Draft genome sequence of a multidrug-resistant novel candidate Pseudomonas sp. NCCP-436 isolated from faeces of a bovine host in Pakistan.

OBJECTIVES

Here we describe the first draft genome analysis of a CRISPR-carrying, multidrug-resistant, candidate novel Pseudomonas sp. NCCP-436 isolated from faeces of a neonatal diarrhoeic calf.

METHODS

The genome of strain NCCP-436 was sequenced using an Illumina NovaSeq PE150 platform and analysed using various bioinformatic tools. The virulence factors and resistome were identified using PATRIC and CARD servers, while CGView Server was used to construct a circular genome map. Antimicrobial susceptibility was determined by the disk diffusion technique.

RESULTS

The draft genome of strain NCCP-436 contains 43 contigs with a total genome size of 3,683,517 bp (61.4% GC content). There are 3,452 predicted genes, including 60 tRNAs, 7 rRNAs and 12 sRNAs. CRISPR analysis revealed two CRISPR arrays with lengths of 1103 bp and 867 bp. Strain NCCP-436 was highly resistant to fluoroquinolone, β-lactam, cephalosporin, aminoglycoside, penicillin, rifamycin, macrolide, glycopeptide, trimethoprim/sulfonamide and tetracycline antibiotic classes. Additionally, 22 antibiotic resistance genes, 313 virulence genes and 253 pathogen-host interactor genes were predicted. Comparison of the average nucleotide identity and digital DNA-DNA hybridisation values with the closely-related strain Pseudomonas khazarica (TBZ2) was found to be 82.08% and 34.90%, respectively, illustrating strain NCCP-436 as a potentially new species of Pseudomonas.

CONCLUSION

Substantial number of antibiotic resistance and virulence genes and homology with human pathogens were predicted, exposing the pathogenic and zoonotic potential of strain NCCP-436 to public health. These findings may be used to better understand the genomic epidemiological features and drug resistance mechanisms of pathogenic Pseudomonas spp. in Pakistan.