Abstract
National surveillance of Shigella flexneri ensures the rapid detection of outbreaks to facilitate public health investigation and intervention strategies. In this study, we used whole-genome sequencing (WGS) to type S. flexneri in order to detect linked cases and support epidemiological investigations. We prospectively analyzed 330 isolates of S. flexneri received at the Gastrointestinal Bacteria Reference Unit at Public Health England between August 2015 and January 2016. Traditional phenotypic and WGS sub-typing methods were compared. PCR was carried out on isolates exhibiting phenotypic/genotypic discrepancies with respect to serotype. Phylogenetic relationships between isolates were analyzed by WGS using single nucleotide polymorphism (SNP) typing to facilitate cluster detection. For 306/330 (93%) isolates there was concordance between serotype derived from the genome and phenotypic serology. Discrepant results between the phenotypic and genotypic tests were attributed to novel O-antigen synthesis/modification gene combinations or indels identified in O-antigen synthesis/modification genes rendering them dysfunctional. SNP typing identified 36 clusters of two isolates or more. WGS provided microbiological evidence of epidemiologically linked clusters and detected novel O-antigen synthesis/modification gene combinations associated with two outbreaks. WGS provided reliable and robust data for monitoring trends in the incidence of different serotypes over time. SNP typing can be used to facilitate outbreak investigations in real-time thereby informing surveillance strategies and providing the opportunities for implementing timely public health interventions.
Highlights
Shigellosis is caused by four species of Shigella, including S. boydii, S. dysenteriae, S. flexneri and S. sonnei, transmitted via the fecal oral route
Cluster 4 comprised five isolates of S. flexneri associated with an outbreak of gastrointestinal symptoms in five captive chimpanzees phenotypically identified as serotype 3a
This study showed whole-genome sequencing (WGS) to be a robust and reliable method for serotyping S. flexneri isolates and provided additional strain discrimination at the single nucleotide polymorphism (SNP) level
Summary
Shigellosis is caused by four species of Shigella, including S. boydii, S. dysenteriae, S. flexneri and S. sonnei, transmitted via the fecal oral route. Symptoms typically start 1–2 days after exposure and include diarrhea, bloody diarrhea abdominal pain, fever, and tenesmus. The burden of shigellosis is highest in developing countries with up to 167 million episodes of diarrhea annually, leading to over a million deaths (Kotloff et al, 1999). A multicenter study of shigellosis in six Asian countries indicated the incidence rate to be highest in children under the age of 4 years old and in adults over 70 years old (von Seidlein et al, 2006). In the United Kingdom, S. flexneri is most commonly associated with causing travelers’ diarrhea and outbreaks of gastrointestinal symptoms in men who have sex with men (MSM) (Simms et al, 2015). There are reports of increased intercontinental dissemination of multidrug resistant S. flexneri (Baker et al, 2015)
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