Colistin resistance in Gram-negative bacteria analysed by five phenotypic assays and inference of the underlying genomic mechanisms

Abstract Background Colistin is used against multi-drug resistant pathogens, yet resistance emerges through dissemination of plasmid-mediated genes (mcr) or chromosomal mutation of genes involved in lipopolysaccharide synthesis (i.e. mgrB, phoPQ, pmrCAB). Phenotypic susceptibility testing is challen...

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Autores principales:	Diana Albertos Torres, Helena M. B. Seth-Smith, Nicole Joosse, Claudia Lang, Olivier Dubuis, Magdalena Nüesch-Inderbinen, Vladimira Hinic, Adrian Egli
Formato:	article
Lenguaje:	EN
Publicado:	BMC 2021
Materias:	Colistin Resistance Antimicrobial susceptibility testing WGS Antimicrobial resistance genes Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/9304e7b785764422a07c56150e8fdb31
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spelling	oai:doaj.org-article:9304e7b785764422a07c56150e8fdb312021-11-21T12:05:34ZColistin resistance in Gram-negative bacteria analysed by five phenotypic assays and inference of the underlying genomic mechanisms10.1186/s12866-021-02388-81471-2180https://doaj.org/article/9304e7b785764422a07c56150e8fdb312021-11-01T00:00:00Zhttps://doi.org/10.1186/s12866-021-02388-8https://doaj.org/toc/1471-2180Abstract Background Colistin is used against multi-drug resistant pathogens, yet resistance emerges through dissemination of plasmid-mediated genes (mcr) or chromosomal mutation of genes involved in lipopolysaccharide synthesis (i.e. mgrB, phoPQ, pmrCAB). Phenotypic susceptibility testing is challenging due to poor diffusion of colistin in agar media, leading to an underestimation of resistance. Performance of five phenotypic approaches was compared in the context of different molecular mechanisms of resistance. We evaluated Vitek 2® (bioMérieux, AST N242), Colistin MIC Test Strip (Liofilchem Diagnostici), UMIC (Biocentric), and Rapid Polymyxin™ NP test (ELITechGroup) against the standard broth microdilution (BMD) method. We used whole genome sequencing (WGS) to infer molecular resistance mechanisms. We analysed 97 Enterobacterales and non-fermenting bacterial isolates, largely clinical isolates collected up to 2018. Data was analysed by comparing susceptibility categories (susceptible or resistant) and minimal inhibitory concentrations (MIC). Susceptibility category concordance is the percentage of test results sharing the same category to BMD. MIC concordance was calculated similarly but considering ±1 MIC titre error range. We determined genomic diversity by core genome multi locus sequencing typing (cgMLST) and identified putative antimicrobial resistance genes using NCBI and CARD databases, and manual annotation. Results Of 97 isolates, 54 (56%) were resistant with standard BMD. Highest susceptibility category concordance was achieved by Rapid Polymyxin™ NP (98.8%) followed by UMIC (97.9%), Colistin E-test MIC strip (96.9%) and Vitek 2® (95.6%). Highest MIC concordance was achieved by UMIC (80.4%), followed by Vitek 2® (72.5%) and Colistin E-test MIC strip (62.9%). Among resistant isolates, 23/54 (43%) were intrinsically resistant to colistin, whereas 31/54 (57%) isolates had acquired colistin resistance. Of these, mcr-1 was detected in four isolates and mcr-2 in one isolate. Non-synonymous mutations in mgrB, phoQ, pmrA, pmrB, and pmrC genes were encountered in Klebsiella pneumoniae, Escherichia coli, and Acinetobacter bereziniae resistant isolates. Mutations found in mgrB and pmrB were only identified in isolates exhibiting MICs of ≥16 mg/L. Conclusions The Rapid Polymyxin™ NP test showed highest categorical concordance and the UMIC test provided MIC values with high concordance to BMD. We found colistin resistance in diverse species occurred predominantly through spontaneous chromosomal mutation rather than plasmid-mediated resistance.Diana Albertos TorresHelena M. B. Seth-SmithNicole JoosseClaudia LangOlivier DubuisMagdalena Nüesch-InderbinenVladimira HinicAdrian EgliBMCarticleColistinResistanceAntimicrobial susceptibility testingWGSAntimicrobial resistance genesMicrobiologyQR1-502ENBMC Microbiology, Vol 21, Iss 1, Pp 1-12 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Colistin Resistance Antimicrobial susceptibility testing WGS Antimicrobial resistance genes Microbiology QR1-502
spellingShingle	Colistin Resistance Antimicrobial susceptibility testing WGS Antimicrobial resistance genes Microbiology QR1-502 Diana Albertos Torres Helena M. B. Seth-Smith Nicole Joosse Claudia Lang Olivier Dubuis Magdalena Nüesch-Inderbinen Vladimira Hinic Adrian Egli Colistin resistance in Gram-negative bacteria analysed by five phenotypic assays and inference of the underlying genomic mechanisms
description	Abstract Background Colistin is used against multi-drug resistant pathogens, yet resistance emerges through dissemination of plasmid-mediated genes (mcr) or chromosomal mutation of genes involved in lipopolysaccharide synthesis (i.e. mgrB, phoPQ, pmrCAB). Phenotypic susceptibility testing is challenging due to poor diffusion of colistin in agar media, leading to an underestimation of resistance. Performance of five phenotypic approaches was compared in the context of different molecular mechanisms of resistance. We evaluated Vitek 2® (bioMérieux, AST N242), Colistin MIC Test Strip (Liofilchem Diagnostici), UMIC (Biocentric), and Rapid Polymyxin™ NP test (ELITechGroup) against the standard broth microdilution (BMD) method. We used whole genome sequencing (WGS) to infer molecular resistance mechanisms. We analysed 97 Enterobacterales and non-fermenting bacterial isolates, largely clinical isolates collected up to 2018. Data was analysed by comparing susceptibility categories (susceptible or resistant) and minimal inhibitory concentrations (MIC). Susceptibility category concordance is the percentage of test results sharing the same category to BMD. MIC concordance was calculated similarly but considering ±1 MIC titre error range. We determined genomic diversity by core genome multi locus sequencing typing (cgMLST) and identified putative antimicrobial resistance genes using NCBI and CARD databases, and manual annotation. Results Of 97 isolates, 54 (56%) were resistant with standard BMD. Highest susceptibility category concordance was achieved by Rapid Polymyxin™ NP (98.8%) followed by UMIC (97.9%), Colistin E-test MIC strip (96.9%) and Vitek 2® (95.6%). Highest MIC concordance was achieved by UMIC (80.4%), followed by Vitek 2® (72.5%) and Colistin E-test MIC strip (62.9%). Among resistant isolates, 23/54 (43%) were intrinsically resistant to colistin, whereas 31/54 (57%) isolates had acquired colistin resistance. Of these, mcr-1 was detected in four isolates and mcr-2 in one isolate. Non-synonymous mutations in mgrB, phoQ, pmrA, pmrB, and pmrC genes were encountered in Klebsiella pneumoniae, Escherichia coli, and Acinetobacter bereziniae resistant isolates. Mutations found in mgrB and pmrB were only identified in isolates exhibiting MICs of ≥16 mg/L. Conclusions The Rapid Polymyxin™ NP test showed highest categorical concordance and the UMIC test provided MIC values with high concordance to BMD. We found colistin resistance in diverse species occurred predominantly through spontaneous chromosomal mutation rather than plasmid-mediated resistance.
format	article
author	Diana Albertos Torres Helena M. B. Seth-Smith Nicole Joosse Claudia Lang Olivier Dubuis Magdalena Nüesch-Inderbinen Vladimira Hinic Adrian Egli
author_facet	Diana Albertos Torres Helena M. B. Seth-Smith Nicole Joosse Claudia Lang Olivier Dubuis Magdalena Nüesch-Inderbinen Vladimira Hinic Adrian Egli
author_sort	Diana Albertos Torres
title	Colistin resistance in Gram-negative bacteria analysed by five phenotypic assays and inference of the underlying genomic mechanisms
title_short	Colistin resistance in Gram-negative bacteria analysed by five phenotypic assays and inference of the underlying genomic mechanisms
title_full	Colistin resistance in Gram-negative bacteria analysed by five phenotypic assays and inference of the underlying genomic mechanisms
title_fullStr	Colistin resistance in Gram-negative bacteria analysed by five phenotypic assays and inference of the underlying genomic mechanisms
title_full_unstemmed	Colistin resistance in Gram-negative bacteria analysed by five phenotypic assays and inference of the underlying genomic mechanisms
title_sort	colistin resistance in gram-negative bacteria analysed by five phenotypic assays and inference of the underlying genomic mechanisms
publisher	BMC
publishDate	2021
url	https://doaj.org/article/9304e7b785764422a07c56150e8fdb31
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Colistin resistance in Gram-negative bacteria analysed by five phenotypic assays and inference of the underlying genomic mechanisms

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