title: Whole genome sequencing of Shigella sonnei through PulseNet Latin America and Caribbean: advancing global surveillance of foodborne illnesses.
abstract: OBJECTIVE
  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.
  
  
  METHODS
  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.
  
  
  RESULTS
  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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: University of Liverpool, Department of Functional and Comparative Genomics, Liverpool, England, United Kingdom; Wellcome Trust Sanger Institute, Pathogen Variation Programme, Hinxton, England, United Kingdom. Electronic address: kbaker@liverpool.ac.uk.
authors.forename: K S
authors.initials: KS
authors.lastname: Baker
authors.affiliation: Instituto Nacional de Enfermedades Infecciosas, ANLIS, Buenos Aires, Argentina.
authors.forename: J
authors.initials: J
authors.lastname: Campos
authors.affiliation: Instituto Nacional de Enfermedades Infecciosas, ANLIS, Buenos Aires, Argentina.
authors.forename: M
authors.initials: M
authors.lastname: Pichel
authors.affiliation: Instituto Nacional de Enfermedades Infecciosas, ANLIS, Buenos Aires, Argentina.
authors.forename: A
authors.initials: A
authors.lastname: Della Gaspera
authors.affiliation: Instituto Costarricense de Investigación y Enseñanza en Nutrición y Salud (Inciensa), Costa Rica.
authors.forename: F
authors.initials: F
authors.lastname: Duarte-Martínez
authors.affiliation: Instituto Costarricense de Investigación y Enseñanza en Nutrición y Salud (Inciensa), Costa Rica.
authors.forename: E
authors.initials: E
authors.lastname: Campos-Chacón
authors.affiliation: Instituto Costarricense de Investigación y Enseñanza en Nutrición y Salud (Inciensa), Costa Rica.
authors.forename: H M
authors.initials: HM
authors.lastname: Bolaños-Acuña
authors.affiliation: Programa de Investigación en Enfermedades Tropicales, Escuela de Medicina Veterinaria, Universidad Nacional, Heredia, Costa Rica; Centro de Investigación en Enfermedades Tropicales, Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica.
authors.forename: C
authors.initials: C
authors.lastname: Guzmán-Verri
authors.affiliation: Wellcome Trust Sanger Institute, Pathogen Variation Programme, Hinxton, England, United Kingdom; University of Cambridge, Department of Veterinary Medicine, Cambridge, England, United Kingdom.
authors.forename: A E
authors.initials: AE
authors.lastname: Mather
authors.affiliation: National Institute of Heath, Lima, Peru.
authors.forename: S
authors.initials: S
authors.lastname: Diaz Velasco
authors.affiliation: National Institute of Heath, Lima, Peru.
authors.forename: M L
authors.initials: ML
authors.lastname: Zamudio Rojas
authors.affiliation: Wellcome Trust Sanger Institute, Pathogen Variation Programme, Hinxton, England, United Kingdom.
authors.forename: J L
authors.initials: JL
authors.lastname: Forbester
authors.affiliation: Organisms and Environment Division, Cardiff University School of Biosciences, Sir Martin Evans Building, Cardiff, Wales, United Kingdom.
authors.forename: T R
authors.initials: TR
authors.lastname: Connor
authors.affiliation: Centre for Enteric Diseases, National Institute for Communicable Diseases and Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
authors.forename: K H
authors.initials: KH
authors.lastname: Keddy
authors.affiliation: Centre for Enteric Diseases, National Institute for Communicable Diseases and Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
authors.forename: A M
authors.initials: AM
authors.lastname: Smith
authors.affiliation: Department of Bacteriology, National Institute of Hygiene 'Rafael Rangel', Ciudad University, Los Chaguaramos, Venezuela.
authors.forename: E A
authors.initials: EA
authors.lastname: López de Delgado
authors.affiliation: Department of Bacteriology, National Institute of Hygiene 'Rafael Rangel', Ciudad University, Los Chaguaramos, Venezuela.
authors.forename: G
authors.initials: G
authors.lastname: Angiolillo
authors.affiliation: Department of Bacteriology, National Institute of Hygiene 'Rafael Rangel', Ciudad University, Los Chaguaramos, Venezuela.
authors.forename: N
authors.initials: N
authors.lastname: Cuaical
authors.affiliation: Molecular Genetics Laboratory, Institute of Public Health of Chile, Santiago, Chile.
authors.forename: J
authors.initials: J
authors.lastname: Fernández
authors.affiliation: Molecular Genetics Laboratory, Institute of Public Health of Chile, Santiago, Chile.
authors.forename: C
authors.initials: C
authors.lastname: Aguayo
authors.affiliation: Department of Foodborne Diseases, National Health Laboratory of Guatemala, Laboratorio Nacional de Salud, Barcenas, Guatemala.
authors.forename: M
authors.initials: M
authors.lastname: Morales Aguilar
authors.affiliation: Department of Foodborne Diseases, National Health Laboratory of Guatemala, Laboratorio Nacional de Salud, Barcenas, Guatemala.
authors.forename: C
authors.initials: C
authors.lastname: Valenzuela
authors.affiliation: Department of Foodborne Diseases, National Health Laboratory of Guatemala, Laboratorio Nacional de Salud, Barcenas, Guatemala.
authors.forename: A J
authors.initials: AJ
authors.lastname: Morales Medrano
authors.affiliation: Bacteriology Laboratory, Departamento de Laboratorios de Salud Pública (DLSP), Ministerio de Salud Pública (MSP), Montevideo, Uruguay.
authors.forename: A
authors.initials: A
authors.lastname: Sirok
authors.affiliation: Department of Bacteriology, Laboratorio Central de Salud Pública, Asuncion, Paraguay.
authors.forename: N
authors.initials: N
authors.lastname: Weiler Gustafson
authors.affiliation: Grupo de Microbiología, Instituto Nacional de Salud, Bogotá, Colombia.
authors.forename: P L
authors.initials: PL
authors.lastname: Diaz Guevara
authors.affiliation: Grupo de Microbiología, Instituto Nacional de Salud, Bogotá, Colombia.
authors.forename: L A
authors.initials: LA
authors.lastname: Montaño
authors.affiliation: Pan American Health Organization/World Health Organization, Department of Health Emergencies, Washington, DC, United States.
authors.forename: E
authors.initials: E
authors.lastname: Perez
authors.affiliation: Wellcome Trust Sanger Institute, Pathogen Variation Programme, Hinxton, England, United Kingdom; London School of Hygiene and Tropical Medicine, London, England, United Kingdom. Electronic address: nrt@sanger.ac.uk.
authors.forename: N R
authors.initials: NR
authors.lastname: Thomson
mesh_terms: D017691:Caribbean Region / Q000453:epidemiology; D004269:DNA, Bacterial / Q000032:analysis / Q000235:genetics; D004196:Disease Outbreaks / Q000517:prevention & control / Q000706:statistics & numerical data; D024881:Drug Resistance, Bacterial; D004405:Dysentery, Bacillary / Q000453:epidemiology / Q000382:microbiology; D005517:Foodborne Diseases / Q000453:epidemiology / Q000382:microbiology; D006801:Humans; D007843:Latin America / Q000453:epidemiology; D062486:Public Health Surveillance; D012189:Retrospective Studies; D012764:Shigella sonnei / Q000187:drug effects / Q000235:genetics*; D000073336:Whole Genome Sequencing
chemical_list: D004269:DNA, Bacterial
keywords: Antimicrobial resistance; Central America; Diarrhoeal disease; Epidemiology; Genomics; Shigellosis; South America