<p>Comparative genomic analysis and multi-drug resistance differences of <em>Acinetobacter baumannii</em> in Chongqing, China</p>

Abstract

IntroductionMultidrug-resistance in Acinetobacter baumannii has emerged as a serious problem to public health. There is still a significant gap in the understanding of the multidrug-resistance and the genome diversity evolutionary process of A. baumannii in China, especially in the central and western regions.MethodsTen A. baumannii strains were collected from three hospitals in Chongqing, China. Whole-genome re-sequencing was used to obtain differences in genomic levels among strains. The diversity were determined by multi-locus sequence typing method, and investigate the genetic relationship between the ten strains and others by phylogenetic analysis. Comparative analysis focused on resistance genes related to insertions and deletions (InDels) and single-nucleotide polymorphisms (SNPs) was performed.ResultsThe overall G+C% content was 39.05%~39.43%, the average sequencing depth was 273.95~428.99, and the alignment ratio of the sequencing data was 92.93%~99.27%. A total of 42 InDels and 11,387 SNPs were detected in the coding sequence region of the isolates. Phylogenetic tree shows that the 10 A. baumannii isolates were divided into four relative groups, and there exist the possibility of cross-regional spread pattern. A total number of 19 drug resistance genes had been found in each strain, and efflux pump-related genes accounted for the most. Only AacA4 underwent a change in InDel. Six types of drug resistance genes were found in the SNPs resistance gene-related loci, among which gene ANT(3’’)-II and QacE mutations were found in each strain.ConclusionIn this study, the main mechanism of A. baumannii multi-drug resistance is due to the multi-drug efflux pump related genes. The point mutations at the SNPs sites of the six types of resistance genes are the main differences in A. baumannii between Chongqing and the eastern coastal areas of China.

The adeH and adeS Efflux Pump Genes in Imipenem and Colistin-Resistant Acinetobacter baumannii Clinical Isolates

“…In China, an evaluation of the relationship between adeDE, adeM, and adeABCefflux pumps among A. baumannii strains showed that 80% of the imipenemresistant strains carried the adeB, adeR, adeS, and adeJ genes, indicating that efflux pumps were associated with antibiotic resistance, consistent with the results of the present study [32].…”

“Omic” Approaches to Bacteria and Antibiotic Resistance Identification

“…Diversity was determined by multi-locus sequence typing, and the genetic relationship between ten strains and others was examined by phylogenetic analysis. They conducted a comparative analysis focused on resistance genes related to insertions and deletions and single nucleotide polymorphisms (SNPs) to identify the primary mechanism of A. baumanii resistance [ 250 ]. Another example is the study by Suzuki et al, who performed genome re-sequencing analyses for each drug-resistant E. coli strain tested to identify fixed mutations and changes in gene expression.…”

Ciprofloxacin induced antibiotic resistance in Salmonella Typhimurium mutants and genome analysis

“…The recent advances in whole genome sequencing and comparing it with the previously sequenced genomes helps to study evolutionary, resistant, pathogenicity as well as virulent mechanism of bacterial pathogen. Advances in sequencing technologies helps to capture sequence variation for each sample under study, providing the potential to detect all changes at all positions in the genome from single nucleotide changes to largescale insertions and deletions (Bryant et al 2012;Pu et al 2019). The WGS gives most precise structural details and de nitive phylogenetic relationships thus helping researchers in understanding molecular mechanisms of antimicrobial resistance (Hendriksen et al 2019) a vital step for this is detection of resistant determinants like single nucleotide polymorphism (SNP), Insertions or Deletions (INDELS) and frame shift mutations.…”