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

Journal of Global Antimicrobial Resistance

Iftikhar Ahmed¹  Saira Abbas²  Muhammad Arshad³  Hamza Tariq⁴  Ahmad Ali⁴  Shuai Li⁵  Lei Dong⁵  Wen-Jun Li⁵  Li Li⁶ 

[1] State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, PR China;Department of Zoology, University of Science and Technology, Bannu, Pakistan;Institute of Environmental Sciences and Engineering, School of Civil and Environmental Engineering, National University of Science and Technology (NUST), Islamabad, Pakistan;National Culture Collection of Pakistan (NCCP), Bio-resources Conservation Institute (BCI), National Agricultural Research Centre (NARC), Park Road, Islamabad, Pakistan;State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, PR China;State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, PR China;

关键词: Pseudomonas;    Multidrug-resistant;    Virulence genes;    Zoonosis;    One Health;    Whole-genome sequencing;   

DOI  :  

来源: DOAJ

【 摘 要 】

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

【 授权许可】

Unknown