Peleg AY, Seifert H, Paterson DL. Acinetobacter baumannii: emergence of a successful pathogen. Clin Microbiol Rev. 2008 Jul;21(3):538-82. doi: 10.1128/CMR.00058-07. PMID: 18625687; PMCID: PMC2493088.
Davis, K. A., Moran, K. A., McAllister, C. K., & Gray, P. J. (2005). Multidrug-resistant Acinetobacter extremity infections in soldiers. Emerging infectious diseases, 11(8), 1218–1224.*Adenoviruses are double-stranded DNA viruses that cause significant respiratory illness across age groups. They account for roughly 5–10% of viral respiratory infections in children (and up to 1–7% in adults) and can lead to outbreaks of bronchitis and pneumonia, sometimes resulting in severe disease or fatal pneumonia in infants and immunocompromised patients. Including adenovirus in a PCR panel ensures rapid and accurate identification of this common pathogen (Khanal et al. 2018).
Khanal, S., Ghimire, P., & Dhamoon, A. S. (2018). The Repertoire of Adenovirus in Human Disease: The Innocuous to the Deadly. Biomedicines, 6(1), 30.
The mecA gene encodes an altered penicillin-binding protein (PBP2a) with low affinity for β-lactams; its presence is the genetic hallmark of methicillin-resistant Staphylococcus aureus (MRSA) and methicillin-resistant coagulase-negative staphylococci. Detecting mecA in respiratory samples allows rapid identification of methicillin-resistant S. aureus (MRSA) by PCR (Wielders et al. 2002, Chambers & Deleo 2009).
Wielders, C. L., Fluit, A. C., Brisse, S., Verhoef, J., & Schmitz, F. J. (2002). mecA gene is widely disseminated in Staphylococcus aureus population. Journal of clinical microbiology, 40(11), 3970–3975.
Chambers, H. F., & Deleo, F. R. (2009). Waves of resistance: Staphylococcus aureus in the antibiotic era. Nature reviews. Microbiology, 7(9), 629–641.
Bacteroides fragilis is a common anaerobic pathogen isolated from chronic and deep wound infections, contributing to abscess formation and tissue destruction. It produces virulence factors that enhance immune evasion and complicate wound healing. Identification of B. fragilis is essential for guiding anaerobic-targeted therapy in wound care (Brook 2008).
Brook I. (2008). Microbiology and management of soft tissue and muscle infections. International journal of surgery (London, England), 6(4), 328–338.
Bordetella parapertussis is a cause of pertussis-like illness that is often milder than B. pertussis infection but can still be clinically significant. U.S. PCR surveillance has shown that about 14% of Bordetella-positive respiratory specimens were B. parapertussis, and recent data indicate a resurgence of B. parapertussis cases. Detecting B. parapertussis via PCR prevents misclassification of whooping cough and explains some cases that might otherwise be labeled vaccine failures. (Noble et al. 2024, Cherry & Seaton 2012).
Noble, B. A., Jiudice, S. S., Jones, J. D., & Timbrook, T. T. (2024). Reemergence of Bordetella parapertussis, United States, 2019-2023. Emerging infectious diseases, 30(5), 1058–1060.
Cherry, J. D., & Seaton, B. L. (2012). Patterns of Bordetella parapertussis respiratory illnesses: 2008-2010. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America, 54(4), 534–537.Bordetella pertussis is the primary agent of whooping cough, a highly contagious respiratory disease that remains an important public health concern. Even with vaccination programs, pertussis causes substantial disease: the U.S. incidence is roughly 20% of pre-vaccine levels, and serologic data suggest on the order of a million B. pertussis infections occur annually. Including B. pertussis allows for rapid confirmation so that appropriate macrolide therapy and public health measures can be implemented (Sounder & Long 2015, Nieves & Heininger 2016).
References:
Souder, E., & Long, S. S. (2015). Pertussis in the Era of New Strains of Bordetella pertussis. Infectious disease clinics of North America, 29(4), 699–713.
Nieves, D. J., & Heininger, U. (2016). Bordetella pertussis. Microbiology spectrum, 4(3),Urinary tract infections: Candida albicans is the most common fungal cause of UTIs, particularly in patients with indwelling catheters, diabetes, recent antibiotic use, or immunosuppression. Candiduria may be asymptomatic or cause symptoms similar to bacterial UTIs, and distinguishing colonization from infection is critical in management. Its frequent identification in hospitalized patients makes it a relevant target in PCR panels for comprehensive UTI diagnostics (Kauffman et al. 2011, Odabasi & Mert 2020).
Wound infections: Candida albicans is a frequent fungal pathogen in chronic wounds, where it forms biofilms that resist antifungal treatment and prolong infection. Its interaction with bacterial species further exacerbates wound severity and delays healing. Accurate detection of C. albicans is critical for implementing effective antifungal strategies in wound management (Gil et al. 2022, James et al. 2008).
Kauffman CA, Fisher JF, Sobel JD, Newman CA. Candida urinary tract infections–diagnosis. Clin Infect Dis. 2011 May;52 Suppl 6:S452-6. doi: 10.1093/cid/cir111. PMID: 21498838.
Odabasi Z, Mert A. Candida urinary tract infections in adults. World J Urol. 2020 Nov;38(11):2699-2707. doi: 10.1007/s00345-019-02991-5. Epub 2019 Oct 25. PMID: 31654220.
Gil, J., Solis, M., Higa, A., & Davis, S. C. (2022). Candida albicans Infections: a novel porcine wound model to evaluate treatment efficacy. BMC microbiology, 22(1), 45.
James, G. A., Swogger, E., Wolcott, R., Pulcini, E.d, Secor, P., Sestrich, J., Costerton, J. W., & Stewart, P. S. (2008). Biofilms in chronic wounds. Wound repair and regeneration : official publication of the Wound Healing Society [and] the European Tissue Repair Society, 16(1), 37–44.
Candida auris is an emerging multidrug-resistant fungal pathogen increasingly isolated from wound infections, particularly in healthcare settings. It demonstrates high environmental persistence and resistance to multiple antifungal agents, complicating treatment outcomes. Rapid identification of C. auris is crucial for infection control and targeted wound therapy (Chowdhary et al., 2017).
Chowdhary, A., Sharma, C., & Meis, J. F. (2017). Candida auris: A rapidly emerging cause of hospital-acquired multidrug-resistant fungal infections globally. PLoS pathogens, 13(5), e1006290.
Urinary tract infections: Candida glabrata is an emerging non-albicans Candida species increasingly associated with UTIs, especially in older adults and those with diabetes or recent antifungal exposure. It is less susceptible to fluconazole compared to C. albicans, which can impact treatment decisions. Molecular detection is important due to its slower growth in culture and rising prevalence in nosocomial infections (Pfaller & Diekema 2007, Silva et al. 2012).
Wound infections: Candida glabrata is a common non-albicans Candida species associated with chronic wound infections, often displaying reduced susceptibility to azole antifungals. Its ability to persist in biofilms complicates eradication and prolongs infection. Early detection of C. glabrata informs antifungal selection and improves wound care strategies (Hassan et al. 2021, Silva et al. 2012)
Pfaller MA, Diekema DJ. Epidemiology of invasive candidiasis: a persistent public health problem. Clin Microbiol Rev. 2007 Jan;20(1):133-63. doi: 10.1128/CMR.00029-06. PMID: 17223626; PMCID: PMC1797637.
Silva S, Negri M, Henriques M, Oliveira R, Williams DW, Azeredo J. Candida glabrata, Candida parapsilosis and Candida tropicalis: biology, epidemiology, pathogenicity and antifungal resistance. FEMS Microbiol Rev. 2012 Mar;36(2):288-305.
Hassan, Y., Chew, S. Y., & Than, L. T. L. (2021). Candida glabrata: Pathogenicity and Resistance Mechanisms for Adaptation and Survival. Journal of fungi (Basel, Switzerland), 7(8), 667.
Candida lusitaniae is an uncommon cause of infection, but it is noteworthy for its ability to rapidly develop resistance to amphotericin B. It has been reported to cause opportunistic infections, including catheter-related and wound infections, particularly in immunocompromised patients. Including C. lusitaniae in a wound or women’s health PCR panel ensures that this rare but clinically significant yeast is identified and appropriate antifungal treatment is selected (Apsemidou et al. 2020, Krcmeryet al. 2002).
Apsemidou, A., Füller, M. A., Idelevich, E. A., Kurzai, O., Tragiannidis, A., & Groll, A. H. (2020). Candida lusitaniae Breakthrough Fungemia in an Immuno-Compromised Adolescent: Case Report and Review of the Literature. Journal of fungi (Basel, Switzerland), 6(4), 380.
Krcmery, V., & Barnes, A. J. (2002). Non-albicans Candida spp. causing fungaemia: pathogenicity and antifungal resistance. The Journal of hospital infection, 50(4), 243–260.Urinary tract infections: Candida parapsilosis is another non-albicans species that can cause urinary tract infections, particularly in neonates and inviduals with urinary catheters. It is known for its ability to form biofilms on medical devices, contributing to persistent infections. Although less common than C. albicans, its clinical significance is rising, especially in ICU settings, warranting its inclusion in PCR-based detection panels (Trofa et al 2008, Silva et al. 2012).
Wound infections: Candida parapsilosis is a fungus commonly found on human skin that can cause wound infections, especially after surgery or in burn wounds especially in immunocompromised or hospitalized patients. Inclusion of C. parapsilosis in a PCR wound panel is justified because it is an emerging cause of wound and tissue infections (Turkal & Baumgardner 1995, Trofa et al. 2008)
Trofa D, Gácser A, Nosanchuk JD. Candida parapsilosis, an emerging fungal pathogen. Clin Microbiol Rev. 2008 Oct;21(4):606-25. doi: 10.1128/CMR.00013-08. PMID: 18854483; PMCID: PMC2570155.
Silva S, Negri M, Henriques M, Oliveira R, Williams DW, Azeredo J. Candida glabrata, Candida parapsilosis and Candida tropicalis: biology, epidemiology, pathogenicity and antifungal resistance. FEMS Microbiol Rev. 2012 Mar;36(2):288-305.
Turkal, N. W., & Baumgardner, D. J. (1995). Candida parapsilosis infection in a rose thorn wound. The Journal of the American Board of Family Practice, 8(6), 484–485.
Urinary tract infections: Candida tropicalis is a notable fungal pathogen in UTIs among immunocompromised patients, including those with hematologic malignancies or undergoing organ transplants. It can cause both upper and lower urinary tract infections and is often more virulent than other non-albicans species. Its high prevalence in certain hospital populations and potential antifungal resistance make it essential to monitor via molecular diagnostics (Zuza-Alves et al. 2017, Silva et al.2012).
Wound infections: Candida tropicalis is a virulent Candida species often associated with invasive infections in immunocompromised. C. tropicalis can also infect wounds and skin, especially in patients with underlying conditions, leading to persistent infections that may not respond to routine antibacterial therapy. Identification of C. tropicalis in a wound is clinically important because it guides the use of appropriate antifungal treatment and helps prevent progression to systemic infection (Fan et al. 2018).
Zuza-Alves DL, Silva-Rocha WP, Chaves GM. An Update on Candida tropicalis Based on Basic and Clinical Approaches. Front Microbiol. 2017 Oct 13;8:1927. doi: 10.3389/fmicb.2017.01927. PMID: 29081766; PMCID: PMC5645804.
Silva S, Negri M, Henriques M, Oliveira R, Williams DW, Azeredo J. Candida glabrata, Candida parapsilosis and Candida tropicalis: biology, epidemiology, pathogenicity and antifungal resistance. FEMS Microbiol Rev. 2012 Mar;36(2):288-305.
Fan, C., Tian, Q., Huang, G., Zhang, L., Wu, Q., & Zhang, K. (2018). Candida tropicalis burn wound sepsis: A series of histopathology-confirmed cases. Intensive & critical care nursing, 46, 6–9.Chlamydia trachomatis is the most common bacterial STI, often asymptomatic but capable of causing infertility and pelvic inflammatory disease if untreated. Its inclusion in STI panels ensures early detection and treatment to prevent complications and transmission (USPSTF 2021, Workowski et al. 2021).
US Preventive Services Task Force, Davidson, K. W., Barry, M. J., Mangione, C. M., Cabana, M., Caughey, A. B., Davis, E. M., Donahue, K. E., Doubeni, C. A., Krist, A. H., Kubik, M., Li, L., Ogedegbe, G., Pbert, L., Silverstein, M., Simon, M. A., Stevermer, J., Tseng, C. W., & Wong, J. B. (2021). Screening for Chlamydia and Gonorrhea: US Preventive Services Task Force Recommendation Statement. JAMA, 326(10), 949–956.
Workowski, K. A., Bachmann, L. H., Chan, P. A., Johnston, C. M., Muzny, C. A., Park I., Reno, H., Jonathan M. Zenilman J.M.,Bolan, G. A. (2021). Sexually transmitted infections treatment guidelines, 2021. MMWR Recommendations and Reports, 70(4), 1–187.
Chlamydophila pneumoniae is an obligate intracellular bacterium that causes “atypical” respiratory infections, including bronchitis and pneumonia. Infection is often characterized by a prolonged cough and generally responds to antibiotic treatment. Detecting C. pneumoniae by PCR allows clinicians to target therapy for this pathogen specifically (Tagini et al. 2025, Burillo & Bouza 2010).
Tagini, F., Puolakkainen, M., Greub, G., & On Behalf Of The Escmid Study Group For Mycoplasma And Chlamydia Infections Esgmac (2025). From coughs to complications: the story of Chlamydia pneumoniae. Journal of medical microbiology, 74(4), 002006.
Burillo, A., & Bouza, E. (2010). Chlamydophila pneumoniae. Infectious disease clinics of North America, 24(1), 61–71.
Urinary tract infections: Citrobacter freundii can cause both community-acquired and nosocomial UTIs, particularly in individuals with structural abnormalities of the urinary tract or long-term catheterization. While part of the normal gut flora, it becomes pathogenic when introduced into the urinary system and is known for its potential to develop multidrug resistance. Its presence in complicated UTI cases justifies its detection in multiplex PCR assays (Fonton et al. 2024).
Wound infections: Citrobacter freundii is an opportunistic rod that can infect surgical wounds, often in hospitalized patients with weakened immunity. C. freundii and its relatives are frequently isolated from surgical wound infections and are notable for harboring AmpC beta-lactamases. Detecting C. freundii in a wound culture is important because targeted may be needed to effectively eradicate this bacterium (Gajdács & Urbán, 2019, Jabeen et al. 2023)
Fonton P, Hassoun-Kheir N, Harbarth S. Epidemiology of Citrobacter spp. infections among hospitalized patients: a systematic review and meta-analysis. BMC Infect Dis. 2024 Jul 2;24(1):662. doi: 10.1186/s12879-024-09575-8. PMID: 38956542; PMCID: PMC11221093.
Gajdács, M., & Urbán, E. (2019). Resistance Trends and Epidemiology of Citrobacter–Enterobacter–Serratia in Urinary Tract Infections of Inpatients and Outpatients (RECESUTI): A 10-Year Survey. Medicina (Kaunas, Lithuania), 55(6), 285. https://doi.org/10.3390/medicina55060285
Jabeen, I., Islam, S., Hassan, A. K. M. I., Tasnim, Z., & Shuvo, S. R. (2023). A brief insight into Citrobacter species – a growing threat to public health. Frontiers in antibiotics, 2, 1276982.
HCoV-229E is a common cold coronavirus that usually causes mild upper respiratory illness, but can occasionally cause bronchitis or pneumonia in infants, the elderly, and immunocompromised patients. Its inclusion is justified by its role in seasonal respiratory disease and its potential severity in vulnerable hosts (Gaunt et al. 2010, Jo et al. 2022).
References:
Gaunt, E. R., Hardie, A., Claas, E. C., Simmonds, P., & Templeton, K. E. (2010). Epidemiology and clinical presentations of the four human coronaviruses 229E, HKU1, NL63, and OC43 detected over 3 years using a novel multiplex real-time PCR method. Journal of clinical microbiology, 48(8), 2940–2947.
Jo, K. J., Choi, S. H., Oh, C. E., Kim, H., Choi, B. S., Jo, D. S., & Park, S. E. (2022). Epidemiology and Clinical Characteristics of Human Coronaviruses-Associated Infections in Children: A Multi-Center Study. Frontiers in pediatrics, 10, 877759.
HCoV-HKU1 is another endemic coronavirus that causes wintertime “cold” illnesses; although usually mild, it can cause pneumonia or exacerbations of chronic lung disease in older or immunocompromised patients. Identifying HKU1 can explain seasonal respiratory illness clusters and guide infection control (Gaunt et al. 2010, Jo et al. 2022).
Jo, K. J., Choi, S. H., Oh, C. E., Kim, H., Choi, B. S., Jo, D. S., & Park, S. E. (2022). Epidemiology and Clinical Characteristics of Human Coronaviruses-Associated Infections in Children: A Multi-Center Study. Frontiers in pediatrics, 10, 877759.
Gaunt, E. R., Hardie, A., Claas, E. C., Simmonds, P., & Templeton, K. E. (2010). Epidemiology and clinical presentations of the four human coronaviruses 229E, HKU1, NL63, and OC43 detected over 3 years using a novel multiplex real-time PCR method. Journal of clinical microbiology, 48(8), 2940–2947.
HCoV-NL63 commonly infects children and can cause croup (laryngotracheitis) or bronchiolitis, as well as pneumonia in susceptible hosts. It is clinically important because it often presents as severe respiratory illness in young children or the immunocompromised (Gaunt et al. 2010, Sung et al. 2010, Jo et al. 2022).
Sung, J. Y., Lee, H. J., Eun, B. W., Kim, S. H., Lee, S. Y., Lee, J. Y., Park, K. U., & Choi, E. H. (2010). Role of human coronavirus NL63 in hospitalized children with croup. The Pediatric infectious disease journal, 29(9), 822–826. https://doi.org/10.1097/INF.0b013e3181e7c18d
Gaunt, E. R., Hardie, A., Claas, E. C., Simmonds, P., & Templeton, K. E. (2010). Epidemiology and clinical presentations of the four human coronaviruses 229E, HKU1, NL63, and OC43 detected over 3 years using a novel multiplex real-time PCR method. Journal of clinical microbiology, 48(8), 2940–2947. https://doi.org/10.1128/JCM.00636-10
Jo, K. J., Choi, S. H., Oh, C. E., Kim, H., Choi, B. S., Jo, D. S., & Park, S. E. (2022). Epidemiology and Clinical Characteristics of Human Coronaviruses-Associated Infections in Children: A Multi-Center Study. Frontiers in pediatrics, 10, 877759. https://doi.org/10.3389/fped.2022.877759
HCoV-OC43 is the most frequently detected common cold coronavirus and often causes lower respiratory infections. Studies show OC43 predominates among seasonal coronaviruses and is associated with pneumonia in infants and elderly. It is included because OC43 infections can be severe in high-risk patients and its detection completes the panel of endemic coronaviruses (Gaunt et al. 2010, Jo et al. 2022).
Jo, K. J., Choi, S. H., Oh, C. E., Kim, H., Choi, B. S., Jo, D. S., & Park, S. E. (2022). Epidemiology and Clinical Characteristics of Human Coronaviruses-Associated Infections in Children: A Multi-Center Study. Frontiers in pediatrics, 10, 877759. https://doi.org/10.3389/fped.2022.877759
Gaunt, E. R., Hardie, A., Claas, E. C., Simmonds, P., & Templeton, K. E. (2010). Epidemiology and clinical presentations of the four human coronaviruses 229E, HKU1, NL63, and OC43 detected over 3 years using a novel multiplex real-time PCR method. Journal of clinical microbiology, 48(8), 2940–2947. https://doi.org/10.1128/JCM.00636-10
Urinary tract infections: Enterobacter cloacae is an opportunistic rod increasingly identified in complicated and catheter-associated UTIs. It has intrinsic resistance to multiple antibiotics and is known for harboring extended-spectrum β-lactamases (ESBLs) and carbapenemases. Early and accurate detection via PCR is vital for appropriate treatment and infection control in healthcare settings (Davin-Regli & Pagès 2015, Davin-Regli et al. 2019).
Wound infections: Enterobacter cloacae is a common hospital-associated bacterium that can cause wound and surgical site infections. It is part of the ESKAPE group of pathogens known for antibiotic resistance and often produces inducible AmpC enzymes, which can make it resistant to cephalosporins. E. cloacae is frequently isolated from burn wounds and other healthcare-related wound infections. Inclusion of Enterobacter in a wound PCR panel is justified because prompt identification can influence antibiotic choice (Azzopardi et al. 2014).
Davin-Regli A, Pagès JM. Enterobacter aerogenes and Enterobacter cloacae; versatile bacterial pathogens confronting antibiotic treatment. Front Microbiol. 2015 May 18;6:392. doi: 10.3389/fmicb.2015.00392. PMID: 26042091; PMCID: PMC4435039.
Davin-Regli A, Lavigne JP, Pagès JM. Enterobacter spp.: Update on Taxonomy, Clinical Aspects, and Emerging Antimicrobial Resistance. Clin Microbiol Rev. 2019 Jul 17;32(4):e00002-19. doi: 10.1128/CMR.00002-19. PMID: 31315895; PMCID: PMC6750132.
Azzopardi, E. A., Azzopardi, E., Camilleri, L., Villapalos, J., Boyce, D. E., Dziewulski, P., Dickson, W. A., & Whitaker, I. S. (2014). Gram negative wound infection in hospitalised adult burn patients–systematic review and metanalysis-. PloS one, 9(4), e95042. Mezzatesta ML, Gona F, Stefani S. Enterobacter cloacae complex: clinical impact and emerging antibiotic resistance. Future Microbiol. 2012 Jul;7(7):887-902. doi: 10.2217/fmb.12.61. PMID: 22827309.Urinary tract infections: Enterococcus faecalis is frequently implicated in healthcare-associated UTIs, particularly in patients with urinary catheters or structural urologic abnormalities. It is capable of forming biofilms and exhibiting resistance to many antibiotics, including vancomycin. Its role in persistent and recurrent infections underscores the need for sensitive detection in diagnostic panels (Codelia-Anjum et al. 2023, Hourigan et al. 2024, Arias & Murray 2012).
Wound infections: Enterococcus faecalis is frequently isolated from chronic wound infections and surgical sites, especially in chronic wounds like diabetic foot ulcers. Enterococci are common in diabetic foot infections and are associated with delayed healing and increased risk of complications. E. faecalis can form biofilms in wound environments and exhibits resistance to some antibiotics. PCR detection of E. faecalis is crucial because it is one of the most common bacteria in non-healing wounds (Melo et al. 2021, Celik et al. 2024)
Codelia-Anjum, A., Lerner, L. B., Elterman, D., Zorn, K. C., Bhojani, N., & Chughtai, B. (2023). Enterococcal Urinary Tract Infections: A Review of the Pathogenicity, Epidemiology, and Treatment. Antibiotics (Basel, Switzerland), 12(4), 778.
Hourigan, D., Stefanovic, E., Hill, C., & Ross, R. P. (2024). Promiscuous, persistent and problematic: insights into current enterococcal genomics to guide therapeutic strategy. BMC microbiology, 24(1), 103.
Arias CA, Murray BE. The rise of the Enterococcus: beyond vancomycin resistance. Nat Rev Microbiol. 2012 Mar 16;10(4):266-78. doi: 10.1038/nrmicro2761. PMID: 22421879; PMCID: PMC3621121.
Fisher K, Phillips C. The ecology, epidemiology and virulence of Enterococcus. Microbiology (Reading). 2009 Jun;155(Pt 6):1749-1757. doi: 10.1099/mic.0.026385-0. Epub 2009 Apr 21. PMID: 19383684.
Melo, L. D. R., Ferreira, R., Costa, A. R., Oliveira, H., & Azeredo, J. (2021). Author Correction: Efficacy and safety assessment of two enterococci phages in an in vitro biofilm wound model. Scientific reports, 11(1), 11008.
Celik, C., Lee, S. T. T., Tanoto, F. R., Veleba, M., Kline, K., & Thibault, G. (2024). Decoding the complexity of delayed wound healing following Enterococcus faecalis infection. eLife, 13, RP95113.
Urinary tract infections: Enterococcus faecium is less commonly encountered in UTIs than E. faecalis but poses greater treatment challenges due to its multidrug resistance, including vancomycin-resistant strains (VRE). It is primarily associated with nosocomial infections and often colonizes the urinary tract in immunocompromised individuals. Its detection is important for infection control and antimicrobial stewardship (Codelia-Anjum et al. 2023, Hourigan et al. 2024, Arias & Murray 2012).
Wound infections: Enterococcus faecium is another significant enterococcal species in wound infections, especially in hospital-acquired and chronic wound settings. It is frequently multidrug-resistant, including strains resistant to vancomycin (VRE), making treatment more complex. E. faecium can colonize open wounds and surgical sites, especially in immunocompromised patients. Its inclusion in wound PCR panels allows for early detection and isolation precautions when necessary to limit nosocomial transmission (CDC 2019, Melo et al. 2021).
Codelia-Anjum, A., Lerner, L. B., Elterman, D., Zorn, K. C., Bhojani, N., & Chughtai, B. (2023). Enterococcal Urinary Tract Infections: A Review of the Pathogenicity, Epidemiology, and Treatment. Antibiotics (Basel, Switzerland), 12(4), 778.
Hourigan, D., Stefanovic, E., Hill, C., & Ross, R. P. (2024). Promiscuous, persistent and problematic: insights into current enterococcal genomics to guide therapeutic strategy. BMC microbiology, 24(1), 103.
Arias CA, Murray BE. The rise of the Enterococcus: beyond vancomycin resistance. Nat Rev Microbiol. 2012 Mar 16;10(4):266-78. doi: 10.1038/nrmicro2761. PMID: 22421879; PMCID: PMC3621121.
Fisher K, Phillips C. The ecology, epidemiology and virulence of Enterococcus. Microbiology (Reading). 2009 Jun;155(Pt 6):1749-1757. doi: 10.1099/mic.0.026385-0. Epub 2009 Apr 21. PMID: 19383684.
CDC. Antibiotic Resistance Threats in the United States, 2019. Atlanta, GA: U.S. Department of Health and Human Services, CDC; 2019
Melo, L. D. R., Ferreira, R., Costa, A. R., Oliveira, H., & Azeredo, J. (2021). Author Correction: Efficacy and safety assessment of two enterococci phages in an in vitro biofilm wound model. Scientific reports, 11(1), 11008.
Human enteroviruses (e.g. Coxsackie, echovirus) are common causes of respiratory illness, meningitis, rashes, and myocarditis, and often present as “enteroviral” pneumonia or bronchiolitis in children. Detecting enterovirus helps diagnose outbreaks and rule out other causes (e.g. distinguishing enterovirus D68 vs rhinovirus in clinical syndromes). Charlton et al. 2018, Sanchez et al 2023).
Charlton, C. L., Babady, E., Ginocchio, C. C., Hatchette, T. F., Jerris, R. C., Li, Y., Loeffelholz, M., McCarter, Y. S., Miller, M. B., Novak-Weekley, S., Schuetz, A. N., Tang, Y. W., Widen, R., & Drews, S. J. (2018). Practical Guidance for Clinical Microbiology Laboratories: Viruses Causing Acute Respiratory Tract Infections. Clinical microbiology reviews, 32(1), e00042-18. https://doi.org/10.1128/CMR.00042-18
Sanchez, R., Capossela, E., Speziale, M., O’Donnell, J., Moodley, A., Morales, C., Wadford, D. A., Glaser, C., Shah, S., Beatty, M. E., & Pong, A. (2024). Notes from the Field: Respiratory Viral Panel as an Early Diagnostic Tool for Neonatal Enterovirus Infection – San Diego, California 2023. MMWR. Morbidity and mortality weekly report, 73(27), 607–608. https://doi.org/10.15585/mmwr.mm7327a2
Enterovirus D68 is a non-polio enterovirus that can cause seasonal respiratory outbreaks, especially in children, sometimes leading to severe illness. Including enterovirus targets aids in outbreak detection and surveillance of these clinically important virus (Grizer et al 2024, Martin et al. 2016).
Martin, G., Li, R., Cook, V. E., Carwana, M., Tilley, P., Sauve, L., Tang, P., Kapur, A., & Yang, C. L. (2016). Respiratory Presentation of Pediatric Patients in the 2014 Enterovirus D68 Outbreak. Canadian respiratory journal, 2016, 8302179. https://doi.org/10.1155/2016/8302179
Grizer, C. S., Messacar, K., & Mattapallil, J. J. (2024). Enterovirus D68 – A reemerging non-polio enterovirus that causes severe respiratory and neurological disease in children. Frontiers in Virology, 4, 1328457frontiersin.org.
Urinary tract infections: Escherichia coli is the most common cause of uncomplicated and complicated UTIs, responsible for up to 80–90% of community-acquired infections. Uropathogenic E. coli (UPEC) strains possess virulence factors like adhesins, toxins, and iron acquisition systems that facilitate colonization and persistence in the urinary tract. Due to its prevalence and clinical significance, E. coli is a core target in all UTI molecular diagnostic panels (Flores et al. 2015, Timm et al. 2025).
Wound infections: Escherichia coli is a frequent cause of wound infections, particularly in wounds contaminated with fecal material or in abdominal surgeries. It is often part of polymicrobial infections and can complicate wound healing due to its virulence and potential resistance mechanisms, such as extended-spectrum beta-lactamases (ESBLs). E. coli’s inclusion in a PCR wound panel is justified because it is frequently present in infected wounds and often carries multidrug resistance genes underscoring its clinical relevance (Petkovsek et al. 2009).
Flores-Mireles AL, Walker JN, Caparon M, Hultgren SJ. Urinary tract infections: epidemiology, mechanisms of infection and treatment options. Nat Rev Microbiol. 2015 May;13(5):269-84.
Timm, M.R., Russell, S.K. & Hultgren, S.J. Timm, M.R., Russell, S.K. & Hultgren, S.J. Urinary tract infections: pathogenesis, host susceptibility and emerging therapeutics. Nat Rev Microbiol 23, 72–86 (2025).
Petkovsek, Z., Elersic, K., Gubina, M., Zgur-Bertok, D., & Starcic Erjavec, M. (2009). Virulence potential of Escherichia coli isolates from skin and soft tissue infections. Journal of clinical microbiology, 47(6), 1811–1817.Haemophilus ducreyi causes chancroid, a painful genital ulcer disease that can facilitate HIV transmission. Although rare in many regions, it is included in PCR panels for comprehensive genital ulcer diagnosis (Workowski et al. 2021).
Workowski, K. A., Bachmann, L. H., Chan, P. A., Johnston, C. M., Muzny, C. A., Park I., Reno, H., Jonathan M. Zenilman J.M.,Bolan, G. A. (2021). Sexually transmitted infections treatment guidelines, 2021. MMWR Recommendations and Reports, 70(4), 1–187. https://doi.org/10.15585/mmwr.rr7004a1
Haemophilus influenzae (type b and nontypeable) remains an important respiratory pathogen in children and adults. Hib in particular used to cause severe pediatric pneumonia and meningitis. Its inclusion is justified by its role in community-acquired pneumonia and the importance of vaccine-preventable Hib disease (Morris et al 2017, Borgogna & Voyich 2022).
Morris, D. E., Cleary, D. W., & Clarke, S. C. (2017). Secondary Bacterial Infections Associated with Influenza Pandemics. Frontiers in microbiology, 8, 1041. https://doi.org/10.3389/fmicb.2017.01041
Borgogna, T., & M. Voyich, J. (2022). Examining the Executioners, Influenza Associated Secondary Bacterial Pneumonia. IntechOpen. doi: 10.5772/intechopen.101666Herpes simplex virus type 1 (HSV-1) typically causes orolabial herpes (cold sores) and is often acquired non-sexually in childhood, but it can also be transmitted via oral-genital contact and increasingly causes genital herpes in young adults. Detecting HSV-1 in an STI panel (especially during evaluation of genital ulcers) is important because differentiating it from HSV-2 informs prognosis and counseling (CDC 2024b, Workowski et al. 2021).
Workowski, K. A., Bachmann, L. H., Chan, P. A., Johnston, C. M., Muzny, C. A., Park I., Reno, H., Jonathan M. Zenilman J.M.,Bolan, G. A. (2021). Sexually transmitted infections treatment guidelines, 2021. MMWR Recommendations and Reports, 70(4), 1–187. https://doi.org/10.15585/mmwr.rr7004a1
Centers for Disease Control and Prevention (CDC). (2024b). Genital herpes – CDC detailed fact sheet.Retrieved from https://www.cdc.gov/herpes
Herpes simplex virus type 2 (HSV-2) is the primary cause of genital herpes and causes a lifelong infection characterized by periodic reactivation of painful genital ulcers after an initial exposure. HSV-2 is routinely included in STI panels for patients with genital ulcers because accurate diagnosis enables appropriate antiviral therapy, which can reduce outbreak frequency and transmission risk to partners (CDC 2024b, Workowski et al. 2021).
Centers for Disease Control and Prevention (CDC). (2024b). Genital herpes – CDC detailed fact sheet.Retrieved from https://www.cdc.gov/herpes
Workowski, K. A., Bachmann, L. H., Chan, P. A., Johnston, C. M., Muzny, C. A., Park I., Reno, H., Jonathan M. Zenilman J.M.,Bolan, G. A. (2021). Sexually transmitted infections treatment guidelines, 2021. MMWR Recommendations and Reports, 70(4), 1–187. https://doi.org/10.15585/mmwr.rr7004a1
HMPV is a paramyxovirus discovered in 2001 that causes seasonal respiratory infections (bronchiolitis, pneumonia) similar in severity to RSV, especially in young children and the elderly. It is clinically relevant to include because HMPV accounts for a significant fraction of pediatric hospitalizations (on the order of 5–10% annually) and can cause outbreaks of severe lower respiratory disease Charlton et al. 2018, Panda et al. 2014).
Charlton, C. L., Babady, E., Ginocchio, C. C., Hatchette, T. F., Jerris, R. C., Li, Y., Loeffelholz, M., McCarter, Y. S., Miller, M. B., Novak-Weekley, S., Schuetz, A. N., Tang, Y. W., Widen, R., & Drews, S. J. (2018). Practical Guidance for Clinical Microbiology Laboratories: Viruses Causing Acute Respiratory Tract Infections. Clinical microbiology reviews, 32(1), e00042-18. https://doi.org/10.1128/CMR.00042-18
Panda, S., Mohakud, N. K., Pena, L., & Kumar, S. (2014). Human metapneumovirus: review of an important respiratory pathogen. International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases, 25, 45–52. https://doi.org/10.1016/j.ijid.2014.03.1394
Influenza A viruses are a major inclusion in respiratory panels because seasonal epidemics and occasional pandemics, leading to millions of US cases each year, hundreds of thousands of hospitalizations, and tens of thousands of deaths. Early detection is essential because influenza A is treatable with antivirals and its presence impacts infection control and vaccination strategies (Uyeki et al. 2018, Cozza et al. 2021).
Uyeki, T. M., Bernstein, H. H., Bradley, J. S., Englund, J. A., File, T. M., Fry, A. M., Gravenstein, S., Hayden, F. G., Harper, S. A., Hirshon, J. M., Ison, M. G., Johnston, B. L., Knight, S. L., McGeer, A., Riley, L. E., Wolfe, C. R., Alexander, P. E., & Pavia, A. T. (2019). Clinical Practice Guidelines by the Infectious Diseases Society of America: 2018 Update on Diagnosis, Treatment, Chemoprophylaxis, and Institutional Outbreak Management of Seasonal Influenzaa. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America, 68(6), e1–e47. https://doi.org/10.1093/cid/ciy866
Cozza, V., Campbell, H., Chang, H. H., Iuliano, A. D., Paget, J., Patel, N. N., Reiner, R. C., Troeger, C., Viboud, C., Bresee, J. S., & Fitzner, J. (2021). Global Seasonal Influenza Mortality Estimates: A Comparison of 3 Different Approaches. American journal of epidemiology, 190(5), 718–727. https://doi.org/10.1093/aje/kwaa196
Influenza B viruses co-circulate with influenza A each season and also cause significant illness, especially in children; they lead to seasonal flu outbreaks and can cause severe pneumonia and hospitalizations. Despite lower overall incidence, B strains are included because they contribute substantially to seasonal influenza burden and have distinct vaccine and treatment considerations (Owusu et al. 2019, Charlton et al. 2018).
References:
Charlton, C. L., Babady, E., Ginocchio, C. C., Hatchette, T. F., Jerris, R. C., Li, Y., Loeffelholz, M., McCarter, Y. S., Miller, M. B., Novak-Weekley, S., Schuetz, A. N., Tang, Y. W., Widen, R., & Drews, S. J. (2018). Practical Guidance for Clinical Microbiology Laboratories: Viruses Causing Acute Respiratory Tract Infections. Clinical microbiology reviews, 32(1), e00042-18. https://doi.org/10.1128/CMR.00042-18
Owusu, D., Hand, J., Tenforde, M. W., Feldstein, L. R., DaSilva, J., Barnes, J., Lee, G., Tran, J., Sokol, T., Fry, A. M., Brammer, L., & Rolfes, M. A. (2020). Early Season Pediatric Influenza B/Victoria Virus Infections Associated with a Recently Emerged Virus Subclade – Louisiana, 2019. MMWR. Morbidity and mortality weekly report, 69(2), 40–43. https://doi.org/10.15585/mmwr.mm6902e1
Urinary tract infections: Klebsiella aerogenes is implicated in hospital-acquired UTIs, particularly among patients with indwelling catheters or compromised immune systems. It is known for rapid acquisition of multidrug resistance, including extended-spectrum β-lactamases (ESBL) and carbapenemase production. Its ability to colonize the urinary tract and cause ascending infections supports its inclusion in comprehensive PCR diagnostics (Davin-Regli & Pagès 2015, Davin-Regli et al. 2019, Intra et al. 2023)
Wound infections: Klebsiella aerogenes can cause wound and surgical site infections, especially in nosocomial settings. It is part of the ESKAPE group and exhibits notable resistance to antibiotics, particularly due to AmpC beta-lactamase production. K. aerogenes has been implicated in infections in burns and open wounds, requiring careful antimicrobial stewardship (Davin-Regli & Pagès 2015, Tamma et al. 2019)
Davin-Regli A, Pagès JM. Enterobacter aerogenes and Enterobacter cloacae; versatile bacterial pathogens confronting antibiotic treatment. Front Microbiol. 2015 May 18;6:392. doi: 10.3389/fmicb.2015.00392. PMID: 26042091; PMCID: PMC4435039.
Davin-Regli A, Lavigne JP, Pagès JM. Enterobacter spp.: Update on Taxonomy, Clinical Aspects, and Emerging Antimicrobial Resistance. Clin Microbiol Rev. 2019 Jul 17;32(4):e00002-19. doi: 10.1128/CMR.00002-19. PMID: 31315895; PMCID: PMC6750132.
Intra, J., Carcione, D., Sala, R. M., Siracusa, C., Brambilla, P., & Leoni, V. (2023). Antimicrobial Resistance Patterns of Enterobacter cloacae and Klebsiella aerogenes Strains Isolated from Clinical Specimens: A Twenty-Year Surveillance Study. Antibiotics (Basel, Switzerland), 12(4), 775.
Tamma, P. D., Doi, Y., Bonomo, R. A., Johnson, J. K., Simner, P. J., & Antibacterial Resistance Leadership Group (2019). A Primer on AmpC β-Lactamases: Necessary Knowledge for an Increasingly Multidrug-resistant World. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America, 69(8), 1446–1455.Urinary tract infections: Klebsiella oxytoca is an opportunistic uropathogen associated with both community-acquired and nosocomial UTIs. Though less common than K. pneumoniae, it can cause severe infections and carries a high risk of antimicrobial resistance. Differentiating K. oxytoca from other Klebsiella species is important due to its unique resistance and virulence profiles (Singh et al. 2016).
Wound infections: Klebsiella oxytoca is a less common but clinically important pathogen in wound infections. It shares many virulence traits with K. pneumoniae, including the ability to form biofilms and produce beta-lactamases. K. oxytoca has been recovered from infected surgical sites and chronic wounds, especially in individuals with underlying illnesses (Podschun & Ullman, 1998).
Singh L, Cariappa MP, Kaur M. Klebsiella oxytoca: An emerging pathogen? Med J Armed Forces India. 2016 Dec;72(Suppl 1):S59-S61. doi: 10.1016/j.mjafi.2016.05.002. Epub 2016 Jun 14. PMID: 28050072; PMCID: PMC5192185.
Podschun, R., & Ullmann, U. (1998). Klebsiella spp. as nosocomial pathogens: epidemiology, taxonomy, typing methods, and pathogenicity factors. Clinical microbiology reviews, 11(4), 589–603.Respiratory infections: Klebsiella pneumoniae causes severe pneumonia, particularly in people with alcoholism, diabetes, or compromised lung function. It accounts for a notable share of community-acquired and nosocomial pneumonias (approximately 3–5% of CAP in Western countries, higher in developing regions) and is included because of its association with high-mortality pneumonia and outbreaks in hospitals (Kumar & Zhang 2024, Ashurst & Dawson 2023).
Urinary tract infections: Klebsiella pneumoniae is a major cause of both uncomplicated and complicated UTIs, particularly in hospital settings. It produces various virulence factors such as capsules, adhesins, and siderophores, and it is a common carrier of multidrug resistance mechanisms including extended-spectrum β-lactamase (ESBL)s and carbapenemase. Its clinical significance makes it an essential target in any UTI molecular panel (Paczosa & Mecsas 2016, Timm et al. 2025).
Wound infections: Klebsiella pneumoniae is a significant pathogen in wound infections and surgical sites, particularly in hospitalized patients. It is known for its thick capsule, which enhances virulence, and its frequent multidrug resistance, including carbapenem-resistant strains. Infected wounds with K. pneumoniae can result in delayed healing and serious complications. Its detection is vital for infection control and targeted treatment (Podschun & Ullman, 1998, CDC 2019).
Li, Y., Kumar, S., & Zhang, L. (2024). Mechanisms of Antibiotic Resistance and Developments in Therapeutic Strategies to Combat Klebsiella pneumoniae Infection. Infection and drug resistance, 17, 1107–1119.
Ashurst JV, Dawson A. Klebsiella Pneumonia. [Updated 2023 Jul 20]. In: StatPearls [Internet]. Treasure Island (FL): StatPearls Publishing; 2025 Jan-.
Paczosa MK, Mecsas J. Klebsiella pneumoniae: Going on the Offense with a Strong Defense. Microbiol Mol Biol Rev. 2016 Jun 15;80(3):629-61. doi: 10.1128/MMBR.00078-15. PMID: 27307579; PMCID: PMC4981674.
Timm, M.R., Russell, S.K. & Hultgren, S.J. Timm, M.R., Russell, S.K. & Hultgren, S.J. Urinary tract infections: pathogenesis, host susceptibility and emerging therapeutics. Nat Rev Microbiol 23, 72–86 (2025).
Flores-Mireles AL, Walker JN, Caparon M, Hultgren SJ. Urinary tract infections: epidemiology, mechanisms of infection and treatment options. Nat Rev Microbiol. 2015 May;13(5):269-84.
Podschun, R., & Ullmann, U. (1998). Klebsiella spp. as nosocomial pathogens: epidemiology, taxonomy, typing methods, and pathogenicity factors. Clinical microbiology reviews, 11(4), 589–603.
CDC. Antibiotic Resistance Threats in the United States, 2019. Atlanta, GA: U.S. Department of Health and Human Services, CDC; 2019
Moraxella catarrhalis is typically a commensal organism in the human respiratory tract but can act as a pathogen under certain conditions. It is a major cause of otitis media (middle ear infection) in children and contributes to lower respiratory tract infections in adults (Murphy & Parameswaran 2009, Karalus & Campagnari 2000)
Murphy, T. F., & Parameswaran, G. I. (2009). Moraxella catarrhalis, a human respiratory tract pathogen. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America, 49(1), 124–131. https://doi.org/10.1086/599375
Karalus, R., & Campagnari, A. (2000). Moraxella catarrhalis: a review of an important human mucosal pathogen. Microbes and infection, 2(5), 547–559. https://doi.org/10.1016/s1286-4579(00)00314-2
Urinary tract infections: Morganella morganii can cause UTIs, especially in elderly or catheterized patients. It is often resistant to multiple antibiotics and has intrinsic resistance to certain β-lactams. Although it is not a leading cause of UTIs, its presence in polymicrobial and healthcare-associated infections justifies its inclusion in diagnostic testing (Liu et al. 2016, Zhu et al. 2025) .
Wound infections: Morganella morganii is part of the Enterobacterales family and an uncommon but documented cause of wound infections. It has been implicated in serious skin and soft tissue infections like necrotizing fasciitis and is often described in postoperative or trauma-related wound infections. M. morganii has intrinsic resistance to certain antibiotics and can be mistaken as a contaminant if not properly identified. (Kakurai et al. 2025).
Liu H, Zhu J, Hu Q, Rao X. Morganella morganii, a non-negligent opportunistic pathogen. Int J Infect Dis. 2016 Sep;50:10-7. doi: 10.1016/j.ijid.2016.07.006. Epub 2016 Jul 12. PMID: 27421818.
Zhu W, Liu Q, Liu J, Wang Y, Shen H, Wei M, Pu J, Gu L, Yang J. Genomic epidemiology and antimicrobial resistance of Morganella clinical isolates between 2016 and 2023. Front Cell Infect Microbiol. 2025 Jan 31;14:1464736. doi: 10.3389/fcimb.2024.1464736. PMID: 39958990; PMCID: PMC11826060.
Armbruster, C. E., Brauer, A. L., Humby, M. S., Shao, J., & Chakraborty, S. (2021). Prospective assessment of catheter-associated bacteriuria clinical presentation, epidemiology, and colonization dynamics in nursing home residents. JCI insight, 6(19), e144775.
Kakurai, M., Takeyama, S., & Moriyama, Y. (2025). Necrotizing Soft Tissue Infections Caused by Morganella morganii: A Case Report and Review of the Literature. Cureus, 17(3), e80718.
Mycoplasma genitalium is an emerging STI pathogen linked to urethritis, cervicitis, and pelvic inflammatory disease, with increasing antimicrobial resistance (Workowski et al., 2021). Its inclusion in STI panels supports diagnosis and guides targeted treatment when standard therapies fail.
Workowski, K. A., Bachmann, L. H., Chan, P. A., Johnston, C. M., Muzny, C. A., Park I., Reno, H., Jonathan M. Zenilman J.M.,Bolan, G. A. (2021). Sexually transmitted infections treatment guidelines, 2021. MMWR Recommendations and Reports, 70(4), 1–187. https://doi.org/10.15585/mmwr.rr7004a1
Mycoplasma hominis is a fastidious bacterium lacking a cell wall, which can colonize the genitourinary tract and occasionally cause UTIs, especially in immunosuppressed or pregnant individuals. Because it cannot be detected using standard culture methods and is intrinsically resistant to β-lactam antibiotics, molecular detection via PCR is crucial. Its involvement in persistent, atypical urinary symptoms makes it a relevant diagnostic target (Valentine-King & Brown 2017, Abankwa et al. 2024)
Abankwa A, Sansone S, Aligbe O, Hickner A, Segal S. The Role of Ureaplasma and Mycoplasma Species in Recurrent Lower Urinary Tract Infection in Females: A Scoping Review. Reprod Sci. 2024 Jul;31(7):1771-1780. doi: 10.1007/s43032-024-01513-y. Epub 2024 Mar 20. PMID: 38509400.
Valentine-King MA, Brown MB. Antibacterial Resistance in Ureaplasma Species and Mycoplasma hominis Isolates from Urine Cultures in College-Aged Females. Antimicrob Agents Chemother. 2017 Sep 22;61(10):e01104-17. doi: 10.1128/AAC.01104-17. PMID: 28827422; PMCID: PMC5610494.
Waites KB, Katz B, Schelonka RL. Mycoplasmas and ureaplasmas as neonatal pathogens. Clin Microbiol Rev. 2005 Oct;18(4):757-89. doi: 10.1128/CMR.18.4.757-789.2005. PMID: 16223956; PMCID: PMC1265909.
Mycoplasma pneumoniae is an “atypical” bacterium that causes respiratory infections across all ages and is a leading cause of community-acquired pneumonia in school-aged children and young adults. It infects about 1% of the U.S. population each year (millions of cases); while most are mild, 5–10% of infected patients develop pneumonia. Testing for M. pneumoniae guides therapy and helps explain outbreaks of “walking pneumonia.” (Yun 2024, CDC 2024).
Yun K. W. (2024). Community-acquired pneumonia in children: updated perspectives on its etiology, diagnosis, and treatment. Clinical and experimental pediatrics, 67(2), 80–89. https://doi.org/10.3345/cep.2022.01452
CDC. (2024). Mycoplasma pneumoniae infection surveillance and trends. Retrieved November 14, 2024, from https://www.cdc.gov/mycoplasma/php/surveillance/index.html.
Abdulhadi B, Kiel J. Mycoplasma Pneumonia. [Updated 2023 Jan 16]. In: StatPearls [Internet]. Treasure Island (FL): StatPearls Publishing; 2025 Jan-. Available from: https://www.ncbi.nlm.nih.gov/books/NBK430780/
Neisseria gonorrhoeae often presents asymptomatically but can cause severe reproductive complications and has shown alarming antimicrobial resistance (CDC, 2024a). PCR detection enables timely, appropriate therapy and supports surveillance efforts (Workowski et al., 2021).
Workowski, K. A., Bachmann, L. H., Chan, P. A., Johnston, C. M., Muzny, C. A., Park I., Reno, H., Jonathan M. Zenilman J.M.,Bolan, G. A. (2021). Sexually transmitted infections treatment guidelines, 2021. MMWR Recommendations and Reports, 70(4), 1–187. https://doi.org/10.15585/mmwr.rr7004a1
Human parainfluenza viruses (HPIV 1–3) cause a broad spectrum of respiratory diseases – notably croup, tracheobronchitis, bronchiolitis, and pneumonia in children. Inclusion of HPIV 1–3 is important because they account for a large fraction of pediatric respiratory hospitalizations (croup, bronchiolitis, pneumonia) each year (Elboukari H, Ashraf M 2023, Charlton et al. 2018).
Elboukari H, Ashraf M. Parainfluenza Virus. [Updated 2023 Jul 17]. In: StatPearls [Internet]. Treasure Island (FL): StatPearls Publishing; 2025 Jan-. Available from: https://www.ncbi.nlm.nih.gov/books/NBK560719/
Charlton, C. L., Babady, E., Ginocchio, C. C., Hatchette, T. F., Jerris, R. C., Li, Y., Loeffelholz, M., McCarter, Y. S., Miller, M. B., Novak-Weekley, S., Schuetz, A. N., Tang, Y. W., Widen, R., & Drews, S. J. (2018). Practical Guidance for Clinical Microbiology Laboratories: Viruses Causing Acute Respiratory Tract Infections. Clinical microbiology reviews, 32(1), e00042-18. https://doi.org/10.1128/CMR.00042-18
Proteus mirabilis is a Gram-negative bacterium well known for causing wound and urinary tract infections.
Urinary tract infections: Proteus mirabilis is a common cause of complicated UTIs, especially in patients with long-term catheterization or structural abnormalities of the urinary tract. It produces urease, which hydrolyzes urea to ammonia, raising urine pH and promoting the formation of struvite stones. These properties, combined with swarming motility and biofilm formation, contribute to chronic and recurrent infections, making it a key pathogen in molecular UTI diagnostics (Yang et al. 2024, Armbruster & Mobley, 2012)
Wound infections: In wounds, it is often part of polymicrobial infections and produces a characteristic ammonia-like odor due to its urease activity, which may delay healing. It is often involved in polymicrobial infections and may carry resistance genes, reinforcing its relevance in wound diagnostics. (O’Hara et al. 2000, Armbruster & Mobley, 2012)
Yang A, Tian Y, Li X. Unveiling the hidden arsenal: new insights into Proteus mirabilis virulence in UTIs. Front Cell Infect Microbiol. 2024 Nov 13;14:1465460. doi: 10.3389/fcimb.2024.1465460. PMID: 39606746; PMCID: PMC11599158.
Armbruster CE, Mobley HL. Merging mythology and morphology: the multifaceted lifestyle of Proteus mirabilis. Nat Rev Microbiol. 2012 Nov;10(11):743-54. doi: 10.1038/nrmicro2890. Epub 2012 Oct 8. PMID: 23042564; PMCID: PMC3621030.
O’Hara CM, Brenner FW, Miller JM. Classification, identification, and clinical significance of Proteus, Providencia, and Morganella. Clin Microbiol Rev. 2000 Oct;13(4):534-46. doi: 10.1128/CMR.13.4.534. PMID: 11023955; PMCID: PMC88947.
Urinary tract infections: Proteus vulgaris is a less frequent but clinically significant uropathogen, particularly in hospitalized or catheterized individuals. It shares many virulence traits with P. mirabilis, including urease activity and biofilm formation, and is often multidrug resistant. Its role in polymicrobial and persistent infections supports its inclusion in broad-spectrum UTI testing (O’Hara et al. 2000)
Wound infections: Proteus vulgaris is less frequently encountered than P. mirabilis but still a relevant opportunistic pathogen in wounds. It has been isolated from chronic ulcers, surgical sites, and polymicrobial infections. Its resistance to multiple antibiotics and potential to form biofilms makes early detection crucial for treatment planning. Differentiation from other Proteusspecies is important due to differences in susceptibility profiles (Bowler et al. 2021)
O’Hara CM, Brenner FW, Miller JM. Classification, identification, and clinical significance of Proteus, Providencia, and Morganella. Clin Microbiol Rev. 2000 Oct;13(4):534-46. doi: 10.1128/CMR.13.4.534. PMID: 11023955; PMCID: PMC88947.
Bowler, P. G., Duerden, B. I., & Armstrong, D. G. (2001). Wound microbiology and associated approaches to wound management. Clinical microbiology reviews, 14(2), 244–269.Providencia stuartii is an opportunistic gram-negative pathogen frequently associated with catheter-associated UTIs in elderly, institutionalized patients. It is known for urease production and the ability to form biofilms, contributing to encrustation and catheter blockage. Additionally, it often exhibits resistance to multiple antibiotics, making PCR-based detection important for managing infection risks (Armbruster et al. 2021, (O’Hara et al. 2000).
O’Hara CM, Brenner FW, Miller JM. Classification, identification, and clinical significance of Proteus, Providencia, and Morganella. Clin Microbiol Rev. 2000 Oct;13(4):534-46. doi: 10.1128/CMR.13.4.534. PMID: 11023955; PMCID: PMC88947.
Armbruster, C. E., Brauer, A. L., Humby, M. S., Shao, J., & Chakraborty, S. (2021). Prospective assessment of catheter-associated bacteriuria clinical presentation, epidemiology, and colonization dynamics in nursing home residents. JCI insight, 6(19), e144775. https://doi.org/10.1172/jci.insight.144775
Urinary tract infections: Pseudomonas aeruginosa is a highly adaptable gram-negative bacterium that causes complicated UTIs, especially in immunocompromised patients or those with urinary catheters. It is notorious for antibiotic resistance and for forming biofilms on urinary devices, leading to chronic infections. Its relevance in hospital-acquired UTIs and need for targeted therapy make its detection via molecular methods essential (Mittal et al. 2009, Timm et al. 2025).
Wound infections: Pseudomonas aeruginosa is one of the most common and challenging pathogens in wound care due to its multidrug resistance and biofilm-forming ability. It frequently infects burn wounds and chronic ulcers, causing delayed healing and increased morbidity. P. aeruginosa thrives in moist environments and produces toxins that damage tissue. Prompt identification enables initiation of antipseudomonal therapy and mitigates risk of dissemination (Azzopardi et al. 2014).
Timm, M.R., Russell, S.K. & Hultgren, S.J. Timm, M.R., Russell, S.K. & Hultgren, S.J. Urinary tract infections: pathogenesis, host susceptibility and emerging therapeutics. Nat Rev Microbiol 23, 72–86 (2025).
Azzopardi, E. A., Azzopardi, E., Camilleri, L., Villapalos, J., Boyce, D. E., Dziewulski, P., Dickson, W. A., & Whitaker, I. S. (2014). Gram negative wound infection in hospitalised adult burn patients–systematic review and metanalysis-. PloS one, 9(4), e95042.RSV (A and B) is the leading cause of bronchiolitis and viral pneumonia in infants and young children and also cause significant disease in elderly adults. Nearly all children are infected by age 2, and RSV annually causes about 33 million pediatric LRTI episodes. It is the single largest cause of infant hospitalization in the U.S., making RSV detection by PCR crucial because it confirms the diagnosis and guiding supportive care and infection control (Schweitzer & Justice 2023, Charlton et al. 2018).
Charlton, C. L., Babady, E., Ginocchio, C. C., Hatchette, T. F., Jerris, R. C., Li, Y., Loeffelholz, M., McCarter, Y. S., Miller, M. B., Novak-Weekley, S., Schuetz, A. N., Tang, Y. W., Widen, R., & Drews, S. J. (2018). Practical Guidance for Clinical Microbiology Laboratories: Viruses Causing Acute Respiratory Tract Infections. Clinical microbiology reviews, 32(1), e00042-18. https://doi.org/10.1128/CMR.00042-18
Jain H, Schweitzer JW, Justice NA. Respiratory Syncytial Virus Infection in Children. [Updated 2023 Jun 20]. In: StatPearls [Internet]. Treasure Island (FL): StatPearls Publishing; 2025 Jan-.
Rhinoviruses are by far the most common cause of the “common cold” (responsible for ~50–80% of URIs) and circulate year-round. Although typically causing mild illness, rhinovirus can infect lower airways and is a leading trigger of asthma and chronic airway. Testing for rhinovirus helps interpret respiratory symptoms and can identify outbreaks (Tobin et al. 2025, Esneau et al 2022).
Tobin, E. H., Thomas, M., & Bomar, P. A. (2025). Upper Respiratory Tract Infections With Focus on The Common Cold. In StatPearls. StatPearls Publishing.
Esneau, C., Duff, A. C., & Bartlett, N. W. (2022). Understanding Rhinovirus Circulation and Impact on Illness. Viruses, 14(1), 141. https://doi.org/10.3390/v14010141
RNase P is a human gene present in all nucleated cells and is commonly used as an internal control in PCR-based assays. Its amplification confirms that the sample contains human nucleic acid and that the nucleic acid extraction and PCR steps were successful. Please note that even though RNase P is a gold standard endogenous control for PCR assays, but it is not reliable in urine samples due to their typically low human DNA content. Assays using urine often require additional or alternative controls to ensure accurate validation of negative results (Vogels et al 2020, FDA 2023).
Vogels, C. B. F., Brito, A. F., Wyllie, A. L., Fauver, J. R., Ott, I. M., Kalinich, C. C., Petrone, M. E., Casanovas-Massana, A., Catherine Muenker, M., Moore, A. J., Klein, J., Lu, P., Lu-Culligan, A., Jiang, X., Kim, D. J., Kudo, E., Mao, T., Moriyama, M., Oh, J. E., Park, A., … Grubaugh, N. D. (2020). Analytical sensitivity and efficiency comparisons of SARS-CoV-2 RT-qPCR primer-probe sets. Nature microbiology, 5(10), 1299–1305. https://doi.org/10.1038/s41564-020-0761-6
Nalla, A. K., Casto, A. M., Huang, M. W., Perchetti, G. A., Sampoleo, R., Shrestha, L., Wei, Y., Zhu, H., Jerome, K. R., & Greninger, A. L. (2020). Comparative Performance of SARS-CoV-2 Detection Assays Using Seven Different Primer-Probe Sets and One Assay Kit https://journals.asm.org/doi/epub/10.1128/jcm.00557-20. Journal of clinical microbiology, 58(6), e00557-20. https://doi.org/10.1128/JCM.00557-20
SARS-CoV-2 (COVID-19) is a coronavirus that causes viral pneumonia and systemic illness; it remains a significant respiratory pathogen. Even after the pandemic emergency, it continues to circulate seasonally in the U.S., leading to thousands of hospitalizations and deaths each year. Detecting SARS-CoV-2 is essential for patient care and public health (CDC2024, Hanage & Schaffner 2025).
CDC. (2024). Preliminary estimates of COVID-19 burden for 2024–2025. Retrieved December 6, 2024, from https://www.cdc.gov/covid/php/surveillance/burden-estimates.html
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Urinary tract infections: Serratia marcescens is an opportunistic, gram-negative pathogen increasingly recognized in nosocomial UTIs, particularly in ICU patients or those with indwelling devices. It produces a red pigment (prodigiosin) and is capable of biofilm formation and resistance to multiple antibiotics, including β-lactams. Although less common, its role in outbreaks and persistent infections warrants its inclusion in diagnostic panels (Su et al. 2003, Tavares-Carreon et al. 2023).
Wound infections: Serratia marcescens is a gram-negative bacillus that causes opportunistic wound infections, particularly in healthcare environments. It is associated with contamination of medical equipment and antiseptics and has been responsible for outbreaks. S. marcescens is notable for its resistance mechanisms and ability to survive in harsh environments. Early detection in wound panels is important for preventing nosocomial spread (Drummond et al. 2023, Kim et al. 2020)
Su LH, Ou JT, Leu HS, Chiang PC, Chiu YP, Chia JH, Kuo AJ, Chiu CH, Chu C, Wu TL, Sun CF, Riley TV, Chang BJ; Infection Control Group. Extended epidemic of nosocomial urinary tract infections caused by Serratia marcescens. J Clin Microbiol. 2003 Oct;41(10):4726-32. doi: 10.1128/JCM.41.10.4726-4732.2003. PMID: 14532211; PMCID: PMC254321.
Tavares-Carreon, F., De Anda-Mora, K., Rojas-Barrera, I. C., & Andrade, A. (2023). Serratia marcescens antibiotic resistance mechanisms of an opportunistic pathogen: a literature review. PeerJ, 11, e14399.
Drummond, S. E., Maliampurakal, A., Jamdar, S., Melly, L., & Holmes, S. (2023). Serratia marcescens causing recurrent superficial skin infections in an immunosuppressed patient. Skin health and disease, 3(6), e283.
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Wound infections: Staphylococcus aureus is one of the most prevalent causes of wound infections and can lead to a range of conditions from mild cellulitis to life-threatening sepsis. Methicillin-resistant S. aureus (MRSA) is of particular concern in both community and healthcare settings. S. aureus produces multiple virulence factors, including toxins and enzymes that degrade tissue. PCR detection enables rapid diagnosis and appropriate antimicrobial management (Del Guidice 2020, Tong et al. 2015).
Urinary tract infections: Staphylococcus aureus is not a frequent cause of community-acquired UTIs but is increasingly implicated in healthcare-associated and complicated cases, particularly in patients with catheters, diabetes, or immunosuppression. It can enter the urinary tract hematogenously or via instrumentation and may lead to severe outcomes like pyelonephritis or bacteremia. The inclusion of S. aureus in PCR panels is important for early detection and intervention, especially in high-risk settings (Tong et al. 2015 , Timm et al. 2025).
Morris, D. E., Cleary, D. W., & Clarke, S. C. (2017). Secondary Bacterial Infections Associated with Influenza Pandemics. Frontiers in microbiology, 8, 1041. https://doi.org/10.3389/fmicb.2017.01041
Borgogna, T., & M. Voyich, J. (2022). Examining the Executioners, Influenza Associated Secondary Bacterial Pneumonia. IntechOpen. doi: 10.5772/intechopen.101666 Del Giudice P. (2020). Skin Infections Caused by Staphylococcus aureus. Acta dermato-venereologica, 100(9), adv00110. Tong, S. Y., Davis, J. S., Eichenberger, E., Holland, T. L., & Fowler, V. G., Jr (2015). Staphylococcus aureus infections: epidemiology, pathophysiology, clinical manifestations, and management. Clinical microbiology reviews, 28(3), 603–661.Timm, M.R., Russell, S.K. & Hultgren, S.J. Timm, M.R., Russell, S.K. & Hultgren, S.J. Urinary tract infections: pathogenesis, host susceptibility and emerging therapeutics. Nat Rev Microbiol 23, 72–86 (2025).
Urinary tract infections: Staphylococcus saprophyticus is a leading cause of uncomplicated UTIs in young, sexually active women, second only to E. coli. It adheres strongly to uroepithelial cells and can persist in the urinary tract without significant symptoms, sometimes leading to delayed diagnosis. Given its frequency in this demographic and its resistance to certain antibiotics, it is a crucial component of targeted molecular testing (Zhang et al. 2023, Flores et al. 2015).
Wound infections: Staphylococcus saprophyticus is primarily associated with urinary tract infections but has been identified in wound infections, particularly in immunocompromised individuals. It is coagulase-negative and may be overlooked in polymicrobial cultures. S. saprophyticus can cause wound infections following trauma or surgery and may demonstrate resistance to common antibiotics (Zhang et al. 2023).
Zhang K, Potter RF, Marino J, Muenks CE, Lammers MG, Dien Bard J, Dingle TC, Humphries R, Westblade LF, Burnham C-AD, Dantas G. Comparative genomics reveals the correlations of stress response genes and bacteriophages in developing antibiotic resistance of Staphylococcus saprophyticus. mSystems. 2023 Dec 21;8(6):e0069723. doi: 10.1128/msystems.00697-23. Epub 2023 Dec 5. PMID: 38051037; PMCID: PMC10734486.
Flores-Mireles AL, Walker JN, Caparon M, Hultgren SJ. Urinary tract infections: epidemiology, mechanisms of infection and treatment options. Nat Rev Microbiol. 2015 May;13(5):269-284.
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