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Wang S, Zeng X, Jiang Y, Wang W, Bai L, Lu Y, Zhang L, Tan GY. Unleashing the potential: type I CRISPR-Cas systems in actinomycetes for genome editing. Nat Prod Rep 2024. [PMID: 38888887 DOI: 10.1039/d4np00010b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/20/2024]
Abstract
Covering: up to the end of 2023Type I CRISPR-Cas systems are widely distributed, found in over 40% of bacteria and 80% of archaea. Among genome-sequenced actinomycetes (particularly Streptomyces spp.), 45.54% possess type I CRISPR-Cas systems. In comparison to widely used CRISPR systems like Cas9 or Cas12a, these endogenous CRISPR-Cas systems have significant advantages, including better compatibility, wide distribution, and ease of operation (since no exogenous Cas gene delivery is needed). Furthermore, type I CRISPR-Cas systems can simultaneously edit and regulate genes by adjusting the crRNA spacer length. Meanwhile, most actinomycetes are recalcitrant to genetic manipulation, hindering the discovery and engineering of natural products (NPs). The endogenous type I CRISPR-Cas systems in actinomycetes may offer a promising alternative to overcome these barriers. This review summarizes the challenges and recent advances in CRISPR-based genome engineering technologies for actinomycetes. It also presents and discusses how to establish and develop genome editing tools based on type I CRISPR-Cas systems in actinomycetes, with the aim of their future application in gene editing and the discovery of NPs in actinomycetes.
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Affiliation(s)
- Shuliu Wang
- State Key Laboratory of Bioreactor Engineering (SKLBE), School of Biotechnology, East China University of Science and Technology (ECUST), Shanghai 200237, China.
| | - Xiaoqian Zeng
- State Key Laboratory of Bioreactor Engineering (SKLBE), School of Biotechnology, East China University of Science and Technology (ECUST), Shanghai 200237, China.
| | - Yue Jiang
- State Key Laboratory of Bioreactor Engineering (SKLBE), School of Biotechnology, East China University of Science and Technology (ECUST), Shanghai 200237, China.
| | - Weishan Wang
- State Key Laboratory of Microbial Resources and CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing 100101, China
| | - Linquan Bai
- State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yinhua Lu
- College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Lixin Zhang
- State Key Laboratory of Bioreactor Engineering (SKLBE), School of Biotechnology, East China University of Science and Technology (ECUST), Shanghai 200237, China.
| | - Gao-Yi Tan
- State Key Laboratory of Bioreactor Engineering (SKLBE), School of Biotechnology, East China University of Science and Technology (ECUST), Shanghai 200237, China.
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2
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Khan MU, Romance M, Polash MAUZ, Zahan N, Ali MS, Raihan J, Sarker S, Haque MH. Draft genome sequence of carbapenems-resistant Acinetobacter baumannii Hakim RU_CBWP strain isolated from a pond surface water in Bangladesh. Microbiol Resour Announc 2024:e0044024. [PMID: 38864657 DOI: 10.1128/mra.00440-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2024] [Accepted: 05/10/2024] [Indexed: 06/13/2024] Open
Abstract
We have revealed the genomic sequence of Acinetobacter baumannii strain Hakim RU_CBWP isolated from pond surface water. Our assembled genome covers 3.787 Mb with 45.5629× coverage, showcasing an average GC content of 38.60%. This genome contains two CRISPR arrays, 17 prophages, 22 antibiotic resistance genes, and 20 virulence factor genes.
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Affiliation(s)
- Muhib Ullah Khan
- Department of Veterinary and Animal Sciences, University of Rajshahi, Rajshahi, Bangladesh
| | - M Romance
- Department of Veterinary and Animal Sciences, University of Rajshahi, Rajshahi, Bangladesh
| | | | - Nusrat Zahan
- Department of Veterinary and Animal Sciences, University of Rajshahi, Rajshahi, Bangladesh
| | - Md Sumon Ali
- Department of Veterinary and Animal Sciences, University of Rajshahi, Rajshahi, Bangladesh
| | - Jafor Raihan
- Department of Veterinary and Animal Sciences, University of Rajshahi, Rajshahi, Bangladesh
| | - Subir Sarker
- Biomedical Sciences & Molecular Biology, College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, Queensland, Australia
| | - Md Hakimul Haque
- Department of Veterinary and Animal Sciences, University of Rajshahi, Rajshahi, Bangladesh
- Biomedical Sciences & Molecular Biology, College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, Queensland, Australia
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Islam MS, Pramanik PK, Rana ML, Ullah MA, Neloy FH, Ramasamy S, Schreinemachers P, Oliva R, Rahman MT. Draft genome sequence of Escherichia coli MTR_GS_S1457 strain isolated from a soil sample of a vegetable garden in Gazipur, Bangladesh. Microbiol Resour Announc 2024; 13:e0002124. [PMID: 38757962 DOI: 10.1128/mra.00021-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Accepted: 04/29/2024] [Indexed: 05/18/2024] Open
Abstract
We announce the sequence of the Escherichia coli MTR_GS_S1457 strain isolated from a soil sample of a vegetable gardening system for the first time in Bangladesh. With a length of 4,918,647 bp, this strain contained one plasmid, two CRISPR arrays, 54 predicted antibiotic resistance genes, and 81 predicted virulence factor genes.
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Affiliation(s)
- Md Saiful Islam
- Department of Microbiology and Hygiene, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh, Bangladesh
- Department of Animal Sciences, University of California-Davis, Davis, California, USA
| | - Pritom Kumar Pramanik
- Department of Microbiology and Hygiene, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Md Liton Rana
- Department of Microbiology and Hygiene, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Md Ashek Ullah
- Department of Microbiology and Hygiene, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Fahim Haque Neloy
- Department of Microbiology and Hygiene, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Srinivasan Ramasamy
- Safe and Sustainable Value Chains Flagship Program, World Vegetable Center, Shanhua, Tainan, Taiwan
| | - Pepijn Schreinemachers
- Healthy Diets and Enabling Impact Flagship Programs, World Vegetable Center-East and Southeast Asia, Bangkok, Thailand
| | - Ricardo Oliva
- Safe and Sustainable Value Chains Flagship Program, World Vegetable Center, Shanhua, Tainan, Taiwan
| | - Md Tanvir Rahman
- Department of Microbiology and Hygiene, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh, Bangladesh
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Romance M, khan MU, Islam MS, Islam MF, Haque MH. Draft genome sequence of multidrug-resistant Klebsiella pneumoniae Hakim-RU strain isolated from a patient with urinary tract infections in Bangladesh. Microbiol Resour Announc 2024; 13:e0008924. [PMID: 38534153 PMCID: PMC11080560 DOI: 10.1128/mra.00089-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 03/17/2024] [Indexed: 03/28/2024] Open
Abstract
We unveil the genomic sequence of the Klebsiella pneumoniae Hakim-RU strain isolated from a patient with urinary tract infections. Our assembled genome spans 4.3 Mb with 73.0× coverage, an average GC content of 57.41%, 4 plasmids, 2 CRISPR arrays, 10 prophages, 41 antibiotic resistance genes, and 6 virulence factor genes.
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Affiliation(s)
- M. Romance
- Department of Veterinary and Animal Sciences, University of Rajshahi, Rajshahi, Bangladesh
| | - Muhib Ullah khan
- Department of Veterinary and Animal Sciences, University of Rajshahi, Rajshahi, Bangladesh
| | - Md. Shamsul Islam
- Department of Veterinary and Animal Sciences, University of Rajshahi, Rajshahi, Bangladesh
| | - Md. Faridul Islam
- Department of Veterinary and Animal Sciences, University of Rajshahi, Rajshahi, Bangladesh
| | - Md. Hakimul Haque
- Department of Veterinary and Animal Sciences, University of Rajshahi, Rajshahi, Bangladesh
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Ren K, Zhou F, Zhang F, Yin M, Zhu Y, Wang S, Chen Y, Huang T, Wu Z, He J, Zhang A, Guo C, Huang Z. Discovery and structural mechanism of DNA endonucleases guided by RAGATH-18-derived RNAs. Cell Res 2024; 34:370-385. [PMID: 38575718 PMCID: PMC11061315 DOI: 10.1038/s41422-024-00952-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 03/09/2024] [Indexed: 04/06/2024] Open
Abstract
CRISPR-Cas systems and IS200/IS605 transposon-associated TnpBs have been utilized for the development of genome editing technologies. Using bioinformatics analysis and biochemical experiments, here we present a new family of RNA-guided DNA endonucleases. Our bioinformatics analysis initially identifies the stable co-occurrence of conserved RAGATH-18-derived RNAs (reRNAs) and their upstream IS607 TnpBs with an average length of 390 amino acids. IS607 TnpBs form programmable DNases through interaction with reRNAs. We discover the robust dsDNA interference activity of IS607 TnpB systems in bacteria and human cells. Further characterization of the Firmicutes bacteria IS607 TnpB system (ISFba1 TnpB) reveals that its dsDNA cleavage activity is remarkably sensitive to single mismatches between the guide and target sequences in human cells. Our findings demonstrate that a length of 20 nt in the guide sequence of reRNA achieves the highest DNA cleavage activity for ISFba1 TnpB. A cryo-EM structure of the ISFba1 TnpB effector protein bound by its cognate RAGATH-18 motif-containing reRNA and a dsDNA target reveals the mechanisms underlying reRNA recognition by ISFba1 TnpB, reRNA-guided dsDNA targeting, and the sensitivity of the ISFba1 TnpB system to base mismatches between the guide and target DNA. Collectively, this study identifies the IS607 TnpB family of compact and specific RNA-guided DNases with great potential for application in gene editing.
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Affiliation(s)
- Kuan Ren
- HIT Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang, China
| | - Fengxia Zhou
- HIT Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang, China
- Westlake Center for Genome Editing, Westlake Laboratory of Life Sciences and Biomedicine, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
| | - Fan Zhang
- HIT Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang, China.
| | - Mingyu Yin
- HIT Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang, China
| | - Yuwei Zhu
- HIT Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang, China
| | - Shouyu Wang
- HIT Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang, China
| | - Yan Chen
- HIT Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang, China
| | - Tengjin Huang
- HIT Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang, China
| | - Zixuan Wu
- Westlake Center for Genome Editing, Westlake Laboratory of Life Sciences and Biomedicine, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
| | - Jiale He
- Westlake Center for Genome Editing, Westlake Laboratory of Life Sciences and Biomedicine, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
| | - Anqi Zhang
- HIT Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang, China
| | - Changyou Guo
- HIT Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang, China
| | - Zhiwei Huang
- HIT Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang, China.
- Westlake Center for Genome Editing, Westlake Laboratory of Life Sciences and Biomedicine, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China.
- New Cornerstone Science Laboratory, Shenzhen, Guangdong, China.
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Islam MS, Pramanik PK, Rana ML, Ullah MA, Neloy FH, Ramasamy S, Schreinemachers P, Oliva R, Rahman MT. Draft genome sequence of antibiotic-resistant Shigella flexneri MTR_GR_V146 strain isolated from a tomato ( Solanum lycopersicum) sample collected from a peri-urban area of Bangladesh. Microbiol Resour Announc 2024; 13:e0009924. [PMID: 38411069 PMCID: PMC11008221 DOI: 10.1128/mra.00099-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Accepted: 02/11/2024] [Indexed: 02/28/2024] Open
Abstract
This study announces the genome sequence of the Shigella flexneri MTR_GR_V146 strain isolated from a tomato (Solanum lycopersicum) sample in Bangladesh. This strain has a 4,624,521 bp genome length (coverage: 73.07×), 2 CRISPR arrays, 1 plasmid, 52 predicted antibiotic resistance genes, and 53 virulence factor genes.
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Affiliation(s)
- Md. Saiful Islam
- Department of Microbiology and Hygiene, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh, Bangladesh
- Department of Animal Sciences, University of California—Davis, Davis, California, USA
| | - Pritom Kumar Pramanik
- Department of Microbiology and Hygiene, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Md. Liton Rana
- Department of Microbiology and Hygiene, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Md. Ashek Ullah
- Department of Microbiology and Hygiene, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Fahim Haque Neloy
- Department of Microbiology and Hygiene, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | | | | | | | - Md. Tanvir Rahman
- Department of Microbiology and Hygiene, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh, Bangladesh
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Islam MS, Pramanik PK, Rana ML, Ramasamy S, Schreinemachers P, Oliva R, Rahman MT. Draft genome sequences of five multidrug-resistant Escherichia coli strains isolated from vegetable samples in Bangladesh. Microbiol Resour Announc 2024; 13:e0098223. [PMID: 38095874 DOI: 10.1128/mra.00982-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Accepted: 11/09/2023] [Indexed: 01/18/2024] Open
Abstract
Reports indicate that vegetables are becoming a source of multidrug-resistant (MDR) bacteria, including Escherichia coli. Here, we present genome sequences of five MDR E. coli strains to assist future genomic analysis of this bacterium. These E. coli strains were isolated from vegetable samples of different gardening systems in Dhaka, Bangladesh.
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Affiliation(s)
- Md Saiful Islam
- Department of Microbiology and Hygiene, Faculty of Veterinary Science, Bangladesh Agricultural University , Mymensingh, Bangladesh
- Department of Animal Sciences, University of California-Davis , Davis, California, USA
| | - Pritom Kumar Pramanik
- Department of Microbiology and Hygiene, Faculty of Veterinary Science, Bangladesh Agricultural University , Mymensingh, Bangladesh
| | - Md Liton Rana
- Department of Microbiology and Hygiene, Faculty of Veterinary Science, Bangladesh Agricultural University , Mymensingh, Bangladesh
| | | | | | | | - Md Tanvir Rahman
- Department of Microbiology and Hygiene, Faculty of Veterinary Science, Bangladesh Agricultural University , Mymensingh, Bangladesh
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Ahmed T, Islam MS, Nuruzzaman M, Sadekuzzaman M, Kabir SML, Rahman MT, Khan MSR. Draft genome sequence of multidrug-resistant Citrobacter portucalensis BAU_133-2 strain isolated from a domestic duck ( Anas platyrhynchos domesticus) in Bangladesh. Microbiol Resour Announc 2023; 12:e0058723. [PMID: 37909718 PMCID: PMC10720505 DOI: 10.1128/mra.00587-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 10/02/2023] [Indexed: 11/03/2023] Open
Abstract
We announce the genome sequence of the Citrobacter portucalensis BAU_133-2 strain isolated from a domestic duck. Our assembled genome contained a length of 4.8 Mb, 110.0× genome coverage, 51.91% of an average GC content, 1 plasmid, 1 CRISPR array, 8 prophages, 27 antibiotic resistance genes, and 75 virulence factor genes.
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Affiliation(s)
- Tarana Ahmed
- Department of Microbiology and Hygiene, Bangladesh Agricultural University, Mymensingh, Bangladesh
- Department of Livestock Services, Ministry of Fisheries & Livestock, Government of the Peoples Republic of Bangladesh, Krishi Khamar Sarak, Farmgate, Dhaka, Bangladesh
| | - Md. Saiful Islam
- Department of Microbiology and Hygiene, Bangladesh Agricultural University, Mymensingh, Bangladesh
- Department of Animal Sciences, University of California—Davis, Davis, California, USA
| | | | - Mohammad Sadekuzzaman
- Department of Livestock Services, Central Disease Investigation Laboratory (CDIL), Ministry of Fisheries & Livestock, Government of the Peoples Republic of Bangladesh, Krishi Khamar Sarak, Farmgate, Dhaka, Bangladesh
| | - S. M. Lutful Kabir
- Department of Microbiology and Hygiene, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Md. Tanvir Rahman
- Department of Microbiology and Hygiene, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Md. Shahidur Rahman Khan
- Department of Microbiology and Hygiene, Bangladesh Agricultural University, Mymensingh, Bangladesh
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Anika TT, Noman ZA, Islam MS, Sultana N, Ashraf MN, Pervin M, Islam MA, Hossain MM, Rahman MT, Khan MAHNA. Draft genome sequence of multidrug-resistant Escherichia coli MAHK_SCM_BAU_30A strain isolated from a subclinical mastitis cow in Bangladesh. Microbiol Resour Announc 2023; 12:e0071323. [PMID: 37889012 PMCID: PMC10652913 DOI: 10.1128/mra.00713-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 09/21/2023] [Indexed: 10/28/2023] Open
Abstract
This study announces the sequence of a multidrug-resistant Escherichia coli MAHK_SCM_BAU_30A strain isolated from bovine subclinical mastitis milk in 2022 in Bangladesh. Our assembled genome had a length of 4,884,948 bp, three plasmids, two CRISPR arrays, five prophages, 51 predicted antibiotic resistance, and 72 predicted virulence factor genes.
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Affiliation(s)
- Tasnia Tabassum Anika
- Department of Pathology, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Zakaria Al Noman
- Bangladesh Council of Scientific and Industrial Research, Dhaka, Bangladesh
| | - Md. Saiful Islam
- Department of Microbiology and Hygiene, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh, Bangladesh
- Department of Animal Sciences, University of California—Davis, Davis, California, USA
| | - Nazneen Sultana
- Department of Pathology, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Md. Nahid Ashraf
- Department of Microbiology and Hygiene, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Munmun Pervin
- Department of Pathology, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Mohammad Ariful Islam
- Department of Medicine, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Mokbul Md. Hossain
- Department of Pathology, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Md. Tanvir Rahman
- Department of Microbiology and Hygiene, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh, Bangladesh
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