Application of whole genome sequencing to epidemiologic investigation of infectious disease

Scope of investigations covered by next generation molecular epidemiology Identifying …  risk factors that could not be identified by conventional or early-generation molecular biology

Lecture 15: Application of whole genome sequencing to  epidemiologic investigation of infectious disease

National Institute of Infectious Disease

January 19, 2017

Scope of investigations covered by next generation molecular

epidemiology

Identifying …

 risk factors that could not be identified by conventional or early-generation molecular biology laboratory methods

 direction or chain of transmission of an infectious agent

 endogenous reactivation vs exogenous reinfection

 ecological niches from which clonal pathogenic strains are selected and disseminate

 pathogen microbial population structures associated with a syndrome

 host commensal microbial population structures that determine non-communicable disease outcomes

WGS vs other genotyping methods to conduct epidemiologic investigations: Examples

 WGS vs PFGE in healthcare-associated infections

 WGS vs MIRU-VNTR to characterize TB transmission

 WGS vs MLST to investigate MRSA hospital outbreak

WGS vs PFGE in healthcare-associated outbreaks (Salipante, et al J Clin Micro 2015)

 Number of outbreaks of

 Acinetobacter baumanii (15)

 Vancomycin-resistant Enterococcus faecium (19)

 Methicillin-resistant Staphylococcus aureus (17)

Criteria for interpreting PFGE patterns (Tenover et al, J Clin Microbiol 1995;33:2233)

mutations number of

band differences

WGS vs PFGE (Salipante et al, 2015)

Organism Indistinguishable by

PFGE (n=90)

Different by PFGE (n= 81)

WGS Clonal Non-Clonal

WGS Clonal Non-Clonal

VRE 55 9 0 18

MRSA 5 15 0 35

A baumanii 4 2 0 28

Total 64 26 0 81

WGS vs PFGE (Salipante et al, 2015)

Organism Closely related by

PFGE (n=148)

Possibly related by PFGE (n=93)

WGS Clonal Non-Clonal

WGS Clonal Non-Clonal

VRE 0 81 0 8

MRSA 0 23 0 58

A baumanii 12 32 4 23

Total 12 136 4 89

WGS vs other genotyping methods to conduct epidemiologic

investigations: Examples

 WGS vs PFGE in healthcare-associated infections

 WGS vs MIRU-VNTR to characterize TB transmission

 WGS vs MLST to investigate MRSA hospital outbreak

Identifying hidden transmission pathways and social networks that facilitate transmission

www.worldatlas.com

Example 4: TB outbreak in British Columbia, Canada, 2006-08

(Gardy et al, NEJM, 2011)

 Between May 2006-Dec 2008, 41 new cases of TB

identified, all with an identical MIRU-VNTR genotype pattern

 Whole genome sequencing done

on 36

TB outbreak in British Columbia, Canada, 2006-08 (Gardy et al,

NEJM, 2011)

Two major lineages of M tuberculosis identified; transmission sustained

by a social network involving cocaine use.

WGS vs other genotyping methods to conduct epidemiologic investigations: Examples

 WGS vs PFGE in healthcare-associated infections

 WGS vs MIRU-VNTR to characterize TB transmission

 WGS vs MLST to investigate MRSA hospital

outbreak

MRSA outbreak in a hospital (Harris, SR et al, Lancet ID, 2013)

 Problem:

 Putative MRSA outbreak in a special care baby unit (SCBU) in Cambridge, UK over 6-months in 2011

 Conventional epidemiologic analysis performed at SCBU

 12 infants colonized and suspected to be linked but not

confirmed

 MLST showed it to belong to new ST (2371, contains PVL); related to ST22

MRSA outbreak in a hospital…cont.

 WGS of all SCBU and community isolates of MRSA with identical drug-susceptibility profile done.

 26 related cases found in SCBU, postnatal ward, and

community

Harris SR et al, Lancet ID, 2013

Harris SR et al, Lancet ID, 2013

Harris SR et al, Lancet ID, 2013

MRSA outbreak in a hospital summary

 Suspected MRSA outbreak confirmed by WGS analysis

 WGS analysis helped to fill the gaps in transmission chain.

 Transmission occurred between mothers in postnatal ward.

 Community transmission documented (involved family

members)

 Healthcare worker implicated in transmission route—

contributed to persistence of the outbreak, even after deep clean of SCBU.

 Number of SNPs increased over time of the outbreak

MRSA outbreak in a hospital—caveats of WGS analysis

outbreak

putative outbreak.

• Salipante SJ et al. Application of Whole‐Genome Sequencing for 

Bacterial Strain Typing in Molecular Epidemiology. J Clin Microbiol. 

2015; 53:1072–1079.

• Gardy JL et al. Whole‐Genome Sequencing and Social‐Network Analysis 

of a Tuberculosis Outbreak. New Engl J Med. 2011;364:730‐9.

• Harris, SR et al. Whole‐genome sequencing for analysis of an outbreak 

of meticillin‐resistant Staphylococcus aureus: a descriptive study. 

Lancet ID, 2013;13:130‐136.