Genotyping methods for monitoring the epidemic evolution of A. baumannii strains.

Salman Shaheer Ahmed,Emine Alp

doi:10.3855/jidc.6201

Salman Shaheer Ahmed, Emine Alp

Open Access

https://doi.org/10.3855/jidc.6201

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Abstract

Acinetobacter baumannii is clustered with other phenotypically similar species into what has commonly become known as the ACB complex: A. calcoaceticus, A. pittii and, A. nosocomialis. The ecology and pathology of most of these species are not well understood, mainly because current specific phenotypic techniques have, to date, been insufficient. This has inhibited both the precise identification of, as well as the ability to discriminate between, these clinically important and closely related Acinetobacter strains.However, new genotypic methods have greatly enhanced our capacity to identify the ACB complex. This has resulted in the implementation of more rational infection control programs. Several genotypic identification methods are explored in this study, including non-polymerase chain reaction (PCR)-based and PCR-based methods. These methods include ribotyping, pulsed-field gel electrophoresis, 16S rRNA identification, multilocus sequence typing, single locus sequence typing, restriction fragment length polymorphism analysis, restriction analysis of 16S-23S rRNA intergenic spacer sequences, rapid amplification of polymorphic DNA, and repetitive extragenic palindromic PCR; however, there is no current single ideal genotyping method. Each one has its own advantages and disadvantages. With this in mind we reviewed current and new genotyping methods used to characterize the Acinetobacter species.

Highlights

The clinically important and closely related genus of the Acinetobacter strain, Acinetobacter baumannii, is a most troublesome pathogen, causing hospitalacquired infections worldwide [1]
This study demonstrated that internal transcribed spacer (ITS) sequences have better discriminatory power than a 16S rRNA gene
In recent years, substantial improvements in genotyping methods have changed the current approaches to identifying Acinetobacter species

Summary

Introduction

The clinically important and closely related genus of the Acinetobacter strain, Acinetobacter baumannii, is a most troublesome pathogen, causing hospitalacquired infections worldwide [1]. In another study [24], 99 well-identified strains of ACB complex were studied to assess inter- and intra-species variability using the rpoB gene for resultant comparison and 16S rRNA differential sequencing. It was found that rpoB sequencing identified ACB complex strains more accurately than did the 16S rRNA gene sequencing methodology This is a high-resolution genotypic method for sequencing microorganisms; it has been applied successfully for clinical characterization of many important nosocomial pathogens including the Acinetobacter species. MLST is a powerful tool to discriminate closely related genomic species, and it is comparable to PFGE and amplification and restriction fragment length polymorphism analysis (AFLP) [26]. Several sequences within the genome are targeted, including 16S rDNA, 16S-23S intergenic spacer sequences, 16-23S rDNA, and the recA gene [17]

Amplification and restriction fragment length polymorphism analysis

Findings

Conclusions