Infectious diseases diagnosis One way to detect these pathogens is detect part of their genome by<unk> s sequencing (Next Generation Sequencing-mNGS), which can be targeted or untargeted. Targeted Because of that, the sensitivity to detect microorganisms that are being targeted usually increases, but this comes with a limitation of the amount of identifiable pathogens. Untargeted The untargeted analysis is a<unk>  "shotgun" approach. The whole DNA and/or RNA is sequenced with this approach using universal primers. The resultant mNGS reads can be assembled into partial or complete genomes. These genome sequences allow to monitor hospital outbreaks to facilitate infection control and public health surveillance. Also, they can be used for subtyping (identificate a specific genetic variant of a microorganism). Untargeted mNGS is the most promising approach to analyse<unk>  samples and provide a comprehensive diagnosis of infections. Various groups have validated mNGS in<unk>  Laboratory Improvement Amendments ( CLIA), such as meningitis or encephalitis, sepsis and pneumonia. This method can be very helpful in the settings where no exact infectious etiology is suspected. For example, in patients with suspected pneumonia, identification of the underlying infectious etiology as in COVID-19 has important<unk>  and public health implications. The traditional method consists on formulating a differential diagnosis on the basis of the patient's history, a<unk>  presentation, imaging findings and laboratory testing. But here it is suggested a different way of diagnosis;<unk>  next-generation sequencing (NGS) is a promising method because a comprehensive spectrum of a potential causes (viral, bacterial; fungus and parasitic) can be identify by a single assay. Below are some examples of the<unk>  sequencing application in infectious diseases diagnosis. Examples Diagnosis of meningitis and encephalitis The traditional method that is used to the diagnosis of infectious diseases has been challenged in some cases: neuroinflamatory diseases, lack of diagnostic tests for rare pathogens and the limited availability and volume of the Central Nervous System (CNS) samples, because of the requirement for invasive procedures. Owing to these problems, some assays suggest a different way of diagnosis, which is the<unk>  next-generation sequencing (NGS); this is a promising method for diagnosis because a comprehensive spectrum of potential causes (bacterial, viral, fungus and parasitic) can be identify by a single study. Summarising, NGS can identify a broad range of pathogens in a single test. In some articles they evaluate the<unk>  usefulness of<unk>  NGS for diagnosis neurologic infections, in parallel with conventional microbiologic testing. It has been seen that the highest diagnostic yield resulted from a combination of<unk> s NGS of CSF and conventional testing, including serologic testing and testing of sample types other than CSF. Moreover, some findings from different studies have shown that neurologic infections remain undiagnosed in a proportion of patients despite conventional testing and they demonstrate the potential usefulness of<unk><unk>  NGS testing in these patients. The results of<unk>  NGS can also be valuable even when concordant with results of conventional testing, not only providing reassurance that the conventionally obtained diagnosis is correct but also potentially detecting or ruling out coinfections, specially in immunocompromised patients.<unk>  is fundamentally a direct-detection method and relies on the presence of nucleic acid form the causative pathogen in the CSF samples. Study of antimicrobial resistance Antimicrobial resistance is a health problem needed to resolve. Nowadays to detect resistances of different microbes is used a technique called Antibiotic Sensitivity (AST), but several studies have discovered that bacterial resistance is in the genoma and it is transferred by horizontal way (HGT), so sequencing methods are being developed to ease the identification and characterization of those genomes and metagenomes. For the moment exist the following methods to detect antimicrobial resistances: * AST: an advantage about this method is that it gives information for patients treatment. There are also some disadvantages, one of them is that this technique is only useful in cultivable bacteria or that is needed competent personal. * Sequencing methods: some advantages of those methods over the AST technique are that it is rapid and sensible, it is useful on both bacteria that grow on artificial media and those that do not, and it permits compare studies in several organisms. One type of sequencing method can be used in preference to another depending on the type of the sample, for a genomic sample assembly-based methods is used; for a<unk>  sample it is preferable to use read-based methods. It is noted that<unk>  sequencing methods have provided better results than genomics ones, due to these present less number of negative falses. Within<unk> s sequencing, functional<unk>  is a powerful approach for characterizing resistomes; a<unk>  library is generated by cloning the total community DNA extracted from a sample into an expression vector, this library is assayed for antimicrobial resistance by plating on selective media that are lethal to the wild-type host. The selected inserts from the surviving recombinant, antimicrobial-resistant host cells are then sequenced, and resulting sequences are subsequently assembled and annotated (PARFuMS). Functional<unk> s has enabled the discovery of several new antimicrobial resistance mechanisms and their related genes, one such example is the recently discovered tetracycline resistance mechanism by tetracycline destructases. In conclusion is important to incorporate not only the antimicrobial resistance gene sequence and mechanism but also the genomic context, host bacterial species and geographic location (metagenome). Pandemic preparedness Potentially dangerous pathogens such as ebolaviruses, coronaviruses etc., and the closest genetic relative for unknown pathogens, could be identified immediately, prompting further follow-up. Its role in the future of pandemic preparedness is anticipated and could exist as the earliest surveillance system we may have to detect outbreaks of unknown etiology and to respond in an opportune manner.<unk>  microbiome analyses The use of mNGS to characterize the microbiome has made possible the development of bacterial probiotics to be administrated as pills, for example, as a treatment of Clostridium difficile-associated diseases. Human host response analyses The studying of genes expression allows us to characterize a lot of infections, for example infections due to Staphylococcus aureus, Lyme disease, candidiasis, tuberculosis and influenza. Also, this approach can be used for cancer classification. RNAseq analysis have a lot of other purposes and applications such as to identify novel or under appreciated host–microbial interactions directly from<unk>  samples, to make indirect diagnosis on the basis of a pathogen specific human host response and to discriminate infectious versus noninfectious causes of acute illness. Applications in oncology
Clinical metagenomic sequencing
Molecular risk assessment
Functional molecular infection epidemiology
Multiplexed point-of-care testing
Point-of-care testing
Pharmacomicrobiomics
Whole genome sequencing
Microscopic Observation Drug Susceptibility assay