Whole genome sequencing of Shigella sonnei through PulseNet Latin America and Caribbean: advancing global surveillance of foodborne illnesses.

Baker, KS; Campos, J; Pichel, M; Della Gaspera, A; Duarte-Martínez, F; Campos-Chacón, E; Bolaños-Acuña, HM; Guzmán-Verri, C; Mather, AE; Diaz Velasco, S; Zamudio Rojas, ML; Forbester, JL; Connor, TR; Keddy, KH; Smith, AM; López de Delgado, EA; Angiolillo, G; Cuaical, N; Fernández, J; Aguayo, C; Morales Aguilar, M; Valenzuela, C; Morales Medrano, AJ; Sirok, A; Weiler Gustafson, N; Diaz Guevara, PL; Montaño, LA; Perez, E; Thomson, NR; (2017) Whole genome sequencing of Shigella sonnei through PulseNet Latin America and Caribbean: advancing global surveillance of foodborne illnesses. Clinical microbiology and infection. ISSN 1198-743X DOI: https://doi.org/10.1016/j.cmi.2017.03.021

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Shigella sonnei is a globally important diarrhoeal pathogen tracked through the surveillance network PulseNet Latin America and Caribbean (PNLA&C), which participates in PulseNet International. PNLA&C laboratories use common molecular techniques to track pathogens causing foodborne illness. We aimed to demonstrate the possibility and advantages of transitioning to whole genome sequencing (WGS) for surveillance within existing networks across a continent where S. sonnei is endemic. We applied WGS to representative archive isolates of S. sonnei (n = 323) from laboratories in nine PNLA&C countries to generate a regional phylogenomic reference for S. sonnei and put this in the global context. We used this reference to contextualise 16 S. sonnei from three Argentinian outbreaks, using locally generated sequence data. Assembled genome sequences were used to predict antimicrobial resistance (AMR) phenotypes and identify AMR determinants. S. sonnei isolates clustered in five Latin American sublineages in the global phylogeny, with many (46%, 149 of 323) belonging to previously undescribed sublineages. Predicted multidrug resistance was common (77%, 249 of 323), and clinically relevant differences in AMR were found among sublineages. The regional overview showed that Argentinian outbreak isolates belonged to distinct sublineages and had different epidemiologic origins. Latin America contains novel genetic diversity of S. sonnei that is relevant on a global scale and commonly exhibits multidrug resistance. Retrospective passive surveillance with WGS has utility for informing treatment, identifying regionally epidemic sublineages and providing a framework for interpretation of prospective, locally sequenced outbreaks.

Item Type: Article
Faculty and Department: Faculty of Infectious and Tropical Diseases > Dept of Pathogen Molecular Biology
Research Centre: Antimicrobial Resistance Centre (AMR)
PubMed ID: 28389276
Web of Science ID: 413739600014
URI: http://researchonline.lshtm.ac.uk/id/eprint/3959279


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