Tracking the establishment of local endemic populations of an emergent enteric pathogen

Abstract

Shigella sonnei is a human-adapted pathogen that is emerging globally as the dominant agent of bacterial dysentery. To investigate local establishment, we sequenced the genomes of 263 Vietnamese S. sonnei isolated over 15 y. Our data show that S. sonnei was introduced into Vietnam in the 1980s and has undergone localized clonal expansion, punctuated by genomic fixation events through periodic selective sweeps. We uncover geographical spread, spatially restricted frontier populations, and convergent evolution through local gene pool sampling. This work provides a unique, high-resolution insight into the microevolution of a pioneering human pathogen during its establishment in a new host population.enteric disease | drug resistance | phylogeography | genomics

Travel- and Community-Based Transmission of Multidrug-ResistantShigellasonneiLineage among International Orthodox Jewish Communities

“…The lineage was monophyletic and had a strong time signature, consistent with a point introduction and subsequent epidemic emergence. This pattern was similar to that observed in Vietnam after the introduction of another global III S. sonnei sublineage (15,17). The date of the emergence of the OJC-associated lineage (1988 [95% highest posterior distribution [1985][1986][1987][1988][1989][1990]) is consistent with that estimated in a previous study where a 2-isolate lineage emerged in the Middle East during 1983 (16).…”

“…Strains from Israel and strains from nearly all previously reported OJC outbreaks elsewhere formed a distinct OJC-associated sublineage that emerged ≈30 years ago. Unlike other described emergent Shigella sublineages (17,28), the OJC-associated lineage lacked a defining association with AMR.…”

“…Root-to-tip distances were generated by using Path-O-Gen version 1.4 (32). BEAST results shown are from 4 chains of 100 million Markov chain Monte Carlo generations run according to a general time reversible plus gamma substitution model, with a relaxed normal clock and Bayesian Skyline Population model, previously used for this pathogen (16,17). Chains were sampled every 1,000 generations with a 10% initial burn-in for root-height (time to most recent common ancestor) analysis.…”

“…Subtyping of S. sonnei by using whole-genome sequencing has defined a global population structure that is divided into 4 lineages; the third lineage, global III, disseminated globally after acquiring multidrug resistance (MDR) (16). This advanced subtyping and established global context was used to show that the rise of S. sonnei in Vietnam was attributable to the point introduction and subsequent expansion of a single sublineage in the 1980s (17), demonstrating the effectiveness of this approach for characterizing epidemiologic phenomena.…”

Genomic Analysis of Bacterial Outbreaks

“…(Snitkin et al, 2012;Espedido et al, 2013;Onori et al, 2015) Legionella pneumophila 3.5 Illumina HiSeq 2x100 bp Illumina MiSeq 2x250 bp, 2x150bp SOLiD 5500XL SE 75bp (Reuter et al, 2013a;Reuter et al, 2013b;Sánchez-Busó et al, 2014;Bartley et al, 2016) Listeria monocytogenes 3 Roche 454 GS-FLX (Gilmour et al, 2010;Schmid et al, 2014;Kwong et al, 2016 (Holt et al, 2008;Lienau et al, 2011;Quick et al, 2015;Allard et al, 2013;Cao et al, 2013;Allard et al, 2012;Taylor et al, 2015;Bekal et al, 2016) Salmonella Typhimurium 4.7 Illumina GA II system (Okoro et al, 2012) Shigella sonnei 5.06 Illumina GAII PE 2x54 bp Illumina MiSeq Illumina HiSeq2000 (Holt et al, 2012;Holt et al, 2013;McDonnell et al, 2013) 32 (Harris et al, 2010;Eyre et al, 2012;McAdam et al, 2012;Young et al, 2012;Köser et al, 2012;Holden et al, 2013;Nübel et al, 2013;Harris et al, 2013;Price et al, 2014;Azarian et al, 2015;Paterson et al, 2015;Senn et al, 2016;Kinnevey et al, 2016;Reuter et al, 2016) Streptococcus pneumoniae 1. Hendriksen et al, 2011;Chin et al, 2011;…”