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Partial genomic characterization of Chromobacterium piscinae from India reveals multi drug resistance

  • Environmental Microbiology - Research Paper
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Abstract

Species of genus Chromobacterium have been isolated from diverse geographical settings, which exhibits significant metabolic flexibility as well as biotechnological and pathogenic properties. This study describes the isolation, characterization, draft assembly, and detailed sequence analysis of Chromobacterium piscinae strain W1B-CG-NIBSM isolated from water samples from multi use community pond. The organism was characterized by biochemical tests, Matrix Assisted Laser Desorption/Ionization Time of Flight Mass Spectrometry (MALDI TOF–MS) and partial genome sequencing. The partial genomic data of Chromobacterium pisciane isolate W1B NIBSM strain was submitted to GenBank with Bio project number PRJNA803347 and accession no CP092474. An integrated genome analysis of Chromobacterium piscinae has been accomplished with PATRIC which indicates good quality genome. DNA sequencing using the illumina HiSeq 4000 system generated total length of 4,155,481 bp with 63 contig with G + C content is 62.69%. This partial genome contains 4,126 protein-coding sequences (CDS), 27 repeats region and 78 transfer RNA (tRNA) genes as well as 3 ribosomal RNA (rRNA) genes. The genomic annotation of Chromobacterium W1B depicts 2,925 proteins with functional assignments and 1201 hypothetical proteins. A repertoire of specialty genes implicated in antibiotic resistance (45 genes), drug target (6 genes), Transporter (3 genes) and virulence factor (10 genes). The genomic analysis reveals the adaptability, displays metabolic varied pathways and shows specific structural complex and various virulence factors which makes this strain multi drug resistant. The isolate was found to be highly resistant to β-lactam antibiotics whereas it showed sensitivity towards aminoglycosides and fluoroquinolone antibiotics. Hence, the recovery of Chromobacterium piscinae from community pond evidenced for uncertain hidden source of public health hazard. To the best of authors knowledge this is first report of isolation and genomic description of C. piscinae from India.

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Data availability

The bacterial partial genome sequence for Chromobacterium spp. has been deposited under the bio project number PRJNA803347 and BioSample number SAMN25648687 and SRA accession number PRJNA803347 and in NCBI/DDBJ/EMBL GenBank under accession number CP092474.

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Acknowledgements

The authors gratefully acknowledge the Director and Joint Director (Research) of ICAR-NIBSM, Raipur, for providing the all-necessary facilities to carry out this work. This research article is contribution number ICAR-NIBSM-PME/RP-41/2022-5 from ICAR-NIBSM, Raipur, India.

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  1. Binod Kumar Choudhary, Mamta Choudhary and Asheesh Shanker contributed equally to be the first author.

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  1. Indian Council of Agricultural Research-National Institute of Biotic Stress Management, Baronda, Raipur, 493 225, Chhattisgarh, India

    Binod Kumar Choudhary & Mamta Choudhary

  2. ICAR-National Research Centre On Meat, Hyderabad, 500092, India

    Sukhadeo B. Barbuddhe

  3. Department of Bioinformatics, Central University of South Bihar, Gaya, Bihar, 824236, India

    Asheesh Shanker

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Conceptualization, BKC, MC, SBB; methodology, BKC, MC, SBB, AS; formal analysis and data curation AS, BKC, MC and SBB; writing original draft preparation BKC, MC, SBB and AS; writing, review and editing, BKC, MC, SBB and AS. All authors have read and approved the manuscript.

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Correspondence to Binod Kumar Choudhary.

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Choudhary, B.K., Choudhary, M., Barbuddhe, S.B. et al. Partial genomic characterization of Chromobacterium piscinae from India reveals multi drug resistance. Braz J Microbiol (2024). https://doi.org/10.1007/s42770-024-01288-z

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