The manufacturing process for ointments typically involves a series of heating, cooling, and mixing steps. Precise control of the level of mixing through homogenization and the cooling rate, as well as temperature at different stages, is important in delivering ointments with the desired quality attributes, stability, and performance. In this work, we investigated the influence of typical plant processing conditions on the microstructure, stability, and sensorial properties of a model ointment system through a Design of Experiments (DoE) approach. Homogenization speed at the cooling stage after the addition of the solvent  was found to be the critical processing parameter that affects stability and the rheological and sensorial properties of the ointment. A lower PG addition temperature was also found to be beneficial. The stabilization of the ointment at a lower PG addition temperature was hypothesized to be due to more effective encapsulation by crystallizing mono- and diglycerides at the lower temperature. The in vitro release profiles were found to be not influenced by the processing parameters, suggesting that for the ointment platform studied, processing affects the microstructure, but the effects do not translate into the release profile, a key performance indicator. Our systematic study represents a Quality-by-Design (QbD) approach to the design of a robust manufacturing process for delivering stable ointments with the desired performance attributes and properties. The typical ointment formulation is an oil-based formulation with a semi-solid texture comprising a solvent phase dispersed in an oil phase stabilized by emulsifying agents. A drug or an active ingredient can be dissolved in the solvent phase and dispersed in the external oil phase. The typical oil phase of ointment comprises petrolatum and stiffening agents and/or emulsifying agents such as glyceride derivatives that provide the desired stiffness/strength to keep the solvent phase dispersed. In addition, to provide emollience for skin, mineral oil is typically used in ointments .The manufacturing process for ointments involves heating to melt the petrolatum and waxes, followed by addition of other liquid components, such as polar solvents, with mixing/homogenization for uniform dispersion. The ointment is then cooled to room temperature before filling into containers such as jars and tubes. It is anticipated that homogenization should affect the distribution or dispersion of the various components at the different stages, and both heating and cooling, along with homogenization, affect the distribution and crystallization of emulsifying wax and stiffening agents around the solvent droplets and the oil phase. Although the term microstructure has been recently used to characterize semi-solid topical products such as ointments, its definition is not clearly articulated and agreed upon . The micBesides influencing the active release and skin permeation behavior, the microstructural properties—including droplet size, structure, and distribution of the stiffening and emulsifying agents around the oil droplet—also affect the sensorial properties as the product is applied to skin. In addition, congealing of petrolatum and distribution of the waxes and stiffening agents as they crystallize would generate a viscoelastic system with different rheological properties. The rheological properties would influence the phase separation of dispersed solvent due to various de-mixing phenomena such as coalescence, sedimentation, and/or creaming, and potentially impact the bio-performance, i.e., in vitro release and skin permeation. While the in vitro release and permeation profile of a drug (flux) influences drug delivery and hence efficacy, sensorial properties are also an important concern, as they affect consumer perception and acceptance of the product.The objective of this study was, therefore, to study the influence of typical plant processing conditions of various unit processes on the microstructure, stability, and sensorial properties of a topical ointment formulation through a systematic DoE approach. The focus of the current study is the effect of processing on the microstructure of the ointment formulation. However, if significant impacts of process conditions on microstructure are observed, the second study would involve an assessment of the performance attributes, such as API release.Both the white petrolatum and paraffin wax used in this study were Ph. Eur grades manufactured by H&R Gruppe  and VWR International (Singapore), respectively. Mono-and-Diglycerides (Geleol™) was purchased from Gattefosse . Propylene glycol (Ph. Eur grade) was purchased from Thermo Fisher Scientific . The active pharmaceutical ingredient, lidocaine, was purchased from Sigma Aldrich (Singapore). All the ingredients were used directly as supplied for ointment preparation.High-speed mixing emulsifying equipment  consisting of a glass-jacketed vessel equipped with a high-speed shearing homo-mixer and a scraper/paddle mixer was used as the representative manufacturing container for ointments. The equipment was capable of manufacturing semi-solid products under vacuum. The temperature was controlled by a water circulator  with an attached thermocouple (Julabo Pt100). The ointment was prepared in two stages, namely compounding and post compounding, as shown in the schematic in Step 1:Charge white petrolatum, paraffin wax and Mono-and-Diglycerides into the jacketed mixing vessel and heat to 75 ± 5 °C while mixing until all materials are fully melted.Step 2:Transfer melted waxes into the main vessel and mix (90 rpm) at 75 ± 5 °C for at least 10 min.Compounding1] to [F4] represent set points of various processing parameters/factors investigated for their effect on ointment properties with a statistically appropriate DoE study.Step 3:1] to cool the contents of the main vessel while mixing at 90 rpm. When the temperature reaches 50 ± 3 °C, homogenize at [F2] for 5 min while continuing mixing at 90 rpm until the temperature reaches [F3]. [F1], [F2], and [F3] are critical process parameters investigated for the effect on drug product quality attributes.The cooling rate is set at [FStep 4:3]. After the addition is completed, homogenize at [F2] for 20 min at every 30 min interval. Homogenization is repeated twice for a total mixing and homogenization duration of 60 min.Dissolve lidocaine in propylene glycol. Charge propylene glycol into main vessel while mixing (90 rpm) at [FStep 5:4] is applied for 5 min when the temperature reaches 36 ± 3 °C.The cooling rate is set at 0.5 ± 0.1 °C/min to cool the contents to 32 ± 3 °C while mixing (50 rpm). Homogenization at  was varied from 2500 to 8000 rpm while the cooling rate [F1] was set at 0.8 °C/min, and the compounding shear temperature [F3] was fixed at 43 °C. The maximum homogenization speed at the final cooling stage [F4] was limited to 5000 rpm because the mixture became highly viscous at that stage, and higher homogenization would result in a significant temperature rise in the mixture. No significant temperature rise was detected in the mixture inside the main vessel, even at the highest homogenization speed and longest duration applied in this study.Runs OT1, OT2, and OT3  technology, and its instability index was determined via SEPView 6 software. Oscillatory rheology measurements were performed to study the viscoelastic behavior of the ointments. Storage modulus (G′) and loss modulus (G″) were calculated from the small angle oscillatory shear (SAOS) measurements. The complex shear modulus (G*), which is an indication of the material stiffness as a function of strain, was then computed by the equation below:cross), the ointment lost its structural integrity, and the viscous characteristics dominated over the elastic response. The viscoelastic parameters obtained for OT1-3 are shown in 4] at 5000 rpm to investigate if varying the cooling rate [F1] and homogenization speed [F2] will shift the formulation properties to the desirable range. The compounding shear temperature [F3] was set at 40 °C, which is the lower limit set by the manufacturer. During PG addition, homogenization was applied twice for 20 min duration, with 30 min between each application. The operating conditions of OT4 to OT9 are shown in cross . Most importantly, OT4 to OT9 exhibited similar stability as assessed by the instability index measured by the LUMiSizer. From these findings, we believe that the homogenization speed of 5000 rpm or above at the final cooling step during the compounding stage may have damaged the microstructure built up in the previous steps, thus masking the effect of the other three operating parameters on the stability of the ointment. Hence, lower homogenization speeds should be employed at step 5 in subsequent experiments.From the results of OT1-OT3, the operating conditions at OT3 yielded the most drastic changes to the properties of the ointment compared to OT1 and OT2. Therefore, the subsequent set of experiments (OT4-OT9) was designed based on OT3 by fixing [F4] was capped at 2500 rpm in the final DoE. The cooling rate [F1] did not significantly affect the properties of the ointment, so the cooling rate [F1] was fixed at 0.8 °C/min, which is more practically achievable in the plant than the faster rate of 1.5 °C/min. Homogenization speed at steps 3 and 4 [F2] was varied from 2500 to 8000 rpm. During PG addition, the homogenization was applied twice for 20 min duration, with 30 min between each application. Propylene glycol addition temperature [F3] was assessed at two levels, 40 °C and 46 °C, which are the lower and upper limits of the manufacturing process. The operating conditions or factors of the final DoE are shown in Based on the preliminary runs OT1-OT9, the homogenization speed at step 5 [F3], the stability of the ointment increases (instability index decreases) when the homogenization speed at step 5 [F4] was lowered. An exception was when the homogenization speed at the previous steps [F2] was at 8000 rpm, [F4] no longer had any influence on the stability. This means that if the mixture is subjected to a high level of shear before or during the addition of propylene glycol, either the formation process of the microstructure is being hindered or the microstructures already formed are destroyed before reaching step 5; therefore, the damage cannot be reversed, even if no homogenization is applied at step 5. Even though our results suggest that no homogenization at step 5 is beneficial to the stability of the ointment, this is not practical in a manufacturing plant. Some degree of gentle homogenization is still required to ensure homogeneity within the mixing vessel and the final ointment product.The instability indices of the ointments produced in the final DoE are shown in 3] was at 46 °C, the homogenization speed at step 5 [F4] did not affect the stability of the ointment since the instability indices were almost the same . Similar to the observation when [F3] was set at 40 °C, at the same homogenization speed at step 5, the instability index increased significantly when the homogenization speed [F2] was increased from 2500 to 8000 rpm. In addition, the mixing duration of the PG addition step also influenced the stability of the ointment. The stability of the ointment was improved when the mixing duration was reduced from 60 min to 30 min.When the propylene glycol addition temperature . This can be better visualized graphically in cross decrease with increasing homogenization speed [F2], regardless of the homogenization speed at step 5. This shows that shear at the steps before step 5 also plays a part in controlling the rheological properties of the ointment. The same can also be observed for samples OS-7 to OS-12.From the rheological properties listed in −1 and then reduced back to 0 using a stepwise shear ramp. −1 are also shown in To understand why step 5 heavily influences the rheological properties and stability of the ointment, thixotropy tests were performed on petrolatum, which is the dominant component in the formulation. The tests were conducted using a rough parallel plate geometry with a 1 mm gap between plates. The shear rate was increased from 0 to 100 sThe effect of PG addition mixing duration at 46 °C on complex shear modulus and crossover stress is shown in 4]  is the same as that observed in textural properties of the ointments. This similarity is because textural properties are largely dependent on the bulk rheological properties of the ointments.The sensorial attributes measured for ointments in the final DoE are shown in 4] . Going fperature , which a4], PG additional temperature [F3], and PG addition mixing duration on the CoF are illustrated graphically in The coefficient of friction (CoF) as a function of probe displacement on the bioskin plate without the application of ointment is shown in v/v ethanol:water solution was chosen as the receptor medium to ensure that the solubility of lidocaine is high enough to provide sink condition for the release studies. In vitro release studies were performed using the most stable (OS5-4) and least stable (OS5-8) ointments in the final DoE to investigate if the stability of the ointment would affect the drug release performance. The assumption is that the less stable formulation is due to inadequate microstructure and not appropriate rheological properties. Lidocaine, a local anaesthetic agent, was chosen as the model drug for this study. It was predissolved in propylene glycol and incorporated into the ointment during PG addition at step 4 of the compounding stage  are negatively correlated with linear rheological response and the measured textural properties. This suggests that lower homogenization speeds should result in ointments that are more rigid and less susceptible to shear damage (higher complex shear modulus and crossover stress) while giving a skin feel of being more adhesive, firmer, and more cohesive and spreadable. It is clear from the biplot that the textural properties are correlated positively with the linear rheological response , as their vectors form acute angles. Among the textural properties, adhesive force is most highly correlated with complex shear modulus and crossover stress.Given the large number of measured properties and operating conditions, PCA analysis was performed to understand how the various operating parameters are correlated to the measured properties. The scree plot shown as the inset in 3] is also positively correlated with the instability index, although not as highly correlated as the homogenization speed, since the angle between the instability index and PG addition temperature is larger than the angles between the instability index and homogenization speeds. Unlike homogenization speed, PG addition temperature correlates highly with the coefficient of friction. Hence, if PG is added at a lower temperature, a more stable and lubricating ointment can be achieved, although an ointment with a lower coefficient of friction may also be perceived as greasy during application on skin. PG addition temperature does not have much influence on the rheological properties and the pick-up characteristics , although it correlates negatively, to a certain extent, with the rubout characteristics (cohesion strength and spreadability).PG addition temperature  can also be explained by our proposed hypothesis. In step 5, the MDG crystals begin to crystallize and encapsulate the PG droplets. Homogenization, subsequently, may disrupt the formation process of the microstructure or destroy the microstructure already formed. Therefore, we observed that a lower step 5 homogenization speed resulted in more stable ointment.The effect of step 5 homogenization speed [FThis study demonstrated the significant effects that selected processing parameters have on the critical quality attribute of ointment drug product. However, not all processing parameters are equal and have an equivalent significant effect on all or some critical quality attributes, including performance, stability, and sensorial properties. It appears that the temperature of addition of solvent and homogenization speed during cooling at the compounding stage had the most significant effect on rheological properties, stability, and sensorial properties. These were attributed to the complex dynamics of stabilizing agents (MDG) crystallizing at different temperatures during/after addition of solvent to enable droplet encapsulation and stabilization. Once the optimal microstructure is formed, additional homogenization (speed and time) may disrupt the structure to cause instability. Rheological properties and instability, as measured by the LUMiSizer, appear to correlate well and provide insight into the formed microstructure of the ointment DP. However, based upon similar in vitro release profiles for the suboptimal DP compared to the most stable DP, it appears that the variations in microstructure in the ranges affected by changes in the processing parameters studied may have no influence on delivery performance. This suggests that it is difficult to obtain an ideal product profile from key quality attributes, including performance, stability, and sensorial properties, by modifications of process alone. From a manufacturing scale-up perspective, we have demonstrated how a typical semi-solid manufacturing process can be studied and optimized to achieve the target product profile from a quality and performance attributes perspective.


Pseudomonas aeruginosa; however, real-world comparative-effectiveness data are lacking.Ceftolozane-tazobactam (CT) and ceftazidime-avibactam (CZA) are front-line agents for treatment of multidrug-resistant (MDR) P. aeruginosa. CT and CZA patients were matched 1:1 within each study site by the presence/absence of septic shock/severe sepsis, infection site, and time to treatment initiation. The primary outcome was clinical success at day 30 defined as survival, resolution of signs/symptoms with the intended treatment course, and absence of recurrent infections. Patients with cystic fibrosis or COVID-19 infection within 90 days were excluded.CACTUS is a retrospective, matched, multicenter study to compare the efficacy of CT and CZA among patients with bacteremia or pneumonia due to MDR Table 1). The overall median age was 61 years, 61% were male, and the median Charlson score was 5. At study drug initiation, 77% of patients were in the ICU, 67% received mechanical ventilation and the median SOFA score was 7. 79% of patients were treated for pneumonia; 72% of which occurred in ventilated patients. The median time from index culture to treatment initiation was 72 hours in both groups; CT patients were more likely to receive a prolonged infusion of ≥3 hours . Clinical success occurred in 62% and 55% of patients receiving CT and CZA, respectively . Corresponding rates of success for pneumonia were 63% and 52%, respectively . All-cause, 30-day mortality rate was 20% and 19%, respectively. Microbiologic failures, recurrent infections, and development of resistance within 90 days were similar between groups. Time to a composite endpoint of recurrent infection or death within 90 days was similar between groups in the overall analysis and the subgroup of patients with pneumonia .234 patients were included from 20 sites. Patient demographics, severity of illness, infection types, and treatment durations were similar for patients treated with CT or CZA , Merck: Advisor/Consultant Erin K. McCreary, PharmD, Abbvie: Advisor/Consultant|Ferring: Advisor/Consultant|GSK: Honoraria|La Jolla (Entasis): Advisor/Consultant|LabSimply: Advisor/Consultant|Merck: Advisor/Consultant|Shionogi: Advisor/Consultant|Shionogi: Honoraria Christopher Polk, MD, ViiVHealthcare: Job change to work for ViiV as Medical Director Michael J. Satlin, MD, AbbVie: IDMC member|Biomerieux: Grant/Research Support|Merck: Grant/Research Support|SNIPRBiome: Grant/Research Support Michael Veve, PharmD, MPH, National Institutes of Health: Grant/Research Support|Paratek Pharmaceuticals: Grant/Research Support jason M. Pogue, PharmD, AbbVie: Advisor/Consultant|Entasis: Advisor/Consultant|Ferring: Advisor/Consultant|GSK: Advisor/Consultant|Merck: Advisor/Consultant|Merck: Grant/Research Support|Qpex: Advisor/Consultant|Shionogi: Advisor/Consultant


Routinely-collected healthcare data provide a valuable resource for epidemiological research. Validation studies have shown that for most conditions, simple lists of clinical codes can reliably be used for case finding in primary care, however, studies exploring the robustness of this approach are lacking for diseases such as idiopathic pulmonary fibrosis (IPF) which are largely managed in secondary care.Using the UK’s Clinical Practice Research Datalink (CPRD) Aurum dataset, which comprises patient-level primary care records linked to national hospital admissions and cause-of-death data, we compared the positive predictive value (PPV) of eight diagnostic algorithms. Algorithms were developed based on the literature and IPF diagnostic guidelines using combinations of clinical codes in primary and secondary care (SNOMED-CT or ICD-10) with/without additional information. The positive predictive value (PPV) was estimated for each algorithm using the death record as the gold standard. Utilization of the reviewed codes across the study period was observed to evaluate any change in coding practices over time.A total of 17,559 individuals had a least one record indicative of IPF in one or more of our three linked datasets between 2008 and 2018. The PPV of case-finding algorithms based on clinical codes alone ranged from 64.4% (95%CI:63.3–65.3) for a “broad” codeset to 74.9% (95%CI:72.8–76.9) for a “narrow” codeset comprising highly-specific codes. Adding confirmatory evidence, such as a CT scan, increased the PPV of our narrow code-based algorithm to 79.2% (95%CI:76.4–81.8) but reduced the sensitivity to under 10%. Adding evidence of hospitalisation to the standalone code-based algorithms also improved PPV, . IPF coding practices changed over time, with the increased use of specific IPF codes.High diagnostic validity was achieved by using a restricted set of IPF codes. While adding confirmatory evidence increased diagnostic accuracy, the benefits of this approach need to be weighed against the inevitable loss of sample size and convenience. We would recommend use of an algorithm based on a broader IPF code set coupled with evidence of hospitalisation.The online version contains supplementary material available at 10.1186/s12890-023-02550-0. Idiopathic pulmonary fibrosis (IPF) is characterised by worsening respiratory symptoms  and irreversible loss of lung function due to progressive architectural distortion and aberrant cellular proliferation within the interstitium of the lung. The prognosis for people diagnosed with this chronic lung condition is poor, with a median survival of only 3–5 years if left untreated –3. GlobaAnalysis of primary care data for 2000–2012 suggests a UK IPF prevalence at the higher end of global estimates, between 19.9 and 38.8 cases per 100,000 people, with approximately 5,000 new cases diagnosed each year  . DespiteWhile routinely-collected healthcare data represent a valuable resource for epidemiological study and research, their utility relies on the quality of case ascertainment. Validation studies are important to assess the reliability of diagnostic coding of diseases and the majority of validation studies conducted to date indicate that case ascertainment based on the use of simple lists of clinical diagnostic codes in primary care records results in acceptable positive predictive values (PPVs) for the majority of diseases and conditions, especially those that are predominantly managed in primary care . HoweverThe aim of this study was to assess the reliability of recording IPF in a UK primary care database. Specifically, to determine whether a list of clinical diagnostic codes alone was sufficient or whether a more complex algorithm – one that includes additional information such as radiology or hospital admission data is required to improve the accuracy of IPF case identification in primary care data. To do this, we used ONS mortality data as our reference or “gold standard”, relying on the assumption that a person with IPF on their death certificate is highly likely to have been diagnosed with IPF during their lifetime.We used data from the Clinical Practice Research Datalink (CPRD) Aurum database (November 2020 build). This dataset contains pseudonymized primary care electronic health records for nearly 40 million patients, including around 13 million current patients representing 19% of the UK population . CPRD AuCPRD Aurum primary care data are routinely linked to a number of other patient-level datasets, including Hospital Episode Statistics (HES) and ONS mortality data using a deterministic methodology . Linked This analysis uses a cohort study design. The study population was drawn from patients registered at English CPRD practices that had consented to HES/ONS linkage. To be eligible for inclusion in the study patients had to have evidence of a diagnosis of IPF in one or more of our three linked electronic health datasets, CPRD Aurum, HES APC or ONS, and be aged at least 18 years at the start of the study period (1 January 2008–31 December 2018) and prior to their IPF diagnosis. A period of “useable” follow up (1 day) was defined for each patient based in their primary care record, starting on the latest of 1 January 2008, date of IPF diagnosis (the earliest IPF code in Aurum), start of current registration at a linked GP practice or date of 18th birthday and ending on 31 December 2018, date of death, last day of data collection at the practice or patient’s transfer out date, whichever came first.https://github.com/NHLI-Respiratory-Epi/SNOMED-CT-codelists). In short, initial text-based search terms were derived in consultation with two respiratory clinicians with expert knowledge of ILDs. Codes found by searching of the Aurum medical browser using these search terms were cross-checked against published IPF code lists, and any codes not captured by the test-based search added to form a list of potential codes [A set of clinical SNOMED CT diagnostic codes denoting IPF created for this study was used to define cases. This code set was developed using an established methodology . We defined two IPF primary care cohorts, one based on the “broad” set of Aurum codes, the other on the “narrow” Aurum code set.Consistent with previous electronic health records-based studies that have used sets of clinical codes to define IPF cohorts, , 8, 16 ahttps://github.com/NHLI-Respiratory-Epi/Validation-of-the-recording-of-Idiopathic-Pulmonary-Fibrosis-in-routinely-collected-electronic-healt) to define IPF hospitalizations and deaths in HES APC and ONS mortality data, respectively. To be included in the HES APC cohort, a patient had to have one of the three qualifying ICD-10 codes recorded as either the first or second clinical diagnosis in any “episode” of hospital care within their stay (“spell”) in hospital within their follow up period. We chose to restrict our case definitions to the first and second diagnostic codes in order to be more certain that we were selecting patients where IPF was the reason for their admission. In HES-APC data, codes mentioned further down the list of recorded diagnoses are more likely to reflect coexisting conditions/comorbidities that might impact hospital care and are known to have lower diagnostic accuracy. In a sensitivity analysis, we also created a cohort which included patients who had a least one qualifying ICD-10 IPF code in any diagnostic position .We used the International Classification of Diseases, 10th revision (ICD-10) codes, J84.1, J84.8 and J84.9  and comorbidities  as recorded in primary care. Smoking status was based on the closest available record to the date of IPF diagnosis; patients were assumed to have a given comorbidity if they had a relevant diagnostic code at any point prior to their IPF diagnosis. All codelists are available via GitHub .To gain insight into possible changes in coding practices in primacy care over time, we examined the frequency of use of IPF codes in Aurum for each year of our study period (2008–2018).We totalled the number of patients who met our cohort inclusion criteria in each of our three concurrent linked data sets using the case definitions described above. To assess concordance, the Aurum and HES-APC cohorts were restricted to those who had died within our study period. We investigated the concordance of recording of IPF in ONS, Aurum and HES-APC in terms of the number of patients with at least one IPF record in (i) just Aurum, (ii) just HES-APC and (iii) just ONS, (iv) both Aurum and HES-APC, (v) Aurum and ONS, (vi) HES-APC and ONS, and (vii) Aurum, HES-APC and ONS.In total we defined eight diagnostic algorithms (DAs) based on either our “broad” or “narrow” clinical code sets plus any one or more of the following: evidence of HRCT (high-resolution computed tomography) of the thorax, absence of other known causes of interstitial lung disease , and/or evidence of hospitalisation for IPF, i.e. record in HES-APC Table .PPV was calculated as the number of IPF cases correctly identified by the algorithm (i.e. confirmed by a record in ONS) divided by the total number of IPF cases identified by that algorithm. Sensitivity was defined as the number of “true” IPF cases correctly identified by the algorithm divided by the total number of ONS IPF deaths. Given that a death is our reference standard, this analysis was limited to those patients who died.All analyses were conducted using Stata version 17.0.Between 2008 and 2018, the most frequently used coding terms were; diffuse pulmonary fibrosis, pulmonary fibrosis, idiopathic fibrosing alveolitis and idiopathic pulmonary fibrosis. These four codes combined accounted for nearly 80% of all GP-coded IPF consultations during this period , of whom 9,498 died (of any cause). A slightly higher number, 14,719 had evidence of at least one hospital admission for IPF. Among this population, 10,714 people died. Our study population thus comprised a total of 17,559 individuals who died and had a IPF record in at least one of our three linked datasets  within the time frame of our study. The patient attrition for the three sources is in Supplementary Fig. Sn = 4,304) had evidence of IPF in all three of our linked concurrent data sets  also had at least one clinical code denoting IPF in Aurum prior to death (or within 60 days after their death). Slightly more, 6,651 or 58.9% of the ONS population had been admitted to hospital ostensibly for IPF at some point prior to their death. Although only 38.1%  of our ONS IPF population had evidence of an IPF diagnosis in both Aurum and HES-APC, 74.9%  had IPF records in either Aurum or HES-APC , around a third  had no mention of IPF on their death certificate. The most common underlying reason for death in these patients was pneumonia, bronchopneumonia or malignant neoplasm of unspecified part of bronchus or lung . Other frequently reported causes were chronic obstructive pulmonary disease (COPD) (J44.9), “other general symptoms and signs” (R68.8), and “respiratory failure, not elsewhere classified” (J96.9). For those patients who were hospitalized with IPF but had no mention of IPF on their death certificate , the top three underlying causes were again J18.9, J18.0 and C34.9; for this group other frequently reported causes included myocardial infarction, heart failure and sepsis .Conversely, of the Aurum IPF patients who died  reduced the absolute number of patients in multiple datasets . Similarly, the number patients who were admitted to hospital with a diagnosis for IPF who also died of IPF, reduced to 4,756 or 44.4% of the HES-APC population  when the wider definition of the ONS population was used). Concordance across all three data sets also reduced when measured in terms of the absolute number of patients, from 4,304 to 3,119, which represents just 19.5% of the total study population . On the basis of this analysis, which suggests that a higher proportion of Aurum and HES-APC cases are captured and “confirmed” in ONS when we define an ONS IPF death as one in which IPF is listed anywhere on the death certificate (as opposed to the underlying cause), we adopted the former definition as our gold standard.Restricting our ONS reference population to those who had IPF listed as their underlying cause of death n = 7,09 reducedThe results of our second sensitivity analysis, in which we assessed the concordance of extending our HES-APC case definition to include patients who had episodes of hospital care in which IPF was listed further down the list of clinical diagnoses (beyond the first and second positions) impacted the diagnostic accuracy quite significantly. When we included patients with IPF codes  in the top three diagnostic positions the size of the HES-APC cohort increased from 10,714 to 13,957, but the proportion of patients who also had a record in ONS decreased from 62.1 to 55.8%  but reduced the sensitivity to just 28.2% .Among the diagnostic algorithms based on a broad list of IPF codes (DA1 and DA2), there was little variation in the estimated PPVs. The PPV for DA1 was 64.3%  with a sensitivity of 53.5% . Refining the criteria, that is, restricting cases to people with no known causes of ILD and who also had evidence of a HRCT scan (DA2), had a modest effect on the PPV , but a proportionally greater impact on the number of patients identified. Adding stricter case finding criteria halved the sample size from 1,828 to 891, reducing the sensitivity to under 10% , produced notably higher PPVs compared with the corresponding broad-code-based algorithms (PPVDA8 =81.8%) but a sensitivity of just 8.6% (Table The probability that a person with IPF codes in both Aurum and HES- APC (DA7) “truly” has IPF (measured against a death in ONS), was estimated to be 78.4% , Using a narrow set of Aurum codes plus evidence of a hospitalisation for IPF gave the highest PPV of all eight algorithms (PPVTable DA6=62.4% (95% CI: 61.1–63.0) and the highest by an algorithm based on a limited set of primary care clinical codes coupled with evidence of a hospitalisation for IPF (PPVDA8=to 81.8% (95%CI: 79.5–84.0). While the two IPF patient cohorts defined by these two algorithms do not differ significantly in terms of their demographic characteristics or comorbidity profiles, the former (the secondary care-based cohort) has a slightly lower median survival time, implying that patients with more advanced disease might be overrepresented in a cohort derived using this algorithm.The primary aim of this study was to investigate the diagnostic accuracy of the recording of IPF in UK primary and secondary care records. The lowest PPV was achieved using an algorithm based on secondary care data only  achieved a reasonable PPV of 64.4%. Restricting the code set to a smaller number of highly specific IPF diagnostic codes (DA3) increased the PPV to 74.9%, similar to other conditions , 17. HowAttempts to improve diagnostic accuracy of our baseline broad and narrow clinical code-based algorithms by adding additional criteria produced only marginal improvements in the PPVs but had a significant impact on sensitivity. Adding evidence of a hospital admission had a relatively greater impact on the PPV of our baseline algorithms but without compromising sample size to the same extent. Therefore, we would recommend, that algorithms based on a narrow set of highly specific IPF clinical codes would be appropriate for studies which demand high case validity. For studies where sample size is a primary consideration, and certainly for estimating IPF incidence and prevalence, use of a broader code list combined with evidence of a hospitalisation represents a good compromise between acceptable case validity and capture (DA7).A relatively high validity of a positive IPF diagnosis in primary care is not totally unexpected, even though most GPs will have limited experience of IPF . It is u%) had been hospitalised for IPF prior to their death.The relatively high baseline PPV of a hospitalisation for IPF relative to a record in CPRD Aurum (62% v 64%) against an ONS death was consistent with earlier research which suggests that a high proportion of hospitalised patients who were assigned an IPF diagnostic code did indeed have the disease (c. 80%) . HoweverWe noted some improvement in the PPVs for algorithms which included additional information relative to our baseline clinical-code-only algorithms, but this was relatively modest. This mirrors findings of other validation studies, including one for COPD that likewise reported that requiring evidence of spirometry and/or COPD medications only marginally improved the accuracy of simple diagnostic code-based algorithms (89.4% vs. 87.5% vs. 86.5%) . Other sOver the period of this study, we observed shifts in code use frequencies, most noticeably a gradual decline in the use of codes associated with now obsolete terms such as “cryptogenic fibrosing alveolitis” and a corresponding increase in codes associated with the term “idiopathic pulmonary fibrosis”. It is important to be aware of such trends when selecting appropriate codes for IPF case finding, especially for studies which cover a 10-year-plus time span. While changes in code frequencies related to changes in nomenclature are easier to rationalise, it is likely that some code shifts are being driven by more subtle or nuanced changes in GP coding practice that are harder to predict. Anecdotal evidence suggests that in the UK some GPs select a more generic code to document a given condition, especially if that code appears at the top of a drop-down menu. The shift towards the use of more specific codes for IPF might be a consequence of the introduction of antifibrotics and a desire of GPs to ensure that their patients met the eligibility criteria for prescription of an antifibrotic.This study has several strengths and limitations. Its main strength stems from the use of a large population-based, representative healthcare datasets. Secondly, by selecting a study period which spans the period 2008–2018, we have been able to assess whether there have been any changes in coding practices over time, in the wake of the introduction and adoption of updated international IPF guidelines in 2011/18and the licensed use of anti-fibrotic drugs . The incWe also acknowledge that our recommended approach to case finding likely risks including some cases that have a non-IPF fibrotic ILD. Given a tendency among some healthcare practitioners noted previously to choose less specific codes, this is to a certain extent inevitable and represents a further limitation. We would advise researchers whose study question requires a highly specific IPF study population to also consider excluding people who have known causes of pulmonary fibrosis, such as a connective tissue disease.This is the first study to validate the completeness and quality of the recording of IPF in routinely-collected health data from the UK. It is important to conduct studies of this type and ensure the reliability of coding and case finding in UK electronic health records, given that these data are used to estimate disease prevalence and thus inform health service planning and resource allocation. More specifically, this work has demonstrated that for many observational research purposes, it is acceptable/feasible to use a simple set of clinical codes to define a cohort of patients with IPF in primary care data alone. However, those wishing to conduct observational research using UK health data are advised to tailor their choice of individual codes to their particular research objectives and study design and to consider the relative merits of using linked hospital data to improve diagnostic accuracy of a primary care study population.Additional file 1.


These results provide a new strategy for the development of graphene array-based room-temperature terahertz photodetectors.Graphene, known for its high carrier mobility and broad spectral response range, has proven to be a promising material in photodetection applications. However, its high dark current has limited its application as a high-sensitivity photodetector at room temperature, particularly for the detection of low-energy photons. Our research proposes a new approach for overcoming this challenge by designing lattice antennas with an asymmetric structure for use in combination with high-quality monolayers of graphene. This configuration is capable of sensitive detection of low-energy photons. The results show that the graphene terahertz detector-based microstructure antenna has a responsivity of 29 V·W Terahertz (THz) waves are characterized by frequencies ranging from 0.1 to 10 THz, spanning the region between infrared and microwave regions of the electromagnetic spectrum. The distinct optical and electrical properties of these waves make THz technology highly promising for a range of applications in various domains, such as biomedicine, information security, environmental monitoring, security inspection, non-destructive testing, and defense technology ,3,4,5,6.5 cm2/V·s) for monolayer graphene, a bandgap of zero, broad spectral response, and limited surface dangling bonds, it has garnered significant attention in the field of photonics [Graphene, a seminal two-dimensional material composed of monolayer carbon atoms, has garnered significant interest due to its distinctive structural attributes. Boasting high strength, exceptional conductivity, elevated carrier mobility  from a copper substrate to a substrate. The specific method is as follows: the graphene grown on a copper substrate is coated with polymethyl methacrylate (PMMA) by spin coating, and then the copper substrate is etched as the base with ferric chloride solution. The etching time is about twenty-four hours, and the sample is cleaned with dilute hydrochloric acid. Then, the graphene covered with PMMA is transferred to the prepared Si/SiOrate see .−1, in agreement with previous studies, attesting to its high quality and serving as a basis for the development of high-performance detectors [y axis. It is important that, for computational efficiency, the boundary conditions are set as periodic and the material comprising the antenna is assumed to be a perfect electrical conductor (PEC). The electromagnetic field distribution of the structure is shown in As shown in etectors ,35. GrapThe electrical properties of the device were evaluated with a semiconductor parameter analyzer, as shown in As shown in In addition, the optical response of the device was studied at different power density and bias voltage conditions. In VR) is calculated as:AR represents photocurrent responsivity, r, phI, P0, and S0 represent resistance, photocurrent, power density, and effective area of the detector, respectively [−1 and 29 V·W−1, respectively. Additionally, we validated that the device operates in self-powered mode, with good stability in the photocurrent waveform over time. Applying a small bias voltage of 0.1 V significantly improved the photocurrent, however, graphene’s inherent nature as a semi-metal inevitably increased the dark current, which is detrimental for detecting weak low-energy photons. The asymmetric graphene effectively absorbed THz light under the modulation of grid-like microstructure, generating more photon-generated carriers. Then, the internal potential, driven by the temperature gradient, can effectively drive the nonequilibrium carrier, providing a basis for the device to generate high photocurrent values under zero-bias conditions. Our detector demonstrates high self-powered photo-detection ability under 0.04 THz and 0.12 THz radiation, offering a pre-condition for realizing arrayed monolayer graphene THz detectors. Responsivity is an important indicator for evaluating the sensitivity of photodetectors. Thus, the photocurrent voltage responsivity (ectively . The resj) and dark current-induced noise are considered [Bk is the Boltzmann constant, T is the thermodynamic temperature, r is the device resistance, q is the elementary charge, and darkI is the dark current. The smaller the value of NEP is, the better the performance of the detector will be. The NEP value calculated is only 8.5 pW/Hz1/2 without bias voltage , and equivalent noise power of less than 8.5 pW/Hz1/2 in the self-powered mode. This work provides a viable approach to large-scale device integration and is one of the potential candidates for implementing graphene terahertz detection in focal plane arrays.In summary, by introducing asymmetric optical coupling, we design microstructured antennas to achieve a non-uniform distribution of the terahertz local field. In addition, the artificial grid antenna can focus the terahertz field at the microscale, increasing the interaction between the monolayer graphene and terahertz light and achieving sensitive detection of low-energy photons. At room temperature, the graphene-based photodetector demonstrates a voltage responsivity of 29 V·W


The Iberian harbour porpoise is currently threatened by accidental captures in fisheries (bycatch). Because monitoring cetacean bycatch is particularly challenging, marine mammal stranding networks may provide important information. Between 2000 and 2020, 756 porpoises washed ashore (stranded) on Portuguese and Galician coastlines. The post-mortem analyses of stranded porpoises revealed that the most representative cause of stranding  was fishery interaction and another 10.99% was identified as probable fishery interaction. Combining this information with porpoise annual abundance estimates in Portugal available for the period between 2011 and 2015, an estimated average of 207 porpoises died each year due to bycatch in Portuguese waters alone. This estimate greatly surpassed the maximum annual number of porpoise strandings due to human interactions (22 porpoises) that were predicted to occur without negatively affecting the population in Portuguese waters. To prevent porpoise bycatch in Portugal and Spain, fishing effort management is needed and new activities at sea must be carefully considered. Moreover, appropriate measures directed at the conservation of the Iberian harbour porpoise are crucial to ensure the restoration and survival of the population.The Iberian harbour porpoise population is small and fisheries bycatch has been described as one of its most important threats. Data on harbour porpoise strandings collected by the Portuguese and Galician stranding networks between 2000 and 2020 are indicative of a recent mortality increase in the western Iberian coast . Overall, in Portugal and Galicia, individuals stranded due to confirmed fishery interaction represented 46.98% of all analysed porpoises, and individuals stranded due to probable fishery interaction represented another 10.99% of all analysed porpoises. Considering the Portuguese annual abundance estimates available between 2011 and 2015, it was possible to calculate that an annual average of 207 individuals was removed from the population in Portuguese waters alone, which largely surpasses the potential biological removal (PBR) estimates  for the same period. These results are conservative and bycatch values from strandings are likely underestimated. A structured action plan accounting for new activities at sea is needed to limit the Iberian porpoise population decline. Meanwhile, there is an urgent need for a fishing effort reorganization to directly decrease porpoise mortality. Phocoena phocoena meridionalis, has already been proposed to include the so-called Iberian and Mauritanian harbour porpoise groups [Recent genetic studies revealed that the harbour porpoise population in the upwelling areas of the Iberian Peninsula is small and isolated ,2. In fae groups . The smae groups . The hare groups  and endae groups .Fisheries bycatch has been described as the most important threat to small cetaceans ,7,8, parHowever, estimating bycatch rates from strandings is also problematic. Cetaceans that die at sea do not necessarily strand ashore , and theThe objective of the present study was to assess the evolution of harbour porpoise strandings registered in Portugal and Galicia across two decades (2000–2020), particularly focussing on the temporal evolution of porpoises stranded due to fishery interaction. Finally, we also aimed to estimate an annual porpoise population removal rate based on fishery interactions related to mortality identified in porpoise strandings in Portugal.Data recorded between 2000 and 2020 by the National Strandings Network in Portugal  and the Galicia Strandings Network  were used in the present study.Results concerning Portugal are divided between northern and southern sectors because the northern sector had a more constant and dedicated effort from the regional strandings network since the year 2000 , particularly between 2010 and 2020 (SPVS and University of Aveiro). The southern sector had a more dedicated effort in the Algarve region, between 2010 and 2017 (SPVS) and partly in 2020 (University of Algarve). In areas and periods with no dedicated effort, strandings were monitored by maritime police officers or park rangers. In Galicia, the strandings network’s effort was constant during the study period.Both in Portugal and Galicia, detailed necropsies were performed by trained technicians and the cause of stranding was determined based on full external and internal examination . Cause oNeonates were identified by the presence of vibrissae, foetal folds, or umbilical cord, including cord scars . Calves All strandings locations were plotted in QGIS 3.16.16-Hannover  using WGMatrix heatmaps were built as an initial approach to visualize the monthly, seasonal and long-term temporal variations of the total number of harbour porpoise strandings per geographical area  using ggplot2 package version 3.4.2  in R. LoGeneralized additive models (GAMs) were then used to evaluate the influence of explanatory variables on harbour porpoise strandings along the western Iberian coastline  between 2000 and 2020. All data series were explored for outliers, collinearity, and heterogeneity of variance and plotted for visualization of potential relationships between response and explanatory variables . The numbycatch) was estimated [strandings)) were also estimated based on the number of stranded porpoises evaluated for bycatch evidence (strandings), as described in bycatch), carcass detection rate  and APRstrandings were also recalculated considering the total number of stranded porpoises instead of the number of stranded porpoises evaluated for bycatch evidence. Whereas using the total number of observed porpoise strandings to calculate EAM accounts for possible bycaught individuals which could not be evaluated for bycatch (decomposition stage > 3), a more accurate APR estimate can be obtained considering only the number of stranded porpoises which were evaluated for bycatch evidence, despite the lower number of individuals included in the analysis. All parameters were calculated annually and for the overall period (2011–2015). Estimated mortality rates and the average removal values are expressed as 95% confidence intervals.A deeper analysis was dedicated to porpoise strandings data in Portugal, particularly because porpoise annual population abundances were available from 2011 to 2015  in Portustimated  and is mN) and the respective coefficient of variation (CVN) were obtained from aerial surveys performed in Portuguese waters during the period 2011–2015 [Nmin is the minimum population abundance estimate  estimated by:It was also possible to estimate the potential biological removal (PBR) in Portuguese waters because population abundance estimates (011–2015 . To esti011–2015 ), the fomax is the maximum annual net recruitment rate; f is a recovery factor between 0.1 and 1.Rmax) of 4% is the default value used for small cetaceans [f value for depleted and threatened stocks and stocks of unknown status (0.5) was used instead of the f value for endangered or declining species (0.1) [The maximum net recruitment or population growth rate (Retaceans . In ordees (0.1) . Considering the overall dataset, between 2000 and 2020, 756 stranded harbour porpoises were reported on the western Iberian coast  . p < 0.001), year (p < 0.001) and geographical area (p < 0.001) (r2 = 25.3%) on the number of porpoise strandings in the western Iberian coast. Based on the data analysed, in Portugal, the number of stranded porpoises  was more than double the number of porpoises stranded in Galicia  during the study period. In Portugal, most porpoise strandings were registered in the northern sector (n = 453), while in Galicia the highest densities of strandings occurred in the southern Rias Baixas (n = 115) (GAM results emphasized a significant effect of month (n = 115) . The sign = 115) . With ren = 115) a.p < 0.001) and year (p < 0.001) (r2 = 28.8) on the number of porpoise strandings. On the Portuguese coast, the temporal trend in porpoise strandings was similar to the overall dataset with a significant increase over time  and year (p < 0.026) (r2 = 14.7%) on the number of porpoise strandings. Contrary to the monthly pattern observed in Portugal, the peak of porpoise strandings on the Galician coast occurred in winter (January and February), followed by a sharp decrease until September , 40.96% of the analysed porpoises presented evidence of fishery interaction, and porpoises showing probable evidence of fishery interaction represented another 7.23%, out of the 83 analysed porpoises.strandings of 9.19% (CI = 5.25–16.10%) (bycatch), corresponding to an APRstrandings of 5.55% (CI = 3.17–9.72%)  amounts to 207 individuals, corresponding to an APR–16.10%) . However7–9.72%) .For the period between 2011 and 2015, the overall PBR estimates indicate an “acceptable” average annual removal in Portuguese waters of 22 porpoises (CI: 12–43). The maximum annual PBR estimate of 29 porpoises (CI: 14–60) was obtained in 2013 .The present study revealed that 46.98% of all analysed porpoises in Portugal and Galicia presented evidence of fishery interaction, and another 10.99% of all analysed porpoises presented probable evidence of fishery interaction. Also, we estimated that an annual average of 207 individuals were removed from the population in Portuguese waters alone between 2011 and 2015.Considering the western Iberian Peninsula, over the last two decades, most harbour porpoise strandings were concentrated in the northern sector of the Portuguese coast and in the southern Rias Baixas in Galicia (Spain). The increasing incidence of porpoise strandings particularly during the last decade partly relates to the improved response of the national strandings network in Portugal, as already discussed in other regions ,46,47. NThe number of strandings may be related to biotic  or abiotic variables , but is also dependent on other factors such as stranding probability and detection rate, which in turn are influenced by environmental variables  ,24. A fuAs an example of the potential effect of different variables on porpoise strandings, the highest number of porpoises stranded in Portugal in 2014 (particularly in March and April and then in August) may be related to the higher porpoise abundances estimated in October 2013 . HoweverA concerning amount of porpoises stranded with evidence of fishery interaction in the western Iberia area (46.98%) emphasises the need for bycatch mitigation measures to decrease porpoise mortality. Note that another 10.99% were conservatively identified as stranded due to probable fishery interaction and, furthermore, over half of the stranded porpoises were not considered in the cause of stranding evaluation to avoid inaccurate identification of fishery interaction. Therefore, the global estimate (~47%) is a minimum value for porpoises stranded with evidence of fishery interaction in Portugal and Galicia. It is also noteworthy that when only considering the 264 porpoises analysed for their cause of stranding in the northern region of Portugal (where the largest number of strandings were registered), the proportion of porpoises with evidence of fishery interaction rises to 51.51%. If individuals demonstrating probable fishery interaction were considered, the proportion of porpoises interacting with fisheries in the northern region of Portugal would become 63.63% of all analysed porpoises.Future research is needed to assess changes in seasonal Iberian porpoise distribution and in possible imbalances in sex ratio and differences in age classes across different areas. Currently, no further inferences are possible considering the large number of stranded individuals to which no sex or age class was attributed.Using the annual population abundance estimates obtained between 2011 and 2015 in Portugal , the PBRAttempts to highlight the porpoise bycatch situation in the Iberian Peninsula have been made for years . In 2020Given the importance of fishing-related activities in the study region, the primary threat to the Iberian porpoise population has been identified as bycatch, and at the least, strict implementation of EU directives and fisheries legislation is crucial. Recently, the European Commission called on member states to “Adopt national measures or submit joint recommendations to the Commission to minimise by-catch (or reduce it to the level that enables the full recovery of the populations) by the end of 2023 in the case of the harbour porpoise in Iberian Atlantic” . If we aMeanwhile, there is an urgent need for changes in fishing, particularly in those fisheries with highest bycatch rates, namely the polyvalent fleet using gill and trammel nets and beach seines. Fishing effort management measures should be applied within legal frameworks that prevent fisheries from losing profitability, particularly because legal measures are needed within an effective timeframe.Stranding data are essential to understand the impact of threats, particularly on small and isolated marine populations, and to support science-based conservation and management strategies. In the present study, an increasing number of porpoise strandings was detected in Galicia (Spain) and Portugal. In Portuguese waters, the estimated annual population removal due to bycatch during the evaluated period indicated that the potential biological removal estimates for harbour porpoises was exceeded. There are still many gaps in knowledge concerning the Iberian porpoise population  which should be urgently addressed to understand the potential resilience of this already-depleted population. The present study highlights the urgent need for reliable transboundary conservation and monitoring efforts with appropriate legal support.


Liver abscesses (LAs) are one of the most common and important problems faced by the beef industry. The most efficacious method for the prevention of LAs in North America is through dietary inclusion of low doses of antimicrobial drugs such as tylosin, but the mechanisms by which this treatment prevents LAs are not fully understood. LAs are believed to result from mucosal barrier dysfunction in the gastrointestinal tract (GIT) allowing bacterial translocation to the liver via the portal vein, yet differences in the GIT microbiome of cattle with and without LAs have not been explored. Here, we characterized microbial communities from LAs, rumen, ileum, and colon from the same cattle for the first time.Bifidobacterium spp.—a bacteria commonly associated with a healthy GIT in several species—were more abundant in the rumen and ileum of animals without LAs compared to those with LAs.Results demonstrate that tylosin supplementation was associated with differences in microbial community structure in the rumen and small intestine, largely because of differences in the predominance of Clostridia. Importantly, we show for the first time that microbial communities from multiple LAs in one animal’s liver are highly similar, suggesting that abscesses found at different locations in the liver may originate from a localized source in the GIT (rather than disparate locations). A large portion of abscesses were dominated by microbial taxa that were most abundant in the hindgut. Further, we identified taxa throughout the GIT that were differentially abundant between animals with and without liver abscesses. Together these results provide the first direct comparison of GIT and LA microbial communities within the same animal, add considerable evidence to the hypothesis that some LA microbial communities arise from the hindgut, and suggest that barrier dysfunction throughout the GIT may be the underlying cause of LA formation in cattle.The online version contains supplementary material available at 10.1186/s42523-023-00278-0. Liver abscesses (LAs) are one of the most important and costly problems faced by the beef industry. In addition to condemned products, LAs can cause significant losses in the feedlot. Severe abscessation can reduce carcass yield and grade , 2, and While tylosin is effective in reducing the prevalence of abscesses, the mechanisms by which it prevents LAs are not fully understood. All sequencing-based studies to date have concluded that there is no change in the diversity or composition of LA microbial communities resulting from in-feed supplementation of tylosin –13. AntiFusobacteria necrophorum is widely considered the most common causative agent of LAs given its ubiquitous presence in culture-based investigations of LAs in cattle [Fusobacterium is still the most abundant community member when averaged across all LAs, the most recent investigations of microbial community structures of individual LAs have shown that a large proportion of LAs are actually dominated by members of Bacteroidetes (largely Bacteroides or Porphyromonas); microbial taxa more commonly associated with more distal portions of the GIT [Historically, the accepted pathogenesis of liver abscesses has been attributed to a gut barrier dysfunction (GBD) in the rumen caused by acidosis. Extended feeding diets with high concentrations of fermentable starches are often thought to be the principal cause of this metabolic disorder and subsequent translocation of bacteria to the liver . Fusobacn cattle , 17–19. n cattle . While F the GIT . Yet, toThis study utilized 16S rRNA gene sequencing to (1) investigate the impact of tylosin on microbial communities in LAs, and the rumen, ileum, and colon in the same animals, (2) compare microbial community structure among multiple LAs from one liver, (3) quantify prevalent LA taxa throughout the GIT, and (4) evaluate differences in microbial communities between abscessed and non-abscessed animals in the rumen, ileum, and colon. Importantly, it leverages samples collected as part of a randomized, controlled intervention trial and represents the first to investigate microbial diversity and composition in both multiple GIT locations and LAs of the same animals.Rumen microbial communities. Both the richness and diversity of luminal and epithelial microbial communities in the rumen were lower in animals receiving tylosin supplementation, and except for richness in luminal communities (p = 0.07), the decreases were statistically significant . Based on generalized UniFrac distances, the overall composition of luminal and epithelial communities in the rumen were significantly different between animals that received tylosin supplementation and those that did not .Hierarchal clustering further revealed that there were two major clades of both luminal and epithelial rumen communities. The two clades of luminal communities were largely the result of differences in the relative abundance of Lachnospiraceae Fig. . The clap < 0.05).Across all luminal communities, 15 families comprised more than 1% of the overall community and together these 15 families represented 89.03% of the luminal community in the rumen. Lachnospiraceae was the most abundant family, followed Prevotellaceae, Atopobiaceae, Oscillospiraceae, Methanobacteriaceae, Anaerovoracaceae, Ruminococcaceae, Muribaculaceae, Clostridia UCG-014, Erysipelotrichaceae .Within rumen epithelial communities, the two major clades formed largely on differences in the relative abundance of Succinivibrionaceae and less abundant families Fig. . The clap < 0.05). With the exception of Ruminococcus, all genera exhibited the same response to tylosin supplementation  in both luminal and epithelial rumen communities . Erysipelotrichaceae UCG-009 was more abundant within luminal rumen communities from tylosin supplemented animals but was below 0.5% relative abundance in epithelial communities. Members of the Ruminococcus gauvreauii group and Shuttleworthia were more abundant within luminal and epithelial communities from the rumen of animals receiving tylosin supplementation, but the difference was only significant in luminal communities . Only members of Rikenellaceae RC9 gut group had significantly lower relative abundances in both luminal and epithelial communities. While members of Eubacterium coprostanoligenes group, Eubacterium nodatum group, Family XIII AD3001 group, Bacteroidales RF16 group, F082, NK4A214 group, and Prevotellaceae UCG-001 all decreased, the difference was only statistically significant in either luminal or epithelial communities . In both luminal and epithelial rumen communities, low abundance genera (< 0.5% RA) were significantly less abundant collectively in animals that received tylosin supplementation. Interestingly, most of the differentially abundant genera across all rumen communities were all members of the same class; with 10 of the 18 genera being members of the class Clostridia . While diversity was lower in both luminal and epithelial communities from the ileum of animals that received tylosin, this difference was not statistically significant. Based on generalized UniFrac distances, the composition of luminal communities in the ileum were significantly different between animals given diet supplemented with tylosin and those not receiving tylosin . Despite the lack of statistical significance (p = 0.09) the amount of variation in community composition explained by tylosin supplementation in the epithelium of the ileum (R2 = 0.06) was similar to statistically significant differences in the rumen and lumen of the ileum .Hierarchal clustering further revealed that two clades containing nearly equal numbers of communities formed for luminal communities in the ileum Fig. . The clap < 0.05).In ileum epithelial communities, hierarchal clustering revealed that the two major clades formed based on differing relative abundances of Lachnospiraceae, Peptostreptococcaceae, Clostridiaceae, Atopobiaceae, Erysipelotrichaceae, and Anaerovoracaceae as was the case in luminal communities Fig. . Howeverp < 0.05). In general, there was considerably greater animal to animal variation in community structure in ileum communities compared to the rumen and large intestine. As a result of this variation, there were no genera with statistically higher relative abundance in luminal communities from animals that received tylosin, though some of the most abundant genera  all exhibited a trend of increase relative abundance . Ruminococcus was in significantly lower relative abundance in cattle that received tylosin in both luminal and epithelial communities, while relative abundances of Family XIII AD3001 group and Methanobrevibacter were significantly lower in just luminal communities, and Mogibacterium was significantly lower in epithelial communities only . Collectively, low abundance genera (< 0.5% RA) had significantly lower relative abundance within animals that received tylosin. The majority of differentially abundant genera in the ileum between animals that received tylosin and those that did not belonged to the class Clostridia . Based on generalized UniFrac distances, there was no significant difference in overall community structure in colon luminal or epithelial communities from animals that received tylosin compared to those that did not .There were no significant differences in the richness or diversity of luminal or epithelial communities in the colon of animals that received tylosin compared to those that did not .Within epithelial communities in the colon, the major clades also formed largely as a result of differing relative abundances of Bacteroidaceae Fig. . CommuniOlsenella, Turicibacter, and Methanobrevibacter were in significantly higher relative abundance in luminal and epithelial communities from animals that received tylosin . Similar to the rumen and ileum, low abundance genera (< 0.5% RA) were once again collectively less abundant in luminal and epithelial communities from the colon of animals that received tylosin . Unlike in the rumen and small intestine however, none of the differentially abundant genera in the large intestine belonged to Clostridia . Six genera  each comprised more than 0.5% of the overall community, and collectively they represented 97.5% of the liver abscess community. None of these six genera were differentially abundant between animals that received tylosin and those that did not .Based on generalized UniFrac distances, there were no significant differences in community composition within LA purulent material from animals that received tylosin compared to those that did not . However, Fusobacteriaceae were in significantly higher relative abundance within rumen epithelium communities as compared to colon epithelium communities . Given the sparsity of detection and extremely low relative abundance  of Fusobacteriaceae the biological significance of this finding should be interpreted with caution. Bacteroidaceae was in significantly higher relative abundance within luminal and epithelial communities in the large intestine compared to both the rumen and small intestine . Bacteroidaceae was almost entirely comprised of Bacteroides, and unsurprisingly that genus was also significantly more abundant in the large intestine . In fact, Bacteroides was nearly absent across all rumen (0.011% ± 0.006 SEM) and small intestine communities (0.010% ± 0.005 SEM), while comprising 8.49% ± 0.572 SEM of the overall community in the large intestine. Prevalent families within clade 3 abscess communities were in significantly higher relative abundances within small intestine epithelial communities than rumen and large intestine epithelial communities . Within luminal communities, clade 3 prevalent families were more abundant in the small intestine than both the rumen and colon, and also significantly more abundant in the rumen as compared to large intestine luminal communities .To investigate potential sources of liver abscesses communities, the prevalent families within each of the three liver abscesses community types  were quantified in luminal and epithelial communities of the rumen, small intestine, and large intestine. Fusobacteriaceae was the only prevalent family within clade 1 abscesses and Bacteroidaceae was the only family within clade 2 abscesses. Porphyromonadaceae, Peptostreptococcales-Tissierellales, Peptostreptococcaceae, Actinomycetaceae, and Atopobiaceae were the prevalenet families within clade 3. There were no significant differences in the abundance of Fusobacteriaceae in luminal communities within the rumen, small intestine, or large intestine  were differentially abundant within luminal communities, and only unclassified Bacteroidales was differentially abundant in epithelial communities. Acetitomaculum and unclassified Lachnospiraceae were more abundant in the lumen of the ileum from animals without LAs, while the NK4A214 group was more in luminal communities from the colon of animals with LAs. Bifidobacterium was more abundant within luminal communities in the rumen and ileum of animals without LAs compared to those with LAs . Unclassified Bacteroidales was more abundant within the epithelial communities of the rumen from animals with LAs, and represented the only differentially abundant epithelial taxa .Linear discriminant analysis effect size identified five genera that were differentially abundant between animals with and without LAs in rumen, ileum, or colon communities Fig. . Four gep < 0.05). While a significant PERMDISP suggests that unequal dispersions of variance  is at least partially responsible for the significant PERMANOVA, the distinct clustering of these two groups .Based on generalized UniFrac distances, significant differences in the community composition existed in the lumen of the ileum between animals that did not have liver abscesses and those that had clade 1 (high Fusobacteria) abscesses  were members of the class Clostridia and were also identified as differentially abundant in our study. However, we observed an opposite trend in the abundances of Lachnospiraceae and Erysipelotrichaceae, where these families and the genera comprising them were largely more abundant following tylosin supplementation. A possible explanation for the contrasting results is that the previous study utilized an enzyme-based DNA enrichment method [Ruminococcus, both core members of the rumen microbiome [Tylosin supplementation had no impact on the microbial flora of LAs but did change the composition of microbial communities in the rumen and ileum, largely through influencing the predominance of members of the class Clostridia. In the colon, tylosin impacted a few genera but did not shift overall community composition. Interestingly, members of  rodents —was more rodents , 11–13. piraceae . Interest method  to deplet method , while wt method –25. Regacrobiome , 27 and crobiome . Furthercrobiome –32. Due Bacteroides and the other (clade 3 in this study) comprised of Bacteroides, Porphyromonas, and taxa from other phyla . Given the apparent trial to trial variation in the proportions of different LA community types, there are likely external factors  influencing LA community structure. It is well established that these external factors impact the taxonomy and function of GIT microbial communities in ruminants [Here, we add to the concept that microbial taxa other than members of Fusobacteria dominate the communities within a significant portion of LAs, which we initially demonstrated in a previous trial  and is suminants –36, but Fusobacterium, Porphyromonas) are in extremely low abundance throughout the GIT of cattle. However, the predominance of Bacteroides in the hindgut and its near absence in the rumen of cattle has been demonstrated in numerous studies [Bacteroides is virtually absent from the rumen, suggesting that these LAs with abundant Bacteroides may originate in the hindgut.Bacterial translocation from the lumen of the GIT into the portal vein provides a means for GIT microbiota to seed the liver , and the studies –41, and Bifidobacterium, which is widely considered to exhibit protective effects against GBD in humans and are commonly identified as discriminant of healthy GIT communities [Bifidobacterium spp. are commonly used as probiotics in efforts to reduce GBD-related disease in humans [Bifidobacterium here as the only taxa differentially abundant in two GIT locations from cattle without LAs suggest it may play a similarly protective role again GBD in cattle. As is the case with any 16S rRNA based investigation we must acknowledge the limitations of such work, specifically that we are limited to relative abundance and lack absolute abundance values. Further work investigating the role of GBD throughout the GIT of cattle should incorporate techniques to provide absolute quantification values for important taxa of interest and include complimentary assays to quantify gut inflammatory responses.Alterations in the GIT microbiota (dysbiosis) are ubiquitously found to be associated with gut barrier dysfunction (GBD)-related liver disease in humans , 43, thomunities –47. Due n humans , 49. TheFusobacterium dominated liver abscess communities may in part be seeded from the hindgut of cattle and that multiple abscesses within an individual animal may arise from the same source in the GIT.Dietary inclusion of tylosin (the most common intervention used to prevent and reduce LA occurrence) impacted the microbial communities of the rumen, small intestine, and large intestine of cattle, with the largest impact being observed in the rumen. Furthermore, the first analysis of cattle GIT and liver abscesses microbial communities from the same individual animals suggested that liver abscess communities may be seeded from the hindgut of cattle. The results presented here present the first direct evidence that non-The study reported here was conducted using a subset of animals enrolled in a blinded, randomized controlled trial evaluating the efficacy of different tylosin supplementation strategies for prevention of LAs using methods meeting Good Clinical Research Practice (GCP) expectations. The subset of cattle used in this investigation were part of the animals randomly assigned to two treatment groups at the time they arrived at the feedlot. The two treatment groups were housed separately in different pens, and the finishing diet of one group was supplemented with tylosin phosphate , whereas the diet of the other group was not supplemented with tylosin. Except for this difference, the management protocols were identical for all cattle. The clinical trial methods and management of study animals were reviewed and approved by the West Texas A&M Institutional Animal Care and Use Committee (approved protocol # 2021.08.002) prior to initiation of the study. When cattle reached target harvest weight and body condition, both study groups were harvested on the same day at a federally-inspected commercial abattoir. During carcass evisceration, 10 individual cattle with LAs and 10 without LAs were selected from both treatment groups for inclusion in this study . Purulent material from up to 5 LAs were collected from cattle with LAs, and samples of luminal contents and epithelial surface were collected from rumen, ileum, and colon from all animals. All samples were analyzed using 16S rRNA gene sequencing to characterize the microbial communities, and statistical analyses were performed to address the study objectives. Study personnel involved in cattle management, sampling, analysis, and data interpretation were blinded to treatment group assignments throughout the study, from enrollment until after data analyses were completed.Bos taurus steers  with minimal Bos indicus influence that weighed 800–950 lb at the time of purchase and were previously raised without substantial grain supplementation. After shipping to a very large commercial feedlot located in Colorado, individual cattle were randomly assigned to one of four study groups, with cattle housed separately by group. The subset of cattle selected for this study were enrolled at the same time, including animals from 10 different marketing groups that were randomly assigned by computer algorithm to pens that housed ~ 250 animals each. At the time of arrival, each animal received a unique identification tag, weighed individually, and administered standard preventive treatments including anthelmintics (ivermectin and fenbendazole), vaccines targeting respiratory disease agents and clostridial bacteria (Bovishield® IBR/BVD Gold and UltraChoice® 7), and a hormone implant to optimize weight gain and feed efficiency . Care and management of animals was overseen by the cattle managers and a veterinarian. Additionally, trained animal healthcare personnel visually evaluated every animal daily while riding through pens on horseback. Animals that were potentially ill or injured were moved to the dedicated veterinary facility for examination, and animals meeting established case definitions were treated under the supervision of the feedlot veterinarian using standardized treatment protocols.Cattle enrolled in the clinical trial were purchased through commercial marketing sources, targeting English and continental beef breed The feedlot facilities were constructed to meet or exceed industry standards for beef feedlots, including pens with 130–160 sq-ft of housing space per animal and 7–9 in of linear space of feed bunk per animal. Clean drinking water was provided ad libitum. Diets fed to animals were formulated by animal nutritionists to meet or exceed National Academies of Science nutritional requirements for growing beef cattle, , and ratAll cattle were fed the same diets, except for differences in supplementation with the test article, tylosin phosphate, according to treatment group assignments. At the time of arrival, cattle were fed starting ration that was high in forage (hay and silage) until enrollment for ~ 2 weeks, at which time a series of rations were introduced over ~ 21d, which gradually increased the amount of starch so as to prevent the occurrence of acute ruminal acidosis. At that time, the finishing rations for the treatment groups was introduced, including supplementation with tylosin phosphate at 90 mg/animal/day that treatment group. Finishing rations consisted of steam-flaked corn as the grain constituent, corn silage as roughage, dry distillers grains as a protein supplement, whey permeate, a fat source, and supplement containing mineral and vitamins. Monensin (an ionophore) was included in all diets (30 mg/kg of dietary dry matter) to improve feed efficiency, per industry standards. Feed was delivered twice daily in specialized feed trucks containing onboard scales and computers to ensure accurate delivery of appropriate amounts of feed, and feed consumption was adjusted at least biweekly to ensure appropriate supplementation of tylosin phosphate to meet the intended dosing (90 mg/hd/day). At 33d prior to harvest, ractopamine hydrochloride  was supplemented in all diets to improve rate of weight gain, feed efficiency, and carcass leanness; this supplementation was removed from rations 2d prior to slaughter, per FDA regulations. It should be noted that monensin and ractopamine supplementation have not been demonstrated to be associated with significant changes in the occurrence of LAs. Nutrient composition of rations were analyzed throughout the study to indirectly assess and refine delivery of the targeted amount of tylosin phosphate in final mixed rations by comparison to the target composition of the ration formula.Cattle were on feed for 185 days prior harvest, and their average daily gain in body weight over this period was 3.0 lbs per day. The average live body weight of cattle at harvest was 1464 lbs for the untreated pen and 1468 lbs for the pen treated with tylosin. At harvest, the average hot carcass weight (standard deviation) for the two pens was 931 lbs (74 lbs) and 928 lbs (73 lbs), respectively.Study cattle were euthanized and harvested at a USDA–FSIS inspected commercial abattoir using approved and supervised methods. All animals from each study group were processed separately, and during carcass evisceration, a study investigator (PSM) selected by convenience 10 individual cattle with LAs and 10 without LAs from both treatment groups for inclusion in this study . Among those with LAs, cattle with severe abscessation (A or A + based on the Elanco scoring system) were preferentially selected for inclusion. A study ID number was assigned to each animal at the time of selection and used to identify all samples collected from the same individuals. Blocks of liver tissue containing abscesses were excised, placed in sterile bags, and refrigerated on ice. The rumen was opened onsite at the slaughter facility, and samples of luminal content and mucosal surface swabs , were collected aseptically from the ventral rumen sac, placed in sterile tubes, and refrigerated on ice. Approximately 20 cm proximal to the cecum, sections of ileum (15–20 cm in length) were tied off and excised, placed in sterile bags, and refrigerated on ice. Similarly, 15–20 cm of the distal colon loop was tied off, excised, placed in sterile bags, and refrigerated on ice. All samples were transported to laboratory facilities at Colorado State University for further processing within 6 h of collection.Prior to collecting samples for sequencing, external surfaces of tissues were flame sterilized after spraying with 70% ethanol. Tissues were opened using sterile disposable scalpels, and LA purulent material and intestinal contents were collected aseptically using sterile disposable spatulas and placed in sterile cryotubes. A total of 53 abscesses, up to 5 per steer, were collected from the livers of the 20 cattle with LAs. A large (1.3 cm diameter) rayon tipped swab was used to aseptically sample the epithelial surfaces of the ileum and colon and placed in sterile tubes. Epithelial surfaces were not rinsed prior to swabbing to reduce contamination potential, but this does mean there was potential for luminal community members to be present. However, given significant differences in community composition between luminal and epithelial communities in the rumen (see below) we don’t believe this has impact our conclusions. All samples were frozen at − 80 °C after collection until further processed for sequencing.DNA was isolated from all samples using the QIAamp PowerFecal Pro DNA kit and a QIAcube Connect  automated isolation system for nucleic acid recovery according to the manufacturer’s instructions. Following isolation, DNA was quantified (ng·μL-1) using a Qubit Flex fluorometer . An extraction blank was included for each sample type  that were included in subsequent library preparation steps and sequencing.The V3-V4 region of the 16S rRNA gene was amplified using the 341f/785r primer pair  and 400 p > 0.05), and no difference in the number of ASVs per sample between liver abscesses classified as high Fusobacteria or high Bacteroidetes . Similarly, there was no significant difference in the number of ASVs per samples between animals receiving tylosin and those that did not . Over 91% of all ASVs were classified at the level of genus and > 99% of all ASVs were classified at the ranks of family, order, class, and phylum from all four body sites sampled . Luminal and epithelial communities were significantly different from each other in the rumen , and as such all luminal and epithelial communities were analyzed separately.Demultiplexed 16S rRNA gene sequence reads were imported into QIIME2 version 2022.2 . BecauseRichness (observed ASVs) and Faith’s phylogenetic distance (FPD) were calculated for all remaining samples n = 256) with phyloseq and the ‘estimate_pd’ function from the btools package. ASV counts were then normalized using cumulative sum scaling  with phy, 58. FroDifferentially abundant genera were identified in the rumen, ileum, and colon between animals with and without LAs using linear discriminant analysis effect size (LEfSe) performed with the online LEfSe tool on the Galaxy server under default settings. In an effort to avoid potential false positives, a more conservative pairwise Wilcoxon rank-sum test was used to statistically test differences genera identified as differentially abundant with LEfSe between animals with and without LAs.Unless specified otherwise, R version 4.2.1 was used for statistical analysis of data. Kruskal–Wallis analysis of variance (for comparisons between 2 variables) or Pairwise Wilcoxon rank-sum tests were performed with a Benjamini–Hochberg correction for multiple comparisons (for comparisons between more than 2 variables). Differences in beta-diversity were tested using pairwise PERMANOVA with a Benjamini–Hochberg correction for multiple comparisons and 9999 permutations. Additionally, pairwise PERMDISPs were carried out for all significant PERMANOVA outcomes using 9999 permutations to test for differences in the variability of dispersions.Additional file 1. Table S1 Relative abundances of taxonomic families comprising more than 1% of the overall community across all rumen samples. The mean relative abundance and standard error of the mean are displayed for each family from luminal and epithelial communities of the rumen from animals that received tylosin supplementation and those that did not. Significant p-values are bold .Additional file 2. Table S2 Taxonomic information for the 20 genera differentially abundant across all sample sites between animals receiving tylosin supplementation and those that did not.Additional file 3. Table S3 Relative abundances of taxonomic families comprising more than 1% of the overall community across all small intestine samples. The mean relative abundance and standard error of the mean are displayed for each family from luminal and epithelial communities of the small intestine from animals that received tylosin supplementation and those that did not. Significant p-values are bolded .Additional file 4. Table S4 Relative abundances of taxonomic families comprising more than 1% of the overall community across all large intestine samples. The mean relative abundance and standard error of the mean are displayed for each family from luminal and epithelial communities of the small intestine from animals that received tylosin supplementation and those that did not. Significant p-values are bolded .Additional file 5. Fig. S1 Non-metric multidimensional scaling (NMDS) of generalized UniFrac distances illustrates differences in overall microbial community structure of liver abscesses between treatment groups. The NMDS demonstrates clustering of 16S rRNA gene sequences from animals that received tylosin (purple) and those that did not (gold). There were no significant differences in overall community composition . The bar plot demonstrates the mean relative abundance of all genera within liver abscesses that comprised at least 0.5% of the overall microbial community between animals that received tylosin supplementation and those that did not. Error bars represent the standard error of the mean. There were no significant differences detected . To limit the effect of some animals having multiple  abscess communities, values were based on normalized ASV counts generated by averaging counts from each liver abscess within an individual animal.Additional file 6. Fig. S2 Bar plots demonstrating the relative abundances of taxonomic families within purulent material from individual abscesses (n = 47) from the 14 animals that contained multiple liver abscesses were collected. The eight most abundant families are displayed in the legend.Additional file 7. Fig. S3 Boxplots demonstrating the relative abundance of Bacteroides across luminal and epithelial microbial communities in the rumen, ileum, and colon. Significant differences are illustrated by different letters .


Sarcoidosis is a granulomatous disease involving multiple organ systems. In its classic form, sarcoidosis is associated with non-caseating granuloma. Several differential diagnostic entities exist for sarcoidosis, including tuberculosis (TB), as well as lymphomas. In this report, we present a case of sarcoidosis in a 55-year-old male with diffuse lymphadenopathy and hepatosplenic involvement, highlighting the differential diagnostic point for this disease. Sarcoidosis is a multisystem disease with an unclear etiology with pulmonary and extrapulmonary manifestations. Extrapulmonary sarcoidosis can impact the lymph nodes, leading to lymphadenopathy, and systemic features may include fever, malaise, night sweats, and dry cough. Non-caseating granuloma is found to be most commonly associated with sarcoidosis . LymphomHere, we present a case of a 55-year-old male with initial clinical features and physical findings suggestive of lymphoma. Further investigation, including lymph node excisional biopsy, resulted in a diagnosis of sarcoidosis with extrapulmonary involvement.A 55-year-old male with diabetes was hospitalized for an infected diabetic foot ulcer. Initial vitals were unremarkable. Physical examination was significant for diffuse, palpable, non-tender lymphadenopathy and right second toe ulcer.Laboratory results showed a significant elevation of erythrocyte sedimentation rate (ESR) of 55 mm/hour (reference range: 0-20 mm/hour) and C-reactive protein (CRP) of 9 mg/L (reference range: 0-8 mg/L). Chest X-ray Figure  revealedOn further history-taking, he reported unquantified unintentional weight loss and intermittent night sweats for the past three years. He denied fever, chills, cough, or other upper respiratory infection symptoms. He works as a bulldozer mechanic, lives with two dogs and nine cats, and denied tobacco, alcohol, and illicit drug use. He was born in the Caribbean and moved to the United States over 30 years ago, and traveled back and forth often.CT of the abdomen and pelvis with contrast revealed innumerable hypodense lesions throughout the liver and spleen Figure , 1D withMycobacterium tuberculosis (MTB) polymerase chain reaction (PCR) was negative  and non-HL (NHL) . TypicalAlthough sarcoidosis and lymphoma are two seemingly separate entities, there have been reports in the literature that sarcoidosis may occur together with lymphoma, mainly NHL, but usually, lymphoma occurs after sarcoidosis with a median interval of 24 months. It was named sarcoidosis-lymphoma syndrome by Brincker in 1986. It was also found that there is a fivefold increased risk of developing lymphoma among patients with chronic active sarcoidosis [Mycobacterium tuberculosis (MTB). The major type of TB is pulmonary TB, while extrapulmonary TB accounts for approximately 20%-30% of all TB cases, with lymphadenitis being the most common form [Tuberculosis (TB) is another common granulomatous disease. TB is a contagious disease caused by mon form ,11. Consmon form ,13.Other differential diagnoses to consider include berylliosis, granulomatous arteritis, cat scratch disease, and fungal infection .Both lymphoma and sarcoidosis can present with B symptoms, diffuse lymphadenopathy, and hepatosplenic involvement. Differentiating these two diseases become more challenging, and rarely, lymphoma and sarcoidosis coexist. Although rare, sarcoidosis should be considered a differential diagnosis entity in the presence of lymphadenopathy and a clinical picture that is overall suggestive of lymphoma.


The Accreditation Council for Graduate Medical Education (ACGME) and the Infectious Diseases Society of America (IDSA) require infectious diseases fellowship programs to include a core curriculum as part of their requirements for clinical training, though recommendations regarding content and structure are limited. Despite advances in online tools available for asynchronous learning in medical education, there remains a scarcity of published ready-to-teach content. We hypothesized that case-based clinical reasoning sessions covering core clinical topics would improve the attitudes and confidence of infectious diseases fellows.We conducted an informal needs assessment of current fellows, reviewed published recommendations and other fellowship curricula. Then, we developed a series of case-based clinical reasoning sessions for clinical and research fellows based on constructivist theory and emphasizing adult learning principles. Topics were rooted in published guidelines and evidence-based practice, prioritizing complex and high-yield clinical topics. Content was peer-reviewed by faculty and sessions were facilitated by senior fellows. Facilitation guides were created to allow for dissemination in the future. Faculty and pharmacists attended the sessions as expert discussants. Fellows completed anonymous surveys assessing attitudes and confidence after each session.Three sessions covering Endemic Mycoses, Non-tuberculous Mycobacteria, and Toxoplasmosis were completed with 6-8 fellows in attendance at each. Surveyed fellows felt that the sessions were valuable and improved their confidence in clinical management of the topics presented . Participants also provided narrative feedback (Table 1).Post-session Survey ResultsPost-session Narrative FeedbackThis curriculum represents a novel initiative by trainee physicians to create a series of peer-facilitated, discussion-based sessions for learners at the level of subspecialty fellowship. We demonstrated that these sessions improve the attitudes and confidence of fellows in a single-program pilot. Future directions will include studying the intervention in other fellowship programs and sharing this program broadly within the infectious diseases education community.Eileen K. Maziarz, MD, Karius, Inc: Advisor/Consultant