Emergence and spread of carbapenem-resistant Acinetobacter baumannii international clones II and III in Lima, Peru

Abstract

Carbapenem-resistant Acinetobacter baumannii is the top-ranked pathogen in the World Health Organization priority list of antibiotic-resistant bacteria. It emerged as a global pathogen due to the successful expansion of a few epidemic lineages, or international clones (ICs), producing acquired class D carbapenemases (OXA-type). During the past decade, however, reports regarding IC-I isolates in Latin America are scarce and are non-existent for IC-II and IC-III isolates. This study evaluates the molecular mechanisms of carbapenem resistance and the epidemiology of 80 non-duplicate clinical samples of A. baumannii collected from February 2014 through April 2016 at two tertiary care hospitals in Lima. Almost all isolates were carbapenem-resistant (97.5%), and susceptibility only remained high for colistin (95%). Pulsed-field gel electrophoresis showed two main clusters spread between both hospitals: cluster D containing 51 isolates (63.8%) associated with sequence type 2 (ST2) and carrying OXA-72, and cluster F containing 13 isolates (16.3%) associated with ST79 and also carrying OXA-72. ST2 and ST79 were endemic in at least one of the hospitals. ST1 and ST3 OXA-23-producing isolates were also identified. They accounted for sporadic hospital isolates. Interestingly, two isolates carried the novel OXA-253 variant of OXA-143 together with an upstream novel insertion sequence (ISAba47). While the predominant A. baumannii lineages in Latin America are linked to ST79, ST25, ST15, and ST1 producing OXA-23 enzymes, we report the emergence of highly resistant ST2 (IC-II) isolates in Peru producing OXA-72 and the first identification of ST3 isolates (IC-III) in Latin America, both considered a serious threat to public health worldwide.

These authors contributed equally: Saúl Levy-Blitchtein, Ignasi Roca.

These authors contributed equally: Saúl Levy-Blitchtein, Ignasi Roca.

Acknowledgements

This study was supported by Cienciactiva of CONCYTEC, contract no. 164-2016-FONDECYT; Planes Nacionales de I+D+i 2008-2011/2013-2016, Instituto de Salud Carlos III, Subdirección General de Redes y Centros de Investigación Cooperativa, Ministerio de Economía y Competitividad, Spanish Network for Research in Infectious Diseases (REIPI RD12/0015/0013 and REIPI RD16/0016/0010); the 2017 call for Strategic Action on Health (PI17/01932), co-financed by European Development Regional Fund “A way to achieve Europe” and operative program Intelligent Growth 2014-2020; and grant 2014 SGR 0653 from the Departament d’Universitats, Recerca i Societat de la Informació, of the Generalitat de Catalunya. I.R. was supported by the Department of Health, Generalitat de Catalunya, grant SLT002/16/00349. Part of these data have been presented as a poster communication at the 18th International Congress on Infectious Diseases, 3–4 March, 2018, Buenos Aires, Argentina, and at the XXVIII-European Congress of Clinical Microbiology and Infectious Diseases (ECCMID), Madrid (Spain), 21–24 April, 2018.

Authors’ contributions

Collected the samples: S.L.-B., S.P.-R., W.V.-T., J.V.-P. Conceived and designed the experiments: I.R., L.M., J.d.V.-M., J.V. Performed the experiments: S.L.-B., I.R., S.P.-R., L.M., J.M.-M., M.J.P. Analyzed the data: S.L.-B., I.R., S.P.-R., W.V.-T., J.V.-P., J.M.-M., M.J.P., J.d.V.-M., J.V. Wrote the paper: S.L.-B., I.R., J.d.V.-M., J.V. All authors critically revised the manuscript for intellectual content. All authors read and approved the final manuscript.

Conflict of interest

The funders had no role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript. The authors declare that they have no conflict of interest.

Ethics approval

This study was performed on clinical laboratory isolates. The authors had no contact or interaction with the patients. Personal information of the patients was not collected, to guarantee anonymity and confidentiality. Ethics approval was obtained from the Committee of the Instituto de Investigación Nutricional (IIN), Lima, Peru.