Abstract
Antibiotic resistant bacteria (ARBs) carrying resistance genes (ARGs) have increasingly been detected in activated sludge. Bacillus subtilis, a gram-positive and spore-produced bacterium, is commonly found as one of the dominant bacterial group in activated sludge of wastewater treatment plants. These Bacillus strains are always categorized with various antimicrobial resistance phenotypes and mechanisms, and thought as one of the important carriers to spread ARGs of sludge to environment. This study aimed to characterize the ARGs, MGEs, and HMRGs of a multidrug-resistant Bacillus subtilis M3 strain, which was isolated from an activated sludge. The Bacillus subtilis M3 genome was sequenced and assembled, and then annotated in the RAST server. Simultaneously, SARG 2.0, INTEGRALL, and BacMet databases were used to identify the ARGs, MGEs, and HMRGs. The analysis showed that Bacillus subtilis M3, with a genome length of 5,728,923 bp, harbors ten types of ARGs involving resistance to aminoglycoside, multidrug, bacitracin, beta-lactamase, vancomycin, and tetracycline. Along with this, more than 41 types of MGEs and 23 types of HMRG were also identified. The genome sequence reported here will provide useful information better to understand antibiotics resistance profiles of the Bacillus strains from the sludge. Results highlighted that the spread of ARGs, MGEs, and HMRG in activated sludge deserved more public health attention.
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Data availability
The Bacillus subtilis M3 genome was submitted and deposited in NCBI database under GenBank Accession Number JAJHUI000000000. The Assembled genome of the Bacillus subtilis M3 was deposited in NCBI under accession number PRJNA775613.
Abbreviations
- ARBs:
-
Antimicrobial-resistant bacteria
- ARGs:
-
Antimicrobial resistance genes
- MGEs:
-
Mobile genetics elements
- HMRGs:
-
Heavy metal resistance genes
- rRNA:
-
Ribosomal ribonucleic acid
- DNA:
-
Deoxyribonucleic acid
- RAST:
-
It is an automatic annotation server for microbial genomes Rapid Annotations using Subsystems Technology
- SARG:
-
It is an online analysis pipeline used for rapid characterization and quantification of antibiotic resistance genes in sequencing data and stands for structural antibiotic resistance genes database
- INTEGRALL:
-
INTEGRALL is a database used for the detection of integrase genes
- BacMet:
-
BacMet is database used for the detection of heavy metals
- AR genes:
-
Antibiotics resistance genes
- LB:
-
LB stands for Lysogeny broth, and it is a nutritionally rich medium primarily used for the growth of bacteria
- PCR:
-
Polymerase chain reaction
- CLC genomic workbench:
-
CLC Genomics Workbench is a comprehensive analysis package for the analysis and visualization of sequencing data
- NCBI:
-
National center for biotechnology information
- ARDB:
-
it is a database used for the detection of antibiotic resistance genes and stands for Antibiotic resistance genes database
- CARD:
-
Card is a database used for the detection of antibiotic resistance genes and stands for comprehensive antibiotic resistance database
- RNA:
-
Ribonucleic acid
- ATP:
-
Adenosine triphosphate
- MSF gene:
-
Major facilitator protein
- vanR:
-
it is a type of vancomycin resistance gene
- tetB and tetL:
-
These both are the types of Tetracycline resistance genes
- aadK:
-
aadk IS A TYPE OF Aminoglycoside resistance genes
- copY and copZ:
-
These both are transposable elements along with TnpY and TnpZ
- BlastN:
-
BlastN stands for Basic local alignment search tool and is used to find local similarities between sequences
- ISAba20, ISAba6, and ISAmde2:
-
mobile genetics element
- Cu:
-
stand for Copper
- Cr:
-
stand for Chromium
- As:
-
stand for Arsenic
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Acknowledgements
We are grateful to Xingyuan Agriculture and Animal Husbandry Technology Co., Ltd. (Fuqing City, China) for their supporting and providing the activated sludge samples.
Funding
This research was sponsored by funds from the Forestry Science and Technology, and Natural Science Foundation of Fujian Province, China (Nos. 2021FKJ31; 2020J01173; 2019J01101), and the Innovation Program of Fujian Academy of Agricultural Sciences (Nos. YC2019011; CXTD2021043).
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TB and HH designed the main ideas and wrote the manuscript. HH, TZ and YL performed Analysis and data visualization. WH, SM, and YZ conducted a collection of samples, bacterial culture, and genome sequencing. HH, TB, YS and DL critically review the manuscript. TB, YS and DL provided platforms and resources. All the authors approved the publication of the manuscript.
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Ul Haq, H., Huang, W., Li, Y. et al. Genetic and genomic characterization of multidrug resistant Bacillus subtilis M3 isolated from an activated sludge reactor treating wastewater. Biologia 77, 1151–1160 (2022). https://doi.org/10.1007/s11756-021-01006-2
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DOI: https://doi.org/10.1007/s11756-021-01006-2