Lower respiratory tract infections are the leading cause of infectious disease deaths worldwide and are the fifth leading cause of death overall. This is despite conditions such as pneumococcal infections and influenza being largely preventable with the use of appropriate vaccines. The mainstay of treatment for the most important bacterial lower respiratory tract infections, namely acute exacerbations of chronic obstructive pulmonary disease (AECOPD) and community-acquired pneumonia (CAP), is the use of antibiotics. Yet despite a number of recent publications, including clinical studies as well as several systematic literature reviews and meta-analyses, there is considerable ongoing controversy as to what the most appropriate antibiotics are for the empiric therapy of CAP in the different settings . Furthermore, in the case of AECOPD, there is a need for consideration of which of these exacerbations actually need antibiotic treatment. This article describes these issues and makes suggestions for appropriately managing these conditions, in the setting of the need for antimicrobial stewardship initiatives designed to slow current emerging rates of antibiotic resistance, while improving patient outcomes. The Global Burden of Disease Study evaluated evidence for the global, regional, and national morbidity and mortality of LRTIs and indicated that, for 2015, LRTIs were the leading infectious disease cause of death and the fifth leading cause of death overall3. They estimated that LRTIs caused 2.74 million deaths and 103.0 million disability-adjusted life years (DALYs). While the burden had decreased in children younger than 5 years of age, it had increased in many regions for individuals older than 70 years. The study specifically investigated four etiologies—two bacterial and two viral—and noted that pneumococcal pneumonia was the most common etiology, which led to 1,517,388 deaths or 55.4% of LRTI deaths in all ages. Pneumococcal pneumonia was also a cause of a significant number of deaths in the elderly population worldwide . LRTIs are largely preventable causes of death, as vaccines are available against both influenza and pneumococcal pneumonia. Furthermore, while antiviral therapy is available for the treatment of influenza infections once they occur, the mainstay of treatment for community-acquired pneumonia (CAP) and acute bacterial exacerbations of chronic obstructive pulmonary disease (COPD), which are the focus of this overview of the recent literature, is the use of antibiotics.Lower respiratory tract infections (LRTIs), which generally are considered to include acute bronchitis, bronchiolitis, influenza, and pneumonia, are a significant cause of morbidity and mortality in patients worldwide5. This has resulted in numerous antimicrobial stewardship (AMS) programs—both in South Africa and internationally—designed to slow the rate at which organisms develop resistance and at the same time improve outcomes7. AMS programs consist of two major pillars: first, infection prevention and control and then appropriate use of antibiotics, the latter of which will be the focus of this article. Appropriate use implies the correct indication, dose, duration, and administration method .Overuse of antibiotics both in and out of hospital has resulted in an exponential increase in resistance globally. This has, and will, impact upon the ability to treat infections and be directly associated with increasing morbidity and mortality9.The actual antibiotic choice for bacterial LRTIs depends upon the likely organism; however, it is recognized that distinguishing viral from bacterial infections, both in CAP and in acute exacerbations of COPD, and recognizing non-infective COPD exacerbations are not always clear-cut processes. In fact, as many as 60% of COPD exacerbations may be due to viral infections, in particular rhinovirus, and in winter the influenza virus, and there is an increasing recognition of the important role for viruses in the etiology of CAP10. The European guideline on LRTIs indicates that out of the hospital setting, where chest radiographic confirmation of CAP is usually not available, a measurement of CRP in a patient suspected of having CAP can be performed (a point-of-care test is currently available)11. They recommend that a level of less than 20 mg/L at presentation, in the presence of symptoms for at least 24 hours, makes pneumonia highly unlikely but that a level of more than 100 mg/L makes pneumonia likely.Although they are beyond the scope of this article, a brief review of biomarkers and the role they may play in the decision regarding the need for initiation, discontinuation, or duration of antibiotic treatment are of interest. Of the various biomarkers described, perhaps the most studied are C-reactive protein (CRP) and procalcitonin (PCT). One systematic review and meta-analysis evaluated the use of CRP to guide antibiotic therapy in patients presenting to primary care with symptoms of acute respiratory infections and reported a significant reduction in antibiotic use with a slight increase in hospital admissions12. The authors concluded that the use of PCT to guide initiation and duration of antibiotic treatment was associated with a lower risk of mortality, lower antibiotic consumption, and lower risk of antibiotic side effects. The authors, when using a patient-level meta-analysis, reached similar conclusions13. However, a recent study of PCT-guided use of antibiotics in the treatment of patients with suspected LRTIs did not result in less use of antibiotics than did usual care14. Furthermore, there is no point-of-care test available for the measurement of PCT, which is also costly.With regard to PCT, there are some differences in the conclusions reached in the various studies. One systematic review and meta-analysis assessed the safety and efficacy of PCT for starting and stopping antibiotics in a range of patients with varying severity of acute respiratory tract infections in different clinical settings16. It is clear when evaluating the guidelines that differences exist with regard to the various recommendations, including those for initial empiric antibiotic therapy17.Antibiotics are the mainstay of therapy for CAP, and the initial antibiotic treatment needs to be empiric, as the causative organism or organisms are unknown at the time of presentation. However, there has been ongoing debate over a considerable period of time as to the most appropriate choice of initial empiric antibiotic treatment in the different settings: outpatient, inpatient, and intensive care unit (ICU). A number of national and international guidelines, which describe the appropriate management of CAP, have been developed; some of these have been updated recently or are in the process of being updatedStreptococcus pneumoniae (DRSP) infections. Furthermore, a respiratory fluoroquinolone or a beta-lactam plus a macrolide is recommended in the presence of certain comorbidities or risk factors for DRSP infections15. This is in contrast with the European guideline, which recommends amoxicillin or tetracycline for outpatient use with a macrolide or tetracycline being used only in the case of penicillin allergy, in settings with low levels of pneumococcal macrolide resistance11. Similarly, the South African guideline recommends amoxicillin as the treatment of choice, and a macrolide is to be used in the case of penicillin allergy in settings with low levels of pneumococcal macrolide resistance and other options are reserved for the elderly or for those with comorbidities or recent antibiotic use or both16. A recent literature review from Europe described the etiology and management of CAP in adults, which included both primary care and hospitalized cases18. The authors noted differences in antibiotic prescribing habits in the various regions of Europe. Beta-lactams were the most commonly prescribed class of antibiotics, and monotherapy was more common than combination therapy, but hospitalized patients more commonly received combination therapy than did outpatients. These differences in antibiotic recommendations could be ascribed to differences in the microbial etiology of CAP in the different regions, differences in the prevalence of antibiotic-resistant pathogens, differing patient populations, differences in national guideline recommendations, and other local factors, including regulatory requirements. A recent Cochrane review concluded that there was insufficient evidence from randomized controlled trials to make evidence-based recommendations regarding appropriate treatment in adult outpatients with CAP19. Owing to the low number of studies comparing the same antibiotic pairs, pooling of the data was also not possible; in general, the individual studies did not suggest any significant differences in the efficacy of the various antibiotics studied.For outpatient antibiotic therapy of CAP, the Infectious Diseases Society of America/American Thoracic Society (IDSA/ATS) guideline recommends a macrolide or tetracycline for previously healthy patients with no risk factors for drug-resistant15; the European and South African guidelines have the addition of a macrolide to the beta-lactam as an option16. Most of the guidelines recommend a combination therapy of a beta-lactam and macrolide or fluoroquinolone in those requiring ICU admission, and additional options are for possible pseudomonal infection20. The most controversial area has been whether the use of a macrolide antibiotic should be an obligatory component of initial antibiotic treatment21. Earlier studies of hospitalized patients with moderately severe pneumonia suggested that beta-lactam monotherapy was not inferior to beta-lactam–macrolide combination therapy23. However, as has been indicated by several investigators, those studies had certain limitations that make it difficult to accept their conclusions21. A recent review highlighted all the studies documenting a benefit of combination therapy among inpatients; most of these studies were among CAP patients hospitalized in the ward and not the ICU17. Furthermore, Okumuraet al. documented that in hospitalized CAP patients at low risk of drug-resistant pathogens, beta-lactam–macrolide combination treatment lowered 30-day mortality compared with beta-lactam therapy alone: adjusted odds ratio (OR) 0.28, 95% confidence interval (CI) 0.09–0.8724.For inpatients with CAP, the IDSA/ATS guideline recommends the use of either a beta-lactam-macrolide combination or fluoroquinolone monotherapy for non-critically ill cases26. In the first, Gattarelloet al. compared the outcome of two cohorts of critically ill patients with pneumococcal CAP from different time periods (2001–2002 and 2008–2013)25. The investigators noted that the mortality rate decreased by 18% from the earlier to the later cohort (together with other outcome benefits). This was determined on multivariate analysis to be associated with giving of the first dose of antibiotic within 3 hours  and to the use of combination therapy , which occurred more commonly in the second time period. The most frequently used antibiotic regimen was the combination of a cephalosporin with a macrolide, but other combinations included a cephalosporin and a fluoroquinolone. The second study was on patients with severe non-pneumococcal CAP, and the results were essentially similar26. Once again, the most commonly used antibiotic regimen was a cephalosporin and a macrolide. Early antibiotic treatment  and combined antibiotic therapy , which occurred more commonly in the second time period, were independently associated with a lower ICU mortality.There may still be some debate as to the need for adding a macrolide in less severely ill hospitalized cases. However, two matched case-control studies were published by the CAPUCI II Consortium on severe CAP patients admitted to the ICU28, several recent studies have confirmed the benefit of combination therapy in this situation31. For example, Pereiraet al. documented that combination antibiotic therapy together with a macrolide was independently associated with a reduction in hospital stay  and 6-month mortality 31.Whereas a few studies have documented that combination therapy with a beta-lactam and a macrolide or fluoroquinolone has no additional benefit in critically ill patients with CAPp = 0.0232. When macrolide monotherapy was excluded, the mortality benefit of macrolides was still maintained. There was a trend towards better mortality with beta-lactam–macrolide therapy compared with beta-lactam–fluoroquinolone therapy: mortality with beta-lactam–macrolide therapy 20%  versus 23%  with beta-lactam–fluoroquinolone therapy 32. A number of more recent systematic reviews of antibiotic therapy in patients with CAP have been undertaken. Some that did not restrict the study to severely ill cases documented no benefit on 30-day mortality of beta-lactam–macrolide or beta-lactam–fluoroquinolone combination therapies over fluoroquinolone monotherapy34. However, Horitaet al. concluded that, compared with beta-lactam monotherapy, combination therapy with a beta-lactam plus macrolide may decrease all-cause mortality only in severe CAP35. The authors did recommend caution in this interpretation, as the conclusion was based mainly on observational studies. Lastly, Leeet al., in their systematic review and meta-analysis of patients with severe CAP, noted that the overall mortality of the beta-lactam–macrolide group was lower than that of the beta-lactam–fluoroquinolone group (19.4% versus 26.8%) 36. Furthermore, length of hospital stay was shorter in the former group compared with the latter group, although there was no difference in length of ICU stay. However, despite these positive findings, the authors did indicate the need for caution with the conclusions because of the high risk of bias in the trials and methodological limitations.With regard to systematic reviews and meta-analyses of antibiotic therapy in critically ill patients with CAP, an early study concluded that there was a significant reduction in mortality when macrolides were used as part of treatment: 21%  versus 24% , risk ratio 0.82, 95% CI 0.70–0.97,37. For this reason, other investigators have studied the timing of combination antibiotic treatment39. Such investigators have theorized that administering macrolides some time prior to the beta-lactam agent may improve patient outcomes because of the anti-inflammatory effects that attenuate the inflammatory response initiated by the beta-lactam-induced lysis of bacteria. Meterskyet al. undertook a retrospective cohort study using electronic health records from a large database, comparing the outcome of CAP cases receiving a macrolide 1 hour before a cephalosporin compared with cases receiving a cephalosporin 1 hour before the macrolide38. The adjusted mortality was about 30% lower in the former group compared with the latter group, although this did not reach statistical significance. There were also trends towards lower combined in-hospital mortality/hospice discharge and reduced length of stay. The authors concluded that it was worth pursuing this investigation with a larger cohort and perhaps in subsets of severe pneumonia cases. Furthermore, Peyraniet al. undertook a secondary analysis of data from the Community-Acquired Pneumonia Organisation (CAPO) database39. They documented that, in CAP cases in whom a macrolide had been administered before the beta-lactam, compared with the reverse, the time to clinical stability , length of hospital stay  and mortality  were lower.The reason for the potential benefit of macrolide combination therapy in patients with CAP is unclear, but it is known that macrolide antibiotics have additional anti-inflammatory, immunomodulatory effects and do not directly lyse bacteria, which may play an important role. In the case of the pneumococcal infections, for example, lytic antibiotics increase the release of the pro-inflammatory toxin pneumolysin as well as cell-wall components, which may be associated with host tissue injury21, we would recommend that a combination of a beta-lactam and a macrolide be used in hospitalized and severely ill cases with CAP and that the macrolide be given prior to initiation of the beta-lactam. Furthermore, the antibiotics should be started as soon as possible after confirmation of the diagnosis of CAP. With regard to the fluoroquinolones, careful consideration needs to be given to their routine use for suspected CAP in areas in which tuberculosis (TB) is endemic because it is frequently difficult to clinically differentiate TB from CAP on initial presentation of patients40. Therefore, there is concern that the use of fluoroquinolone in someone with TB but suspected of having CAP may lead to a delay in the diagnosis of TB and, moreover, be associated with the development of drug-resistant TB41. Clearly, the above discussion has focused on empiric antibiotic therapy, and once the results of microbiological testing become available, antibiotic treatment should be tailored appropriately to the findings.Based on the findings of the majority of the studies, and in line with the recommendations of other investigators42, this contention is not supported by the majority of additional studies44. All of the studies from the CAPUCI II Consortium of critically ill patients with CAP indicated that early antibiotic administration (<3 hours) was independently associated with a lower ICU mortality43. An additional study of hospitalized patients with CAP indicated that delay of the first dose of antibiotics beyond 4 hours was one of the independent predictors of mortality (adjusted OR 3.9)44. Furthermore, the systematic review by Leeet al.34, assessing three aspects of antibiotic therapy in hospitalized patients with CAP, noted that administration of antibiotics within 4 to 8 hours of hospital arrival was associated with a reduction in mortality, although the quality of evidence was assessed as being relatively poor. Thus, while it is clear that patients with severe CAP  should receive antibiotics as soon as possible20, the impact of time to antibiotic initiation on outcome in less severely ill cases is not clear20. It seems prudent to initiate antibiotics as soon as possible in patients suspected of having CAP; however, it should not be at the expense of an adequate consideration of possible alternative diagnoses, including acute bronchitis, influenza, pulmonary embolism, and heart failure20. In such patients, administration of an antibiotic would have no benefit, would be associated with potentially serious consequences, and would be contrary to AMS initiatives.Two additional aspects of antibiotic therapy in patients with CAP need mention. The first is the importance of time to initiation/administration of antibiotics relative to the time of presentation with CAP. Although there has been the odd study suggesting that time to initiation of antibiotics has no impact on various patient outcomes45. One recent multicenter non-inferiority randomized controlled trial of hospitalized patients with CAP randomly assigned patients at day 5 to an intervention or to a control group. The former were treated with antibiotics for a minimum of 5 days, and the antibiotic was stopped when the temperature had been 37.8°C or less for 48 hours and the patients had no more than one CAP-associated sign of clinical instability (this being in line with the recommendation of the IDSA/ATS guideline on CAP management)46. The antibiotic treatment in the control group of patients was determined by the individual patient’s physician. The results demonstrated non-inferiority of the shorter antibiotic course and supported the IDSA/ATS recommendations. In terms of potential limitations of the study, 60% of the patients were in low Pneumonia Severity Index (PSI) risk groups I–III and had a predicted mortality of less than 1%, and also there was a low rate of comorbid illnesses in the study population, which would limit generalizability to patients with significant comorbidity.Lastly, some consideration should be given to the appropriate duration of antibiotic therapy for patients with CAP which has varied over time, even though earlier studies and even two meta-analyses indicated that shorter duration of therapy  could be safely and effectively used in patients with mild to moderately severe pneumonia47. The latter had antibiotics discontinued 48 hours after reaching clinical stability, having had at least 5 days of antibiotics. The study was stopped early because of apparent inferiority of the individualized treatment over the standard treatment with regard to the primary outcome, which was early failure within 30 days. This difference  was not statistically significant, but the safety committee interrupted the study because at the time this was the first study to evaluate clinical stability as a proxy to shorten antibiotic exposure in patients hospitalized with CAP and the 30-day mortality was higher in the individualized versus the standard group.However, conversely, a more recent multicenter, non-inferiority, randomized controlled trial was undertaken in hospitalized CAP patients who had reached clinical stability within 5 days of hospitalization, who were randomly assigned to a standard or individualized group49. One group of investigators documented that an implementation strategy, tailored to identify previous barriers to early switch, was associated with a reduced duration of intravenous therapy50. Another implemented a dedicated CAP team to manage low-risk, hospitalized CAP patients, which resulted in a reduced hospital length of stay, time to switch from intravenous antibiotics, and antibiotic duration without any adverse events51.However, other studies and reviews have supported shorter duration of antibiotic therapy in patients with CAP and suggested that the use of biomarkers, such as PCT, may be useful in guiding both the initiation and the duration of antibiotic treatment53. Most recently, the Cochrane database of systematic reviews updated its 2011 review of randomized controlled trials of systemic CS therapy, as adjunct to antibiotic therapy versus placebo or no CS, and concluded that CS therapy significantly reduces morbidity (various end-points) and mortality  in adults with severe CAP; the number needed to treat for additional beneficial outcome was 18 patients (95% CI 12–49) to prevent one death54. CSs also significantly reduced morbidity, but not mortality, for non-severe CAP in adults, and although there were more adverse events in the CS group , the harms did not outweigh the benefits. The South African CAP guideline makes some specific recommendations for the use of CSs in patients with severe CAP16, and it would seem likely that as the older CAP guidelines are updated, more specific recommendations regarding adjunctive therapy for CAP will be included.It is interesting to briefly mention non-antibiotic adjunctive therapies, which—though clearly beyond the scope of this review—continue to be evaluated in critically ill patients with CAP, in whom the mortality remains high despite apparently appropriate antibiotic treatment. A number of such therapies have been studied, of which the use of corticosteroids (CSs) appears to be most promising, and a number of positive randomized controlled trials and systematic literature reviews have been published in recent years56. Although the study by Anthonisenet al.56 is old, various other studies have confirmed the value of antibiotics, particularly in the severe exacerbation; however, perhaps the most important of these criteria is sputum purulence and, as mentioned above, the presence of an elevated CRP60 (p <0.0001) without increasing clinical failure and mortality61. Readmission rates and subsequent exacerbations were similar in the two groups. As discussed previously, a reduction of antibiotic use is a critical component of AMS.Antibiotics are used in two instances in COPD: in order to treat an infection associated with an acute exacerbation (acute exacerbations of COPD [AECOPD]) and for prophylaxis. We have previously described a treatment algorithm designed to limit antibiotic use and assist clinicians in the outpatient setting. This algorithm was based upon severity of symptoms according to the Anthonisen criteria and point-of-care testing using the CRP where the clinical criteria are equivocal regarding severity CRP60 . In addiHaemophilus influenzae andS. pneumoniae; however,Moraxella catarrhalis and the atypical organisms may also be seen62. Viral infections may predispose patients to bacterial infections, and the specific bacteria isolated depend on factors such as age of more than 65 years, steroid use, comorbid illness such as cardiac disease, structural lung disease, or more severe COPD—Global Initiative for Chronic Obstructive Lung Disease (GOLD) 3–4 lung functions—and previous antibiotic use in the past 3 months (as would be the case in frequent exacerbators)65. In fact, some studies indicate that more resistant organisms such asKlebsiella pneumoniae,Staphylococcus aureus,Pseudomonas aeruginosa,Escherichia coli, andAcinetobacter andEnterobacter species are increasingly being seen, particularly in developing countries, even without these risk factors69. This implies that the choice of agent depends on both risk factors and local epidemiology. However, we would recommend that therapy be initiated withH. influenzae andS. pneumoniae in mind70.The most common bacterial organisms isolated in AECOPD remainH. influenzae is prevalent) or a fluoroquinolone. However, the US Food and Drug Administration has recommended that the latter be used only as a last resort agent and be reserved for use in patients who have no other treatment options because of both side effects and potential collateral damage71.As such, the initial antibiotic choice would be amoxicillin  shorter courses have had equivalent outcomes with fewer adverse events78. The concept of “short-course high-dose antibiotic therapy” embodies these principles and should be employed wherever possible.The dosing of each antibiotic should be according to pharmacokinetic principles. The beta-lactams are time-dependent agents; as such, the target should be to exceed the minimum inhibitory concentration by as much time as possible, both to limit resistance and to improve outcome. The fluoroquinolones, as concentration-dependent agents, should preferably be administered once daily to achieve a maximal area under the inhibitory curve (AUIC) or an area under the curve-to-MIC ratio (AUC/MIC). Unfortunately, owing to toxicity issues, this is not possible with all agents in practice. For example, if an agent such as ciprofloxacin is going to be used, it must be administered twice daily because of suspected or documented infection with some of the Gram-negative pathogens described above79.Of interest, established guidelines for the management of COPD exacerbations such as those of the GOLD initiative are generally not well adhered to and this includes antibiotic strategies. In a recent study evaluating compliance, 64 (68.1%) of the 94 patients received antibiotics, of which only 71.9% were appropriateP. aeruginosa demonstrated a 42% decrease in AECOPD compared with the previous 6 months and also a marked reduction in markers of inflammation, indicating a potential role for this modality of therapy80.Inhaled antibiotics have not been well evaluated; however, one study that used nebulized tobramycin twice daily for 14 days in patients with severe COPD colonized with multidrug-resistant81. Numerous agents used for COPD have been shown to reduce exacerbations, and these include the long-acting antimuscarinic agents, inhaled CSs, and the phosphodiesterase 4 inhibitors. Antibiotics, specifically the macrolides, have also been shown to provide benefit; however, the exact mechanism has not been fully elucidated84. Different anti-inflammatory effects have been investigatedin vitro but not provenin vivo86.An alternative use for antibiotics in patients with COPD has been prophylaxis for exacerbations, which are predictive of a worse outcome in COPD, and any means that might reduce them may potentially also improve long-term survival and quality of life85. However, when used in selected patients, the macrolides are safe and cost effective87.Doses vary, but the most frequent doses of azithromycin administered have been 250 or 500 mg three times a week. There are possible side effects from the use of these agents for this purpose, and these include resistance of bacteria and non-tuberculous mycobacteria, drug–drug interactions, QT prolongation, reversible deafness, and gastrointestinal upset88. In addition, a meta-analysis of the use of an oral, whole-cell, non-typeableH. influenzae (NTHi) vaccine versus placebo in patients with AECOPD found a statistically significant 80% increase in antibiotic courses per person in the placebo group  was noted89.In line with stewardship principles, vaccination strategies, if effective, would be valuable in reducing antibiotic use. Whereas vaccination with the pneumococcal polysaccharide vaccine has provided inconsistent benefit in COPD, influenza vaccine—in particular, when combined with the pneumococcal polysaccharide vaccine (studies using the conjugate vaccine are not available but it would be expected to be better)—reduces hospitalization for pneumonia, death, death from influenza, and death from pneumoniaCAP and bacterial AECOPD are significant LRTIs associated with considerable morbidity and mortality. Despite numerous clinical studies as well as systematic reviews and meta-analyses, there is still ongoing debate as to the appropriate treatment of CAP, particularly in severely ill cases, and additionally which AECOPD actually need antibiotics. These issues are discussed in detail in the article, and recommendations are given on the basis of the authors’ collective experience. Furthermore, it is important to remember that, with regard to antibiotic use, these agents are a potentially life-saving resource that must be used wisely both in terms of the specific agent, duration, and dose and in the correct circumstances.


Are antibiotics appropriately prescribed for infection prophylaxis before dental procedures?In this cohort study of 91 438 patients who received antibiotic prophylaxis for 168 420 dental visits from 2011 to 2015, a total of 90.7% of dental visits had manipulation of the gingiva or tooth periapex, but only 20.9% of patients had a cardiac condition at the highest risk of adverse outcome from infective endocarditis. Therefore, 80.9% of antibiotic prophylaxis prescriptions were discordant with guidelines.Most antibiotics prescribed for infection prophylaxis before dental procedures are unnecessary. This cohort study assesses the appropriateness of antibiotic prophylaxis prescriptions for infection prophylaxis before dental procedures using Truven, a US national integrated health claims database. Antibiotics are recommended before certain dental procedures in patients with select comorbidities to prevent serious distant site infections.To assess the appropriateness of antibiotic prophylaxis before dental procedures using Truven, a national integrated health claims database.Retrospective cohort study. Dental visits from 2011 to 2015 were linked to medical and prescription claims from 2009 to 2015. The dates of analysis were August 2018 to January 2019. Participants were US patients with commercial dental insurance without a hospitalization or extraoral infection 14 days before antibiotic prophylaxis .Presence or absence of cardiac diagnoses and dental procedures that manipulated the gingiva or tooth periapex.Appropriate antibiotic prophylaxis was defined as a prescription dispensed before a dental visit with a procedure that manipulated the gingiva or tooth periapex in patients with an appropriate cardiac diagnosis. To assess associations between patient or dental visit characteristics and appropriate antibiotic prophylaxis, multivariable logistic regression was used. A priori hypothesis tests were performed with an α level of .05.From 2011 to 2015, antibiotic prophylaxis was prescribed for 168 420 dental visits for 91 438 patients . Overall, these 168 420 dental visits were associated with 287 029 dental procedure codes . Most dental visits were classified as diagnostic (70.2%) and/or preventive (58.8%). In 90.7% of dental visits, a procedure was performed that would necessitate antibiotic prophylaxis in high-risk cardiac patients. Prevalent comorbidities include prosthetic joint devices (42.5%) and cardiac conditions at the highest risk of adverse outcome from infective endocarditis (20.9%). Per guidelines, 80.9% of antibiotic prophylaxis prescriptions before dental visits were unnecessary. Clindamycin was more likely to be unnecessary relative to amoxicillin . Prosthetic joint devices , tooth implant procedures , female sex , and visits occurring in the western United States  were associated with unnecessary antibiotic prophylaxis.More than 80% of antibiotics prescribed for infection prophylaxis before dental visits were unnecessary. Implementation of antimicrobial stewardship in dental practices is an opportunity to improve antibiotic prescribing for infection prophylaxis. The rationale for prophylaxis was that patients with these conditions have an increased risk for serious distant site infections  secondary to bacteremia introduced during dental care. However, guidelines for the use of antibiotics for the prevention of infective endocarditis and prosthetic joint infections were revised in 2007 and 2013, respectively.11 no study has evaluated the appropriateness of antibiotic prescribing by dentists. Therefore, the objective of this study was to assess the appropriateness of antibiotic prophylaxis before dental procedures.While studies in outpatient primary medical care settings have demonstrated that 30% of antibiotics prescribed are unnecessary,15 the dental domain is a convenience sample of 8 million persons with enrollment in both medical  and dental  health plans. This is the only national data set with detailed data on dental claims and links medical and prescription claims.16 Per other health services research performed by the American Dental Association,20 we collected individual-level demographics (patient age and sex), inpatient and outpatient medical diagnoses , medical procedures , retail and mail-order prescription claims, and dental claims . Dental visit CDT codes were aggregated into categories per a standardized coding structure established by the American Dental Association. Because multiple CDT codes could be coded for a visit, our analyses assessed visits with a specific CDT category coded as compared with visits without the CDT category coded. For all analyses herein, ICD-9 codes before October 1, 2015, were converted to ICD-10-CM codes per guidance from the Centers for Disease Control and Prevention.21 This study followed the Strengthening the Reporting of Observational Studies in Epidemiology (STROBE) reporting guideline. The University of Illinois at Chicago Investigational Review Board deemed that this study was exempt from review and informed consent.In this retrospective cohort study, we performed an analysis of adult patients with visits to a dentist from 2011 to 2015 using Truven MarketScan commercial claims and encounters, Medicare supplemental, and coordination of benefits. Truven is a national integrated health claims database of deidentified outpatient medical, hospital, prescription, and dental claims. While the medical claims are nationally representative of the insured US population in terms of age, sex, and geographic area,22 Antibiotics with a days’ supply of 2 days or less dispensed within 7 days before the dental visit met our definition of use for antibiotic prophylaxis vs treatment of an oral or systemic infection (requiring ≥3 days’ treatment).22 We further excluded visits at which patients had a recent hospitalization or active or recent extraoral infection  defined by diagnosis codes from any outpatient encounter. A recent hospitalization or extraoral infection was defined as occurring within 14 days before the antibiotic dispense date.24Prescription claims were identified in the Truven prescription claims data, and dental procedures were identified in the Truven dental commercial claims data (2011-2015), with prevalence of cardiac or other conditions identified in the Truven medical and hospital claims data (2009-2015) before the dispensing of antibiotic prescriptions for the dental visit. The dates of analysis were August 2018 to January 2019. Eligible study patients were those with 12 months of continuous enrollment in plans with medical and prescription coverage and 30 days with dental coverage before and including the date of the visit with a dentist. We identified patients with a prescription claim for any systemic antibiotic with a days’ supply of 2 days or less that occurred within 7 days before the dental visit. In this study, these antibiotics were defined as being prescribed for preprocedural infection prophylaxis and meet the standard from prior studies, manual review of dental records, and per guidance from clinical experts.Because dental visits are typically connected , we combined all dental visits occurring within 7 days from each other into a single observation or an episode of care. All codes from each visit were combined and represented in the episode of care. For example, a diagnostic dental visit that is followed by a tooth implant dental visit 3 days later is combined into an episode of care with diagnostic and implant codes. Clustering visits into episodes of care excluded 13 825 visits  . Of the 25 For antibiotic prophylaxis to be indicated for the prevention of infective endocarditis, both the dental procedure and the medical history need to be consistent with guidelines.26 Dental procedures for which infective endocarditis prophylaxis is considered appropriate are all procedures that involve manipulation of gingival tissue or the periapical region of teeth or perforation of the oral mucosa .5 All CDT, Current Procedural Terminology, and Healthcare Common Procedure Coding System codes associated with dental visits during the study period were assessed for gingival manipulation by 6 general and 6 specialty dentist raters. When raters disagreed, consensus was determined by an additional rater team of 3 general dentists and 1 oral surgeon. Patients with cardiac conditions that are associated with the highest risk of adverse outcome from endocarditis are recommended to receive antibiotic prophylaxis for dental procedures that involve gingival manipulation. Cardiac conditions for which antibiotics are indicated per guidelines include prosthetic cardiac valve or material used for cardiac valve repair, previous infective endocarditis, certain congenital heart diseases, and cardiac transplant recipients with cardiac valvulopathy.5 Cardiac conditions occurring from 2009 until the date the antibiotic was dispensed were evaluated and defined consistent with previous investigators.39Guidelines on the use of antibiotics for infective endocarditis prophylaxis are based on specific planned dental procedures and medical history. Recommendations in current and previous guidelines for the use of antibiotic prophylaxis before dental procedures are summarized in 8 defined as recent (prior 2 years) or historical claims  in patients with an appropriate cardiac diagnosis as indicated by guidelines.5 In the absence of cardiac conditions, antibiotic prophylaxis was considered unnecessary in the primary analysis.8Antibiotics are not recommended for prosthetic joint infection prophylaxis,l claims . Before l claims . Hospita8 we conducted sensitivity analyses varying the definition of what would qualify as an indication for joint-related prophylaxis (1) defining a 2-year window of appropriate antibiotic prescription after prosthetic joint placement (the highest-risk period for infection)7 and (2) using prior guidelines25 per recommendations by Lockhart.44 Other sensitivity analyses estimating the appropriateness of antibiotic prophylaxis included varying selection criteria within plausible scenarios of (1) continuous medical plan enrollment throughout the entire study period, (2) stratified years of estimates to reflect changes in practice and guideline recommendations, and (3) stratification of patients with and without a history of prosthetic joint diagnoses or procedures.Given the varying guidelines and recommendations occurring over the course of the study period (updated prosthetic joint infection prophylaxis guidelines were published in 2013 and reaffirmed in 2015),t test for continuous variables and χ2 test for categorical variables. Missing data (55 observations) were included in the analysis and are labeled in the multivariable analysis as unknown. Multivariable logistic regression models were used to calculate adjusted odds ratios (ORs) and 95% CIs with robust standard errors for association between patient-level and visit-level characteristics and appropriate antibiotic use. Also, in analyses that included multiple visits per patient , generalized estimating equations with a first-order autoregressive working matrix were used to estimate corresponding ORs and 95% CIs.45 Variables significant in unadjusted analyses or identified as factors associated with unnecessary antibiotic prophylaxis were included in the model. The most parsimonious model was selected by only including those final variables significantly associated with prescribing. SAS, version 9.4 (SAS Institute Inc), was used for all analyses. A priori hypothesis tests were performed with a 2-sided α level of .05.Descriptive characteristics of groups with visits identified as having an appropriate use of antibiotic prophylaxis and those that did not were compared using independent-samples More than 3 million dental visits and antibiotic prescriptions were identified in the Truven commercial dental database during the study period of 2011 to 2015. After applying inclusion and exclusion criteria, 168 420 eligible dental visits (or episodes of care) with antibiotic prophylaxis for 91 438 unique patients were included in this analysis . The chaP < .001) , followed by clindamycin (16.0%) . Only 19 < .001) .CDT procedure categories; adjunctive general services, implant services , prosthodontics, orthodontics, and maxillofacial prosthetics had higher odds of unnecessary prescribing. Unnecessary antibiotic prophylaxis was less common in patients with diabetes, immunocompromised conditions, or health care use in the previous 6 months, while having a prosthetic joint device  was associated with unnecessary prescribing compared with those not having a prosthetic joint. Finally, unnecessary antibiotic prophylaxis was most associated with antibiotics falling into the “other” category, followed by clindamycin , compared with amoxicillin.In multivariable analyses, unnecessary antibiotic prophylaxis decreased over time . Patient25 The results were similar after modifying our definition of appropriate antibiotic prophylaxis with recommendations in the 2003 prosthetic joint infection guidelines25 . The highest-risk period of a prosthetic joint infection after joint implant placement is 2 years.25 After including prosthetic joint placement within 2 years in our definition of appropriate antibiotic prophylaxis, 80.9% of antibiotics prescribed for infection prophylaxis before dental visits were unnecessary. A subanalysis of the cohort with visits clustered into episodes of care (n = 13 825), 82.7% of patients at the first visit, 84.6% at the second visit, and 84.3% at the third visit received unnecessary antibiotic prophylaxis. Stratifying the overall cohort by the presence or absence of a prosthetic joint, 11.2% of patients with a prosthetic joint received appropriate antibiotic prophylaxis secondary to a concomitant cardiac condition (n = 71 651). After excluding those with a prosthetic joint, the percentage of visits with unnecessary antibiotic prophylaxis decreased to 75.0% (n = 96 769). Similar characteristics were found to be associated with unnecessary antibiotic prophylaxis as identified in the full analysis  of the cohort were included, and 80.2% of antibiotic prophylaxis prescriptions were defined as unnecessary. The 2003 guidelines for the prevention of prosthetic joint infections also changed during our study period (updated guidelines were published in 2013 [released online in 2012]) .8,25 The46 Antibiotics prescribed for infection prophylaxis by dentists have been associated with community-associated C difficile infection.48 One dose of clindamycin has an equivalent risk of C difficile compared with a prolonged course.49 Therefore, it is alarming that clindamycin was more likely to be inappropriately prescribed than amoxicillin. However, there was a significant decrease in antibiotic prophylaxis over the study period. This may indicate that the 2013 guidelines for the prevention of prosthetic joint infections are being applied to patient care.Our results demonstrate that most antibiotics prescribed for infection prophylaxis before dental visits are unnecessary. These findings are concerning because dentists prescribe a significant proportion of antibiotics and are the top prescribers of clindamycin in the United States.58 However, dentists are knowledgeable about and generally satisfied with the antibiotic prophylaxis guidelines.59 Regardless, 70% of dentists surveyed reported prescribing antibiotic prophylaxis when not indicated.59 Dentists in the United States identified factors associated with guideline-consistent antibiotic prescribing to be postgraduate education, urban locale, and a smaller patient panel.60 Reasons for higher antibiotic prescribing rates included increasing use of dental implants, an aging population, underinsurance driving antibiotics as an oral surgery substitute, slow adoption of new guidelines, lack of awareness of the role of dentists in antibiotic resistance, and physician and patient pressure.61 These characteristics are similar to those associated with physician antibiotic overprescribing.62 Therefore, antibiotic stewardship strategies shown to be effective in outpatient medical clinics may also improve antibiotic prescribing in dentistry. In fact, a recent example has provided early evidence that implementing the Centers for Disease Control and Prevention’s Core Elements of Outpatient Antibiotic Stewardship in dental practices was effective.63These results are consistent with those from other countries, where 58% to 81% of dental antibiotic prescriptions are inconsistent with guidelines, particularly for infection prophylaxis.65 As a result, these persons are not included in our sample unless supplemental commercial dental benefits were purchased. Due to limitations in the data set, the prescriptions cannot be directly linked with the health care encounter or prescriber. We adapted methods used by other investigators to link antibiotic prescriptions to health care encounters and exclude other indications for antibiotics. To increase the specificity of our antibiotic-related dental visits, we conservatively defined a cohort in which other indications for antibiotics are unlikely. In contrast to medical care providers, dentists rarely use diagnostic codes (ICD-9 or ICD-10-CM) and are reimbursed based on procedure codes (CDT).67 Therefore, it is difficult to associate a diagnosis with the prescription. To increase the likelihood that an antibiotic was prescribed for infection prophylaxis , the days’ supply for the antibiotic prescription was limited to 2 days or less . We did not assess dental visits at which an antibiotic was indicated but not dispensed. Although the 2007 infective endocarditis guidelines significantly decreased the number of patients with a prophylaxis indication,5 data are conflicting regarding the association of this change with the incidence of endocarditis.70 However, the sole study70 with results identifying an increase in infective endocarditis in the United States did not include dental visit data and was not able to adjust for increases in infective endocarditis observed with the opioid epidemic. So, it is difficult to elucidate the causal factor . We did not apply 2017 (after our study period) expert panel recommendations of clinical scenarios in which antibiotic prophylaxis may be appropriate in patients with prosthetic joints.71 All scenarios include patients with multiple comorbidities . Because the comorbidities in the expert panel recommendations71 are similar to those in the 2003 prosthetic joint guidelines,25 we anticipate the results from the expert panel recommendations to be similar to the results from the 2003 prosthetic joint guidelines. Due to the difficulty in identifying specific diagnoses, we broadened the definition for certain conditions to include all cardiac transplantation , all diabetes (vs just type 1), and all congenital heart diseases. Therefore, unnecessary prescribing is likely higher than our results indicate.These results are not without limitations. The cohort is a convenience sample of US patients with commercial dental insurance. Therefore, our results may not be representative of the uninsured and underrepresents persons with Medicaid and Medicare benefits. Medicare does not generally cover dental care, and the state provision of dental benefits to adults with Medicaid is optional.49 a decrease in unnecessary antibiotic prophylaxis will significantly decrease overall antibiotic prescribing by dentists. Therefore, specific antibiotic stewardship strategies and prescribing tools targeted to dentists and dental practices should be developed, implemented, and assessed for effectiveness in improving prescribing of antibiotics for infection prophylaxis before dental procedures.These findings have strong public health implications. To our knowledge, this is the first national analysis of overprescribing of antibiotics for infection prophylaxis before dental procedures and should initiate a call to action to the public health and dental communities to improve prescribing of antibiotics for infection prophylaxis. Because dentists primarily prescribe antibiotics for infection prophylaxis,More than 80% of antibiotic prophylaxis prescriptions before dental procedures are unnecessary: clindamycin use, the presence of prosthetic joints, and residence in the western United States were associated with unnecessary prescribing. While antibiotic prophylaxis is appropriately prescribed for indicated dental procedures in patients with cardiac conditions, most antibiotic prophylaxis is prescribed to patients in whom guideline-identified risk factors are not present. Although prescribing is slowly improving, the high proportion of antibiotics that were found to be unnecessary in our study is worrisome. Implementing antimicrobial stewardship efforts in dental practices is an opportunity to improve antibiotic prescribing for infection prophylaxis.


Primary sclerosing cholangitis (PSC) is recognized as an autoimmune-mediated liver disease characterized by progressive biliary inflammation and fibrosis. Some PSC cases with elevated immunoglobulin G4 (IgG4) levels are likely to be misdiagnosed with immunoglobulin G4-related sclerosing cholangitis (IgG4-SC). Thus, distinguishing these 2 diseases is particularly important.A 34-year-old male presented with right hypochondrium abdominal intermittent pain and jaundice lasting for 1 month. Here, we present a case of PSC with increased IgG4 levels with improvement of quality of life upon liver transplantation (LT).The diagnosis of PSC was confirmed based on clinical symptoms, laboratory test results, imaging findings, pathologic results and a lack of response to steroid therapy.LT surgery was performed successfully when his vital parameters were stabilized. Immunosuppressive agents were routinely used after LT.Three years after LT, liver function values show that alanine aminotransferase (ALT) and aspartate aminotransferase (AST) were in the normal range. An abdominal ultrasonography showed no obvious abnormalities.There are similar biochemical characteristics and cholangiographic findings between PSC and IgG4-SC. Therefore, distinguishing these 2 diseases is particularly important. LT remains the only option for end-stage PSC. Early diagnosis and effective treatment can achieve a good prognosis. PSC, recognized as a sclerosing cholangitis without steroid efficacy, has been usually confused with IgG4-SC clinically due to similar biochemical characteristics and cholangiographic findings.,4 Therefore, differential diagnosis between PSC and IgG4-SC is particularly significant. Here, we present a case of PSC with increased IgG4 levels with improvement of quality of life upon liver transplantation (LT). Informed consent was obtained from the patient for this publication. The ethics committee of our hospital approved this case report.Immunoglobulin G4-related sclerosing cholangitis (IgG4-SC) is characterized by abundant immunoglobulin G4 (IgG4)-positive plasma cells with effective steroid therapy.2A 34-year-old male presented with right hypochondrium abdominal intermittent pain and jaundice lasting for 1 month. The patient had no remarkable past history including special drug or consumption of alcohol. The levels of serum IgG4 were increased in his younger sister, his daughter and the patient himself. Physical examination revealed dim and blackish complexion, jaundice, abdominal bulge, and positive shifting dullness. Note that the rebound tenderness sign and Murphy sign were negative. Laboratory results are shown in Table At first, considering these clinical data, we suspected IgG4-SC and began oral steroid therapy at 40 mg/day. The serum IgG4 levels became normal after steroid therapy, but the jaundice did not improve. The patient's general condition gradually deteriorated, and he eventually developed severe complications after steroid therapy. Therefore, we conducted endoscopic retrograde cholangiopancreatography (ERCP), in which irregular narrowing of the intrahepatic bile ducts, that is, a pruned-tree appearance, was observed. Then, endoscopic nasobiliary drainage (ENBD) was performed. Severe esophageal and gastric varices were shown by gastroscopy. A colonoscopy confirmed chronic colitis. Thus, the diagnosis of PSC was strongly suspected based on a lack of response to steroid therapy and ERCP. Then, the patient successfully underwent LT when his vital parameters were stabilized. Histopathological findings of the liver during operation showed fibrotic change, atrophied biliary epithelial cells and onion-skin fibrosis in the enlarged portal area Fig. A, IgG imOne year after LT, the serum IgG4 levels of his younger sister, his daughter and the patient himself were above the upper limit of normal (ULN) range, as follows: 10.20 g/L, 8.86 g/L, and 11.90 g/L, respectively. HLA-DRB1∗07:01, 07:01 was found in both his younger sister and the patient himself, and HLA-DRB1∗07:01, 09:01 was found in his daughter. Three years after LT, liver function values show that alanine aminotransferase (ALT) and aspartate aminotransferase (AST) were in the normal range. An abdominal ultrasonography showed no obvious abnormalities.3 The potential etiologies of PSC have not yet been identified, which may be due to interactions among genetic and environmental factors. Owing to the application of genome-wide association studies, a large number of disease susceptibility genes for PSC have been confirmed.–8 The risk of PSC in first-degree relatives of patients is increased 9 to 39 times. Evidence from a genome-wide association study indicated a significant association of HLA-DRB1∗07:01 with PSC. In addition, recent progress has found that some PSC patients with increased serum IgG4 levels also carry HLA-DRB1∗07:01. Based on this patient and his first-degree relatives, we hypothesize that HLA-DRB1∗07:01 may be associated with the elevated levels of IgG4 in PSC, a hypothesis that needs to be further confirmed. Approximately half of the patients with PSC have no obvious clinical symptoms in the early stage. Jaundice, fatigue and vague upper abdominal discomfort are most common among the symptomatic patients, who may also have gastrointestinal bleeding. Liver function tests suggest evidence of cholestasis, especially the elevation of alkaline phosphatase and gamma-glutamyl transferase. Elevated bilirubin levels indicate that the disease has developed to the middle and late stages or that dominant biliary strictures can be seen in these patients. The serum IgG4 levels of a small number of PSC patients may be elevated. Compared with patients with PSC with normal IgG4 levels, patients with elevated IgG4 levels had a lower frequency of inflammatory bowel disease (IBD), higher severity of this disease and shorter time to liver transplantation, which were compatible with this case. Typical imaging findings are extrahepatic and/or intrahepatic biliary strictures. MRCP has been recommended for the diagnosis of PSC, but ERCP is still essential in some dominant biliary strictures for its diagnostic and therapeutic utility. The only current medical therapy for PSC patients is ursodeoxycholic acid, which can improve liver enzyme levels; however, it cannot slow the progression of this disease, and LT remains the only option for end-stage PSC. In this case, based on clinical symptoms, laboratory test results, imaging findings, pathologic results and a lack of response to steroid therapy, the diagnosis of PSC was definitive. After LT, the patient's quality of life improved markedly.PSC is a chronic and progressive cholestatic liver disease that predominantly occurs in 30- to 40-year-old men. ever reported 3 PSC individuals with elevated serum IgG4 levels. However, our case has the following advantages. First, the efficiency and safety of LT was also apparently confirmed in PSC patients, which provided us with a warning regarding the importance of differential diagnosis with IgG4-SC and avoiding blindly administering steroid therapy. Second, we tested the HLA-DRB1∗ alleles and serum IgG4 levels for the patient's first-degree relatives and the patient himself, which provides cautionary information for clinicians to consider the role of HLA-DRB1∗07:01 in PSC with elevated IgG4 levels.Koyabu et alWe thank the patient and his family, who gave their informed consent for publication.Data curation: Xiao-Xue Zhang, Li-Na Feng.Formal analysis: Rui Zhong.Writing – original draft: Qing-Ling Chen.Writing – review & editing: Xiao-Yu Wen, Qing-Long Jin.


The role of spliced leaders (SL) within the cell is unclear and an accurate assessment of SL occurrence within an organism is possible only after extensive sequencing data are available, which is not currently the case for many nematode species. SL discovery is further complicated by an absence of SL sequences from high-throughput sequencing results due to incomplete sequencing of the 5’-ends of transcripts during RNA-seq library preparation, known as 5′-bias. Existing datasets and novel methodology were used to identify both conserved SLs and unique hypervariable SLs within Heterodera glycines, the soybean cyst nematode. In H. glycines, twenty-one distinct SL sequences were found on 2,532 unique H. glycines transcripts. The SL sequences identified on the H. glycines transcripts demonstrated a high level of promiscuity, meaning that some transcripts produced as many as nine different individual SL-transcript combinations. Most uniquely, transcriptome analysis revealed that H. glycines is the first nematode to demonstrate a higher SL trans-splicing rate using a species-specific SL over well-conserved Caenorhabditis elegans SL-like sequences.Spliced leader  Trans-splicing is less widespread and results in the fusion of RNA molecules that are transcribed from different genomic loci. The most prevalent form of trans-splicing involves the addition of a short, spliced leader (SL) sequence to the 5′ end of mRNA transcripts, referred to as spliced leader trans-splicing (SLTS). SLTS has evolved independently in a diverse set of phyla including Nematoda, Platyhelminthes, Trypanosoma, Cnidaria, Rotifera, Chordata, Arthropoda and Dinoflagellata8.Pre-mRNA splicing is a vital mechanism associated with the expression and regulation of eukaryotic genes. The most widely deployed splicing mechanism is cis-splicing, which enables the removal of intron sequences from mRNA molecules. 11. SL RNAs maintain a conserved secondary structure comprised of hairpins and a single-stranded Sm binding site (5′-purine-AU4–6G-purine-3), which allows the SL RNA to interact with proteins that are required for SLTS13.SLs originate from SL RNA genes, whose transcripts are divided into two parts by a donor splice site: a 5′ exon-like SL region and a 3′ intron-like regionCaenorhabditis elegans, acting as a prerequisite for subsequent translation14. In C. elegans, approximately 70% of transcripts are trans-spliced to a 22nt SL: SL1 or SL217. However, operon resolution is not the sole function of SLTS in C. elegans, as only 17% of C. elegans transcripts originate from operons18. It has been hypothesized that SLTS is involved in many translational regulation mechanisms, including the replacement of deleterious sequences in the 5′-untranslated region, addition of translational motifs from within the SL sequence, or by replacing a transcript’s 5′-monomethylated cap with a 5′-hypermodified cap structure24.It is evident that SLTS has a role in resolving polycistonic mRNAs in trans-splicing. In all nematodes, SLs with similarity to SL1 and/or SL2 are found, with an exception of Trichinella spiralis, which uses non-canonical spliced leaders32. Interestingly, sequence analysis of the potato cyst nematodes Globodera rostochiensis and G. pallida, identified multiple hypervariable SL sequences in addition to SL1 and SL233. The diversity of SL sequences found in Globodera spp. and the dearth of information regarding their functionality highlights a need to improve our understanding through the investigation of nematode genomic and transcriptomic data. Previous studies have identified SL1 in the soybean cyst nematode, Heterodera glycines, a highly damaging plant parasite closely related to Globodera spp.34. Subsequently, the SL1 sequence has been used to successfully generate H. glycines cDNA libraries .Sequence data indicate that all nematode species studied to date utilize SL H. glycines genome35 and the RNA-seq reads from an early-life stages transcriptome36 to extensively characterize SLs and their usage in H. glycines. Serendipitous observation of variation in the 5′-end of two previously sequenced H. glycines transcripts led to the discovery of a novel SL. Through subsequent bioinformatic approaches utilizing both H. glycines genomic and transcriptomic data, this report shows that H. glycines possesses at least twenty-one SLs, found on a total of 2,532 H. glycines transcripts, which account for approximately one-third of H. glycines genes. Functional analysis of the H. glycines SL trans-spliced transcripts reveals involvement in a variety of biological processes. Interestingly, around 45% of the transcripts are promiscuously trans-spliced by SLs suggesting that there is functional redundancy amongst SL RNA molecules. Furthermore, H. glycines is the first nematode to show a transcriptome-wide preference for a species-specific SL sequence over the well-conserved C. elegans SL-like sequences.In this current study, we utilize the recently assembled H. glycines expressed sequence tags on NCBI revealed two transcripts coding for chorismate mutase proteins (AY16022537 & MH119144), which are important enzymes for parasitism in multiple plant-parasitic nematodes42. Alignment of the 5′ end of MH119144 and the SL1 primer sequence used to clone AY160225 revealed divergent 5′ ends, suggesting the presence of a novel SL sequence  to distinguish it from C. elegans SL1-like and SL2-like sequences in other nematode species.Collectively, three tiers of evidence support the legitimacy of this novel SL, including: mapping of the putative SL and the remainder of the transcript to separate locations within the genome, the similarity of the putative SL RNA sequence to known SL RNAs, and the absence of a SL chorismate mutase PCR product when using gDNA. This novel SL will subsequently be named H. glycines, all known SLs from C. elegans and Globodera spp. were mapped to the H. glycines genome. SL1 mapped to 180 loci in the H. glycines genome, twenty-two sequences of which were located within close proximity to a Sm motif13. The only Globodera spp. SL variant present in the H. glycines genome was SL1b, which lacked a proximal Sm motif . The use of truncated SLs has been demonstrated to circumvent the low availability of complete 5′-ends in RNA-seq data26.To assess SLTS in H. glycines transcriptome36. A two-tiered third approach that involved SL queries to trimmed Illumina reads with subsequent mapping to the 5′ end of transcripts  rediscovery rate of ESTs within the transcriptome . It is interesting that of the 9,042 SL trans-spliced genes, approximately one-third  co-align with annotated repeats in the H. glycines genome. The ten most abundant repeats comprised 27.7% of the 3,013 trans-spliced genes. The most abundant functionally annotated repeat is associated with a LINE/CR1 retrotransposon (3.4%), suggesting that a significant portion of SL trans-spliced transcripts are associated with transposons  of bona fide effector genes are subject to SL trans-splicing. Previous hypotheses indicate that species use SL trans-splicing as a form of translational control to respond to changing environments, particularly in response to nutrient availability20. The existence of two subsets of effector transcripts, one SL trans-spliced and one not, may provide H. glycines with a way to mitigate host defense responses through differentially regulating the two subsets of effectors.This study was prompted by the discovery of HgSL3 at the 5′-end of a chorismate mutase effector cDNA, leading to the identification of a unique set of hypervariable HgSLs. Novel hypervariable SLs have previously been discovered in the potato cyst nematode H. glycines SL trans-spliced transcripts, SLs were first truncated at the 5′-ends before being queried using BLAST against H. glycines sequences. The use of truncated SLs was previously utilized in G pallida26. Before truncating the SLs in H. glycines, we first verified that this approach was necessary by using the full-length SLs as query sequences against the H. glycines ESTs and transcriptome. Only fifteen sequences, none of which were SL1, were identified across both databases (available in GitHub). The failure to recover full-length SL1 supports the lack of 5′-ends within the H. glycines datasets, as SL1 is present in H. glycines and other related nematodes27. The read-based approach further verified the lack of complete 5′-ends within the H. glycines transcriptome by showing that the truncated SLs were predominantly located at the first nucleotide of raw reads that were underrepresented in mature transcripts. To further complicate transcriptome assembly in SLTS organisms, this study revealed that 45.5% of SL trans-spliced transcripts do not have one unique SL-transcript combination. The promiscuous nature of SLs on otherwise identical transcripts may cause high ambiguity in the assembly step, resulting in 5′ truncations or the assembly of a transcript that reflects only the most abundant SL-transcript while discarding lower expressed SL-transcripts.To identify H. glycines ESTs, transcriptome and raw reads used in this study concluded that HgSL3 is the most prevalent SL in H. glycines, with 30.9% of the SL trans-spliced transcripts being trans-spliced by HgSL3. The predominant use of a non-SL1 sequence is unique to H. glycines and contrasts with findings in C. elegans and the animal-parasitic nematode Ascaris suum, as well as G. pallida where SL1 and SL1 variants were identified on >90% of the SL-containing G. pallida reads26.Analysis of the available C. elegans operon genes, which are resolved into monocistronic transcripts using SL trans-splicing, are upregulated during recovery from growth-arrested states50. Operon arrangement is believed to be advantageous in C. elegans during times of limited resources as there are less promoters competing for transcriptional resources50. In the case of H. glycines, SL trans-spliced transcripts were found to be involved in ‘Embryo development ending or egg hatching’ and ‘Nematode larval development,’ suggesting that SL trans-splicing may also be involved in initiating developmental changes in H. glycines. Operon arrangement has not yet been defined in H. glycines, however the clustering of SL trans-spliced transcripts in the genome suggests the presence of operon-like structures.52, we developed a SL identification pipeline that utilizes generic RNA-seq, assembled transcripts, and ESTs, rather than requiring SL trapping prior to sequencing54. This method provides an alternative to existing pipelines by utilizing the propensity for SLs to be trans-spliced at 5′ ends and avoiding the requirement of unmapped reads having dual genomic mapping51. Additionally, using both pre-existing and predicted SL sequences that follow canonical SL RNA structures, we allow for the identification of novel SLs. A drawback of this approach may lie in the requirement of SLs to reside at 5′ ends, which is reliant on accurate adaptor trimming and prior knowledge of the anticipated SL length.To both adapt and improve upon existing SL identification pipelinesH. glycines possesses a unique set of hypervariable SLs, which are promiscuously trans-spliced to the 5′ end of >2,000 H. glycines transcripts, equivalent to approximately one-third of H. glycines genes. A robust identification of SLs was possible through novel methodology and the availability of H. glycines genome and transcriptome sequences. As more data becomes available for H. glycines and other parasitic and non-parasitic nematodes, the functional significance of SLTS may become more apparent and potentially lead to novel control measures.In summary, G. rostochiensis26, C. elegans (PRJNA13758) SL sequences and the 22nt SL sequence from MH119144 were queried to the H. glycines genome with BLASTn V2.4.0 + 55. SL hits and the adjacent 3′ 98 nucleotides were extracted using Samtools V1.456. Secondary structure was predicted using RNAfold V2.1.9 with unpaired bases participating in at most one dangling end. All extracted sequences were analyzed for a downstream Sm motif (5′-purine-AU4–6G-purine-3′)57.All H. glycines was propagated on Williams 82 soybean. To isolate mixed-stage nematodes, root tissue was macerated with a blender, sieved and separated with a sucrose gradient58. Nematodes were ground in liquid nitrogen and total RNA was extracted using a RNeasy Mini Kit . One μg of total RNA was treated with DNase I  and cDNA was synthesized using qScript cDNA SuperMix . Genomic DNA was also extracted from ground nematode tissue using QIAamp DNA Mini Kit (Qiagen). RT-PCR was performed on a Bio-Rad S1000TM thermal cycler with reactions containing 1X PCR buffer, 1.5 mM MgCl2, 0.2 mM dNTP, and 1 unit of Taq DNA Polymerase (ThermoFisher Scientific). Thermocycler conditions were: 94 °C for 3 min, 35 cycles of 95 °C for 45 s, 55 °C for 30 s and 72 °C for 1 min, followed by 10 min at 72 °C.To confirm the functionality of putative SL on transcript MH119144 OP50 H. glycines NCBI EST database, referred to as EST BLAST59 and a H. glycines de novo Trinity transcriptome assembled from NCBI SRA accession SRP122521, referred to as Direct BLAST36. BLAST hits were filtered to within the first thirteen nucleotides of the transcript, and with a 10nt minimum alignment length. ESTs and trinity transcripts were mapped to the genome using GMAP 20170317, and transcript to gene relationships were identified using exon to exon overlaps with Bedtools intersect V2.26.060. Genes were clustered by location using custom bash scripts.All putative SL sequences were queried with BLASTn to the 61, paired-end reads  used in generating a H. glycines trinity transcriptome55. The subject start position for hits was graphed using GraphPad Prism 4. BLAST output was filtered by a 10 bp minimum alignment length and hits within 12 bp of the appropriate read end. Putative SL-containing reads were queried with BLASTn V2.4.0+ to the transcriptome and filtered by 80 bp min alignment length, and within 12 bp of the 5′ transcript end55.In the method referred to as Read-to-transcript, SLs were truncated to the 11 3′ nucleotides and queried with BLASTn V2.4.0+ to Sickle-trimmed (default)62. GO enrichment for trans-spliced genes was performed using Ontologizer V2.0 with gene functions from the H. glycines genome63.Functional annotation was performed using Blast2go V4.1. All transcript sequences were searched against the NCBI NR database using Blastx (e-value 1.0–5. Interpro scan was performed using all default applications, and sequences were annotated with an annotation cutoff of 55 and a GO weight of 5trans-spliced repetitive genes from a Repeatmodeler V1.0.8 tracks of the genome64. Effector genes were mapped to the genome using GMAP 2017031744, and were subjected to bedtools intersect V2.26.0 and custom bash scripts to identify trans-splicing effectors60.Bedtools intersect V2.26.0 and custom bash scripts were used to identify Figure S1Dataset 1Dataset 2Dataset 3Dataset 4


The influence of geographic origin on the risk of severe illness and death on cART has not been explored in European countries.We studied antiretroviral-naïve heterosexual HIV-1-infected individuals enrolled in the FHDH-ANRS CO4 cohort in France who started cART between 2006 and 2011. Individuals originating from France (French natives), sub-Saharan Africa (SSA) and non-French West-Indies (NFW) were studied until 2012. Crude and adjusted rate ratios (aRR) of severe morbid events/deaths (AIDS-related and non-AIDS-related) were calculated using Poisson regression models stratified by sex, comparing each group of migrants to French natives.Among 2334 eligible men, 1379 (59.1%) originated from France, 838 (35.9%) from SSA and 117 (5.0%) from NFW. SSA male migrants had a higher aRR for non-AIDS infections, particularly bacterial infections (aRR 1.56 (95% CI 1.07–2.29), p = 0.0477), than French natives. Among 2596 eligible women, 1347 (51.9%) originated from France, 1131 (43.6%) from SSA, and 118 (4.5%) from NFW. SSA and NFW female migrants had a higher aRR for non-AIDS infections, particularly non-bacterial infections  and 7.87 (2.54–24.4), p = 0.0010), than French natives. We observed no other significant differences related to geographic origin as concerns the aRRs for AIDS-related infections or malignancies, or for other non-AIDS events/deaths such as cardiovascular disease, neurological/psychiatric disorders, non-AIDS malignancies and iatrogenic disorders, in either gender.Heterosexual migrants from SSA or NFW living in France have a higher risk of non-AIDS-defining infections than their French native counterparts. Special efforts are needed to prevent infectious diseases among HIV-infected migrants. In high-income countries, HIV-infected adults with controlled infection and high CD4 cell counts currently live longer than ever before , and theCreated in 1989, the French Hospital Database on HIV  is a large prospective cohort of HIV-infected individuals receiving care in one of 70 French participating hospitals, collecting standardized clinical, therapeutic and biological variables at each outpatient visit or hospital admission and/or at least every 6 months . The onlSevere events included any AIDS-defining event or death from AIDS  and any http://www.cphiv.dk/Portals/0/files/Code%20Protocol%202.3.pdf), adapted to take AIDS and severe non-AIDS events into account, in addition to death. We grouped causes as follows: AIDS-defining infection (CoDe 01.1), AIDS-defining malignancy (CoDe 01.2), non-AIDS bacterial infection (CoDe 02.1), other non-AIDS infection (CoDe 02.2), liver-related disorder (CoDe 03 and 14), non-AIDS malignancy (CoDe 04), cardiovascular disease , respiratory disease (CoDe 13 and 25), renal failure and urogenital disease (CoDe 15 and 28), central neurological and psychiatric disorders , gastrointestinal disorders (CoDe 10 and 26), skin, rheumatic and peripheral neurological disorders (CoDe 27), haematological disease (CoDe 20), accidental/violent events (CoDe 16 and 17) and endocrine and metabolic disease , as proposed elsewhere [Severe events were categorized according to the Coding of Death in HIV (CoDe)  of severe events (per 1000 person-years of follow-up) were calculated. Person-years of follow-up were calculated from the date of cART initiation to the date of death for known deceased individuals, last follow-up visit for individuals with no follow-up visit during the 6-month period before 31 December 2012 (last database update) or 31 December 2012 for the remainder of the cohort. Crude and adjusted IRs were estimated according to geographic origin, in men and in women. Poisson regression models were used to identify differences in morbidity/mortality according to geographic origin, in men and in women. Incidence rates (IRs) and rate ratios (RRs) were adjusted for the following characteristics at cART initiation: age, region of care , CD4 cell count, pVL, AIDS status, hepatitis B and/or C infection and smoking status for each category of events/deaths, plus the body mass index for cardiovascular diseases. All analyses were done with SAS v9.4 software . A p value <0.05 was considered to denote statistical significance.A total of 2334 men and 2596 women fulfilled the inclusion criteria for this study. The men’s geographic origin was France in 1379 cases (59.1%), SSA in 838 (35.9%) and NFW in 117 (5.0%). The women’s geographic origin was France in 1347 cases (51.9%), SSA in 1131 (43.6%) and NFW in 118 (4.5%) . In eachDuring 6524 person-years of follow-up, a total of 771 severe events, including 27 deaths, were recorded in 495 men, of whom 299 were French natives, 167 SSA migrants and 29 NFW migrants. Overall, crude IRs of severe events were 118.7 per 1000 person-years for French natives, 116.4 for SSA migrants and 125.8 for NFW migrants. Adjusted IR of severe events was highest among SSA migrants , with an adjusted rate ratio (aRR) of severe events among SSA migrants estimated as 1.23 : 1.04–1.47) compared to French natives. When AIDS events and severe non-AIDS events were considered separately, SSA migrants had a higher aRR of both AIDS events (1.38 (95%CI: 0.96–1.99)) and non-AIDS events (1.19 (95%CI: 0.98–1.44)) than French natives. Within the different non-AIDS events categories, there was a higher aRR of non-AIDS infections among SSA migrants (1.58 (95%CI: 1.15–2.15)) than among French natives, due to a higher aRR of non-AIDS bacterial infections in SSA migrants than in French natives . The maiDuring a follow-up of 7324 person-years, a total of 624 severe events, including 48 deaths, were recorded in 413 women, of whom 213 were French natives, 181 SSA migrants and 18 NFW migrants. Overall, crude IRs of severe events were 87.0 per 1000 person-years among French natives, 82.2 among SSA migrants and 96.3 among NFW migrants. Within the different non-AIDS events categories, there was a higher aRR of non-AIDS infections among SSA and NFW migrants (respectively 1.40 (95%CI: 0.99–1.97) and 2.91 (95%CI: 1.36–6.22)) than among French natives, due to a higher aRR of non-AIDS non-bacterial infections . The maiWe found that the likelihood of non-AIDS infections, and particularly bacterial infections, was significantly higher among male migrant from sub-Saharan Africa than among male French natives. The likelihood of non-AIDS infections, particularly non-bacterial infections, was significantly higher among female migrants from sub-Saharan Africa and non-French West Indies than among female French natives.A recent collaborative cohort study comparing mortality in Western Europe according to geographic origin, sex and HIV transmission category  showed tNon-AIDS-defining events, and especially bacterial infections, now represent the leading cause of severe morbidity among HIV-infected patients ,23,24. IThis study has several limitations. First, no data on treatment adherence are available in the FHDH database. However, we recently showed that in women and in non homosexual men followed in France, SSA and NFW migrants had no difference in time to viral undetectability than their native French counterparts . MoreoveIn summary, after cART initiation, heterosexual men and women from sub-Saharan Africa and non-French West Indies have a higher risk of non-AIDS infections than their native France counterparts. However, we found no other substantial differences in terms of severe AIDS or non-AIDS events/deaths in either gender. Special attention should thus be paid to the prevention of infectious diseases among migrants, including screening of vaccination status and completion of vaccine schedules , pre-tra


To determine the efficacy and safety of different prophylactic systemic antibiotics in adult and pediatric patients receiving chemotherapy or undergoing hematopoietic stem cell transplantation (HSCT).We conducted a systematic review and performed searches of Ovid MEDLINE, MEDLINE in‐process and Embase; and Cochrane Central Register of Controlled Trials. Studies were included if patients had cancer or were HSCT recipients with anticipated neutropenia, and the intervention was systemic antibacterial prophylaxis. Strategies synthesized included fluoroquinolone vs no antibiotic/nonabsorbable antibiotic; fluoroquinolone vs trimethoprim‐sulfamethoxazole; trimethoprim‐sulfamethoxazole vs no antibiotic; and cephalosporin vs. no antibiotic. Fluoroquinolone vs cephalosporin and levofloxacin vs ciprofloxacin were compared by network meta‐analysis. Primary outcome was bacteremia.Clostridium difficile infection  or invasive fungal disease  but did increase resistance to fluoroquinolone among bacteremia isolates . Heterogeneity in fluoroquinolone effect on bacteremia was not explained by evaluated study, population, or methodological factors. Network meta‐analysis revealed no direct comparisons for pre‐specified analyses; superior regimens were not identified.Of 20 984 citations screened, 113 studies comparing prophylactic antibiotic to control were included. The following were effective in reducing bacteremia: fluoroquinolone vs no antibiotic/nonabsorbable antibiotic (risk ratio (RR) 0.56, 95% confidence interval (CI) 0.41‐0.76), trimethoprim‐sulfamethoxazole vs no antibiotic  and cephalosporin vs no antibiotic . Fluoroquinolone was not significantly associated with increased Fluoroquinolone, trimethoprim‐sulfamethoxazole, and cephalosporin prophylaxis reduced bacteremia. A clinical practice guideline to facilitate prophylactic antibiotic decision‐making is required. Also, adverse effects associated with specific antibiotic classes such as fluoroquinolone‐related musculoskeletal toxicities warrant consideration.Bacteremia and infectious complications are important causes of morbidity and death in children and adults receiving intensive chemotherapy and undergoing hematopoietic stem cell transplant (HSCT).There are many randomized trials that have evaluated systemic antibiotic prophylaxis in patients with cancer and HSCT recipients. Furthermore, the Children's Oncology Group recently published a large randomized trial of 624 high‐risk pediatric patients evaluating levofloxacin prophylaxis, thus substantially increasing the pediatric evidence base around antibiotic prophylaxis.Consequently, our objectives were to determine the efficacy and safety of different prophylactic systemic antibiotics in patients receiving chemotherapy or undergoing HSCT.2For this systematic review, we followed the Preferred Reporting Items for Systematic Reviews and Meta‐Analyses (PRISMA) recommendations for reporting.2.1With the assistance of a library scientist, we searched Ovid MEDLINE, MEDLINE in‐process and Embase; and Wiley Cochrane Central Register of Controlled Trials for articles indexed up to 26 November 2018. The search strategy included the Medical Subject Heading terms and text words that identified patients with cancer or HSCT recipients receiving antibacterial prophylaxis , systemic antibiotic prophylaxis with trimethoprim‐sulfamethoxazole required administration at least once daily. Reasons for excluding studies were as follows: (a) not a full text publication; (b) not a randomized trial with a parallel group design; (c) less than 90% patients receiving chemotherapy for cancer or undergoing HSCT; (d) intervention not a systemic antibacterial agent administered for prophylaxis; (e) antibacterial agent given as peri‐procedural prophylaxis only; (e) duplicate study; and (f) published before 1980.We defined inclusion and exclusion criteria a priori. Studies were included if the manuscript was a fully published primary randomized or quasi‐randomized trial with a parallel group design; if the study compared the administration of a systemic antibacterial agent to any control group as prophylaxis; and if at least 90% of participants were patients undergoing chemotherapy for cancer or HSCT for any indication. As trimethoprim‐sulfamethoxazole can be administered as both prophylaxis against bacterial infection (daily) and Two reviewers (GE and PDR) independently evaluated the titles and abstracts of publications identified by the search strategy and all potentially relevant publications were retrieved in full. Disagreements between the two reviewers were resolved by consensus and adjudicated by a third reviewer (LS) if required. We described agreement with study inclusion between the two reviewers using the kappa statistic and agreement was defined as slight (0 to 20%), fair (21 to 40%), moderate (41 to 60%), substantial (61 to 80%) or almost perfect (81 to 100%).2.3C difficile infection, invasive fungal disease (as defined by each study), musculoskeletal adverse effects and antibiotic resistance. Antibiotic resistance to the intervention antibiotic among all bacteremia isolates tested was abstracted from intervention and control groups. This outcome was not evaluated in studies comparing two systemic prophylactic antibiotics.Two reviewers (GE and PDR) abstracted all data in duplicate and any discrepancies were resolved by consensus. A third reviewer (LS) resolved any outstanding discrepancies if required. Efficacy outcome measures were bacteremia, fever, neutropenic fever, infection‐related mortality, and overall mortality. Episodes of fever and neutropenic fever were abstracted into different categories as some studies described any fever irrespective of neutrophil count while other studies only described fever if it occurred during neutropenia. Adverse outcome measures were Study‐level factors collected included year of study publication, number of randomized groups, country of study conduct, age group , age range, treatment group  and cancer diagnosis or HSCT type. Pediatric studies were defined as those in which all participants were less than 25 years of age while adult studies were defined as those in which all participants were older than 15 years of age.2.4Based upon the available data and clinical relevance, comparisons at the group level focused broadly on fluoroquinolone‐based and non‐fluoroquinolone‐based evaluations. The fluoroquinolone analysis concentrated on the comparison between fluoroquinolone vs no antibiotic or nonabsorbable antibiotic. These control groups were combined as we presumed that nonabsorbable antibiotic would have minimal impact on the efficacy and safety outcomes of interest, and combining them would improve power to identify sources of heterogeneity. However, we also presented the analysis stratified by no antibiotic and nonabsorbable antibiotic control groups separately. No antibiotic controls included both placebo and usual care (no antibiotic prophylaxis). Next, we evaluated the impact of levofloxacin and ciprofloxacin specifically vs no antibiotic. Finally, we compared fluoroquinolone vs trimethoprim‐sulfamethoxazole prophylaxis.In terms of non‐fluoroquinolone‐based comparisons, we compared trimethoprim‐sulfamethoxazole vs no antibiotic, cephalosporin vs no antibiotic, parenteral glycopeptide vs no antibiotic and rifampin plus fluoroquinolone vs fluoroquinolone.For trials with more than two study arms the following hierarchical rules were used to determine the intervention and control groups for conventional meta‐analysis although all arms were used for network meta‐analysis. Control group was chosen in the following order: (a) placebo; (b) no antibiotic; and (c) nonabsorbable antibiotic. If different fluoroquinolones were examined, the fluoroquinolone with the broadest spectrum of activity was considered the intervention.2.5Two reviewers (GE and PDR) assessed study quality and any discrepancies were resolved by consensus. Outstanding discrepancies were resolved by a third reviewer (LS) if required. Study quality was evaluated at the level of the study using the Cochrane Collaboration's tool for assessing the risk of bias in randomized trials.2.62 value, which describes the percentage of total variation across studies due to heterogeneity rather than chance.We combined data at the study level for this meta‐analysis. Synthesis was conducted when there were at least three studies that reported an outcome for a main comparison and at least two studies that reported an outcome within each stratum in the stratified analysis. Data were synthesized using the risk ratio (RR) as the effect measure with its 95% confidence interval (CI). The Mantel‐Haenszel approach was used to estimate treat effects and effects were weighted by the inverse variance. In this analysis, RR < 1 suggests that the intervention is better than the control group. As we anticipated heterogeneity between studies, a random effects model (DerSimonian and Laird)For stratified analysis, we a priori prioritized evaluation of fluoroquinolone based on the large number of available trials, broad Gram‐negative coverage and fewer myelosuppression concerns.For network meta‐analysis, we focused on comparisons of interest in which direct comparison was limited or not available because of the paucity/absence of head‐to‐head trials. These included comparison of fluoroquinolone vs cephalosporin and levofloxacin vs ciprofloxacin. Only studies that assessed any of these antibiotic types were included in the network. Network meta‐analysis was restricted to the primary outcome of bacteremia.Potential publication bias was explored by visual inspection of funnel plots when at least 10 studies were available.We synthesized data for conventional meta‐analysis using Review Manager 5.3 . Network meta‐analysis was conducted using a Bayesian approach using R through the library gemtc.3The flow of study identification and selection is illustrated in Figure Table C difficile infection, invasive fungal disease or musculoskeletal toxicity. However, fluoroquinolone resistance was increased among bacteremia isolates in the prophylaxis group . These results were almost identical to comparison of fluoroquinolone vs. no antibiotic control separately. In evaluating specific fluoroquinolones, levofloxacin significantly reduced bacteremia , fever  and neutropenic fever  without significantly reducing overall mortality  while ciprofloxacin did not significantly reduce bacteremia, neutropenic fever or overall mortality compared to no antibiotic. To evaluate whether specific fluoroquinolone  explained heterogeneity in the effect of fluoroquinolone prophylaxis vs no antibiotic to reduce bacteremia, the P value for interaction was 0.74. Comparison between fluoroquinolone and trimethoprim‐sulfamethoxazole did not show significant differences in bacteremia, fever, infection‐related mortality, or invasive fungal disease.Table Table Table Potential publication bias was observed for the comparison of fluoroquinolone vs. no antibiotic or nonabsorbable antibiotic controls for the outcomes of bacteremia . Supplemental Appendix 4C difficile infection, invasive fungal disease or musculoskeletal adverse effects when compared to no antibiotic or nonabsorbable antibiotic controls. However, fluoroquinolone prophylaxis increased fluoroquinolone resistance in bacteremia isolates. We also found that at least once daily trimethoprim‐sulfamethoxazole prophylaxis was effective in reducing bacteremia and infection‐related mortality when compared to no antibiotic controls although it did increase trimethoprim‐sulfamethoxazole resistance in bacteremia isolates. Cephalosporin prophylaxis reduced bacteremia but did not significantly reduce infection‐related mortality, with antibiotic resistance not being evaluable. The fluoroquinolone prophylaxis effect was similar among sub‐groups evaluated related to bacteremia and overall survival. Finally, fluoroquinolone vs cephalosporin and levofloxacin vs ciprofloxacin had similar effects in terms of bacteremia prevention in network meta‐analysis.In this systematic review, we found that fluoroquinolone prophylaxis was effective at reducing bacteremia, fever and infection‐related mortality without significantly increasing Our systematic review is important as it not only includes the most recent randomized trials, but in addition, evaluates heterogeneity in the fluoroquinolone prophylaxis effect and includes a network meta‐analysis to contrast therapies in which no direct comparative trials exist. Prior systematic reviews focused on specific patient populations such as those with hematological malignancyWe did not find that the following explained heterogeneity in the effect of fluoroquinolone prophylaxis to reduce bacteremia: patient group , age (adult or pediatric), year of publication (early or late), or risk of bacteremia in the control arm (low or high). This suggests that prophylaxis can be considered in a broad group of patients. However, it is important to note that we evaluated RRs in this study and that as the prevalence of bacteremia decreases, the RR associated with prophylaxis may remain constant but the absolute risk reduction could be diminished to the point that prophylaxis is no longer worthwhile. For example, a RR of 0.5 represents both decreasing bacteremia risk from 80% to 40% (probably worthwhile) and decreasing risk from 0.2% to 0.1% (probably not worthwhile).We found that fluoroquinolone prophylaxis did not reduce overall mortality either among the entire cohort or among different sub‐groups. We also found evidence of publication bias in this outcome, further supporting a lack of impact on survival. In contrast to our results, one previous meta‐analysis by Gafter‐Gvili demonstrated that fluoroquinolone prophylaxis significantly reduced overall mortality.In our conventional meta‐analysis, the effect of levofloxacin vs no antibiotic to reduce bacteremia was RR 0.54 while the effect of ciprofloxacin vs no antibiotic to reduce bacteremia was RR 0.88. The P value for interaction for the analysis of fluoroquinolone type was not significant. In support of this finding, network meta‐analysis failed to show a difference between levofloxacin and ciprofloxacin. However, it is important to emphasize that network meta‐analysis may be problematic when patients, controls or interventions are heterogeneous.It is important to note that these studies evaluated the efficacy and adverse effects of systemic antibiotic prophylaxis when administered within a finite time frame of a clinical trial among enrolled participants. An important knowledge gap is the long‐term impact on effectiveness, adverse effects, and resistance outcomes when prophylaxis is administered as routine care over multiple treatment cycles in a universal prophylaxis strategy. These outcomes will be important to measure in future research.C difficile infection included few or no studies, thus limiting or precluding the ability to detect an effect. Fourth, we were not able to synthesize results by neoplasm type based upon how studies were conducted and reported. Finally, we measured antibiotic resistance only against the intervention being evaluated. There are two important issues with this approach. First, we did not measure if resistance rates in the control group were increased, which is plausible with greater environmental exposure to an antibiotic. Second, we did not evaluate resistance to other antibiotics in either group.The strengths of our review include its timely and comprehensive nature as well as its rigorous methodology. Furthermore, inclusion of a network meta‐analysis is another strength. However, this review must be interpreted in light of its weaknesses. First, we did not have access to individual level data, which could have allowed better identification of sub‐groups more likely to benefit (or more likely to be harmed) from prophylaxis. Second, as with all meta‐analysis, there is the potential for bias in terms of which outcomes were reported in individual trials. Third, some syntheses such as the evaluation of In conclusion, fluoroquinolone, trimethoprim‐sulfamethoxazole and cephalosporin prophylaxis reduced bacteremia but did not significantly reduce overall mortality. A clinical practice guideline to facilitate prophylactic antibiotic decision‐making is required.5GE, PDR and LS conceptualized the study, designed the study, collected the data, analyzed the data, and wrote the manuscript; JPM and GT conceptualized and conducted the network meta‐analysis and analyzed this data. All authors critically revised the manuscript for important content. All authors approve the final version of the manuscript.GE, PDR, JPDM, SA, RAA, LLD, BP, SC, GT and LS declare no potential conflicts of interest. BTF's institution receives research funding from Pfizer and Merck, and he serves on a Data Safety Monitoring Board for Astellas. TL has received research grants from Gilead Sciences, is a consultant to Astellas, Basilea, Gilead Sciences, and Merck/MSD, and served at the speaker's bureau of Astellas, Gilead Sciences, Merck/MSD, and Pfizer. Click here for additional data file.