Colistin-resistant Escherichia Coli Belonging to Different Sequence Types: Genetic Characterization of Isolates Responsible for Colonization, Community- and Healthcare-acquired Infections

Overview

Journal Rev Inst Med Trop Sao Paulo

Specialty Tropical Medicine

Date 2021 Apr 28

PMID 33909852

Citations 6

Authors

Yrving Paiva

Debora Satie Nagano

Andre Luis Franco Cotia

Thais Guimaraes

Roberta Cristina Ruedas Martins

Lauro Vieira Perdigao Neto

Marina Farrel Cortes

Ana Paula Marchi

Louise Corscadden

Anna Silva Machado

Alexandre Inacio de Paula

Lucas Augusto Moyses Franco

Patricia Regina Neves

Anna Sara Levin

Silvia Figueiredo Costa

Affiliations

Soon will be listed here.

Abstract

The plasmid-mediated colistin-resistance gene named mcr-1 has been recently described in different countries and it became a public health challenge. Of note, few studies have addressed the spread of Escherichia coli harboring the mcr-1 gene in both, community and hospital settings. A total of seven colistin-resistant E. coli carrying mcr-1, collected from 2016 to 2018, from community (n=4), healthcare-acquired infections (n=2) and colonization (n=1) were identified in three high complexity hospitals in Sao Paulo, Brazil. These colistin-resistant isolates were screened for mcr genes by PCR and all strains were submitted to Whole Genome Sequencing and the conjugation experiment. The seven strains belonged to seven distinct sequence types (ST744, ST131, ST69, ST48, ST354, ST57, ST10), and they differ regarding the resistance profiles. Transference of mcr-1 by conjugation to E. coli strain C600 was possible in five of the seven isolates. The mcr-1 gene was found in plasmid types IncX4 or IncI2. Three of the isolates have ESBL-encoding genes (blaCTX-M-2, n=2; blaCTX-M-8, n=1). We hereby report genetically distinct E. coli isolates, belonging to seven STs, harboring the mcr-1 gene, associated to community and healthcare-acquired infections, and colonization in patients from three hospitals in Sao Paulo. These findings point out for the potential spread of plasmid-mediated colistin-resistance mechanism in E. coli strains in Brazil.

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References

Hadjadj L, Riziki T, Zhu Y, Li J, Diene S, Rolain J . Study of mcr-1 Gene-Mediated Colistin Resistance in Enterobacteriaceae Isolated from Humans and Animals in Different Countries. Genes (Basel). 2017; 8(12). PMC: 5748712. DOI: 10.3390/genes8120394. View

Wu C, Wang Y, Shi X, Wang S, Ren H, Shen Z . Rapid rise of the ESBL and mcr-1 genes in Escherichia coli of chicken origin in China, 2008-2014. Emerg Microbes Infect. 2018; 7(1):30. PMC: 5849743. DOI: 10.1038/s41426-018-0033-1. View

Fernandes M, Moura Q, Sartori L, Silva K, Cunha M, Esposito F . Silent dissemination of colistin-resistant Escherichia coli in South America could contribute to the global spread of the mcr-1 gene. Euro Surveill. 2016; 21(17). DOI: 10.2807/1560-7917.ES.2016.21.17.30214. View

Corbella M, Mariani B, Ferrari C, Comandatore F, Scaltriti E, Marone P . Three cases of mcr-1-positive colistin-resistant Escherichia coli bloodstream infections in Italy, August 2016 to January 2017. Euro Surveill. 2017; 22(16). PMC: 5404483. DOI: 10.2807/1560-7917.ES.2017.22.16.30517. View

da Silva Pontes L, Pimenta R, Silveira M, Tavares-Teixeira C, Pereira N, da Conceicao Neto O . Harboring IncHI2 Plasmid Containing Gene-A Novel Reservoir for Colistin Resistance in Brazil. Microb Drug Resist. 2020; 27(5):721-725. DOI: 10.1089/mdr.2020.0041. View

Bertels F, Silander O, Pachkov M, Rainey P, van Nimwegen E . Automated reconstruction of whole-genome phylogenies from short-sequence reads. Mol Biol Evol. 2014; 31(5):1077-88. PMC: 3995342. DOI: 10.1093/molbev/msu088. View

Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M, Sturrock S . Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics. 2012; 28(12):1647-9. PMC: 3371832. DOI: 10.1093/bioinformatics/bts199. View

Dalmolin T, Martins A, Zavascki A, de Lima-Morales D, Barth A . Acquisition of the mcr-1 gene by a high-risk clone of KPC-2-producing Klebsiella pneumoniae ST437/CC258, Brazil. Diagn Microbiol Infect Dis. 2017; 90(2):132-133. DOI: 10.1016/j.diagmicrobio.2017.09.016. View

Zankari E, Hasman H, Kaas R, Seyfarth A, Agerso Y, Lund O . Genotyping using whole-genome sequencing is a realistic alternative to surveillance based on phenotypic antimicrobial susceptibility testing. J Antimicrob Chemother. 2012; 68(4):771-7. DOI: 10.1093/jac/dks496. View

10.

Baez-Ortega A, Lorenzo-Diaz F, Hernandez M, Gonzalez-Vila C, Roda-Garcia J, Colebrook M . IonGAP: integrative bacterial genome analysis for Ion Torrent sequence data. Bioinformatics. 2015; 31(17):2870-3. DOI: 10.1093/bioinformatics/btv283. View

11.

Matuschek E, Ahman J, Webster C, Kahlmeter G . Antimicrobial susceptibility testing of colistin - evaluation of seven commercial MIC products against standard broth microdilution for Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, and Acinetobacter spp. Clin Microbiol Infect. 2017; 24(8):865-870. DOI: 10.1016/j.cmi.2017.11.020. View

12.

Sallem R, Slama K, Rojo-Bezares B, Porres-Osante N, Jouini A, Klibi N . IncI1 plasmids carrying bla(CTX-M-1) or bla(CMY-2) genes in Escherichia coli from healthy humans and animals in Tunisia. Microb Drug Resist. 2014; 20(5):495-500. DOI: 10.1089/mdr.2013.0224. View

13.

Wang Y, Tian G, Zhang R, Shen Y, Tyrrell J, Huang X . Prevalence, risk factors, outcomes, and molecular epidemiology of mcr-1-positive Enterobacteriaceae in patients and healthy adults from China: an epidemiological and clinical study. Lancet Infect Dis. 2017; 17(4):390-399. DOI: 10.1016/S1473-3099(16)30527-8. View

14.

Moreno L, Gomes V, Moreira J, de Oliveira C, Peres B, Silva A . First report of mcr-1-harboring Salmonella enterica serovar Schwarzengrund isolated from poultry meat in Brazil. Diagn Microbiol Infect Dis. 2018; 93(4):376-379. DOI: 10.1016/j.diagmicrobio.2018.10.016. View

15.

Bankevich A, Nurk S, Antipov D, Gurevich A, Dvorkin M, Kulikov A . SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol. 2012; 19(5):455-77. PMC: 3342519. DOI: 10.1089/cmb.2012.0021. View

16.

Carattoli A, Zankari E, Garcia-Fernandez A, Larsen M, Lund O, Villa L . In silico detection and typing of plasmids using PlasmidFinder and plasmid multilocus sequence typing. Antimicrob Agents Chemother. 2014; 58(7):3895-903. PMC: 4068535. DOI: 10.1128/AAC.02412-14. View

17.

Rau R, de Lima-Morales D, Lamb Wink P, Ribeiro A, Barth A . Positive from Food in Brazil: Detection and Characterization. Foodborne Pathog Dis. 2019; 17(3):202-208. DOI: 10.1089/fpd.2019.2700. View

18.

Moffatt J, Harper M, Boyce J . Mechanisms of Polymyxin Resistance. Adv Exp Med Biol. 2019; 1145:55-71. DOI: 10.1007/978-3-030-16373-0_5. View

19.

Perdigao Neto L, Corscadden L, Martins R, Nagano D, Cunha M, Neves P . Simultaneous colonization by Escherichia coli and Klebsiella pneumoniae harboring mcr-1 in Brazil. Infection. 2019; 47(4):661-664. DOI: 10.1007/s15010-019-01309-2. View

20.

Grimstrup Joensen K, Scheutz F, Lund O, Hasman H, Kaas R, Nielsen E . Real-time whole-genome sequencing for routine typing, surveillance, and outbreak detection of verotoxigenic Escherichia coli. J Clin Microbiol. 2014; 52(5):1501-10. PMC: 3993690. DOI: 10.1128/JCM.03617-13. View