Targets

References:

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.

The ACT gene encodes a plasmid-borne AmpC β-lactamase that confers resistance to broad-spectrum cephalosporins. In clinical Klebsiella pneumoniae isolates ACT-1 is inducible by cephalosporins, and when combined with porin loss it can drive high-level carbapenem/cephalosporin resistance. Including ACT in the panel flags AmpC-mediated resistance that may otherwise be missed (Philippon et al. 2002, Reisbig & Hanson 2002).

References:

Philippon, A., Arlet, G., & Jacoby, G. A. (2002). Plasmid-determined AmpC-type beta-lactamases. Antimicrobial agents and chemotherapy, 46(1), 1–11. https://doi.org/10.1128/AAC.46.1.1-11.2002

Reisbig, M. D., & Hanson, N. D. (2002). The ACT-1 plasmid-encoded AmpC beta-lactamase is inducible: detection in a complex beta-lactamase background. The Journal of antimicrobial chemotherapy, 49(3), 557–560. https://doi.org/10.1093/jac/49.3.557

Actinomyces urogenitalis is a rare Actinomyces species first described from urogenital samples. It has been implicated in pelvic/genitourinary infections. Because it is fastidious and resembles other Actinomyces, standard cultures often fail to identify it. Its inclusion on a PCR panel helps detect this unusual pathogen in post-procedure UTIs or abscesses, ensuring appropriate treatment antibiotics (Van Hoecke et al. 2013).

References

Van Hoecke, F., Beuckelaers, E., Lissens, P., & Boudewijns, M. (2013). Actinomyces urogenitalis bacteremia and tubo-ovarian abscess after an in vitro fertilization (IVF) procedure. Journal of clinical microbiology, 51(12), 4252–4254. https://doi.org/10.1128/JCM.02142-13

Actinotignum schaalii (formerly Actinobaculum schaalii) is a fastidious, anaerobic gram-positive rod increasingly recognized in UTIs, especially among the elderly and those with urological comorbidities. It is difficult to culture and often overlooked by standard diagnostic methods, despite being a frequent contributor to symptomatic infections. PCR testing is the most reliable method for detection and proper management (Lotte & Lotte 2016, Sahuquillo-Arce et al. 2024, Wang et al. 2023).

References:

Lotte R, Lotte L, Ruimy R. Actinotignum schaalii (formerly Actinobaculum schaalii): a newly recognized pathogen-review of the literature. Clin Microbiol Infect. 2016 Jan;22(1):28-36.

Sahuquillo-Arce JM, Suárez-Urquiza P, Hernández-Cabezas A, Tofan L, Chouman-Arcas R, García-Hita M, Sabalza-Baztán O, Sellés-Sánchez A, Lozano-Rodríguez N, Martí-Cuñat J, López-Hontangas JL. Actinotignum schaalii infection: Challenges in diagnosis and treatment. Heliyon. 2024 Mar 22;10(7): e28589.

Wang, D., Haley, E., Luke, N., Mathur, M., Festa, R. A., Zhao, X., Anderson, L. A., Allison, J. L., Stebbins, K. L., Diaz, M. J., & Baunoch, D. (2023). Emerging and Fastidious Uropathogens Were Detected by M-PCR with Similar Prevalence and Cell Density in Catheter and Midstream Voided Urine Indicating the Importance of These Microbes in Causing UTIs. Infection and drug resistance, 16, 7775–7795. https://doi.org/10.2147/IDR.S429990

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).

References:

Khanal, S., Ghimire, P., & Dhamoon, A. S. (2018). The Repertoire of Adenovirus in Human Disease: The Innocuous to the Deadly. Biomedicines, 6(1), 30.

Aerococcus urinae is a gram-positive coccus that resembles streptococci but has distinct pathogenic and antibiotic susceptibility traits. It has emerged as a significant pathogen in elderly males and those with urologic abnormalities or catheters, often causing chronic or recurrent UTIs. It is frequently misidentified by conventional methods, making PCR-based diagnostics valuable (Higgins & Garg 2017, Rasmussen 2016, Wang et al. 2023).

References:

Higgins A, Garg T. Aerococcus urinae: An Emerging Cause of Urinary Tract Infection in Older Adults with Multimorbidity and Urologic Cancer. Urol Case Rep. 2017 Apr 12;13:24-25.

Rasmussen M. Aerococcus: an increasingly acknowledged human pathogen. Clin Microbiol Infect. 2016 Jan;22(1):22-27.

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).

References:

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.

The bla_KPC genes encode KPC enzymes and are the most common carbapenemase detected in U.S. KPC enzymes confer high-level resistance to all β-lactams (including penicillins, cephalosporins and carbapenems) and are usually plasmid-borne with other resistance genes. Detection of bla_KPC in a PCR panel identifies a CRE (carbapenem-resistant Enterobacteriaceae) requiring use of last-resort antibiotics and implementation of strict control measures to prevent transmission (Tzouvelekis et al.  2012, Banerjee, & Humphries 2017)

References:

Tzouvelekis, L. S., Markogiannakis, A., Psichogiou, M., Tassios, P. T., & Daikos, G. L. (2012). Carbapenemases in Klebsiella pneumoniae and other Enterobacteriaceae: an evolving crisis of global dimensions. Clinical Microbiology Reviews, 25(4), 682–707.

Banerjee, R., & Humphries, R. (2017). Clinical and laboratory considerations for the rapid detection of carbapenem-resistant Enterobacteriaceae. Virulence, 8(4), 427–439. https://doi.org/10.1080/21505594.2016.1185577

The bla_SHV genes (sulfhydryl-variable β-lactamases) are a family of plasmid-mediated β-lactamases, originally from Klebsiella, that include many extended-spectrum variants (ESBLs). SHV-type ESBLs hydrolyze oxyimino-cephalosporins (e.g. cefotaxime, ceftazidime) and monobactams; they are typically co-transferred with other resistance genes. Detecting bla_SHV in a clinical isolate suggests an ESBL-mediated resistance phenotype, to provide correct antibiotic treatment (Tzouvelekis et al. 2012, Liakopoulos et al.  2016).

References:

Liakopoulos, A., Mevius, D., & Ceccarelli, D. (2016). A Review of SHV Extended-Spectrum β-Lactamases: Neglected Yet Ubiquitous. Frontiers in microbiology, 7, 1374. https://doi.org/10.3389/fmicb.2016.01374

Tzouvelekis, L. S., Markogiannakis, A., Psichogiou, M., Tassios, P. T., & Daikos, G. L. (2012). Carbapenemases in Klebsiella pneumoniae and other Enterobacteriaceae: an evolving crisis of global dimensions. Clinical Microbiology Reviews, 25(4), 682–707.

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).

References

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).

References

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)

References:

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).

References

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.

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).

References

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.

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).

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-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).

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.

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.

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.

The CTX-M group 2 β-lactamases (including CTX-M-2) are extended-spectrum β-lactamases (ESBL) historically more common in South America and parts of Europe, but are rare in U.S. clinical isolates. Like other CTX-M enzymes, they hydrolyze cefotaxime/ceftazidime. Detection of a bla_CTX-M-group-2 gene would indicate an ESBL phenotype and suggest resistance to extended-spectrum cephalosporins. In practice this marker has limited U.S. prevalence, but its presence would similarly guide therapy toward carbapenems or β-lactam/β-lactamase inhibitor combinations (Bush & Bradford 2020, Tzouvelekis et al. 2012)

References:

Bush, K., & Bradford, P. A. (2020). Epidemiology of β-Lactamase-Producing Pathogens. Clinical microbiology reviews, 33(2), e00047-19. https://doi.org/10.1128/CMR.00047-19

Tzouvelekis, L. S., Markogiannakis, A., Psichogiou, M., Tassios, P. T., & Daikos, G. L. (2012). Carbapenemases in Klebsiella pneumoniae and other Enterobacteriaceae: an evolving crisis of global dimensions. Clinical Microbiology Reviews, 25(4), 682–707.

CTX-M group 9 extended-spectrum β-lactamases (ESBL) (e.g. CTX-M-9, CTX-M-14) are globally distributed and have been reported in the U.S., though less frequently than group 1. These enzymes also hydrolyze cefotaxime and related cephalosporins. Detecting bla_CTX-M-group-9 similarly indicates ESBL production; such isolates typically carry resistance to third-generation cephalosporins. Clinically, this mandates selection of carbapenem or other effective agents (as for any ESBL) and reinforces infection control measures to limit spread (Bush & Bradford 2020, Tzouvelekis et al. 2012)

References:

Bush, K., & Bradford, P. A. (2020). Epidemiology of β-Lactamase-Producing Pathogens. Clinical microbiology reviews, 33(2), e00047-19. https://doi.org/10.1128/CMR.00047-19

Tzouvelekis, L. S., Markogiannakis, A., Psichogiou, M., Tassios, P. T., & Daikos, G. L. (2012). Carbapenemases in Klebsiella pneumoniae and other Enterobacteriaceae: an evolving crisis of global dimensions. Clinical Microbiology Reviews, 25(4), 682–707.

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).

References:

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.

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)

References:

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).

References:

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). 

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.

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.

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).

References:

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, 1328457

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.

The ermB gene encodes an rRNA methyltransferase that modifies the macrolide–lincosamide–streptogramin B (MLSB) binding site on the 50S ribosome, conferring high-level resistance to macrolides (erythromycin, azithromycin) and often inducible resistance to clindamycin. ErmB is the most common MLSB resistance gene in streptococci and staphylococci. Detection of ermB in a clinical isolate predicts macrolide resistance and should lead clinicians to avoid these antibiotics (Roberts et al. 1999, Roberts 2008, Hotomi et al. 2009).

References:

Roberts, M. C., Sutcliffe, J., Courvalin, P., Jensen, L. B., Rood, J., & Seppala, H. (1999). Nomenclature for macrolide and macrolide-lincosamide-streptogramin B resistance determinants. Antimicrobial agents and chemotherapy, 43(12), 2823–2830. https://doi.org/10.1128/AAC.43.12.2823

Roberts M. C. (2008). Update on macrolide-lincosamide-streptogramin, ketolide, and oxazolidinone resistance genes. FEMS microbiology letters, 282(2), 147–159.

Hotomi, M., Billal, D. S., Shimada, J., Suzumoto, M., Yamauchi, K., Fujihara, K., & Yamanaka, N. (2005). Increase of macrolide-resistant Streptococcus pneumoniae-expressing mefE or ermB gene in the nasopharynx among children with otitis media. The Laryngoscope, 115(2), 317–320.

Facklamia hominis is a rarely reported gram-positive coccus occasionally isolated from urine; only a few cases of F. hominis urinary infections (including pyelonephritis) have been documented. Because F. hominis resembles viridans streptococci and can be misidentified, it is likely underrecognized, and one report suggests it may be a facultative pathogen whose incidence could rise with better detection. Including F. hominis on the panel helps identify these rare UTI cases that would otherwise be missed (Pérez-Cavazos et al.  2022, Moreland et al. 2023).

Reference:

Pérez-Cavazos, S., Cisneros-Saldaña, D., Espinosa-Villaseñor, F., Castillo-Bejarano, J. I., Vaquera-Aparicio, D. N., Sánchez-Alanís, H., & Mascareñas-De Los Santos, A. (2022). Facklamia hominis pyelonephritis in a pediatric patient: first case report and review of the literature. Annals of clinical microbiology and antimicrobials, 21(1), 4. https://doi.org/10.1186/s12941-022-00497-4

Moreland RB, Choi BI, Geaman W, Gonzalez C, Hochstedler-Kramer BR, John J, Kaindl J, Kesav N, Lamichhane J, Lucio L, Saxena M, Sharma A, Tinawi L, Vanek ME, Putonti C, Brubaker L, Wolfe AJ. 2023. Beyond the usual suspects: emerging uropathogens in the microbiome age. Front Urol 3:1212590

The FOX gene family encodes plasmid AmpC enzymes that hydrolyze third-generation cephalosporins. FOX-type AmpCs confer extended-spectrum cephalosporin resistance, often in species lacking chromosomal AmpC. Its inclusion ensures detection of this additional AmpC-mediated resistance mechanism that can occur in Enterobacteriaceae (Jacoby 2009, Rodríguez-Guerrero et al. 2022) .

References:

Jacoby G. A. (2009). AmpC beta-lactamases. Clinical microbiology reviews, 22(1), 161–182. https://doi.org/10.1128/CMR.00036-08

Rodríguez-Guerrero, E., Callejas-Rodelas, J. C., Navarro-Marí, J. M., & Gutiérrez-Fernández, J. (2022). Systematic Review of Plasmid AmpC Type Resistances in Escherichia coli and Klebsiella pneumoniae and Preliminary Proposal of a Simplified Screening Method for ampC. Microorganisms, 10(3), 611. https://doi.org/10.3390/microorganisms10030611

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).

References

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.

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).

References:

Morris, D. E., Cleary, D. W., & Clarke, S. C. (2017). Secondary Bacterial Infections Associated with Influenza Pandemics. Frontiers in microbiology, 8, 1041.

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).

References

Centers for Disease Control and Prevention (CDC). (2024b). Genital herpes – CDC detailed fact sheet.

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.

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).

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.

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. http

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).

References:

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.

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.

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:

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.

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.

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 (Goldstein et al., 2009,  Karalus & Campagnari 2000)

References:

Goldstein et al., (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.

Karalus, R., & Campagnari, A. (2000). Moraxella catarrhalis: a review of an important human mucosal pathogen. Microbes and infection, 2(5), 547–559.

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).

References:

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.

References

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.

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)

References:

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.

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).

References:

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.

CDC. (2024). Mycoplasma pneumoniae infection surveillance and trends. Retrieved November 14, 2024,

Neisseria gonorrhoeae often presents asymptomatically but can cause severe reproductive complications and has shown alarming antimicrobial resistance (CDC, 2025). PCR detection enables timely, appropriate therapy and supports surveillance efforts (Workowski et al., 2021).

References

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.

The bla_OXA-48–like genes encode class D oxacillinases (carbapenemases) that hydrolyze penicillins and carbapenems (often weakly) but may not raise obvious resistance levels without potentiating factors. These enzymes have since spread globally and are now seen in U.S. Enterobacteriaceae. Detecting any bla_OXA-48–like (including OXA-28, -48, -58) indicates an emerging carbapenemase threat: patients harboring these organisms often require non-β-lactam therapy and enhanced infection control to prevent outbreaks (Logan & Weinstein 2017, Tzouvelekis et al. 2012).

References:

Logan, L. K., & Weinstein, R. A. (2017). The Epidemiology of Carbapenem-Resistant Enterobacteriaceae: The Impact and Evolution of a Global Menace. The Journal of Infectious Diseases, 215(suppl_1), S28–S36.

Tzouvelekis, L. S., Markogiannakis, A., Psichogiou, M., Tassios, P. T., & Daikos, G. L. (2012). Carbapenemases in Klebsiella pneumoniae and other Enterobacteriaceae: an evolving crisis of global dimensions. Clinical Microbiology Reviews, 25(4), 682–707.

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).

References:

Elboukari H, Ashraf M. Parainfluenza Virus. [Updated 2023 Jul 17]. In: StatPearls [Internet]. Treasure Island (FL): StatPearls Publishing; 2025 Jan-.

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.

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)

References:

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)

References:

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.

The qnrA gene encodes a pentapeptide repeat protein that protects DNA gyrase and topoisomerase IV from quinolone inhibition. qnrA (and its relatives qnrB, qnrS) confer low-level resistance to fluoroquinolones (raising MICs modestly) and facilitate the selection of high-level resistance mutations. Detection of qnrA in a pathogen suggests that fluoroquinolone therapy may be less effective and that stepwise mutations to high-level resistance are likely (Strahilevitz et al. 2009, Jacoby et al. 2014, Rodriguez-Martines et al. 2016).

References:

Strahilevitz, J., Jacoby, G. A., Hooper, D. C., & Robicsek, A. (2009). Plasmid-mediated quinolone resistance: a multifaceted threat. Clinical microbiology reviews, 22(4), 664–689.

Jacoby, G. A., Strahilevitz, J., & Hooper, D. C. (2014). Plasmid-mediated quinolone resistance. Microbiology spectrum, 2(5), 10.1128/microbiolspec.PLAS-0006-2013.

Rodríguez-Martínez, J. M., Machuca, J., Cano, M. E., Calvo, J., Martínez-Martínez, L., & Pascual, A. (2016). Plasmid-mediated quinolone resistance: Two decades on. Drug resistance updates : reviews and commentaries in antimicrobial and anticancer chemotherapy, 29, 13–29.

The qnrB gene is one of several qnr alleles (often found on Enterobacteriaceae plasmids) that confer similar protective resistance to quinolones. qnrB-positive strains typically show modest increases in quinolone MICs, which can complicate therapy especially in serious infections. Detection of qnrB in a pathogen indicates a potential to survive fluoroquinolone therapy and select high-level mutants (Strahilevitz et al. 2009, Jacoby et al. 2014, Rodriguez-Martines et al. 2016).

References:

Strahilevitz, J., Jacoby, G. A., Hooper, D. C., & Robicsek, A. (2009). Plasmid-mediated quinolone resistance: a multifaceted threat. Clinical microbiology reviews, 22(4), 664–689.

Jacoby, G. A., Strahilevitz, J., & Hooper, D. C. (2014). Plasmid-mediated quinolone resistance. Microbiology spectrum, 2(5), 10.1128/microbiolspec.PLAS-0006-2013.

Rodríguez-Martínez, J. M., Machuca, J., Cano, M. E., Calvo, J., Martínez-Martínez, L., & Pascual, A. (2016). Plasmid-mediated quinolone resistance: Two decades on. Drug resistance updates : reviews and commentaries in antimicrobial and anticancer chemotherapy, 29, 13–29.

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).

References:

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.

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).

References

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.

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).

References:

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-.

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).

References:

CDC. (2024). Preliminary estimates of COVID-19 burden for 2024–2025. Retrieved December 6, 2024, from

Hanage, W. P., & Schaffner, W. (2025). Burden of Acute Respiratory Infections Caused by Influenza Virus, Respiratory Syncytial Virus, and SARS-CoV-2 with Consideration of Older Adults: A Narrative Review. Infectious diseases and therapy, 14(Suppl 1), 5–37.

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)

References:

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.

Kim, E. J., Park, W. B., Yoon, J. K., Cho, W. S., Kim, S. J., Oh, Y. R., Jun, K. I., Kang, C. K., Choe, P. G., Kim, J. I., Choi, E. H., Oh, M. D., & Kim, N. J. (2020). Outbreak investigation of Serratia marcescens neurosurgical site infections associated with a contaminated shaving razors. Antimicrobial resistance and infection control, 9(1), 64.

Hejazi A, Falkiner FR. Serratia marcescens. J Med Microbiol. 1997 Nov;46(11):903-12. doi: 10.1099/00222615-46-11-903. PMID: 9368530.

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).

References:

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.

Raz R, Colodner R, Kunin CM. Who are you–Staphylococcus saprophyticus? Clin Infect Dis. 2005 Mar 15;40(6):896-8. doi: 10.1086/428353. Epub 2005 Feb 16. PMID: 15736028.

The Streptococcus anginosus group (SAG) – comprising S. anginosus, S. constellatus, and S. intermedius – are part of the genitourinary flora and can cause serious pyogenic infections. Although they are not classic uropathogens, SAG species can cause invasive, abscess-forming UTIs (often polymicrobial) that are missed by standard culture. Including SAG in a PCR panel ensures detection of these underrecognized pathogens in complicated UTIs (Jiang et al. 2020, Pilarczyk-Zurek et al. 2022).

References:

Jiang, S., Li, M., Fu, T., Shan, F., Jiang, L., & Shao, Z. (2020). Clinical Characteristics of Infections Caused by Streptococcus Anginosus Group. Scientific reports, 10(1), 9032. https://doi.org/10.1038/s41598-020-65977-z

Pilarczyk-Zurek M, Sitkiewicz I, Koziel J. The Clinical View on Streptococcus anginosus Group – Opportunistic Pathogens Coming Out of Hiding. Front Microbiol. 2022 Jul 8;13:956677.

Urinary tract infections: Streptococcus agalactiae is increasingly recognized as a cause of UTIs in pregnant women, the elderly, and patients with diabetes. In pregnant individuals, its presence in the urinary tract is a marker for heavy genital tract colonization and increases the risk of neonatal infection. Its detection is essential for both patient management and public health implications (Flores et al. 2015, Mohanty et al. 2021).

Wound infections: Streptococcus agalactiae, is known for neonatal infections but is also implicated in adult skin and soft tissue infections. It is frequently isolated from diabetic foot ulcers and chronic wounds. GBS infections can progress rapidly and require timely antibiotic therapy, often penicillin-based (Raabe & Shane 2019, Akbari et al. 2023).

References:

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.

Mohanty, S., Purohit, G., Rath, S., Seth, R. K., & Mohanty, R. R. (2021). Urinary tract infection due to Group B Streptococcus: A case series from Eastern India. Clinical case reports, 9(10), e04885. https://doi.org/10.1002/ccr3.4885

Raabe, V. N., & Shane, A. L. (2019). Group B Streptococcus (Streptococcus agalactiae). Microbiology spectrum, 7(2), 10.1128/microbiolspec.gpp3-0007-2018.

Akbari, M. S., Keogh, R. A., Radin, J. N., Sanchez-Rosario, Y., Johnson, M. D. L., Horswill, A. R., Kehl-Fie, T. E., Burcham, L. R., & Doran, K. S. (2023). The impact of nutritional immunity on Group B streptococcal pathogenesis during wound infection. mBio, 14(4), e0030423.

Verani JR, McGee L, Schrag SJ; Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention (CDC). Prevention of perinatal group B streptococcal disease–revised guidelines from CDC, 2010. MMWR Recomm Rep. 2010 Nov 19;59(RR-10):1-36. PMID: 21088663.

Wound infections: Streptococcus pyogenes is a major pathogen in wound infections from simple cellulitis to necrotizing fasciitis (“flesh-eating” disease). S. pyogenes produces exotoxins that facilitate tissue invasion and systemic illness. Rapid identification in wound infections is crucial due to its aggressive nature and potential for rapid progression (Walker et al. 2014, Stevens & Bryant, 2016).

Respiratory infections: Group A Streptococcus is primarily a throat and skin pathogen, but it can rarely cause severe invasive infections including pneumonia and toxic shock. In influenza seasons, S. pyogenes has been identified as a fatal co-infecting pathogen; its inclusion helps detect these dangerous cases (Morris et al 2017, Borgogna & Voyich 2022).

References:

Walker, M. J., Barnett, T. C., McArthur, J. D., Cole, J. N., Gillen, C. M., Henningham, A., Sriprakash, K. S., Sanderson-Smith, M. L., & Nizet, V. (2014). Disease manifestations and pathogenic mechanisms of Group A Streptococcus. Clinical microbiology reviews, 27(2), 264–301. https://doi.org/10.1128/CMR.00101-13

Stevens DL, Bryant AE. Impetigo, Erysipelas and Cellulitis. 2016 Feb 10. In: Ferretti JJ, Stevens DL, Fischetti VA, editors. Streptococcus pyogenes : Basic Biology to Clinical Manifestations [Internet]. Oklahoma City (OK): University of Oklahoma Health Sciences Center; 2016-.

Morris, D. E., Cleary, D. W., & Clarke, S. C. (2017). Secondary Bacterial Infections Associated with Influenza Pandemics. Frontiers in microbiology, 8, 1041.

The tet genes (e.g. tet(A), tet(B), tet(M)) encode either tetracycline efflux pumps or ribosomal protection proteins, conferring resistance to tetracyclines. These genes are widespread in both Gram-negative and Gram-positive pathogens. Detection of a tet gene indicates that tetracycline antibiotics (doxycycline, minocycline) will not be effective, and often correlates with multidrug-resistant plasmids. Clinically, this finding leads to avoiding tetracyclines and choosing other agents (such as fluoroquinolones or β-lactams) for treatment (Chopra& Roberts 2001, Grossman 2016).

References:

Grossman T. H. (2016). Tetracycline Antibiotics and Resistance. Cold Spring Harbor perspectives in medicine, 6(4), a025387. https://doi.org/10.1101/cshperspect.a025387

Chopra, I., & Roberts, M. (2001). Tetracycline: mode of action, applications, molecular biology, and epidemiology of bacterial resistance. Microbiology and molecular biology reviews : MMBR, 65(2), 232–260. https://doi.org/10.1128/MMBR.65.2.232-260.2001

Urinary tract infections: Ureaplasma urealyticum is a fastidious organism commonly found in the genitourinary tract and is associated with urethritis, prostatitis, and occasionally UTIs, especially in immunocompromised or pregnant patients. It lacks a cell wall, making it undetectable by Gram stain and resistant to β-lactam antibiotics. Due to these limitations in traditional testing, PCR is essential for accurate detection (Valentine-King & Brown 2017, Abankwa et al. 2024).

Sexually transmitted infections: Ureaplasma urealyticum has been associated with non-gonococcal urethritis in men and adverse reproductive outcomes, although its pathogenic role is still debated. Including it in STI panels helps identify atypical causes of persistent urethritis not detected by standard screening (Horner et al. 2018, Workowski et al. 2021).

References:

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.

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.

Horner, P., Donders, G., Cusini, M., Gomberg, M., Jensen, J. S., & Unemo, M. (2018). Should we be testing for urogenital Mycoplasma hominis, Ureaplasma parvum and Ureaplasma urealyticum in men and women? – a position statement from the European STI Guidelines Editorial Board. Journal of the European Academy of Dermatology and Venereology : JEADV, 32(11), 1845–1851.

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.

The vanB operon encodes a D-Ala-D-Lac ligase that confers inducible vancomycin resistance. vanB-positive Enterococcus exhibit variable high-level resistance to vancomycin. Detection of vanB indicates VRE; like vanA, it mandates use of non-glycopeptide therapy and aggressive infection control. The vanB genotype often signals hospital-acquired vancomycin resistance that can spread via plasmids, underscoring the need for isolation precautions and alternative treatments (Levitus et al. 2023,  Arias & Murray 2012, Hourigan et al. 2024,).

References:

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.

Levitus M, Rewane A, Perera TB. Vancomycin-Resistant Enterococci. [Updated 2023 Jul 17]. In: StatPearls [Internet]. Treasure Island (FL): StatPearls Publishing; 2025 Jan-.

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. https://doi.org/10.1186/s12866-024-03243-2