Utility of whole-genome sequencing in tracking healthcare associated infection outbreaks_West China Medical Journal

Authors：

 QIAO Fu

Infection Prevention & Control Department, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P. R. China;

Corresponding author：

QIAO Fu, Email: qiaofu2005@gmail.com

Keywords：

Whole-genome sequencing; Healthcare-associated infection; Outbreak; Tracking

DOI：

10.7507/1002-0179.201903067

Video：

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Healthcare-associated infection outbreaks are a serious threat to patient safety and often cause serious consequences. The use of genotyping methods to identify the source of infection and the route of transmission in outbreaks is a critical point in controlling outbreaks. Recently, the use of whole-genome sequencing (WGS) makes it faster and much more accurate. Compared with traditional methods, WGS can distinguish highly correlated pathogen lineages, track infection source accurately and help researchers understanding the propagation dynamics model, and even provide more target intervention information. The application of WGS technology in healthcare-associated infection outbreak investigation and control is reviewed in this paper, and its advantages and challenges are also evaluated.

Citation： QIAO Fu. Utility of whole-genome sequencing in tracking healthcare associated infection outbreaks. West China Medical Journal, 2019, 34(3): 334-337. doi: 10.7507/1002-0179.201903067 Copy

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3.	Tang P, Croxen MA, Hasan MR, et al. Infection control in the new age of genomic epidemiology. Am J Infect Control, 2017, 45(2): 170-179.
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6.	Jünemann S, Sedlazeck FJ, Prior K, et al. Updating benchtop sequencing performance comparison. Nat Biotechnol, 2013, 31(4): 294-296.
7.	Eyre DW, Sheppard AE, Madder H, et al. A Candida auris outbreak and its control in an intensive care setting. N Engl J Med, 2018, 379(14): 1322-1331.
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12.	Snitkin ES, Zelazny AM, Thomas PJ, et al. Tracking a hospital outbreak of carbapenem-resistant Klebsiella pneumoniae with whole-genome sequencing. Sci Transl Med, 2012, 4(148): 148ra116.
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14.	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): 207-214.
15.	Martin J, Phan HTT, Findlay J, et al. Covert dissemination of carbapenemase-producing Klebsiella pneumoniae (KPC) in a successfully controlled outbreak: long- and short-read whole-genome sequencing demonstrate multiple genetic modes of transmission. J Antimicrob Chemother, 2017, 72(11): 3025-3034.
16.	Harris SR, Cartwright EJP, Török ME, et al. Whole-genome sequencing for analysis of an outbreak of meticillin-resistant Staphylococcus aureus: a descriptive study. Lancet Infect Dis, 2013, 13(2): 130-136.
17.	Davis RJ, Jensen SO, Van Hal S, et al. Whole genome sequencing in real-time investigation and management of a Pseudomonas aeruginosa outbreak on a neonatal intensive care unit. Infect Control Hosp Epidemiol, 2015, 36(9): 1058-1064.
18.	Yang S, Hemarajata P, Hindler J, et al. Evolution and transmission of carbapenem-resistant Klebsiella pneumoniae expressing the blaOXA-232 gene during an institutional outbreak associated with endoscopic retrograde cholangiopancreatography. Clin Infect Dis, 2017, 64(7): 894-901.
19.	Rosendahl Madsen AM, Holm A, Jensen TG, et al. Whole-genome sequencing for identification of the source in hospital-acquired Legionnaires’ disease. J Hosp Infect, 2017, 96(4): 392-395.
20.	Lee AS, White E, Monahan LG, et al. Defining the role of the environment in the emergence and persistence of vanA vancomycin-resistant Enterococcus (VRE) in an intensive care unit: a molecular epidemiological study. Infect Control Hosp Epidemiol, 2018, 39(6): 668-675.
21.	乔甫, 林吉, 李婧闻, 等. 人工心肺机热交换水箱系统引起心脏手术患者奇美拉分枝杆菌的感染暴发. 中华医学杂志, 2017, 97(42): 3357-3359.
22.	van Ingen J, Kohl TA, Kranzer K, et al. Global outbreak of severe Mycobacterium chimaera disease after cardiac surgery: a molecular epidemiological study. Lancet Infect Dis, 2017, 17(10): 1033-1041.
23.	Li Z, Pérez-Osorio A, Wang Y, et al. Whole genome sequencing analyses of Listeria monocytogenes that persisted in a milkshake machine for a year and caused illnesses in Washington State. BMC Microbiol, 2017, 17(1): 134.
24.	Sommerstein R, Führer U, Lo Priore E, et al. Burkholderia stabilis outbreak associated with contaminated commercially-available washing gloves, Switzerland, May 2015 to August 2016. Euro surveill, 2017, 22(49): pii=17-00213.
25.	Etienne KA, Roe CC, Smith RM, et al. Whole-genome sequencing to determine origin of multinational outbreak of Sarocladium kiliense bloodstream infections. Emerg Infect Dis, 2016, 22(3): 476-481.
26.	Abbo L, Shukla BS, Giles A, et al. Linezolid and vancomycin-resistant Enterococcus faecium in solid organ transplant recipients: infection control and antimicrobial stewardship using whole genome sequencing. Clin Infect Dis, 2018.
27.	Jia H, Du P, Yang H, et al. Nosocomial transmission of Clostridium difficile ribotype 027 in a Chinese hospital, 2012–2014, traced by whole genome sequencing. BMC Genomics, 2016, 17(1): 405.

1. Epstein L, Hunter JC, Arwady MA, et al. New Delhi metallo-beta-lactamase-producing carbapenem-resistant Escherichia coli associated with exposure to duodenoscopes. JAMA, 2014, 312(14): 1447-1455.
2. Kainer MA, Wise M, Ph D, et al. Fungal infections associated with contaminated methylprednisolone injections 2013. N Engl J Med, 2013, 369: 1598-1609.
3. Tang P, Croxen MA, Hasan MR, et al. Infection control in the new age of genomic epidemiology. Am J Infect Control, 2017, 45(2): 170-179.
4. 乔甫, 康梅, 谭成, 等. PFGE 在识别和追踪医院感染暴发及流行中的应用. 现代预防医学杂志, 2007, 34(14): 2-4.
5. Quainoo S, Coolen JPM, van Hijum SAFT, et al. Whole-genome sequencing of bacterial pathogens: the future of nosocomial outbreak analysis. Clin Microbiol Rev, 2017, 30(4): 1015-1063.
6. Jünemann S, Sedlazeck FJ, Prior K, et al. Updating benchtop sequencing performance comparison. Nat Biotechnol, 2013, 31(4): 294-296.
7. Eyre DW, Sheppard AE, Madder H, et al. A Candida auris outbreak and its control in an intensive care setting. N Engl J Med, 2018, 379(14): 1322-1331.
8. Le VTM, Diep BA. Selected insights from application of whole-genome sequencing for outbreak investigations. Curr Opin Crit Care, 2013, 19(5): 432-429.
9. Gilchrist CA, Turner SD, Riley MF, et al. Whole-genome sequencing in outbreak analysis. Clin Microbiol Rev, 2015, 28(3): 541-563.
10. Wyllie DH, Davidson JA, Grace Smith E, et al. A quantitative evaluation of MIRU-VNTR typing against whole-genome sequencing for identifying Mycobacterium tuberculosis transmission: a prospective observational cohort study. EBioMedicine, 2018, 34: 122-130.
11. Köser CU, Holden MTG, Ellington MJ, et al. Rapid whole-genome sequencing for investigation of a neonatal MRSA outbreak. N Engl J Med, 2012, 366(24): 2267-2275.
12. Snitkin ES, Zelazny AM, Thomas PJ, et al. Tracking a hospital outbreak of carbapenem-resistant Klebsiella pneumoniae with whole-genome sequencing. Sci Transl Med, 2012, 4(148): 148ra116.
13. Roe CC, Horn KS, Driebe EM, et al. Whole genome SNP typing to investigate methicillin-resistant Staphylococcus aureus carriage in a health-care provider as the source of multiple surgical site infections. Hereditas, 2016, 153(1): 11.
14. 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): 207-214.
15. Martin J, Phan HTT, Findlay J, et al. Covert dissemination of carbapenemase-producing Klebsiella pneumoniae (KPC) in a successfully controlled outbreak: long- and short-read whole-genome sequencing demonstrate multiple genetic modes of transmission. J Antimicrob Chemother, 2017, 72(11): 3025-3034.
16. Harris SR, Cartwright EJP, Török ME, et al. Whole-genome sequencing for analysis of an outbreak of meticillin-resistant Staphylococcus aureus: a descriptive study. Lancet Infect Dis, 2013, 13(2): 130-136.
17. Davis RJ, Jensen SO, Van Hal S, et al. Whole genome sequencing in real-time investigation and management of a Pseudomonas aeruginosa outbreak on a neonatal intensive care unit. Infect Control Hosp Epidemiol, 2015, 36(9): 1058-1064.
18. Yang S, Hemarajata P, Hindler J, et al. Evolution and transmission of carbapenem-resistant Klebsiella pneumoniae expressing the blaOXA-232 gene during an institutional outbreak associated with endoscopic retrograde cholangiopancreatography. Clin Infect Dis, 2017, 64(7): 894-901.
19. Rosendahl Madsen AM, Holm A, Jensen TG, et al. Whole-genome sequencing for identification of the source in hospital-acquired Legionnaires’ disease. J Hosp Infect, 2017, 96(4): 392-395.
20. Lee AS, White E, Monahan LG, et al. Defining the role of the environment in the emergence and persistence of vanA vancomycin-resistant Enterococcus (VRE) in an intensive care unit: a molecular epidemiological study. Infect Control Hosp Epidemiol, 2018, 39(6): 668-675.
21. 乔甫, 林吉, 李婧闻, 等. 人工心肺机热交换水箱系统引起心脏手术患者奇美拉分枝杆菌的感染暴发. 中华医学杂志, 2017, 97(42): 3357-3359.
22. van Ingen J, Kohl TA, Kranzer K, et al. Global outbreak of severe Mycobacterium chimaera disease after cardiac surgery: a molecular epidemiological study. Lancet Infect Dis, 2017, 17(10): 1033-1041.
23. Li Z, Pérez-Osorio A, Wang Y, et al. Whole genome sequencing analyses of Listeria monocytogenes that persisted in a milkshake machine for a year and caused illnesses in Washington State. BMC Microbiol, 2017, 17(1): 134.
24. Sommerstein R, Führer U, Lo Priore E, et al. Burkholderia stabilis outbreak associated with contaminated commercially-available washing gloves, Switzerland, May 2015 to August 2016. Euro surveill, 2017, 22(49): pii=17-00213.
25. Etienne KA, Roe CC, Smith RM, et al. Whole-genome sequencing to determine origin of multinational outbreak of Sarocladium kiliense bloodstream infections. Emerg Infect Dis, 2016, 22(3): 476-481.
26. Abbo L, Shukla BS, Giles A, et al. Linezolid and vancomycin-resistant Enterococcus faecium in solid organ transplant recipients: infection control and antimicrobial stewardship using whole genome sequencing. Clin Infect Dis, 2018.
27. Jia H, Du P, Yang H, et al. Nosocomial transmission of Clostridium difficile ribotype 027 in a Chinese hospital, 2012–2014, traced by whole genome sequencing. BMC Genomics, 2016, 17(1): 405.

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