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

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.

Accurate Identification of Clinically Important Acinetobacter Spp.: An Update

“…This method involves amplification and restriction of conserved gene sequences using various restriction enzymes. Several gene sequences such as 16S rRNA, 16S–23S ITS and recA are widely used [51].…”

Acinetobacter baumannii Kan İzolatlarının MALDI-TOF MS, ARDRA ve blaOXA-51-benzeri Gene Özgül Gerçek Zamanlı Polimeraz Zincir Reaksiyonu ile Tanımlanması

“…Bununla birlikte, Shehata ve arkadaşları 25 81 klinik A.baumannii izolatını tiplendirdikleri çalışmalarında, ARDRA (kesim enzimleri: Alu I, Mbo I, Msp I) yönteminin ayırt edici gücünün düşük olduğunu belirtmişlerdir. ARDRA yöntemi, tekrarlanabilirlik ve sonuçların laboratuvarlar arası paylaşımı açısından çözülmemiş sorunları olmakla birlikte, Acinetobacter cinsi bakterilerin tür ayrımında doğru, hızlı ve kolay bir yöntem olarak birçok araştırmada kullanılmaktadır 26,27 .…”

Discrimination of hospital isolates of Acinetobacter baumannii using repeated sequences and whole genome alignment differential analysis

“…The presence of tandem DNA repeats in genomes of A. baumannii was confirmed by several groups (Martín-Lozano et al 2002;Turton et al 2009;Irfan et al 2011;Pourcel et al 2011;Minandri et al 2012;Ergin et al 2013;Ahmed and Alp 2015;Villalón et al 2015). Based on these sequences, different methods of differentiation of A. baumannii strains have been developed; however, they take into account only their diversifying power of evolutionary changes of the Acinetobacter genus (Touchon et al 2014).…”