Parcell BJ, Gillespie SH, Pettigrew KA, Holden MTG. Clinical perspectives in integrating whole-genome sequencing into the investigation of healthcare and public health outbreaks – hype or help? J Hosp Infect. 2021;109:1–9. https://doi.org/10.1016/j.jhin.2020.11.001.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Price JR, Didelot X, Crook DW, Llewelyn MJ, Paul J. Whole genome sequencing in the prevention and control of Staphylococcus aureus infection. J of Hosp Infect. 2013;83:14–21.

Article  CAS  Google Scholar 

Quainoo S, Coolen JPM, Sacha AFT van Hijum C, Martijn A, Huynen CWJGM, Willem van Schaik E, Wertheim HFL. Whole-genome sequencing of bacterial pathogens : the future of nosocomial outbreak analysis. Clin Microbiol Rev. 2017;30(4):1015–1064.

Francis RV, Billam H, Clarke M, et al. The impact of real-time whole-genome sequencing in controlling healthcare-associated SARS-CoV-2 outbreaks. J Infect Dis. 2022;225(1):10–8. https://doi.org/10.1093/infdis/jiab483.

Article  CAS  PubMed  Google Scholar 

Popovich KJ, Snitkin ES. Whole genome sequencing—implications for infection prevention and outbreak investigations. Curr Infect Dis Rep. 2017;19(4).  https://doi.org/10.1007/s11908-017-0570-0.

• Price JR, Golubchik T, Cole K, et al. Whole-genome sequencing shows that patient-to-patient transmission rarely accounts for acquisition of staphylococcus aureus in an intensive care unit. Clin Infect Dis. 2014;58(5):609–18. https://doi.org/10.1093/cid/cit807. One of the first studies to employ WGS to understand transmission dynamics on a unit outside of an outbreak situation.

Article  PubMed  Google Scholar 

Hallin M, Friedrich AW, Struelens MJ. spa typing for epidemiological surveillance of Staphylococcus aureus. Methods Mol Biol. 2009;551:189–202. https://doi.org/10.1007/978-1-60327-999-4_15.

Article  CAS  PubMed  Google Scholar 

Price JR, Cole K, Bexley A, et al. Transmission of Staphylococcus aureus between health-care workers, the environment, and patients in an intensive care unit: a longitudinal cohort study based on whole-genome sequencing. Lancet Infect Dis. 2017;17(2):207–14. https://doi.org/10.1016/S1473-3099(16)30413-3.

Article  PubMed  PubMed Central  Google Scholar 

Uhlemann AC, Dordel J, Knox JR, Raven KE, Parkhill J, Holden MT, Peacock SJ, Lowy FD. Molecular tracing of the emergence, diversification, and transmission of S. aureus sequence type 8 in a New York community. Proc Natl Acad Sci U S A. 2014;111(18):6738–43. https://doi.org/10.1073/pnas.1401006111. Epub 2014 Apr 21. PMID: 24753569; PMCID: PMC4020051.

Morgan DJ, Murthy R, Munoz-Price LS, Barnden M, Camins BC, Johnston BL, Rubin Z, Sullivan KV, Shane AL, Dellinger EP, Rupp ME, Bearman G. Reconsidering contact precautions for endemic methicillin-resistant Staphylococcus aureus and vancomycin-resistant Enterococcus. Infect Control Hosp Epidemiol. 2015;36(10):1163–72. https://doi.org/10.1017/ice.2015.156. Epub 2015 Jul 3.

Article  PubMed  Google Scholar 

Warny M, Pepin J, Fang A, Killgore G, Thompson A, Brazier J, Frost E, McDonald LC. Toxin production by an emerging strain of Clostridium difficile associated with outbreaks of severe disease in North America and Europe. Lancet. 2005;366(9491):1079–84. https://doi.org/10.1016/S0140-6736(05)67420-X.

Article  CAS  PubMed  Google Scholar 

• Eyre DW, Cule ML, Wilson DJ, Griffiths D, Vaughan A, O’Connor L, Ip CLC, Golubchik T, Batty EM, Finney JM, Wyllie DH, Didelot X, Piazza P, Bowden R, Dingle KE, Harding RM, Crook DW, Wilcox MH, Peto TEA, Walker AS. Diverse sources of C. difficile infection identified on whole-genome sequencing. N Engl J Med. 2013;369(13):1195–205. https://doi.org/10.1056/NEJMoa1216064. WGS applied to a C. difficile in a health system and community challenged the paradigm of C. difficile infection as a hospital-acquired conditions.

Article  CAS  PubMed  Google Scholar 

Rousseau C, Poilane I, De Pontual L, Maherault AC, Le Monnier A, Collignon A. Clostridium difficile carriage in healthy infants in the community: a potential reservoir for pathogenic strains. Clin Infect Dis. 2012;55(9):1209–15.

Article  PubMed  Google Scholar 

Keel K, Brazier JS, Post KW, Weese S, Songer JG. Prevalence of PCR ribotypes among Clostridium difficile isolates from pigs, calves, and other species. J Clin Microbiol. 2007;45:1963–4.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Stone NE, Sidak-Loftis LC, Sahl JW, Vazquez AJ, Wiggins KB, Gillece JD, et al. More than 50% of Clostridium difficile isolates from pet dogs in Flagstaff, USA, carry toxigenic genotypes. PLoS ONE. 2016;11(10):e0164504. https://doi.org/10.1371/journal.pone.0164504.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Knetsch CW, Kumar N, Forster SC, Connor TR, Browne HP, Harmanus C, Sanders IM, Harris SR, Turner L, Morris T, Perry M, Miyajima F, Roberts P, Pirmohamed M, Songer JG, Weese JS, Indra A, Corver J, Rupnik M, Wren BW, Riley TV, Kuijper EJ, Lawley TD. Zoonotic transfer of Clostridium difficile harboring antimicrobial resistance between farm animals and humans. J Clin Microbiol. 2018;56(3):e01384-e1417. https://doi.org/10.1128/JCM.01384-17.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Snitkin ES, Zelazny AM, Thomas PJ, Stock F, NISC Comparative Sequencing Program Group, Henderson DK, Palmore TN, Segre JA. Tracking a hospital outbreak of carbapenem-resistant Klebsiella pneumoniae with whole-genome sequencing. Sci Transl Med. 2012;4(148):148ra116. https://doi.org/10.1126/scitranslmed.3004129.

Article  PubMed  PubMed Central  Google Scholar 

Conlan S, Thomas PJ, Deming C, Park M, Lau AF, Dekker JP, Snitkin ES, Clark TA, Luong K, Song Y, Tsai YC, Boitano M, Dayal J, Brooks SY, Schmidt B, Young AC, Thomas JW, Bouffard GG, Blakesley RW, NISC Comparative Sequencing Program, Mullikin JC, Korlach J, Henderson DK, Frank KM, Palmore TN, Segre JA. Single-molecule sequencing to track plasmid diversity of hospital-associated carbapenemase-producing Enterobacteriaceae. Sci Transl Med. 2014;6(254):254ra126. https://doi.org/10.1126/scitranslmed.3009845.

Article  CAS  PubMed  PubMed Central  Google Scholar 

•• Cerqueira GC, Earl AM, Ernst CM, Grad YH, Dekker JP, Feldgarden M, Chapman SB, Reis-Cunha JL, Shea TP, Young S, Zeng Q, Delaney ML, Kim D, Peterson EM, O’Brien TF, Ferraro MJ, Hooper DC, Huang SS, Kirby JE, Onderdonk AB, Birren BW, Hung DT, Cosimi LA, Wortman JR, Murphy CI, Hanage WP. Multi-institute analysis of carbapenem resistance reveals remarkable diversity, unexplained mechanisms, and limited clonal outbreaks. Proc Natl Acad Sci U S A. 2017;114(5):1135–40. https://doi.org/10.1073/pnas.1616248114. WGS of gram negative organisms across 4 hospitals revealed remarkable diversity and suggests transmission of resistance mechanisms between bacterial species, and unrecognized outbreaks of these organisms in hospitals.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Marimuthu K, Venkatachalam I, Koh V, et al. Whole genome sequencing reveals hidden transmission of carbapenemase-producing Enterobacterales. Nat Commun. 2022;13(1):1–11. https://doi.org/10.1038/s41467-022-30637-5.

Article  CAS  Google Scholar 

Satoh K, Makimura K, Hasumi Y, Nishiyama Y, Uchida K, Yamaguchi H. Candida auris sp. nov., a novel ascomycetous yeast isolated from the external ear canal of an inpatient in a Japanese hospital. Microbiol Immunol. 2009;53:41–4.

Article  CAS  PubMed  Google Scholar 

Lee WG, Shin JH, Uh Y, Kang MG, Kim SH, Park KH, Jang HC. First three reported cases of nosocomial fungemia caused by Candida auris. J Clin Microbiol. 2011;49(9):3139–42. https://doi.org/10.1128/JCM.00319-11.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Jeffery-Smith A, Taori SK, Schelenz S, Jeffery K, Johnson EM, Borman A, Candida auris Incident Management Team, Manuel R, Brown CS. Candida auris: a review of the literature. Clin Microbiol Rev. 2017;31(1):e00029-17. https://doi.org/10.1128/CMR.00029-17.

Article  PubMed  PubMed Central  Google Scholar 

Lockhart SR, Etienne KA, Vallabhaneni S, et al. Simultaneous emergence of multidrug-resistant Candida auris on 3 continents confirmed by whole-genome sequencing and epidemiological analyses. Clin Infect Dis. 2017;64(2):134–40. https://doi.org/10.1093/cid/ciw691.

Article  CAS  PubMed  Google Scholar 

Berggreen H, Løvestad AH, Helmersen K, Jørgensen SB, Aamot HV. Lessons learned: use of WGS in real-time investigation of suspected intrahospital SARS-CoV-2 outbreaks. J Hosp Infect. 2023;131:81–8. https://doi.org/10.1016/j.jhin.2022.10.003.

Article  CAS  PubMed  Google Scholar 

Marinelli TM, Dolan L, Jenkins F, Lee A, Davis RJ, Crawford S, Nield B, Ronnachit A, Van Hal SJ. The role of real-time, on-site, whole-genome sequencing of severe acute respiratory coronavirus virus 2 (SARS-CoV-2) in guiding the management of hospital outbreaks of coronavirus disease 2019 (COVID-19). Infect Control Hosp Epidemiol. 2022;9:1–5. https://doi.org/10.1017/ice.2022.220.

Article  Google Scholar 

Berbel Caban A, Pak TR, Obla A, Dupper AC, Chacko KI, Fox L, Mills A, Ciferri B, Oussenko I, Beckford C, Chung M, Sebra R, Smith M, Conolly S, Patel G, Kasarskis A, Sullivan MJ, Altman DR, van Bakel H. PathoSPOT genomic epidemiology reveals under-the-radar nosocomial outbreaks. Genome Med. 2020;12(1):96. https://doi.org/10.1186/s13073-020-00798-3.

Article  CAS  PubMed  PubMed Central  Google Scholar 

•• Sundermann AJ, Chen J, Kumar P, Ayres AM, Cho ST, Ezeonwuka C, Griffith MP, Miller JK, Mustapha MM, Pasculle AW, Saul MI, Shutt KA, Srinivasa V, Waggle K, Snyder DJ, Cooper VS, Van Tyne D, Snyder GM, Marsh JW, Dubrawski A, Roberts MS, Harrison LH. Whole-genome sequencing surveillance and machine learning of the electronic health record for enhanced healthcare outbreak detection. Clin Infect Dis. 2022;75(3):476–82. https://doi.org/10.1093/cid/ciab946. Description of a novel implementation of a WGS strategy to identify possible outbreaks of high-risk pathogens in hospitals and comparison to standard surveillance practices.

Article  PubMed  Google Scholar 

Mellmann A, Bletz S, Böking T, Kipp F, Becker K, Schultes A, Prior K, Harmsen D. Real-time genome sequencing of resistant bacteria provides precision infection control in an institutional setting. J Clin Microbiol. 2016;54(12):2874–81. https://doi.org/10.1128/JCM.00790-16.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Gargis AS, Kalman L, Lubin IM. Assuring the quality of next-generation sequencing in clinical microbiology and public health laboratories. J Clin Microbiol. 2016;54(12):2857–65. https://doi.org/10.1128/JCM.00949-16.

Article  PubMed  PubMed Central  Google Scholar 

Dymond A, Davies H, Mealing S, et al. Genomic surveillance of methicillin-resistant Staphylococcus aureus: a mathematical early modeling study of cost-effectiveness. Clin Infect Dis. 2020;70(8):1613–9. https://doi.org/10.1093/cid/ciz480.

Article  CAS  PubMed  Google Scholar 

•• Kumar P, Sundermann AJ, Martin EM, Snyder GM, Marsh JW, Harrison LH, Roberts MS. Method for economic evaluation of bacterial whole genome sequencing surveillance compared to standard of care in detecting hospital outbreaks. Clin Infect Dis. 2021;73(1):e9–18. https://doi.org/10.1093/cid/ciaa512. Cost effectiveness analysis of WGS for detecting/responding to outbreaks compared to standard surveillance and response practices.

Article