Comparative genomic analysis and multi-drug resistance differences of Acinetobacter baumannii in Chongqing, China

The presence of genes encoding carbapenem-hydrolyzing oxacillinase and lack of carbapenem resistance in non-baumannii Acinetobacter misidentified as Acinetobacter baumannii causing bloodstream infections in a tertiary hospital over a 3-year period

OBJECTIVE

This study aims to analyze the genomic and clinical characteristics of Non-baumannii Acinetobacter strains misidentified as A. baumannii, causing bloodstream infections (BSIs) in our hospital.

MATERIALS AND METHODS

Whole genome sequencing was performed and average nucleotide identity (ANI) was analyzed. Susceptibility testing was conducted using micro-broth methods. The distribution of antimicrobial resistance genes (ARGs) and mobile genetic elements (MGEs) was examined using online software tools. The prevalence of virulence factors (VFs) was investigated through nucleotide coding sequence comparisons. Genetic structures of blaOXA genes were analyzed by Gcluster software. Clinical information was collected from electronic medical records for patient characterization.

RESULTS

ANI analysis identified five strains as Acinetobacter pittii, with the remaining four identified as A. geminorum, A. nosocomialis, A. soli and A. bereziniae. The GC content of all isolates was less than 38.9 % except for A. soli 16,294. All Non-baumannii Acinetobacter strains were relatively susceptible to antibiotics, except for one A. pittii isolate. Nine blaOXA variants were identified in seven isolates, with two isolates co-carrying 2 different types of blaOXA. Twenty-four insertion sequences (ISs) were identified, with ISAba and IS17 being the primary ISs. Five A. pittii isolates shared the same genetic structures around blaOXA. Genes related to adherence, immune modulation, and nutritional/metabolic factors were the most frequent. Few VFs were detected in A. soli 16,294 and A.bereziniae 14,325.

CONCLUSIONS

The presence of carbapenem hydrolyzing oxacillinase encoding genes did not confer carbapenem resistance, possibly due to the lack of ISs in the blaOXA flanking sequences. Different blaOXA variants within distinct strains shared the same genetic structures, suggesting potential for multidrug resistance development, which warrants our attention.

“Omic” Approaches to Bacteria and Antibiotic Resistance Identification

The quick and accurate identification of microorganisms and the study of resistance to antibiotics is crucial in the economic and industrial fields along with medicine. One of the fastest-growing identification methods is the spectrometric approach consisting in the matrix-assisted laser ionization/desorption using a time-of-flight analyzer (MALDI-TOF MS), which has many advantages over conventional methods for the determination of microorganisms presented. Thanks to the use of a multiomic approach in the MALDI-TOF MS analysis, it is possible to obtain a broad spectrum of data allowing the identification of microorganisms, understanding their interactions and the analysis of antibiotic resistance mechanisms. In addition, the literature data indicate the possibility of a significant reduction in the time of the sample preparation and analysis time, which will enable a faster initiation of the treatment of patients. However, it is still necessary to improve the process of identifying and supplementing the existing databases along with creating new ones. This review summarizes the use of “-omics” approaches in the MALDI TOF MS analysis, including in bacterial identification and antibiotic resistance mechanisms analysis.

Ciprofloxacin induced antibiotic resistance in Salmonella Typhimurium mutants and genome analysis

Antibiotic resistance of Salmonella species is well reported. Ciprofloxacin is the frontline antibiotic for salmonellosis. The repeated exposure to ciprofloxacin leads to resistant strains. After 20 cycles of antibiotic exposure, resistant bacterial clones were evaluated. The colony size of the mutants was small and had an extended lag phase compared to parent strain. The whole genome sequencing showed 40,513 mutations across the genome. Small percentage (5.2%) of mutations was non-synonymous. Four-fold more transitions were observed than transversions. Ratio of < 1 transition vs transversion showed a positive selection for antibiotic resistant trait. Mutation distribution across the genome was uniform. The native plasmid was an exception and 2 mutations were observed on 90 kb plasmid. The important genes like dnaE, gyrA, iroC, metH and rpoB involved in antibiotic resistance had point mutations. The genome analysis revealed most of the metabolic pathways were affected.