Pangenome of Acinetobacter baumannii uncovers two groups of genomes, one of them with genes involved in CRISPR/Cas defence systems associated with the absence of plasmids and exclusive genes for biofilm formation

Abstract

Acinetobacter baumannii is an opportunistic bacterium that causes hospital-acquired infections with a high mortality and morbidity, since there are strains resistant to virtually any kind of antibiotic. The chase to find novel strategies to fight against this microbe can be favoured by knowledge of the complete catalogue of genes of the species, and their relationship with the specific characteristics of different isolates. In this work, we performed a genomics analysis of almost 2500 strains. Two different groups of genomes were found based on the number of shared genes. One of these groups rarely has plasmids, and bears clustered regularly interspaced short palindromic repeat (CRISPR) sequences, in addition to CRISPR-associated genes (cas genes) or restriction-modification system genes. This fact strongly supports the lack of plasmids. Furthermore, the scarce plasmids in this group also bear CRISPR sequences, and specifically contain genes involved in prokaryotic toxin–antitoxin systems that could either act as the still little known CRISPR type IV system or be the precursors of other novel CRISPR/Cas systems. In addition, a limited set of strains present a new cas9-like gene, which may complement the other cas genes in inhibiting the entrance of new plasmids into the bacteria. Finally, this group has exclusive genes involved in biofilm formation, which would connect CRISPR systems to the biogenesis of these bacterial resistance structures.

Molecular Epidemiology of Acinetobacter calcoaceticus-Acinetobacter baumannii Complex Isolated From Children at the Hospital Infantil de México Federico Gómez

“…Amazingly, we found that the strains that amplify the CRISPR-Cas I-Fb system presented from 1 to 4 plasmids. According to Mangas et al (2019), there is an association between the presence of the CRISPR-Cas system and the absence of plasmids in A. baumannii genomes; as we could see in our results; these systems would limit the transfer of mobile elements such as plasmids.…”

A Diverse Panel of Clinical Acinetobacter baumannii for Research and Development

“…Previous studies have emphasized the high genomic plasticity of A. baumannii and the role it plays in hospital adaptation and pathogenicity (9,11,12,47). This work, and more recent studies analyzing the diversity of thousands of genomes, estimate that the core genome of A. baumannii is comprised of ϳ2,200 genes, while its pangenome is projected to be in the region of 19,000 distinct genes (48). The fact that comparable numbers are observed with just the 100 isolates in this panel is a testament to the diversity of the MRSN repository.…”

Antibiotic Resistance Profiles, Molecular Mechanisms and Innovative Treatment Strategies of Acinetobacter baumannii

“…Unlike the strains from group two, positive for a high number of plasmids, the strains from the first group contain mainly genes involved in regulating the elements of the CRISPR system. This finding led to the idea that the CRISPR system may be involved in the restriction of the plasmid entry into bacterial cells [ 334 ]. Karlapudi et al conducted an in silico study to understand the role of the AbaI gene in biofilm formation in A. baumannii .…”