Abstract
Chromosomal co-existence of metal and antibiotic resistance genes in bacteria offers a new perspective to the bacterial resistance proliferation in contaminated environment. In this study, an arsenotrophic bacterium Achromobacter xylosoxidans BHW-15, isolated from Arsenic (As) contaminated tubewell water in the Bogra district of Bangladesh, was analyzed using high throughput Ion Torrent Personal Genome Machine (PGM) complete genome sequencing scheme to reveal its adaptive potentiality. The assembled draft genome of A. xylosoxidans BHW-15 was 6.3 Mbp containing 5,782 functional genes, 1,845 pseudo genes, and three incomplete phage signature regions. Comparative genome study suggested the bacterium to be a novel strain of A. xylosoxidans showing significant dissimilarity with other relevant strains in metal resistance gene islands. A total of 35 metal resistance genes along with arsenite-oxidizing aioSXBA, arsenate reducing arsRCDAB, and mercury resistance merRTPADE operonic gene cluster and 20 broad range antibiotic resistance genes including β-lactams, aminoglycosides, and multiple multidrug resistance (MDR) efflux gene complex with a tripartite system OM-IM-MFP were found co-existed within the genome. Genomic synteny analysis with reported arsenotrophic bacteria revealed the characteristic genetic organization of ars and mer operonic genes, rarely described in β-Proteobacteria. A transposon Tn21 and mobile element protein genes were also detected to the end of mer (mercury) operonic genes, possibly a carrier for the gene transposition. In vitro antibiotic susceptibility assay showed a broad range of resistance against antibiotics belonging to β-lactams, aminoglycosides, cephalosporins (1st, 2nd, and 3rd generations), monobactams and even macrolides, some of the resistome determinants were predicted during in silico analysis. KEGG functional orthology analysis revealed the potential of the bacterium to utilize multiple carbon sources including one carbon pool by folate, innate defense mechanism against multiple stress conditions, motility, a proper developed cell signaling and processing unit and secondary metabolism-combination of all exhibiting a robust feature of the cell in multiple stressed conditions. The complete genome of the strain BHW-15 stands as a genetic basis for the evolutionary adaptation of metal and the antibiotic coexistence phenomenon in an aquatic environment.
Highlights
With the passage of time, bacteria have acquired a number of mechanisms for both metal and antibiotic resistances upon evolution
Whole genome sequencing of the arsenite oxidizing isolate BHW-15 identified the bacterium as A. xylosoxidans
The assembled filtered draft genome of A. xylosoxidans BHW-15 strain was 6,301,677 bp assembled into 2,049 contigs
Summary
With the passage of time, bacteria have acquired a number of mechanisms for both metal and antibiotic resistances upon evolution. The genetic plasticity of bacteria allows them to acquire such survival strategies by mutations, alteration of gene expression or genetic material acquisition which leads to the harborage of resistance determinants within (Silver & Phung, 1996; Munita & Arias, 2016). Metals are common elements found throughout the earth’s crust naturally, and these are widely distributed in the environment (Tchounwou et al, 2012). Metals including nickel, iron, copper, and zinc are required as trace elements and are essential for some metabolic reactions. Bacterial associations with metals are quite diverse and the genomic level induction for their tolerance or transformation depends on the exposure level
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