A brief primer on genomic epidemiology: lessons learned from<i>Mycobacterium tuberculosis</i>

Guthrie, Jennifer L.; Gardy, Jennifer L.

doi:10.1111/nyas.13273

Cited by 27 publications

(25 citation statements)

References 172 publications

(268 reference statements)

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…The emerging widespread use of WGS has quickly pushed these cut-offs to be considered the new molecular gold standard of recent transmission linking, although SNP distances may vary for technical reasons (e.g. assembly pipelines or filter criteria [ 22 ]) and between study populations e.g. high and low incidence settings [ 19 ].…”

Section: Introductionmentioning

confidence: 99%

The relationship between transmission time and clustering methods in Mycobacterium tuberculosis epidemiology

et al. 2018

View full text Add to dashboard Cite

BackgroundTracking recent transmission is a vital part of controlling widespread pathogens such as Mycobacterium tuberculosis. Multiple methods with specific performance characteristics exist for detecting recent transmission chains, usually by clustering strains based on genotype similarities. With such a large variety of methods available, informed selection of an appropriate approach for determining transmissions within a given setting/time period is difficult.MethodsThis study combines whole genome sequence (WGS) data derived from 324 isolates collected 2005–2010 in Kinshasa, Democratic Republic of Congo (DRC), a high endemic setting, with phylodynamics to unveil the timing of transmission events posited by a variety of standard genotyping methods. Clustering data based on Spoligotyping, 24-loci MIRU-VNTR typing, WGS based SNP (Single Nucleotide Polymorphism) and core genome multi locus sequence typing (cgMLST) typing were evaluated.FindingsOur results suggest that clusters based on Spoligotyping could encompass transmission events that occurred almost 200 years prior to sampling while 24-loci-MIRU-VNTR often represented three decades of transmission. Instead, WGS based genotyping applying low SNP or cgMLST allele thresholds allows for determination of recent transmission events, e.g. in timespans of up to 10 years for a 5 SNP/allele cut-off.InterpretationWith the rapid uptake of WGS methods in surveillance and outbreak tracking, the findings obtained in this study can guide the selection of appropriate clustering methods for uncovering relevant transmission chains within a given time-period. For high resolution cluster analyses, WGS-SNP and cgMLST based analyses have similar clustering/timing characteristics even for data obtained from a high incidence setting.

show abstract

Section: Introductionmentioning

confidence: 99%

The relationship between transmission time and clustering methods in Mycobacterium tuberculosis epidemiology

et al. 2018

View full text Add to dashboard Cite

show abstract

“…Mycobacterium tuberculosis is a great threat to humanity, and it kills about two million people annually ( 1 ). M. tuberculosis is able to subvert the killing machinery of macrophages, a key component of the human innate immune system, and replicate inside the macrophage in an organelle termed the phagosome ( 2 ).…”

Section: Genome Announcementmentioning

confidence: 99%

Genome Sequences of the Mycobacterium tuberculosis H37Rv- ptkA Deletion Mutant and Its Parental Strain

et al. 2017

Self Cite

View full text Add to dashboard Cite

show abstract

“…The 98 widespread use of WGS has quickly pushed these cut-offs to be considered the new molecular 99 gold standard of recent transmission linking, although SNP distances may vary for technical 100 reasons (e.g. assembly pipelines or filter criteria (Guthrie & Gardy, 2017)) and between study 101 populations e.g. high and low incidence settings (Bjorn-Mortensen et al, 2016).…”

Section: Introduction 39mentioning

confidence: 99%

The relationship between transmission time and clustering methods inMycobacterium tuberculosisepidemiology

Meehan

Moris

Köhl

et al. 2018

Preprint

View full text Add to dashboard Cite

BackgroundTracking recent transmission is a vital part of controlling widespread pathogens such as Mycobacterium tuberculosis. Multiple methods with specific performance characteristics exist for detecting recent transmission chains, usually by clustering strains based on genotype similarities. With such a large variety of methods available, informed selection of an appropriate approach for determining transmissions within a given setting/time period is difficult.MethodsThis study combines whole genome sequence (WGS) data derived from 324 isolates collected 2005-2010 in Kinshasa, Democratic Republic of Congo (DRC), a high endemic setting, with phylodynamics to unveil the timing of transmission events posited by a variety of standard genotyping methods. Clustering data based on Spoligotyping, 24-loci MIRU-VNTR typing, WGS based SNP (Single Nucleotide Polymorphism) and core genome multi locus sequence typing (cgMLST) typing were evaluated.FindingsOur results suggest that clusters based on Spoligotyping could encompass transmission events that occurred over 70 years prior to sampling while 24-loci-MIRU-VNTR often represented two or more decades of transmission. Instead, WGS based genotyping applying low SNP or cgMLST allele thresholds allows for determination of recent transmission events in timespans of up to 10 years e.g. for a 5 SNP/allele cut-off.InterpretationWith the rapid uptake of WGS methods in surveillance and outbreak tracking, the findings obtained in this study can guide the selection of appropriate clustering methods for uncovering relevant transmission chains within a given time-period. For high resolution cluster analyses, WGS-SNP and cgMLST based analyses have similar clustering/timing characteristics even for data obtained from a high incidence setting.

show abstract

A brief primer on genomic epidemiology: lessons learned fromMycobacterium tuberculosis

Cited by 27 publications

References 172 publications

The relationship between transmission time and clustering methods in Mycobacterium tuberculosis epidemiology

The relationship between transmission time and clustering methods in Mycobacterium tuberculosis epidemiology

Genome Sequences of the Mycobacterium tuberculosis H37Rv- ptkA Deletion Mutant and Its Parental Strain

The relationship between transmission time and clustering methods inMycobacterium tuberculosisepidemiology

Contact Info

Product

Resources

About