Genetic relatedness in carbapenem-resistant isolates from clinical specimens in Ghana using ERIC-PCR technique.

Francis S Codjoe,Keith Miller,Thomas J Smith,Charles A Brown,Eric S Donkor,Adriano Gianmaria Duse

doi:10.1371/journal.pone.0222168

Abstract

AimEnterobacterial repetitive intergenic consensus (ERIC) sequence analysis is a powerful tool for epidemiological analysis of bacterial species. This study aimed to determine the genetic relatedness or variability in carbapenem-resistant isolates by species using this technique.MethodsA total of 111 non-duplicated carbapenem-resistant (CR) Gram-negative bacilli isolates from a three-year collection period (2012–2014) were investigated by enterobacterial repetitive intergenic consensus-polymerase chain reaction (ERIC–PCR) in four selected hospital laboratories in Ghana. The isolates were also screened for carbapenemase and extended spectrum β-lactamase genes by PCR.ResultsA proportion of 23.4% (26/111) of the genomic DNA extracts were carriers of PCR-positive carbapenemase genes, including 14.4% blaNDM-1, 7.2% blaVIM-1 and 1.8% blaOXA-48. The highest prevalence of carbapenemase genes was from non-fermenters, Acinetobacter baumannii and Pseudomonas aeruginosa. For the ESBL genes tested, 96.4% (107/111) of the CR isolates co-harboured both TEM-1 and SHV-1 genes. The ERIC-PCR gel analysis exhibited 1 to 8 bands ranging from 50 to 800 bp. Band patterns of 93 complex dissimilarities were visually distinguished from the 111 CR isolates studied, while the remaining 18 showed band similarities in pairs.ConclusionOverall, ERIC-PCR fingerprints have shown a high level of diversity among the species of Gram-negative bacterial pathogens and specimen collection sites in this study. ERIC-PCR optimisation assays may serve as a suitable genotyping tool for the assessment of genetic diversity or close relatedness of isolates that are found in clinical settings.

Highlights

enterobacterial repetitive intergenic consensus (ERIC)-PCR fingerprints have shown a high level of diversity among the species of Gram-negative bacterial pathogens and specimen collection sites in this study
The enterobacterial repetitive intergenic consensus (ERIC) technique is a molecular method used for the epidemiological analysis and genotyping of bacterial species
The application of ERIC-PCR has been used to investigate opportunistic pathogens, including Pseudomonas aeruginosa and Acinetobacter baumannii, that are capable of causing outbreaks in hospitals worldwide [11,12,13,14,15,16]

Summary

Introduction

The enterobacterial repetitive intergenic consensus (ERIC) technique is a molecular method used for the epidemiological analysis and genotyping of bacterial species. Enterobacterial repetitive intergenic consensus-polymerase chain reaction (ERIC-PCR) can be used to study human pathogens, in both Gram-positive and -negative bacterial isolates in order to determine their genetic diversity, and occasionally extended to bacterial pathogens in the animal kingdom. For most Gram-negative bacterial strains, diversity/similarity among pathogens have traditionally been determined using antimicrobial resistance patterns, basic microbiological methods or genotyping methods such as by gene expression using microarray technology, multilocus sequence typing (MLST), pulsed field gel electrophoresis (PFGE) and ERIC. This study aimed to broadly determine the genetic relatedness or variability in both carbapenemase PCR-positive isolates and CR isolates without a genetically identified locus (carbapenemase PCR negative), and separately assess clonal similarities for all the PCR-positive species using fingerprint patterns generated by ERIC-PCR amplifications

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Conclusion