Genomic, morphological, and biochemical analyses of a multi-metal resistant but multi-drug susceptible strain of Bordetella petrii from hospital soil

Abstract

Contamination of soil by antibiotics and heavy metals originating from hospital facilities has emerged as a major cause for the development of resistant microbes. We collected soil samples surrounding a hospital effluent and measured the resistance of bacterial isolates against multiple antibiotics and heavy metals. One strain BMCSI 3 was found to be sensitive to all tested antibiotics. However, it was resistant to many heavy metals and metalloids like cadmium, chromium, copper, mercury, arsenic, and others. This strain was motile and potentially spore-forming. Whole-genome shotgun assembly of BMCSI 3 produced 4.95 Mb genome with 4,638 protein-coding genes. The taxonomic and phylogenetic analysis revealed it, to be a Bordetella petrii strain. Multiple genomic islands carrying mobile genetic elements; coding for heavy metal resistant genes, response regulators or transcription factors, transporters, and multi-drug efflux pumps were identified from the genome. A comparative genomic analysis of BMCSI 3 with annotated genomes of other free-living B. petrii revealed the presence of multiple transposable elements and several genes involved in stress response and metabolism. This study provides insights into how genomic reorganization and plasticity results in evolution of heavy metals resistance by acquiring genes from its natural environment.

Figure 1

Multi-drug and multi-metal tolerance capacity of BMCSI 3. Antibiotic sensitivity against different antimicrobial agents (IZ inhibition zone; R resistance) (a); metal tolerance capacity against different heavy metals (b,c).

Figure 2

TYGS result for the BMCSI 3 genome (a). Circular representation of BMCSI 3 genome features as per the CG viewer server (b).

Figure 3

Transmission Electron micrographs showing mature vegetative cells with peritrichous flagellation (a); different stages of cell division (b,c); and free endospores (d) of BMCSI 3.

Figure 4

Genomic Islands (GIs) of BMCSI 3 genome (a); presence of mobile genetic elements (b) and metal resistant genes (c) were marked on the GIs (Developed from Supp. file S2).

Figure 5

Genome information of the genus Bordetella. Host specification (a); disease causing abilities (b); specialty genes (c) (developed from Supp. file S3), and ANI heat map cluster of all representative species including strains of B. petrii (d).

Figure 6

Blast analysis and circular genome comparison of the species of Bordetella.

Figure 7

Pangenome analysis strains representing strain-specific genome size (a), accessory genome size (b), core genome size (c), and functional annotation of Bordetella petrii.