Use of whole-genome sequencing to identify clusters of Shigella flexneri associated with sexual transmission in men who have sex with men in England: a validation study using linked behavioural data

Within the last 2 decades there have been an increasing number of Shigella spp. outbreaks among men who have sex with men (MSM) worldwide. In 2015, Public Health England (PHE) introduced routine whole genome sequencing (WGS) for the national surveillance of Shigella spp.

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Species-wide whole genome sequencing reveals historical global spread and recent local persistence in Shigella flexneri

eLife ◽

10.7554/elife.07335 ◽

2015 ◽

Vol 4 ◽

Cited By ~ 50

Author(s):

Thomas R Connor ◽

Clare R Barker ◽

Kate S Baker ◽

François-Xavier Weill ◽

Kaisar Ali Talukder ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Low Income ◽

Shigella Flexneri ◽

Virulence Gene ◽

Low Income Countries ◽

Whole Genome ◽

Phylogenetic Groups ◽

Gene Acquisition ◽

History Of

Shigella flexneri is the most common cause of bacterial dysentery in low-income countries. Despite this, S. flexneri remains largely unexplored from a genomic standpoint and is still described using a vocabulary based on serotyping reactions developed over half-a-century ago. Here we combine whole genome sequencing with geographical and temporal data to examine the natural history of the species. Our analysis subdivides S. flexneri into seven phylogenetic groups (PGs); each containing two-or-more serotypes and characterised by distinct virulence gene complement and geographic range. Within the S. flexneri PGs we identify geographically restricted sub-lineages that appear to have persistently colonised regions for many decades to over 100 years. Although we found abundant evidence of antimicrobial resistance (AMR) determinant acquisition, our dataset shows no evidence of subsequent intercontinental spread of antimicrobial resistant strains. The pattern of colonisation and AMR gene acquisition suggest that S. flexneri has a distinct life-cycle involving local persistence.

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Whole-genome sequencing reveals transmission of gonococcal antibiotic resistance among men who have sex with men: an observational study

Sexually Transmitted Infections ◽

10.1136/sextrans-2017-053287 ◽

2017 ◽

Vol 94 (2) ◽

pp. 151-157 ◽

Cited By ~ 17

Author(s):

Jason C Kwong ◽

Eric P F Chow ◽

Kerrie Stevens ◽

Timothy P Stinear ◽

Torsten Seemann ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Disease Transmission ◽

Sexual Partners ◽

Whole Genome ◽

Global Public Health ◽

Antibiotic Resistant ◽

Treatment And Prevention ◽

A Genome ◽

Sex With Men

ObjectivesDrug-resistant Neisseria gonorrhoeae are now a global public health threat. Direct transmission of antibiotic-resistant gonococci between individuals has been proposed as a driver for the increased transmission of resistance, but direct evidence of such transmission is limited. Whole-genome sequencing (WGS) has superior resolution to investigate outbreaks and disease transmission compared with traditional molecular typing methods such as multilocus sequence typing (MLST) and N. gonorrhoeae multiantigen sequence (NG-MAST). We therefore aimed to systematically investigate the transmission of N. gonorrhoeae between men in sexual partnerships using WGS to compare isolates and their resistance to antibiotics at a genome level.Methods458 couples from a large prospective cohort of men who have sex with men (MSM) tested for gonorrhoea together between 2005 and 2014 were included, and WGS was conducted on all isolates from couples where both men were culture-positive for N. gonorrhoeae. Resistance-determining sequences were identified from genome assemblies, and comparison of isolates between and within individuals was performed by pairwise single nucleotide polymorphism and pangenome comparisons, and in silico predictions of NG-MAST and MLST.ResultsFor 33 of 34 (97%; 95% CI 85% to 100%) couples where both partners were positive for gonorrhoea, the resistance-determining genes and mutations were identical in isolates from each partner (94 isolates in total). Resistance determinants in isolates from 23 of 23 (100%; 95% CI 86% to 100%) men with multisite infections were also identical within an individual. These partner and within-host isolates were indistinguishable by NG-MAST, MLST and whole genomic comparisons.ConclusionsThese data support the transmission of antibiotic-resistant strains between sexual partners as a key driver of resistance rates in gonorrhoea among MSM. This improved understanding of the transmission dynamics of N. gonorrhoeae between sexual partners will inform treatment and prevention guidelines.

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Author response: Species-wide whole genome sequencing reveals historical global spread and recent local persistence in Shigella flexneri

10.7554/elife.07335.018 ◽

2015 ◽

Author(s):

Thomas R Connor ◽

Clare R Barker ◽

Kate S Baker ◽

François-Xavier Weill ◽

Kaisar Ali Talukder ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Shigella Flexneri ◽

Author Response ◽

Whole Genome ◽

Global Spread

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Whole-Genome Sequencing for National Surveillance of Shigella flexneri

Frontiers in Microbiology ◽

10.3389/fmicb.2017.01700 ◽

2017 ◽

Vol 8 ◽

Cited By ~ 15

Author(s):

Marie A. Chattaway ◽

David R. Greig ◽

Amy Gentle ◽

Hassan B. Hartman ◽

Timothy J. Dallman ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Shigella Flexneri ◽

Whole Genome ◽

National Surveillance

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15. A validation study of copy number variant (CNVs) detection to replace constitutional microarray from low resolution whole genome sequencing data

Cancer Genetics ◽

10.1016/j.cancergen.2018.04.018 ◽

2018 ◽

Vol 224-225 ◽

pp. 56

Author(s):

Alka Chaubey ◽

C. Alexander Valencia ◽

Zeqiang Ma ◽

Gerard Irzyk ◽

Edward Szekeres ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Validation Study ◽

Copy Number ◽

Copy Number Variant ◽

Whole Genome Sequencing Data ◽

Whole Genome ◽

Sequencing Data ◽

Low Resolution

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Decision letter: Species-wide whole genome sequencing reveals historical global spread and recent local persistence in Shigella flexneri

10.7554/elife.07335.017 ◽

2015 ◽

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Shigella Flexneri ◽

Whole Genome ◽

Global Spread

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Is whole genome sequencing the answer for identifying Shigella bacteraemia?

BMJ Case Reports ◽

10.1136/bcr-2019-231596 ◽

2019 ◽

Vol 12 (12) ◽

pp. e231596

Author(s):

Dora Amos ◽

Priya Khanna ◽

Sayeed Adnan Aali ◽

Guduru Gopal Rao

Keyword(s):

Escherichia Coli ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Rare Case ◽

Shigella Flexneri ◽

Genomic Sequencing ◽

Whole Genome ◽

Laboratory Techniques

We present a rare case of Shigella flexneri bacteraemia and the challenges of differentiating Escherichia coli and Shigella spp using conventional and newer laboratory techniques in diagnostic laboratories. The organism was identified only after whole genomic sequencing .

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