b'Gastrointestinal system bacterial pathogens causing atypical pneumonia. Among all Campylobacter species are the most common cause of human368 samples deemed culture- and viral PCR-negative, 7 samples gastroenteritis worldwide and can be fatal among children,tested positive for Bordetella parapertussis, 170 for Bordetella elderly, and immunosuppressed individuals [7]. However, theypertussis, 3 for Chlamydia pneumoniae, 11 for Chlamydia psittaci, are often overlooked due to difficulties in culture diagnosis.20 for Legionella pneumophila, 11 for Legionella spp., and Campylobacter species are fastidious, growing only in146 for Mycoplasma pneumoniae. Moreover, in two patients a microaerobic environments. Culturing of Campylobacter speciesco-infection of Bordetella pertussis and Bordetella parapertussis requires stool sample implantation into a selective mediumwas observed [15]. By accurately identifying causative and incubation at 42C for about 72 hours. Once cultured,pathogens, MDx may improve diagnosis and subsequent bacteria can take an additional 7 days to be identified. In a studypatient management.comparing the performance of culture and culture-independentUrinary systemtests for the diagnosis of Campylobacter enteritis, molecularCulture and MDx differ in their ability to detect co-infection or tests were found to be superior in terms of sensitivity, specificity,polymicrobial infection. In a study that evaluated 582 patients with and positive predictive value. Among the 400 specimens, 41lower urinary tract infections, PCR was found to be significantly were evaluated as Campylobacter positive by PCR. Out of thosemore sensitive than urine culture for detecting polymicrobial Campylobacter-positive specimens, only 21 were culture-positiveinfections. Among the 175 patients with polymicrobial infections, (sensitivity: 51.2%) [8]. PCR reported 95% and culture-only reported 22% of cases. A similar pattern was observed in the Global Enteric MulticenterIn addition, PCR revealed polymicrobial infections in 67 patients Study (GEMS), which investigated 32 entero-pathogens in stoolwith negative culture results [16]. Simultaneous detection of samples by quantitative real-time PCR (qPCR) and traditionalvarious pathogens could aid clinical management, allowing microbiological methods. The pathogen-specific attributablemore specific treatments and fewer recurrent infections resulting incidences of Campylobacter with qPCR were twice that of thefrom inadequate or inappropriate treatments. Furthermore, original microbiological methods. qPCR-derived attributablemultiplex PCR coupled with pooled antibiotic sensitivity can offer incidence surpassed traditional methods for other gastrointestinalclinically relevant microbiological data missed by standard urine pathogens including adenovirus (around five times), Shigellaculture alone [17].spp./Enteroinvasive Escherichia coli (EIEC) (around twoSexually transmitted diseases and other infectionstimes), and heat-stable enterotoxin-producing Escherichia coliFor certain sexually transmitted diseases, such as Chlamydia (around 15 times) [9].trachomatis and Neisseria gonorrhoeae, the CDC highlights The CDC confirms a marked increase in the use ofNAATs as the preferred diagnostic approach [15]. The IDSA is in culture-independent diagnostic tests (CIDTs) for detectingfull support, noting NAATs are the preferred assays for detection Campylobacter, Salmonella, Shigella, and other gastrointestinalbecause of increased sensitivity while retaining specificity in pathogens over the last decade [10-13]. A CDC report onlow-prevalence populations (pregnant patients) and the ability to incidences and trends of foodborne pathogens noted a changescreen with a noninvasive urine specimen [4].in the testing behavior: healthcare providers might be more likelyThe ability to offer quick and accurate results without requiring to order CIDTs because these tests are quicker and easier toaccess to laboratories that can grow cultures has prompted use than traditional culture methods. The report further notedthe WHO to include more MDx in their recommendations. an uptick in the adoption of DNA-based syndromic panels byFor example, the third WHO Model List of Essential In Vitro clinical laboratories [10].Diagnostics includes PCR for the fungus Pneumocystis jirovecii, Respiratory system which causes pneumocystis pneumonia, and a human measles Multiplex molecular panels have proved particularly usefulreverse transcription PCR (RT-PCR) test, which can accurately in detecting the causative agents in atypical pneumonia.confirm cases and help prevent outbreaks [19].Historically, atypical pneumonias were characterized by slightlyIn addition to pathogen detection, MDx can monitor viral load different symptoms, appearing differently on chest X-rays,over time to determine effectiveness of antiviral therapy against and responding poorly to standard antibiotics. Nowadays,HIV and hepatitis viruses. For example, the WHO lists qualitative pneumonias are considered atypical if they are difficult toor quantitative HCV virological nucleic acid tests as essential detect through standard bacterial methods such as culture [14].in vitro diagnostics for diagnosing viremic HCV, monitoring In a study on patients with symptoms of atypical pneumoniatreatment response, and as a test of cure [20].who tested negative for typical agents of pneumonia by culture and viral PCR, researchers used multiplex qPCR to detect key 14 Molecular testing thermofisher.com/infectiousdisease Contents'