Shigellosis is a diarrheal disease caused mainly by Shigella flexneri and Shigella sonnei. Infection is thought to be largely self-limiting, with short-to me-dium-term and serotype-specific immunity provided following clearance. However, cases of men who have sex with men (MSM)-associated shigellosis have been reported where Shigella of the same serotype were serially sampled from individuals between 1 and 1,862 days apart, possibly due to persistent carriage or reinfection with the same serotype. Here, we investigate the accessory genome dynamics of MSM-associated S. flexneri and S. sonnei isolates serially sampled from individual patients at various days apart to shed light on the adaptation of these important pathogens during infection. We find that pairs likely associated with persistent infec-tion/carriage and with a smaller single nucleotide polymorphism (SNP) distance, demonstrated significantly less variation in accessory genome content than pairs likely associated with reinfection, and with a greater SNP distance. We observed anti-microbial resistance acquisition during Shigella carriage, including the gain of an extended-spectrum beta-lactamase gene during carriage. Finally, we explored large chromosomal structural variations and rearrangements in seven (five chronic and two reinfection associated) pairs of S. flexneri 3a isolates from an MSM-associated epidemic sublineage, which revealed variations at several common regions across isolate pairs, mediated by insertion sequence elements and comprising a distinct predicted functional profile. This study provides insight on the variation of accessory genome dynamics and large structural genomic changes in Shigella during persistent infection/carriage. In addition, we have also created a complete reference genome and biobanked isolate of the globally important pathogen, S. flexneri 3a. IMPORTANCE Shigella spp. are Gram-negative bacteria that are the etiological agent of shigellosis, the second most common cause of diarrheal illness among children under the age of five in low-income countries. In high-income countries, shigellosis is also a sexually transmissible disease among men who have sex with men. Within the latter setting, we have captured prolonged and/or recurrent infection with shi-gellae of the same serotype, challenging the belief that Shigella infection is short lived and providing an early opportunity to study the evolution of the pathogen over the course of infection. Using this recently emerged transmission scenario, we comprehensively characterize the genomic changes that occur over the course of individual infection with Shigella and uncover a distinct functional profile of variable genomic regions, findings that have relevance for other Enterobacteriaceae.
Bibliographical noteFunding Information:
This study was supported by a UKRI MRC NIRG award (MR/R020787/1) and a technology directorate voucher from the University of Liverpool. K.S.B. is supported by a Wellcome Trust Clinical Research Career Development Award (106690/A/14/Z) and an Academy of Medical Sciences Springboard award (SBF002/1114). K.S.B., C.J., and T.D. are affiliated with the National Institute for Health Research Health Protection Research Unit (NIHR HPRU) in Gastrointestinal Infections at University of Liverpool in partnership with Public Health England, in collaboration with the University of Warwick. R.J.B. is funded by a Biotechnology and Biological Sciences Research Council Doctoral Training Partnership studentship (BB/M011186/1). G.S. is supported by a studentship from the MRC Discovery Medicine North (DiMeN) Doctoral Training Partnership (MR/N013840/1). The views expressed here are those of the authors and do not necessarily those of the NHS, the NIHR, the Department of Health and Social Care, or Public Health England.
© Crown 2021.
- Persistent infection