Retrospective analysis of whole genome sequencing compared to prospective typing data in further informing the epidemiological investigation of an outbreak of Shigella sonnei in the UK

Abstract

The aim of this study was to retrospectively assess the value of whole genome sequencing (WGS) compared to conventional typing methods in the investigation and control of an outbreak of Shigella sonnei in the Orthodox Jewish (OJ) community in the UK. The genome sequence analysis showed that the strains implicated in the outbreak formed three phylogenetically distinct clusters. One cluster represented cases associated with recent exposure to a single strain, whereas the other two clusters represented related but distinct strains of S. sonnei circulating in the OJ community across the UK. The WGS data challenged the conclusions drawn during the initial outbreak investigation and allowed cases of dysentery to be implicated or ruled out of the outbreak that were previously misclassified. This study showed that the resolution achieved using WGS would have clearly defined the outbreak, thus facilitating the promotion of infection control measures within local schools and the dissemination of a stronger public health message to the community.

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

“…These samples included 22 from a small OJC-associated outbreak (23) and an additional 79 from outbreaks during 2006-2014 that were epidemiologically confirmed to be associated with OJCs by interviews and questionnaires as part of public health investigations. Also included were a set of 45 isolates from patients with no known OJC association (non-OJC).…”

“…Of the recognized Shigella spp., the distribution of S. sonnei makes it particularly relevant for studying international transmission because it is the most commonly isolated species in middle-to high-income nations (5) and causes a substantial disease incidence in low-income nations; for example, 23.7% of all documented shigellosis cases causing moderate to severe diarrhea in children <5 years of age in Africa and Asia (11). Moreover, S. sonnei prevalence increases as nations develop economically (12)(13)(14)(15).…”

“…S. sonnei shigellosis is highly endemic to Israel; its incidence there since the early 1990s has primarily been driven by biennial epidemics within OJCs in Israel (primarily in the 0-4-year age group, in whom the incidence is ≈7 cases/1,000 population/y [19]). In addition to incidence in OJCs in Israel, outbreaks ranging in size from 27 culture-confirmed cases to >13,000 cases of S. sonnei shigellosis have been reported in OJCs in Europe and North America (18,(20)(21)(22)(23)(24). These outbreaks are attributable to highly clonal organisms, determined by using pulsed-field gel electrophoresis (20,22,24) and, in the case of an outbreak in Belgium, linked to prevailing strains from Israel (22).…”

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;…”

Management of patients with suspected infectious diarrhoea in hospitals in England

“…These advances include multiplex polymerase chain reaction (PCR) assays and whole genome sequencing 3,4 . Prior to implementing these new tests, it is important to establish how patients with infectious diarrhoea are currently managed in hospitals in order to assess the implications of more widespread molecular testing.…”