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Whole genome sequencing identifies independent outbreaks of Shigellosis in 2010 and 2011 in La Pampa Province, Argentina

Isabel Chinen, Marcelo Galas, Ezequiel Tuduri, Maria Rosa Viñas, Carolina Carbonari, Anabella Della Gaspera, Daniela Nápoli, David M Aanensen, Silvia Argimón, Nicholas R Thomson, Darren Hughes, Stephen Baker, Caterina Guzmán-Verri, Matthew TG Holden, Alejandra M Abdala, Lucia P Alvarez, Beatriz Alvez, Rosana Barros, Shirley Budall, Constanza Campano, Luciana S Chamosa, Paul Cheddie, Daniel Cisterna, Denise De Belder, Milena Dropa, David Durand, Alan Elena, Gustavo Fontecha, Claudia Huber, Ana Paula Lemos, Luciano Melli, Roxana Elizabeth Paul, Lesly Suarez, Julian Torres Flores, Josefina Campos
doi: https://doi.org/10.1101/049940
Isabel Chinen
1Instituto Nacional de Enfermedades Infecciosas, ANLIS, Buenos Aires, Argentina
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Marcelo Galas
1Instituto Nacional de Enfermedades Infecciosas, ANLIS, Buenos Aires, Argentina
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Ezequiel Tuduri
1Instituto Nacional de Enfermedades Infecciosas, ANLIS, Buenos Aires, Argentina
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Maria Rosa Viñas
1Instituto Nacional de Enfermedades Infecciosas, ANLIS, Buenos Aires, Argentina
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Carolina Carbonari
1Instituto Nacional de Enfermedades Infecciosas, ANLIS, Buenos Aires, Argentina
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Anabella Della Gaspera
1Instituto Nacional de Enfermedades Infecciosas, ANLIS, Buenos Aires, Argentina
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Daniela Nápoli
1Instituto Nacional de Enfermedades Infecciosas, ANLIS, Buenos Aires, Argentina
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David M Aanensen
2Centre for Genomic Pathogen Surveillance, Hinxton, Cambridge, United Kingdom
3Imperial College London, London, United Kingdom
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Silvia Argimón
2Centre for Genomic Pathogen Surveillance, Hinxton, Cambridge, United Kingdom
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Nicholas R Thomson
4The Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
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Darren Hughes
5The Wellcome Genome Campus Advanced Courses, Hinxton, Cambridge, United Kingdom
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Stephen Baker
6The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
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Caterina Guzmán-Verri
7Universidad Nacional, 3000 Heredia, Costa Rica
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Matthew TG Holden
8The University of St. Andrews, St. Andrews, Scotland
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Alejandra M Abdala
9National Institute for Agricultural Technology (INTA)CONICET, Argentina
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Lucia P Alvarez
9National Institute for Agricultural Technology (INTA)CONICET, Argentina
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Beatriz Alvez
10Universidad Central de Venezuela, Caracas, Venezuela
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Rosana Barros
11Fluminense Federal University, Niterio, Brazil
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Shirley Budall
12University of the West Indies, Mona campus, Kingston, Jamaica
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Constanza Campano
13Institute of Public Health of Chile, Santiago, Chile
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Luciana S Chamosa
14Universidad de Buenos Aires, Buenos Aires, Argentina
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Paul Cheddie
15University of Guyana, Georgetown, Guyana
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Daniel Cisterna
1Instituto Nacional de Enfermedades Infecciosas, ANLIS, Buenos Aires, Argentina
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Denise De Belder
1Instituto Nacional de Enfermedades Infecciosas, ANLIS, Buenos Aires, Argentina
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Milena Dropa
16University of Sao Paulo, Sao Paulo, Brazil
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David Durand
17Universidad Peruana Cayetano Heredia, Lima, Perú
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Alan Elena
14Universidad de Buenos Aires, Buenos Aires, Argentina
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Gustavo Fontecha
18Microbiology Research Institute, Universidad Nacional Autónoma de Honduras, Tegucigalpa, Honduras
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Claudia Huber
19Laboratorio Central de Salud Pública, Asunción, Paraguay
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Ana Paula Lemos
20Adolfo Lutz Institute, Sao Paulo, Brazil
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Luciano Melli
21Universidad Nacional de San Martín, Buenos Aires, Argentina
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Roxana Elizabeth Paul
1Instituto Nacional de Enfermedades Infecciosas, ANLIS, Buenos Aires, Argentina
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Lesly Suarez
22Cayetano Heredia University, Lima, Perú
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Julian Torres Flores
22Cayetano Heredia University, Lima, Perú
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Josefina Campos
1Instituto Nacional de Enfermedades Infecciosas, ANLIS, Buenos Aires, Argentina
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  • For correspondence: jcampos@anlis.gov.ar
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Abstract

Shigella sonnei is an emergent cause of diarrheal disease in middle-income countries. The organism causes endemic disease and is also associated with sporadic outbreaks in susceptible populations. In 2010 and 2011 there were two suspected outbreaks of diarrheal disease caused by S. sonnei in La Pampa province in central Argentina. Aiming to confirm these as outbreaks and provide insight into the relationship of the strains causing these infections we combined antimicrobial susceptibility testing and pulsed field gel electrophoresis (PFGE) with whole genome sequencing (WGS). Antimicrobial susceptibility testing suggested the two events were unrelated; organisms isolated in 2010 exhibited resistance to trimethoprim sulphate whereas the 2011 S. sonnei were non-susceptible against ampicillin, trimethoprim sulphate and cefpodoxime. PFGE profiling confirmed the likelihood of two independent outbreaks, separating the isolates into two main XbaI restriction profiles. We additionally performed WGS on 17 isolates associated with these outbreaks. The resulting phylogeny confirmed the PFGE structure and separated the organisms into two comparatively distantly related clones. Antimicrobial resistant genes were common, and the presence of an OXA-1 was likely associated with resistance to cefpodoxime in the second outbreak. We additionally identified novel horizontally transferred genetic material that may impinge on the pathogenic phenotype of the infecting strains. Our study shows that even with a lack of supporting routine data WGS is an indispensible method for the tracking and surveillance of bacterial pathogens during outbreaks and is becoming a vital tool for the monitoring of antimicrobial resistant strains of S. sonnei.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted April 28, 2016.
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Whole genome sequencing identifies independent outbreaks of Shigellosis in 2010 and 2011 in La Pampa Province, Argentina
Isabel Chinen, Marcelo Galas, Ezequiel Tuduri, Maria Rosa Viñas, Carolina Carbonari, Anabella Della Gaspera, Daniela Nápoli, David M Aanensen, Silvia Argimón, Nicholas R Thomson, Darren Hughes, Stephen Baker, Caterina Guzmán-Verri, Matthew TG Holden, Alejandra M Abdala, Lucia P Alvarez, Beatriz Alvez, Rosana Barros, Shirley Budall, Constanza Campano, Luciana S Chamosa, Paul Cheddie, Daniel Cisterna, Denise De Belder, Milena Dropa, David Durand, Alan Elena, Gustavo Fontecha, Claudia Huber, Ana Paula Lemos, Luciano Melli, Roxana Elizabeth Paul, Lesly Suarez, Julian Torres Flores, Josefina Campos
bioRxiv 049940; doi: https://doi.org/10.1101/049940
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Whole genome sequencing identifies independent outbreaks of Shigellosis in 2010 and 2011 in La Pampa Province, Argentina
Isabel Chinen, Marcelo Galas, Ezequiel Tuduri, Maria Rosa Viñas, Carolina Carbonari, Anabella Della Gaspera, Daniela Nápoli, David M Aanensen, Silvia Argimón, Nicholas R Thomson, Darren Hughes, Stephen Baker, Caterina Guzmán-Verri, Matthew TG Holden, Alejandra M Abdala, Lucia P Alvarez, Beatriz Alvez, Rosana Barros, Shirley Budall, Constanza Campano, Luciana S Chamosa, Paul Cheddie, Daniel Cisterna, Denise De Belder, Milena Dropa, David Durand, Alan Elena, Gustavo Fontecha, Claudia Huber, Ana Paula Lemos, Luciano Melli, Roxana Elizabeth Paul, Lesly Suarez, Julian Torres Flores, Josefina Campos
bioRxiv 049940; doi: https://doi.org/10.1101/049940

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