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

被引：31

作者：

Baker, K. S. ^{[1
,2
]}

Campos, J. ^{[3
]}

Pichel, M. ^{[3
]}

Della Gaspera, A. ^{[3
]}

Duarte-Martinez, F. ^{[4
]}

Campos-Chacon, E. ^{[4
]}

Bolanos-Acuna, H. M. ^{[4
]}

Guzman-Verri, C. ^{[5
,6
]}

Mather, A. E. ^{[2
,7
]}

Diaz Velasco, S. ^{[8
]}

Zamudio Rojas, M. L. ^{[8
]}

Forbester, J. L. ^{[2
]}

Connor, T. R. ^{[9
]}

Keddy, K. H. ^{[10
,11
]}

Smith, A. M. ^{[10
,11
]}

Lopez de Delgado, E. A. ^{[12
]}

Angiolillo, G. ^{[12
]}

Cuaical, N. ^{[12
]}

Fernandez, J. ^{[13
]}

Aguayo, C. ^{[13
]}

Morales Aguilar, M. ^{[14
]}

Valenzuela, C. ^{[14
]}

Morales Medrano, A. J. ^{[14
]}

Sirok, A. ^{[15
]}

Weiler Gustafson, N. ^{[16
]}

Diaz Guevara, P. L. ^{[17
]}

Montano, L. A. ^{[17
]}

Perez, E. ^{[18
]}

Thomson, N. R. ^{[2
,19
]}

机构：

[1] Univ Liverpool, Dept Funct & Comparat Genom, Liverpool, Merseyside, England

[2] Wellcome Trust Sanger Inst, Pathogen Variat Programme, Hinxton CB10 1SA, England

[3] ANLIS, Inst Nacl Enfermedades Infecciosas, Buenos Aires, DF, Argentina

[4] Inst Costarricense Invest & Ensenanza Nutr & Salu, Cartago, Costa Rica

[5] Univ Nacl, Escuela Med Vet, Programa Invest Enfermedades Trop, Heredia, Costa Rica

[6] Univ Costa Rica, Fac Microbiol, Ctr Invest Enfermedades Trop, San Jose, Costa Rica

[7] Univ Cambridge, Dept Vet Med, Cambridge, England

[8] Natl Inst Heath, Lima, Peru

[9] Cardiff Univ, Sch Biosci, Organisms & Environm Div, Sir Martin Evans Bldg, Cardiff, S Glam, Wales

[10] Univ Witwatersrand, Natl Inst Communicable Dis, Ctr Enter Dis, Johannesburg, South Africa

[11] Univ Witwatersrand, Fac Hlth Sci, Johannesburg, South Africa

[12] Natl Inst Hyg Rafael Rangel, Dept Bacteriol, Ciudad Univ, Los Chaguaramos, Venezuela

[13] Inst Publ Hlth Chile, Mol Genet Lab, Santiago, Chile

[14] Natl Hlth Lab Guatemala, Dept Foodborne Dis, Lab Nacl Salud, Barcenas, Guatemala

[15] Minist Salud Publ, Dept Lab Salud Publ, Bacteriol Lab, Montevideo, Uruguay

[16] Lab Cent Salud Publ, Dept Bacteriol, Asuncion, Paraguay

[17] Inst Nacl Salud, Grp Microbiol, Bogota, Colombia

[18] WHO, Pan Amer Hlth Org, Dept Hlth Emergencies, Washington, DC USA

[19] London Sch Hyg & Trop Med, London, England

来源：

CLINICAL MICROBIOLOGY AND INFECTION | 2017年 / 23卷 / 11期

基金：

英国生物技术与生命科学研究理事会; 英国惠康基金;

关键词：

Shigellosis; Antimicrobial resistance; Diarrhoeal disease; Epidemiology; South America; Central America; Genomics; PREDICTS ANTIMICROBIAL RESISTANCE; COMMUNITY; CHILDREN; DIARRHEA; DISSEMINATION; TRANSMISSION; COUNTRIES;

D O I：

10.1016/j.cmi.2017.03.021

中图分类号：

R51 [传染病];

学科分类号：

100401 ;

摘要：

Objectives: 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. Crown Copyright (C) 2017 Published by Elsevier on behalf of European Society of Clinical Microbiology and Infectious Diseases.

引用

页码：845 / 853

页数：9

共 32 条

[1] Immunomagnetic separation and PCR detection show shigellae to be common faecal agents in children from urban marginal communities of Costa Rica [J].

Achi, R ;

Mata, L ;

Siles, X ;

Lindberg, AA .

JOURNAL OF INFECTION, 1996, 32 (03) :211-218

[2] Microreact: visualizing and sharing data for genomic epidemiology and phylogeography [J].

Argimon, Silvia ;

Abudahab, Khalil ;

Goater, Richard J. E. ;

Fedosejev, Artemij ;

Bhai, Jyothish ;

Glasner, Corinna ;

Feil, Edward J. ;

Holden, Matthew T. G. ;

Yeats, Corin A. ;

Grundmann, Hajo ;

Spratt, Brian G. ;

Aanensen, David M. .

MICROBIAL GENOMICS, 2016, 2 (11) :e000093

[3] Fluoroquinolone Resistance Mechanisms of Shigella flexneri Isolated in Bangladesh [J].

Azmi, Ishrat J. ;

Khajanchi, Bijay K. ;

Akter, Fatema ;

Hasan, Trisheeta N. ;

Shahnaij, Mohammad ;

Akter, Mahmuda ;

Banik, Atanu ;

Sultana, Halima ;

Hossain, Mohammad A. ;

Ahmed, Mohammad K. ;

Faruque, Shah M. ;

Talukder, Kaisar A. .

PLOS ONE, 2014, 9 (07)

[4]

Baker KS, 2016, EMERG INFECT DIS, V22, P1545, DOI [10.3201/eid2209.1511953, 10.3201/eid2209.151953]

[5] Intercontinental dissemination of azithromycin-resistant shigellosis through sexual transmission: a cross-sectional study [J].

Baker, Kate S. ;

Dallman, Timothy J. ;

Ashton, Philip M. ;

Day, Martin ;

Hughes, Gwenda ;

Crook, Paul D. ;

Gilbart, Victoria L. ;

Zittermann, Sandra ;

Allen, Vanessa G. ;

Howden, Benjamin P. ;

Tomita, Takehiro ;

Valcanis, Mary ;

Harris, Simon R. ;

Connor, Thomas R. ;

Sintchenko, Vitali ;

Howard, Peter ;

Brown, Jeremy D. ;

Petty, Nicola K. ;

Gouali, Malika ;

Duy Pham Thanh ;

Keddy, Karen H. ;

Smith, Anthony M. ;

Talukder, Kaisar A. ;

Faruque, Shah M. ;

Parkhill, Julian ;

Baker, Stephen ;

Weill, Francois-Xavier ;

Jenkins, Claire ;

Thomson, Nicholas R. .

LANCET INFECTIOUS DISEASES, 2015, 15 (08) :913-921

[6] Shigella in Brazilian children with acute diarrhoea: prevalence, antimicrobial resistance and virulence genes [J].

Bernardes Sousa, Mireille Angela ;

Mendes, Edilberto Nogueira ;

Collares, Guilherme Birchal ;

Peret-Filho, Luciano Amedee ;

Penna, Francisco Jose ;

Magalhaes, Paula Prazeres .

MEMORIAS DO INSTITUTO OSWALDO CRUZ, 2013, 108 (01) :30-35

[7] Building PulseNet Latin America and Caribbean Salmonella regional database: First conclusions of genetic subtypes of S. Typhi, S. Typhimurium and S. Enteritidis circulating in six countries of the region [J].

Campos, J. ;

Pichel, M. ;

Vaz, T. M. I. ;

Tavechio, A. T. ;

Fernandes, S. A. ;

Munoz, N. ;

Rodriguez, C. ;

Realpe, M. E. ;

Moreno, J. ;

Araya, P. ;

Fernandez, J. ;

Fernandez, A. ;

Campos, E. ;

Duarte, F. ;

Weiler Gustafson, N. ;

Binsztein, N. ;

Gutierrez, E. Perez .

FOOD RESEARCH INTERNATIONAL, 2012, 45 (02) :1030-1036

[8] Species-wide whole genome sequencing reveals historical global spread and recent local persistence in Shigella flexneri [J].

Connor, Thomas R. ;

Barker, Clare R. ;

Baker, Kate S. ;

Weill, Francois-Xavier ;

Talukder, Kaisar Ali ;

Smith, Anthony M. ;

Stephen Baker ;

Gouali, Malika ;

Duy Pham Thanh ;

Azmi, Ishrat Jahan ;

da Silveira, Wanderley Dias ;

Semmler, Torsten ;

Wieler, Lothar H. ;

Jenkins, Claire ;

Cravioto, Alejandro ;

Faruque, Shah M. ;

Parkhill, Julian ;

Kim, Dong Wook ;

Keddy, Karen H. ;

Thomson, Nicholas R. .

ELIFE, 2015, 4

[9] Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins [J].

Croucher, Nicholas J. ;

Page, Andrew J. ;

Connor, Thomas R. ;

Delaney, Aidan J. ;

Keane, Jacqueline A. ;

Bentley, Stephen D. ;

Parkhill, Julian ;

Harris, Simon R. .

NUCLEIC ACIDS RESEARCH, 2015, 43 (03) :e15

[10] Use of whole-genome sequencing for the public health surveillance of Shigella sonnei in England and Wales, 2015 [J].

Dallman, Timothy J. ;

Chattaway, Marie A. ;

Mook, Piers ;

Godbole, Gauri ;

Crook, Paul D. ;

Jenkins, Claire .

JOURNAL OF MEDICAL MICROBIOLOGY, 2016, 65 :882-884

← 1 2 3 4 →