Whole-genome sequence of a putative pathogenic Bacillus sp. strain SD-4 isolated from cattle feed

Sajid Iqbal; Muhammad Faraz Bhatti; Aneela Javed; Kashif Rahim; Rehan Zafar Paracha; Hussnain Ahmed Janjua

doi:10.1016/j.jgar.2022.04.002

Whole-genome sequence of a putative pathogenic Bacillus sp. strain SD-4 isolated from cattle feed

J Glob Antimicrob Resist. 2022 Jun:29:293-295. doi: 10.1016/j.jgar.2022.04.002. Epub 2022 Apr 9.

Authors

Sajid Iqbal¹, Muhammad Faraz Bhatti², Aneela Javed³, Kashif Rahim⁴, Rehan Zafar Paracha⁵, Hussnain Ahmed Janjua⁶

Affiliations

¹ Department of Industrial Biotechnology, Atta-ur-Raman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad, Pakistan.
² Department of Plant Biotechnology, Atta-ur-Raman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad, Pakistan.
³ Department of Healthcare Biotechnology, Atta-ur-Raman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad, Pakistan.
⁴ Department of Microbiology, Cholistan University of Veterinary and Animal Sciences (CUVAS), Bahawalpur, Pakistan.
⁵ Research Centre for Modelling and Simulation (RCMS), National University of Sciences and Technology (NUST), Islamabad, Pakistan.
⁶ Department of Industrial Biotechnology, Atta-ur-Raman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad, Pakistan. Electronic address: hussnain.janjua@asab.nust.edu.pk.

PMID: 35413450
DOI: 10.1016/j.jgar.2022.04.002

Abstract

Objectives: The present study describes the draft genome sequence of a novel Bacillus sp. strain SD-4 isolated from animal feed. The study aims to get a deeper insight into antimicrobial resistance and secondary metabolite biosynthetic gene clusters (BGCs) and the association between them.

Methods: The strain SD-4 was preliminarily evaluated for antibacterial activities, motility, biofilm formation, and enterotoxin production using in vitro assays. The genome of strain SD-4 was sequenced using the Illumina HiSeq 2500 platform with paired-end reads. The reads were assembled and annotated using SPAdes and PGAP, respectively. The genome was further analysed using several bioinformatics tools, including TYGS, AntiSMASH, RAST, PlasmidFinder, VFDB, VirulenceFinder, CARD, PathogenFinder, MobileElement finder, IslandViewer, and CRISPRFinder.

Results: In vitro assays showed that the strain is motile, synthesises biofilm, and produces an enterotoxin and antibacterial metabolites. The genome analysis revealed that the strain SD-4 carries antimicrobial resistance genes (ARGs), virulence factors, and beneficial secondary metabolite BGCs. Further genome analysis showed interesting genome architectures containing several mobile genetic elements, including two plasmid replicons (repUS22 and rep20), five prophages, and at least four genomic islands (GIs), including one Listeria pathogenicity island LIPI-1. Moreover, the strain SD-4 is identified as a putative human pathogen.

Conclusion: The genome of strain SD-4 harbours several BGCs coding for biologically active metabolites. It also contains antimicrobial resistance genes and is identified as a potential human pathogen. These results can be used to better comprehend antibiotic resistance in environmental bacteria that are not influenced by human intervention.

Keywords: Antimicrobial resistance genes; Bacillus sp; Mobile genetic elements; SD-4; Secondary metabolites biosynthetic gene clusters; Virulence genes.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Animal Feed
Animals
Anti-Bacterial Agents / pharmacology
Bacillus* / genetics
Cattle
Enterotoxins
Genome, Bacterial

Substances

Anti-Bacterial Agents
Enterotoxins