The evolution and international spread of extensively drug resistant Shigella sonnei

Mason, Lewis; Greig, David R.; Cowley, Lauren A.; Partridge, Sally R.; Martínez, Elena; Blackwell, Grace A.; Chong, Charlotte; Silva, Malaka De; Bengtsson, Rebecca J.; Draper, Jenny; Ginn, Andrew N.; Sandaradura, Indy; Sim, Eby; Iredell, Jonathan R.; Sintchenko, Vitali; Ingle, Danielle J.; Howden, Benjamin P; Lefèvre, Sophie; Njamkepo, Elisabeth; Weill, François‐Xavier; Ceyssens, Pieter‐Jan; Jenkins, Claire; Baker, Kate S.

doi:10.21203/rs.3.rs-2057516/v1

Cited by 4 publications

(5 citation statements)

References 65 publications

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“…In addition, it is not possible to rule out better rates of referral by the clinical laboratories participating in this study for patients infected with isolates displaying higher levels of AMR. Our findings therefore require confirmation in a larger study, and changes in the results might be expected if extensively drug-resistant (XDR) Shigella isolates were introduced, as already reported in various parts of the world [9,37,38].…”

Section: Antimicrobial Resistancementioning

confidence: 58%

Genomic analysis of Shigella isolates from Lebanon reveals marked genetic diversity and antimicrobial resistance

Yassine,

Rafei,

Pardos de la Gandara

et al. 2023

Microbial Genomics

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In this study, we characterized 54 clinical isolates of Shigella collected in North Lebanon between 2009 and 2017 through phenotypic and genomic analyses. The most prevalent serogroup was S. sonnei, accounting for 46.3 % (25/54) of the isolates, followed by S. flexneri (27.8 %, 15/54), S. boydii (18.5 %, 10/54) and S. dysenteriae (7.4 %, 4/54). Only three isolates were pan-susceptible, and 87 % (47/54) of the isolates had multidrug resistance phenotypes. Notably, 27.8 % (15/54) of the isolates were resistant to third-generation cephalosporins (3GCs) and 77.8 % (42/54) were resistant to nalidixic acid. 3GC resistance was mediated by the extended-spectrum beta-lactamase genes bla CTX-M-15 and bla CTX-M-3, which were present on various plasmids. Quinolone resistance was conferred by single point mutations in the gyrA DNA gyrase gene, leading to GyrA S83L, GyrA D87Y or GyrA S83A amino acid substitutions. This is the first study, to our knowledge, to provide genomic insights into the serotypes of Shigella circulating in Lebanon and the various antimicrobial resistance determinants carried by these strains.

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Section: Antimicrobial Resistancementioning

confidence: 58%

Genomic analysis of Shigella isolates from Lebanon reveals marked genetic diversity and antimicrobial resistance

Yassine,

Rafei,

Pardos de la Gandara

et al. 2023

Microbial Genomics

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“…In line with other research we find the co-divergence of virulence plasmid, pINV, with the chromosome of S. sonnei (The et al ., 2016), and the movement of small plasmids within the S. sonnei population. Further, we find evidence for multiple MDR plasmid transfer events between S. sonnei lineages, but also between S. sonnei and S. flexneri lineages (Baker et al ., 2015;Ingle et al ., 2019; Locke et al ., 2021; Mason et al ., 2022). Future work could explore where these plasmid are originating from to improve our understanding of how AMR genes move between species, by incorporating other bacterial species into this analyses.…”

Section: Discussionmentioning

confidence: 99%

“…These outbreaks have been driven by the presence of an MDR plasmid, pKSR100 (Baker et al , 2015; Ingle et al , 2019). Recent reports have shown the acquisition of blaCTX-M-27 gene mediating resistance to extended spectrum betalactams on variants of the pKSR100 plasmid driving the outbreaks of extensively drug resistant Shigella sonnei (Mason et al , 2022).…”

Section: Introductionmentioning

confidence: 99%

“…AMR determinants to streptomycin and sulfonamide are encoded on spA (Hawkey et al ., 2021). Additionally, S. sonnei and S. flexneri have been associated with multidrug resistant (MDR) outbreaks, particularly in men who have sex with men (MSM) (Baker et al ., 2015; Ingle et al ., 2019, 2020; Mason et al ., 2022), representing a major public health threat. These outbreaks have been driven by the presence of an MDR plasmid, pKSR100 (Baker et al ., 2015;Ingle et al ., 2019).…”

Section: Introductionmentioning

confidence: 99%

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Tracking the horizontal transfer of plasmids inShigella sonneiandShigella flexneriusing phylogenetics

Müller

Duchêne

Williamson

et al. 2022

Preprint

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There is an urgent need for novel methods to track the emergence and dissemination of antimicrobial resistance (AMR) mechanisms that give rise to multi- and extensively-drug resistant bacterial pathogens. AMR mechanisms are most commonly associated with AMR genes that are carried on mobile elements, such as plasmids. Plasmids may move between lineages of the same or different bacterial species and thus understanding when and where they were introduced into a population, as well as their persistence, is crucial to understanding the changing AMR dynamics in bacterial pathogens. Here we introduce an approach that allows us to reconstruct how plasmids move between bacterial lineages. To do so, we model the co-divergence of chromosomal and plasmid DNA in a Bayesian phylogenetic network approach using a joint coalescent and plasmid transfer process. We apply this new approach to a five year dataset ofShigella sonneiandShigella flexneriisolated in Melbourne, Australia, reconstructing how different plasmids move within and between these species. Specifically, we investigate the long term co-divergence of the virulence plasmid, the gain and loss of small plasmids, and the recent acquisition and dissemination of the multidrug resistant (MDR) plasmid moving betweenS. sonneiandS. flexnerilineages, through multiple introductions from sampled and also unsampled sources. This approach has applications to both emerging and known bacterial pathogens and improves our understanding of where AMR-carrying plasmids are introduced and maintained in bacterial pathogens of human health importance. Our novel approach is implemented in the widely used BEAST2 software.

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“…It included assemblies of over 300,000 genomes which had not previously been available (the raw data only had been available). The assemblies and search indexes allowed multiple other studies of plasmids[5, 6], bacterial adaptation[7, 8, 9, 10], and compression/indexing algorithms[11, 12, 13, 14, 15]. However, there were a few limitations.…”

Section: Introductionmentioning

confidence: 99%

AllTheBacteria - all bacterial genomes assembled, available and searchable

Hunt,

Lima,

Shen

et al. 2024

Preprint

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The bacterial sequence data publicly available at the global DNA archives is a vast source of information on the evolution of bacteria and their mobile elements. However, most of it is either unassembled or inconsistently assembled and QC-ed. This makes it unsuitable for large-scale analyses, and inaccessible for most researchers to use. In 2021 Blackwell et al therefore released a uniformly assembled set of 661,405 genomes, consisting of all publicly available whole genome sequenced bacterial isolate data as of November 2018, along with various search indexes. In this study we extend that dataset by 4.5 years (up to May 2023), tripling the number of genomes. We also expand the scope, as we begin a global collaborative project to generate annotations for different species as desired by different research communities. In this study we describe the initial v0.1 data release of 1,932,812 assemblies (combining 1,271,428 new assemblies with the 661k dataset). All 1.9 million have been uniformly re-processed for quality criteria and to give taxonomic abundance estimates with respect to the GTDB phylogeny. Using an evolution-informed compression approach, the full set of genomes is just 102Gb in batched xz archives. We also provide multiple search indexes. Finally, we outline plans for future annotations to be provided in further releases.

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The evolution and international spread of extensively drug resistant Shigella sonnei

Cited by 4 publications

References 65 publications

Genomic analysis of Shigella isolates from Lebanon reveals marked genetic diversity and antimicrobial resistance

Genomic analysis of Shigella isolates from Lebanon reveals marked genetic diversity and antimicrobial resistance

Tracking the horizontal transfer of plasmids inShigella sonneiandShigella flexneriusing phylogenetics

AllTheBacteria - all bacterial genomes assembled, available and searchable

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