1
|
Islam R, Ferdous FB, Hoque MN, Asif NA, Rana ML, Siddique MP, Rahman MT. Characterization of β-lactamase and virulence genes in Pseudomonas aeruginosa isolated from clinical, environmental and poultry sources in Bangladesh. PLoS One 2024; 19:e0296542. [PMID: 38626002 PMCID: PMC11020970 DOI: 10.1371/journal.pone.0296542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 02/21/2024] [Indexed: 04/18/2024] Open
Abstract
The emergence and spread of multidrug-resistant pathogens like Pseudomonas aeruginosa are major concerns for public health worldwide. This study aimed to assess the prevalence of P. aeruginosa in clinical, environmental, and poultry sources in Bangladesh, along with their antibiotic susceptibility and the profiling of β-lactamase and virulence genes using standard molecular and microbiology techniques. We collected 110 samples from five different locations, viz., BAU residential area (BAURA; n = 15), BAU Healthcare Center (BAUHCC; n = 20), BAU Veterinary Teaching Hospital (BAUVTH; n = 22), Poultry Market (PM; n = 30) and Mymensingh Medical College Hospital (MCCH; n = 23). After overnight enrichment in nutrient broth, 89 probable Pseudomonas isolates (80.90%) were screened through selective culture, gram-staining and biochemical tests. Using genus- and species-specific PCR, we confirmed 22 isolates (20.0%) as P. aeruginosa from these samples. Antibiogram profiling revealed that 100.0% P. aeruginosa isolates (n = 22) were multidrug-resistant isolates, showing resistance against Doripenem, Penicillin, Ceftazidime, Cefepime, and Imipenem. Furthermore, resistance to aztreonam was observed in 95.45% isolates. However, P. aeruginosa isolates showed a varying degree of sensitivity against Amikacin, Gentamicin, and Ciprofloxacin. The blaTEM gene was detected in 86.0% isolates, while blaCMY, blaSHV and blaOXA, were detected in 27.0%, 18.0% and 5.0% of the P. aeruginosa isolates, respectively. The algD gene was detected in 32.0% isolates, whereas lasB and exoA genes were identified in 9.0% and 5.0% P. aeruginosa isolates. However, none of the P. aeruginosa isolates harbored exoS gene. Hence, this study provides valuable and novel insights on the resistance and virulence of circulating P. aeruginosa within the clinical, environmental, and poultry environments of Bangladesh. These findings are crucial for understanding the emergence of β-lactamase resistance in P. aeruginosa, highlighting its usefulness in the treatment and control of P. aeruginosa infections in both human and animal populations.
Collapse
Affiliation(s)
- Raihana Islam
- Department of Microbiology and Hygiene, Faculty of Veterinary Sciences, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Farhana Binte Ferdous
- Department of Microbiology and Hygiene, Faculty of Veterinary Sciences, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - M. Nazmul Hoque
- Department of Gynecology, Obstetrics and Reproductive Health, Faculty of Veterinary Medicine and Animal Science, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, Bangladesh
| | - Nowshad Atique Asif
- Department of Microbiology and Hygiene, Faculty of Veterinary Sciences, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Md. Liton Rana
- Department of Microbiology and Hygiene, Faculty of Veterinary Sciences, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Mahbubul Pratik Siddique
- Department of Microbiology and Hygiene, Faculty of Veterinary Sciences, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Md. Tanvir Rahman
- Department of Microbiology and Hygiene, Faculty of Veterinary Sciences, Bangladesh Agricultural University, Mymensingh, Bangladesh
| |
Collapse
|
2
|
Rahman MM, Siddique N, Akter S, Das ZC, Hoque MN. Draft genome sequencing of Pediococcus pentosaceus strains isolated from cow milk. Microbiol Resour Announc 2024:e0023824. [PMID: 38619270 DOI: 10.1128/mra.00238-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2024] [Accepted: 03/28/2024] [Indexed: 04/16/2024] Open
Abstract
We sequenced the genomes of Pediococcus pentosaceus strains MBBL4 and MBBL6, isolated from raw milk samples of healthy cows. The draft genomes of the MBBL4 and MBBL6 were 1,896,831 bp and 1,849,397 bp, respectively, and were fragmented into 58 and 42 contigs, with coverages of 118.2× and 128.7×, respectively.
Collapse
Affiliation(s)
- Md Morshedur Rahman
- Molecular Biology and Bioinformatics Laboratory, Department of Gynaecology, Obstetrics and Reproductive Health, Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur, Bangladesh
| | - Naim Siddique
- Molecular Biology and Bioinformatics Laboratory, Department of Gynaecology, Obstetrics and Reproductive Health, Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur, Bangladesh
| | - Salma Akter
- Department of Microbiology, Jahangirnagar University, Savar, Dhaka, Bangladesh
| | - Ziban Chandra Das
- Molecular Biology and Bioinformatics Laboratory, Department of Gynaecology, Obstetrics and Reproductive Health, Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur, Bangladesh
| | - M Nazmul Hoque
- Molecular Biology and Bioinformatics Laboratory, Department of Gynaecology, Obstetrics and Reproductive Health, Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur, Bangladesh
| |
Collapse
|
3
|
Habiba MU, Hoque MN, Ahmed S, Islam T, Deb GK, Rahman MM. Draft genome sequence of Leuconostoc falkenbergense isolated from naturally fermented buffalo milk curd. Microbiol Resour Announc 2024:e0014824. [PMID: 38602401 DOI: 10.1128/mra.00148-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Accepted: 03/03/2024] [Indexed: 04/12/2024] Open
Abstract
This study reports the draft genome of Leuconostoc falkenbergense strain BSMRAU-M1L5, isolated from artisanal buffalo milk curd in Bangladesh. The draft genome spans 1,776,471 bp, with 50× coverage and 96 contigs.
Collapse
Affiliation(s)
- Mst Umme Habiba
- Department of Dairy and Poultry Science, Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur, Bangladesh
| | - M Nazmul Hoque
- Molecular Biology and Bioinformatics Laboratory, Department of Gynecology, Obstetrics and Reproductive Health, Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur, Bangladesh
| | - Shabbir Ahmed
- Department of Dairy and Poultry Science, Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur, Bangladesh
| | - Tofazzal Islam
- Institute of Biotechnology and Genetic Engineering, Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur, Bangladesh
| | - Gautam Kumar Deb
- Biotechnology Division, Bangladesh Livestock Research Institute, Savar, Dhaka, Bangladesh
| | - Md Morshedur Rahman
- Department of Dairy and Poultry Science, Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur, Bangladesh
- Institute of Food Safety and Processing, Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur, Bangladesh
| |
Collapse
|
4
|
Hossain MA, Al Amin M, Khan MA, Refat MRR, Sohel M, Rahman MH, Islam A, Hoque MN. Genome-Wide Investigation Reveals Potential Therapeutic Targets in Shigella spp. Biomed Res Int 2024; 2024:5554208. [PMID: 38595330 PMCID: PMC11003385 DOI: 10.1155/2024/5554208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Revised: 02/21/2024] [Accepted: 03/01/2024] [Indexed: 04/11/2024]
Abstract
Shigella stands as a major contributor to bacterial dysentery worldwide scale, particularly in developing countries with inadequate sanitation and hygiene. The emergence of multidrug-resistant strains exacerbates the challenge of treating Shigella infections, particularly in regions where access to healthcare and alternative antibiotics is limited. Therefore, investigations on how bacteria evade antibiotics and eventually develop resistance could open new avenues for research to develop novel therapeutics. The aim of this study was to analyze whole genome sequence (WGS) of human pathogenic Shigella spp. to elucidate the antibiotic resistance genes (ARGs) and their mechanism of resistance, gene-drug interactions, protein-protein interactions, and functional pathways to screen potential therapeutic candidate(s). We comprehensively analyzed 45 WGS of Shigella, including S. flexneri (n = 17), S. dysenteriae (n = 14), S. boydii (n = 11), and S. sonnei (n = 13), through different bioinformatics tools. Evolutionary phylogenetic analysis showed three distinct clades among the circulating strains of Shigella worldwide, with less genomic diversity. In this study, 2,146 ARGs were predicted in 45 genomes (average 47.69 ARGs/genome), of which only 91 ARGs were found to be shared across the genomes. Majority of these ARGs conferred their resistance through antibiotic efflux pump (51.0%) followed by antibiotic target alteration (23%) and antibiotic target replacement (18%). We identified 13 hub proteins, of which four proteins (e.g., tolC, acrR, mdtA, and gyrA) were detected as potential hub proteins to be associated with antibiotic efflux pump and target alteration mechanisms. These hub proteins were significantly (p < 0.05) enriched in biological process, molecular function, and cellular components. Therefore, the finding of this study suggests that human pathogenic Shigella strains harbored a wide range of ARGs that confer resistance through antibiotic efflux pumps and antibiotic target modification mechanisms, which must be taken into account to devise and formulate treatment strategy against this pathogen. Moreover, the identified hub proteins could be exploited to design and develop novel therapeutics against MDR pathogens like Shigella.
Collapse
Affiliation(s)
- Md. Arju Hossain
- Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Tangail 1902, Bangladesh
- Department of Microbiology, Primeasia University, Dhaka 1213, Bangladesh
| | - Md. Al Amin
- Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Tangail 1902, Bangladesh
| | - Md. Arif Khan
- Institute of Epidemiology, Disease Control and Research (IEDCR), Dhaka 1212, Bangladesh
- EcoHealth Alliance, New York, NY 10018, USA
| | - Md. Rashedur Rahman Refat
- Department of Information and Communication Technology, Mawlana Bhashani Science and Technology University, Tangail 1902, Bangladesh
| | - Md Sohel
- Department of Biochemistry and Molecular Biology, Primeasia University, Banani, Dhaka 1213, Bangladesh
- Department of Biochemistry and Molecular Biology, Mawlana Bhashani Science and Technology University, Santosh, Tangail 1902, Bangladesh
| | - Md Habibur Rahman
- Department of Computer Science and Engineering, Islamic University, Kushtia 7003, Bangladesh
- Center for Advanced Bioinformatics and Artificial Intelligence Research, Islamic University, Kushtia 7003, Bangladesh
| | - Ariful Islam
- Institute of Epidemiology, Disease Control and Research (IEDCR), Dhaka 1212, Bangladesh
- EcoHealth Alliance, New York, NY 10018, USA
| | - M. Nazmul Hoque
- Department of Gynecology, Obstetrics and Reproductive Health, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur 1706, Bangladesh
| |
Collapse
|
5
|
Hoque MN, Faisal GM, Jerin S, Moyna Z, Islam MA, Talukder AK, Alam MS, Das ZC, Isalm T, Hossain MA, Rahman ANMA. Unveiling distinct genetic features in multidrug-resistant Escherichia coli isolated from mammary tissue and gut of mastitis induced mice. Heliyon 2024; 10:e26723. [PMID: 38434354 PMCID: PMC10904246 DOI: 10.1016/j.heliyon.2024.e26723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 02/08/2024] [Accepted: 02/19/2024] [Indexed: 03/05/2024] Open
Abstract
Escherichia coli is one of the major pathogens causing mastitis in lactating mammals. We hypothesized that E. coli from the gut and mammary glands may have similar genomic characteristics in the causation of mastitis. To test this hypothesis, we used whole genome sequencing to analyze two multidrug resistant E. coli strains isolated from mammary tissue (G2M6U) and fecal sample (G6M1F) of experimentally induced mastitis mice. Both strains showed resistance to multiple (>7) antibiotics such as oxacillin, aztreonam, nalidixic acid, streptomycin, gentamicin, cefoxitin, ampicillin, tetracycline, azithromycin and nitrofurantoin. The genome of E. coli G2M6U had 59 antimicrobial resistance genes (ARGs) and 159 virulence factor genes (VFGs), while the E. coli G6M1F genome possessed 77 ARGs and 178 VFGs. Both strains were found to be genetically related to many E. coli strains causing mastitis and enteric diseases originating from different hosts and regions. The G6M1F had several unique ARGs (e.g., QnrS1, sul2, tetA, tetR, emrK, blaTEM-1/105, and aph(6)-Id, aph(3″)-Ib) conferring resistance to certain antibiotics, whereas G2M6U had a unique heat-stable enterotoxin gene (astA) and 7192 single nucleotide polymorphisms. Furthermore, there were 43 and 111 unique genes identified in G2M6U and G6M1F genomes, respectively. These results indicate distinct differences in the genomic characteristics of E. coli strain G2M6U and G6M1F that might have important implications in the pathophysiology of mammalian mastitis, and treatment strategies for mastitis in dairy animals.
Collapse
Affiliation(s)
- M. Nazmul Hoque
- Molecular Biology and Bioinformatics Laboratory, Department of Gynecology, Obstetrics and Reproductive Health, Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur, 1706, Bangladesh
| | - Golam Mahbub Faisal
- Molecular Biology and Bioinformatics Laboratory, Department of Gynecology, Obstetrics and Reproductive Health, Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur, 1706, Bangladesh
| | - Shobnom Jerin
- Molecular Biology and Bioinformatics Laboratory, Department of Gynecology, Obstetrics and Reproductive Health, Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur, 1706, Bangladesh
| | - Zannatara Moyna
- Molecular Biology and Bioinformatics Laboratory, Department of Gynecology, Obstetrics and Reproductive Health, Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur, 1706, Bangladesh
| | - Md Aminul Islam
- Advanced Molecular Lab, Department of Microbiology, President Abdul Hamid Medical College, Karimganj, 2310, Bangladesh
| | - Anup Kumar Talukder
- Molecular Biology and Bioinformatics Laboratory, Department of Gynecology, Obstetrics and Reproductive Health, Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur, 1706, Bangladesh
| | | | - Ziban Chandra Das
- Molecular Biology and Bioinformatics Laboratory, Department of Gynecology, Obstetrics and Reproductive Health, Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur, 1706, Bangladesh
| | - Tofazzal Isalm
- Institute of Biotechnology and Genetic Engineering (IBGE), BSMRAU, Gazipur, 1706, Bangladesh
| | - M. Anwar Hossain
- Jashore University of Science and Technology, Jashore, 7408, Bangladesh
| | - Abu Nasar Md Aminoor Rahman
- Molecular Biology and Bioinformatics Laboratory, Department of Gynecology, Obstetrics and Reproductive Health, Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur, 1706, Bangladesh
| |
Collapse
|
6
|
Habiba MU, Hoque MN, Ahmed S, Islam MT, Deb GK, Rahman MM. Genomic insights into antibiotic resistance genes in Leuconostoc citreum strains isolated from artisanal buffalo milk curd in Bangladesh through whole-genome sequencing. Microbiol Resour Announc 2024; 13:e0128923. [PMID: 38358277 DOI: 10.1128/mra.01289-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Accepted: 02/03/2024] [Indexed: 02/16/2024] Open
Abstract
We sequenced the genome of Leuconostoc citreum strains BSMRAU-M1L6 and BSMRAU-M1L13 isolated from artisanal buffalo milk curd in Bangladesh. The draft genomes of BSMRAU-M1L6 and BSMRAU-M1L13 are 1,869,891 and 1,890,611 bp, respectively, with 50.0× coverage (both) and 65 and 75 contigs, respectively.
Collapse
Affiliation(s)
- Mst Umme Habiba
- Department of Dairy and Poultry Science, Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur, Bangladesh
| | - M Nazmul Hoque
- Molecular Biology and Bioinformatics Laboratory, Department of Gynecology, Obstetrics and Reproductive Health, Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur, Bangladesh
| | - Shabbir Ahmed
- Department of Dairy and Poultry Science, Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur, Bangladesh
| | - Md Tofazzal Islam
- Institute of Biotechnology and Genetic Engineering, Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur, Bangladesh
| | - Gautam Kumar Deb
- Biotechnology Division, Bangladesh Livestock Research Institute, Savar, Bangladesh
| | - Md Morshedur Rahman
- Department of Dairy and Poultry Science, Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur, Bangladesh
- Institute of Food Safety and Processing, Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur, Bangladesh
| |
Collapse
|
7
|
Hoque MN, Faisal GM, Das ZC, Sakif TI, Al Mahtab M, Hossain MA, Islam T. Genomic features and pathophysiological impact of a multidrug-resistant Staphylococcus warneri variant in murine mastitis. Microbes Infect 2024; 26:105285. [PMID: 38154518 DOI: 10.1016/j.micinf.2023.105285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Revised: 12/05/2023] [Accepted: 12/22/2023] [Indexed: 12/30/2023]
Abstract
Non-aureus staphylococci (NAS) represent a major etiological agent in dairy animal mastitis, yet their role and impact remain insufficiently studied. This study aimed to elucidate the genomic characteristics of a newly identified multidrug-resistant NAS strain, specifically Staphylococcus warneri G1M1F, isolated from murine feces in an experimental mastitis model. Surprisingly, NAS species accounted for 54.35 % of murine mastitis cases, with S. warneri being the most prevalent at 40.0 %. S. warneri G1M1F exhibited resistance to 10 major antibiotics. Whole-genome sequencing established a genetic connection between G1M1F and S. warneri strains isolated previously from various sources including mastitis milk in dairy animals, human feces and blood across diverse geographical regions. Genomic analysis of S. warneri G1M1F unveiled 34 antimicrobial resistance genes (ARGs), 30 virulence factor genes (VFGs), and 278 metabolic features. A significant portion of identified ARGs (64 %) conferred resistance through antibiotic efflux pumps, while VFGs primarily related to bacterial adherence and biofilm formation. Inoculation with G1M1F in mice resulted in pronounced inflammatory lesions in mammary and colon tissues, indicating pathogenic potential. Our findings highlight distinctive genomic traits in S. warneri G1M1F, signifying the emergence of a novel multidrug-resistant NAS variant. These insights contribute to understanding NAS-related mastitis pathophysiology and inform strategies for effective treatment in dairy animals.
Collapse
Affiliation(s)
- M Nazmul Hoque
- Molecular Biology and Bioinformatics Laboratory, Department of Gynecology, Obstetrics and Reproductive Health, Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur 1706, Bangladesh.
| | - Golam Mahbub Faisal
- Molecular Biology and Bioinformatics Laboratory, Department of Gynecology, Obstetrics and Reproductive Health, Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur 1706, Bangladesh
| | - Ziban Chandra Das
- Molecular Biology and Bioinformatics Laboratory, Department of Gynecology, Obstetrics and Reproductive Health, Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur 1706, Bangladesh
| | | | - Mamun Al Mahtab
- Interventional Hepatology Division, Bangabandhu Sheikh Mujib Medical University, Dhaka 1000, Bangladesh
| | - M Anwar Hossain
- Jashore University of Science and Technology, Jashore 7408, Bangladesh
| | - Tofazzal Islam
- Institute of Biotechnology and Genetic Engineering (IBGE), BSMRAU, Gazipur 1706, Bangladesh
| |
Collapse
|
8
|
Popy NN, Hoque MN, Khan MFR, Biswas L, Rahman MH, Saiduzzaman M, Rahman M, Rahman MB. Draft genome sequencing of a multidrug-resistant Salmonella enterica subspecies enterica serovar Typhimurium strain isolated from chicken in Bangladesh. Microbiol Resour Announc 2024; 13:e0061923. [PMID: 38088574 DOI: 10.1128/mra.00619-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 11/21/2023] [Indexed: 01/18/2024] Open
Abstract
Herein this study, we sequenced the genome of a multidrug-resistant Salmonella enterica serovar Typhimurium strain MBR-MFRK-23 isolated from the liver tissue of a diseased layer chicken. The 4,964,854-bp draft genome comprises 50 contigs with 50.5× coverage and 52.1% GC content and is typed as S. enterica sequence type 19.
Collapse
Affiliation(s)
- Najmun Nahar Popy
- Department of Microbiology and Hygiene, Bangladesh Agricultural University , Mymensingh, Bangladesh
| | - M Nazmul Hoque
- Molecular Biology and Bioinformatics Laboratory, Department of Gynecology, Obstetrics and Reproductive Health, Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU) , Gazipur, Bangladesh
| | | | - Limon Biswas
- Department of Microbiology and Hygiene, Bangladesh Agricultural University , Mymensingh, Bangladesh
| | - Mohammad Habibur Rahman
- Department of Microbiology and Hygiene, Bangladesh Agricultural University , Mymensingh, Bangladesh
| | - Md Saiduzzaman
- Department of Neurology, Mymensingh Medical College Hospital , Mymensingh, Bangladesh
| | - Marzia Rahman
- Department of Microbiology and Hygiene, Bangladesh Agricultural University , Mymensingh, Bangladesh
| | - Md Bahanur Rahman
- Department of Microbiology and Hygiene, Bangladesh Agricultural University , Mymensingh, Bangladesh
| |
Collapse
|
9
|
Islam MS, Ballah FM, Hoque MN, Rahman AMMT, Rahman MT. Draft genome sequence of Staphylococcus gallinarum MTR_B001 strain isolated from breast muscle of a chicken in Bangladesh. Microbiol Resour Announc 2023; 12:e0064723. [PMID: 37846982 PMCID: PMC10652911 DOI: 10.1128/mra.00647-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 09/11/2023] [Indexed: 10/18/2023] Open
Abstract
We announce the genome sequence of the Staphylococcus gallinarum MTR_B001 strain isolated from the breast muscle of a chicken in 2022 in Bangladesh. This assembled genome had an estimated length of 2,889,393 bp (with 50× genome coverage), 15 contigs, 36 predicted antibiotic resistance genes, and 27 predicted virulence factor genes.
Collapse
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
| | - Fatimah Muhammad Ballah
- Department of Microbiology and Hygiene, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - M. Nazmul Hoque
- Department of Gynaecology, Obstetrics and Reproductive Health, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, Bangladesh
| | | | - Md. Tanvir Rahman
- Department of Microbiology and Hygiene, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh, Bangladesh
| |
Collapse
|
10
|
Hoque MN, Faisal GM, Moyna Z, Islam MS, Das ZC, Islam T. Draft genome sequence of a multidrug-resistant Klebsiella pneumoniae fecal isolate from a cow with clinical mastitis. Microbiol Resour Announc 2023; 12:e0073023. [PMID: 37902381 PMCID: PMC10652979 DOI: 10.1128/mra.00730-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 09/24/2023] [Indexed: 10/31/2023] Open
Abstract
Klebsiella pneumoniae is one of the most important mastitis-causing pathogens. The multidrug-resistant K. pneumoniae strain MNH_G2C5F was isolated from the feces of a cow with clinical mastitis. The MNH_G2C5F strain had a genome size of 5,381,832 bp (85.0× coverage) and typed as sequence type 273 (ST273).
Collapse
Affiliation(s)
- M. Nazmul Hoque
- Molecular Biology and Bioinformatics Laboratory, Department of Gynaecology, Obstetrics and Reproductive Health, Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur, Bangladesh
| | - Golam Mahbub Faisal
- Molecular Biology and Bioinformatics Laboratory, Department of Gynaecology, Obstetrics and Reproductive Health, Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur, Bangladesh
| | - Zannatara Moyna
- Molecular Biology and Bioinformatics Laboratory, Department of Gynaecology, Obstetrics and Reproductive Health, Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur, Bangladesh
| | - Md. Sayedul Islam
- Department of Microbiology and Public Health, BSMRAU, Gazipur, Bangladesh
| | - Ziban Chandra Das
- Molecular Biology and Bioinformatics Laboratory, Department of Gynaecology, Obstetrics and Reproductive Health, Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur, Bangladesh
| | - Tofazzal Islam
- Institute of Biotechnology and Genetic Engineering (IBGE), BSMRAU, Gazipur, Bangladesh
| |
Collapse
|
11
|
Islam MA, Marzan AA, Arman MS, Shahi S, Sakif TI, Hossain M, Islam T, Hoque MN. Some common deleterious mutations are shared in SARS-CoV-2 genomes from deceased COVID-19 patients across continents. Sci Rep 2023; 13:18644. [PMID: 37903828 PMCID: PMC10616235 DOI: 10.1038/s41598-023-45517-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 10/20/2023] [Indexed: 11/01/2023] Open
Abstract
The identification of deleterious mutations in different variants of SARS-CoV-2 and their roles in the morbidity of COVID-19 patients has yet to be thoroughly investigated. To unravel the spectrum of mutations and their effects within SARS-CoV-2 genomes, we analyzed 5,724 complete genomes from deceased COVID-19 patients sourced from the GISAID database. This analysis was conducted using the Nextstrain platform, applying a generalized time-reversible model for evolutionary phylogeny. These genomes were compared to the reference strain (hCoV-19/Wuhan/WIV04/2019) using MAFFT v7.470. Our findings revealed that SARS-CoV-2 genomes from deceased individuals belonged to 21 Nextstrain clades, with clade 20I (Alpha variant) being the most predominant, followed by clade 20H (Beta variant) and clade 20J (Gamma variant). The majority of SARS-CoV-2 genomes from deceased patients (33.4%) were sequenced in North America, while the lowest percentage (0.98%) came from Africa. The 'G' clade was dominant in the SARS-CoV-2 genomes of Asian, African, and North American regions, while the 'GRY' clade prevailed in Europe. In our analysis, we identified 35,799 nucleotide (NT) mutations throughout the genome, with the highest frequency (11,402 occurrences) found in the spike protein. Notably, we observed 4150 point-specific amino acid (AA) mutations in SARS-CoV-2 genomes, with D614G (20%) and N501Y (14%) identified as the top two deleterious mutations in the spike protein on a global scale. Furthermore, we detected five common deleterious AA mutations, including G18V, W45S, I33T, P30L, and Q418H, which play a key role in defining each clade of SARS-CoV-2. Our novel findings hold potential value for genomic surveillance, enabling the monitoring of the evolving pattern of SARS-CoV-2 infection, its emerging variants, and their impact on the development of effective vaccination and control strategies.
Collapse
Affiliation(s)
- Md Aminul Islam
- Advanced Molecular Lab, Department of Microbiology, President Abdul Hamid Medical College, Karimganj, Kishoreganj, 2310, Bangladesh.
- COVID-19 Diagnostic Lab, Department of Microbiology, Noakhali Science and Technology University, Noakhali, 3814, Bangladesh.
| | - Abdullah Al Marzan
- Advanced Molecular Lab, Department of Microbiology, President Abdul Hamid Medical College, Karimganj, Kishoreganj, 2310, Bangladesh
- Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet, 3114, Bangladesh
| | - Md Sakil Arman
- Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet, 3114, Bangladesh
| | - Shatila Shahi
- Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet, 3114, Bangladesh
| | - Tahsin Islam Sakif
- Lane Department of Computer Science and Electrical Engineering, West Virginia University, Morgantown, WV, 26506-6109, USA
| | - Maqsud Hossain
- University of Nottingham, Sutton Bonington Campus, LE12 5RD, Loughborough, NG7 2RD, Leicestershire, UK
| | - Tofazzal Islam
- Institute of Biotechnology and Genetic Engineering (IBGE), Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, 1706, Bangladesh.
| | - M Nazmul Hoque
- Molecular Biology and Bioinformatics Laboratory, Department of Gynecology, Obstetrics and Reproductive Health, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, 1706, Bangladesh.
| |
Collapse
|
12
|
Islam T, Hoque MN. Gut and flesh microbiome sequencing of the Bangladesh national fish hilsa ( Tenualosa ilisha). Microbiol Resour Announc 2023; 12:e0044823. [PMID: 37747192 PMCID: PMC10586148 DOI: 10.1128/mra.00448-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 08/15/2023] [Indexed: 09/26/2023] Open
Abstract
The gut and flesh microbiome of the national fish of Bangladesh, Tenualosa ilisha, were analyzed using 16S rRNA gene sequencing. Our findings revealed a significant microbial disparity between sample categories and the habitat of hilsa fish, which will serve as a valuable foundation for further comprehensive studies on the hilsa microbiome.
Collapse
Affiliation(s)
- Tofazzal Islam
- Institute of Biotechnology and Genetic Engineering (IBGE), Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur, Bangladesh
| | - M. Nazmul Hoque
- Department of Gynecology, Obstetrics and Reproductive Health, BSMRAU, Gazipur, Bangladesh
| |
Collapse
|
13
|
Ballah FM, Islam MS, Ievy S, Ferdous FB, Sobur MA, Rahman AMMT, Rahman M, Hoque MN, Hassan J, Rahman MT. Draft genome sequence of biofilm-forming methicillin-resistant Staphylococcus aureus MTR_V1 strain isolated from a ready-to-eat food in Bangladesh. Microbiol Resour Announc 2023; 12:e0059723. [PMID: 37712684 PMCID: PMC10586104 DOI: 10.1128/mra.00597-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 08/08/2023] [Indexed: 09/16/2023] Open
Abstract
This announcement provides the genome sequence of the biofilm-forming methicillin-resistant Staphylococcus aureus MTR_V1 strain isolated from a ready-to-eat food sample in Bangladesh. Our assembled genome had a length of 2.8 Mb, 27 contigs, two CRISPR arrays, 38 predicted antibiotic resistance genes, and 66 predicted virulence factor genes.
Collapse
Affiliation(s)
- Fatimah Muhammad Ballah
- Department of Microbiology and Hygiene, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Md. Saiful Islam
- Department of Microbiology and Hygiene, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Samina Ievy
- Department of Microbiology and Hygiene, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Farhana Binte Ferdous
- Department of Microbiology and Hygiene, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Md. Abdus Sobur
- Department of Microbiology and Hygiene, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | | | - Marzia Rahman
- Department of Microbiology and Hygiene, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - M. Nazmul Hoque
- Department of Gynaecology, Obstetrics, and Reproductive Health, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, Bangladesh
| | - Jayedul Hassan
- 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
| |
Collapse
|
14
|
Islam SMR, Tanzina AY, Foysal MJ, Hoque MN, Rumi MH, Siddiki AMAMZ, Tay ACY, Hossain MJ, Bakar MA, Mostafa M, Mannan A. Author Correction: Insights into the nutritional properties and microbiome diversity in sweet and sour yogurt manufactured in Bangladesh. Sci Rep 2023; 13:17367. [PMID: 37833308 PMCID: PMC10576088 DOI: 10.1038/s41598-023-44099-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2023] Open
Affiliation(s)
- S M Rafiqul Islam
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chattogram, 4331, Bangladesh.
| | - Afsana Yeasmin Tanzina
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chattogram, 4331, Bangladesh
| | - Md Javed Foysal
- School of Molecular and Life Sciences, Curtin University, Bentley, WA, 6102, Australia
- Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet, 3114, Bangladesh
| | - M Nazmul Hoque
- Department of Gynecology, Obstetrics and Reproductive Health, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, 1706, Bangladesh
| | - Meheadi Hasan Rumi
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chattogram, 4331, Bangladesh
| | - A M A M Zonaed Siddiki
- Department of Pathology and Parasitology, Chattogram Veterinary and Animal Sciences University, Chattogram, 4225, Bangladesh
| | - Alfred Chin-Yen Tay
- Helicobacter Research Laboratory, The Marshall Centre, University of Western Australia, Perth, WA, 6009, Australia
| | - M Jakir Hossain
- Forest Chemistry Division, Bangladesh Forest Research Institute, Chattogram, 4211, Bangladesh
| | - Muhammad Abu Bakar
- Bangladesh Council of Scientific and Industrial Research (BCSIR) Laboratories, Chattogram, 4220, Bangladesh
| | - Mohammad Mostafa
- Bangladesh Council of Scientific and Industrial Research (BCSIR) Laboratories, Chattogram, 4220, Bangladesh
| | - Adnan Mannan
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chattogram, 4331, Bangladesh.
| |
Collapse
|
15
|
Diba F, Hoque MN, Rahman MS, Haque F, Rahman KMJ, Moniruzzaman M, Khan M, Hossain MA, Sultana M. Metagenomic and culture-dependent approaches unveil active microbial community and novel functional genes involved in arsenic mobilization and detoxification in groundwater. BMC Microbiol 2023; 23:241. [PMID: 37648982 PMCID: PMC10466822 DOI: 10.1186/s12866-023-02980-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 08/14/2023] [Indexed: 09/01/2023] Open
Abstract
BACKGROUND Arsenic (As) and its species are major pollutants in ecological bodied including groundwater in Bangladesh rendering serious public health concern. Bacteria with arsenotrophic genes have been found in the aquifer, converting toxic arsenite [As (III)] to less toxic arsenate [As (V)] that is easily removed using chemical and biological trappers. In this study, genomic and metagenomic approaches parallel to culture-based assay (Graphical abstract) have made it possible to decipher phylogenetic diversity of groundwater arsenotrophic microbiomes along with elucidation of their genetic determinants. RESULTS Seventy-two isolates were retrieved from six As-contaminated (average As concentration of 0.23 mg/L) groundwater samples from Munshiganj and Chandpur districts of Bangladesh. Twenty-three isolates harbored arsenite efflux pump (arsB) gene with high abundance, and ten isolates possessing arsenite oxidase (aioA) gene, with a wide range of minimum inhibitory concentration, MICAs (2 to 32 mM), confirming their role in arsenite metabolism. There was considerable heterogeneity in species richness and microbial community structure. Microbial taxa from Proteobacteria, Firmicutes and Acidobacteria dominated these diversities. Through these combinatorial approaches, we have identified potential candidates such as, Pseudomonas, Acinetobacter, Stenotrophomonas, Achromobacter, Paraburkholderia, Comamonas and Klebsiella and associated functional genes (arsB, acr3, arsD, arsH, arsR) that could significantly contribute to arsenite detoxification, accumulation, and immobilization. CONCLUSIONS Culture-dependent and -independent shotgun metagenomic investigation elucidated arsenotrophic microbiomes and their functions in As biogeochemical transformation. These findings laid a foundation for further large-scale researches on the arsenotrophic microbiomes and their concurrent functions in As biogeochemical transformation in As-contaminated areas of Bangladesh and beyond.
Collapse
Affiliation(s)
- Farzana Diba
- Department of Microbiology, University of Dhaka, Dhaka, 1000, Bangladesh
- Institute of Tissue Banking and Biomaterial Research, Atomic Energy Research Establishment, Savar, Dhaka, 1349, Bangladesh
| | - M Nazmul Hoque
- Department of Gynecology, Obstetrics and Reproductive Health, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, 1706, Bangladesh
| | - M Shaminur Rahman
- Department of Microbiology, Jashore University of Science and Technology, Jashore, 7408, Bangladesh
| | - Farhana Haque
- Department of Microbiology, University of Dhaka, Dhaka, 1000, Bangladesh
| | | | - Md Moniruzzaman
- Bangladesh Reference Institute for Chemical Measurements (BRiCM), Dr. Qudrat-E-Khuda Road, Dhanmondi, Dhaka, 1205, Bangladesh
| | - Mala Khan
- Bangladesh Reference Institute for Chemical Measurements (BRiCM), Dr. Qudrat-E-Khuda Road, Dhanmondi, Dhaka, 1205, Bangladesh
| | - M Anwar Hossain
- Department of Microbiology, University of Dhaka, Dhaka, 1000, Bangladesh
- Present address: Jashore University of Science and Technology, Jashore, 7408, Bangladesh
| | - Munawar Sultana
- Department of Microbiology, University of Dhaka, Dhaka, 1000, Bangladesh.
| |
Collapse
|
16
|
Hassan J, Bag MAS, Ali MW, Kabir A, Hoque MN, Hossain MM, Rahman MT, Islam MS, Khan MSR. Diversity of Streptococcus spp. and genomic characteristics of Streptococcus uberis isolated from clinical mastitis of cattle in Bangladesh. Front Vet Sci 2023; 10:1198393. [PMID: 37533458 PMCID: PMC10392839 DOI: 10.3389/fvets.2023.1198393] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 06/26/2023] [Indexed: 08/04/2023] Open
Abstract
Introduction Streptococci are the major etiology in mastitis in dairy cattle, a cause of huge economic losses in the dairy industries. This study was aimed to determine the diversity of Streptococcus spp. isolated from clinical mastitis of cattle reared in Bangladesh. Methods A total of 843 lactating cattle reared in four prominent dairy farms and one dairy community were purposively included in this study where 80 cattle were positive to clinical mastitis (CM) based on gross changes in the udder (redness, swelling, and sensitive udder) and/or milk (flakes and/or clots). Milk samples were collected from all the eighty cattle with clinical mastitis (CCM) and twenty five apparently healthy cattle (AHC). Samples were enriched in Luria Bertani broth (LB) and one hundred microliter of the enrichment culture was spread onto selective media for the isolation of Staphylococcus spp., Streptococcus spp., Enterococcus spp., Escherichia coli and Corynebacterium spp., the major pathogen associated with mastitis. Isolates recovered from culture were further confirmed by species specific PCR. Results and Discussion Out of 105 samples examined 56.2% (59/105), 17.14% (18/105), 9.52% (10/105) and 22.9% (24/105) samples were positive for Staphylococcus, Streptococcus, Enterococcus faecalis and E. coli, respectively. This study was then directed to the determination of diversity of Streptococcus spp. through the sequencing of 16S rRNA. A total of eighteen of the samples from CCM (22.5%) but none from the AHC were positive for Streptococcus spp. by cultural and molecular examination. Sequencing and phylogenetic analysis of 16S rRNA identified 55.6, 33.3, 5.6 and 5.6% of the Streptococcus isolates as Streptococcus uberis, Streptococcus agalactiae, Streptococcus hyovaginalis and Streptococcus urinalis, respectively. Considering the high prevalence and worldwide increasing trend of S. uberis in mastitis, in-depth molecular characterization of S. uberis was performed through whole genome sequencing. Five of the S. uberis strain isolated in this study were subjected to WGS and on analysis two novel ST types of S. uberis were identified, indicating the presence of at least two different genotypes of S. uberis in the study areas. On virulence profiling, all the isolates harbored at least 35 virulence and putative virulence genes probably associated with intramammary infection (IMI) indicating all the S. uberis isolated in this study are potential mastitis pathogen. Overall findings suggest that Streptococcus encountered in bovine mastitis is diverse and S. uberis might be predominantly associated with CM in the study areas. The S. uberis genome carries an array of putative virulence factors that need to be investigated genotypically and phenotypically to identify a specific trait governing the virulence and fitness of this bacterium. Moreover, the genomic information could be used for the development of new genomic tools for virulence gene profiling of S. uberis.
Collapse
Affiliation(s)
- Jayedul Hassan
- Department of Microbiology and Hygiene, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Md. Abdus Sattar Bag
- Department of Microbiology and Hygiene, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Md. Wohab Ali
- Department of Microbiology and Hygiene, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Ajran Kabir
- Department of Microbiology and Hygiene, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - M. Nazmul Hoque
- Department of Gynecology, Obstetrics and Reproductive Health, Faculty of Veterinary Medicine and Animal Science, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, Bangladesh
| | - Muhammad Maqsud Hossain
- Department of Biochemistry and Microbiology, North South University, Dhaka, Bangladesh
- NSU Genome Research Institute (NGRI), North South University, Dhaka, Bangladesh
| | - Md. Tanvir Rahman
- Department of Microbiology and Hygiene, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Md. Shafiqul Islam
- Department of Microbiology and Hygiene, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Md. Shahidur Rahman Khan
- Department of Microbiology and Hygiene, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh, Bangladesh
| |
Collapse
|
17
|
Islam T, Fatema, Hoque MN, Gupta DR, Mahmud NU, Sakif TI, Sharpe AG. Improvement of growth, yield and associated bacteriome of rice by the application of probiotic Paraburkholderia and Delftia. Front Microbiol 2023; 14:1212505. [PMID: 37520368 PMCID: PMC10375411 DOI: 10.3389/fmicb.2023.1212505] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 06/28/2023] [Indexed: 08/01/2023] Open
Abstract
Plant probiotic bacteria enhance growth and yield of crop plants when applied at the appropriate time and dose. Two rice probiotic bacteria, Paraburkholderia fungorum strain BRRh-4 and Delftia sp. strain BTL-M2 promote growth and yield of plants. However, no information is available on application of these two bacteria on growth, yield, and diversity and population of bacteriome in roots and rhizosphere soils of the treated rice plants. This study aimed to assess the effect of BRRh-4 and BTL-M2 application on growth, yield and bacteriome in roots and rhizosphere soil of rice under varying doses of N, P and K fertilizers. Application of BRRh-4 and BTL-M2 strains significantly (p < 0.05) increased seed germination, growth and yield of rice compared to an untreated control. Interestingly, the grain yield of rice by these bacteria with 50% less of the recommended doses of N, P, and K fertilizers were statistically similar to or better than the rice plants treated with 100% doses of these fertilizers. Targeted amplicon (16S rRNA) sequence-based analysis revealed significant differences (PERMANOVA, p = 0.00035) in alpha-diversity between the root (R) and rhizosphere soil (S) samples, showing higher diversity in the microbial ecosystem of root samples. Additionally, the bacteriome diversity in the root of rice plants that received both probiotic bacteria and chemical fertilizers were significantly higher (PERMANOVA, p = 0.0312) compared to the rice plants treated with fertilizers only. Out of 185 bacterial genera detected, Prevotella, an anaerobic and Gram-negative bacterium, was found to be the predominant genus in both rhizosphere soil and root metagenomes. However, the relative abundance of Prevotella remained two-fold higher in the rhizosphere soil metagenome (52.02%) than in the root metagenome (25.04%). The other predominant bacterial genera detected in the rice root metagenome were Bacillus (11.07%), Planctomyces (4.06%), Faecalibacterium (3.91%), Deinococcus (2.97%), Bacteroides (2.61%), and Chryseobacterium (2.30%). On the other hand, rhizosphere soil metagenome had Bacteroides (12.38%), Faecalibacterium (9.50%), Vibrio (5.94%), Roseomonas (3.40%), and Delftia (3.02%). Interestingly, we found the presence and/or abundance of specific genera of bacteria in rice associated with the application of a specific probiotic bacterium. Taken together, our results indicate that improvement of growth and yield of rice by P. fungorum strain BRRh-4 and Delftia sp. strain BTL-M2 is likely linked with modulation of diversity, structures, and signature of bacteriome in roots and rhizosphere soils. This study for the first time demonstrated that application of plant growth promoting bacteria significantly improve growth, yield and increase the diversity of bacterial community in rice.
Collapse
Affiliation(s)
- Tofazzal Islam
- Institute of Biotechnology and Genetic Engineering (IBGE), Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur, Bangladesh
| | - Fatema
- Institute of Biotechnology and Genetic Engineering (IBGE), Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur, Bangladesh
| | - M. Nazmul Hoque
- Department of Gynecology, Obstetrics and Reproductive Health, BSMRAU, Gazipur, Bangladesh
| | - Dipali Rani Gupta
- Institute of Biotechnology and Genetic Engineering (IBGE), Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur, Bangladesh
| | - Nur Uddin Mahmud
- Institute of Biotechnology and Genetic Engineering (IBGE), Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur, Bangladesh
| | - Tahsin Islam Sakif
- Lane Department of Computer Science and Electrical Engineering, West Virginia University, Morgantown, WV, United States
| | - Andrew G. Sharpe
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK, Canada
| |
Collapse
|
18
|
Hoque MN, Jerin S, Faisal GM, Das ZC, Islam T, Rahman ANMA. Whole-Genome Sequence of Multidrug-Resistant Escherichia coli Strains Isolated from Mice with Mastitis. Microbiol Resour Announc 2023:e0032023. [PMID: 37314348 DOI: 10.1128/mra.00320-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023] Open
Abstract
We sequenced the genomes of Escherichia coli isolates G2M6U and G6M1F, two multidrug-resistant strains that were isolated from mammary tissue and fecal samples, respectively, from mice with induced mastitis. The complete genomes of G2M6U and G6M1F consist of chromosomes of 4.4 Mbp and 4.6 Mbp, respectively.
Collapse
Affiliation(s)
- M Nazmul Hoque
- Molecular Biology and Bioinformatics Laboratory, Department of Gynaecology, Obstetrics, and Reproductive Health, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, Bangladesh
| | - Shobnom Jerin
- Molecular Biology and Bioinformatics Laboratory, Department of Gynaecology, Obstetrics, and Reproductive Health, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, Bangladesh
| | - Golam Mahbub Faisal
- Molecular Biology and Bioinformatics Laboratory, Department of Gynaecology, Obstetrics, and Reproductive Health, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, Bangladesh
| | - Ziban Chandra Das
- Molecular Biology and Bioinformatics Laboratory, Department of Gynaecology, Obstetrics, and Reproductive Health, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, Bangladesh
| | - Tofazzal Islam
- Institute of Biotechnology and Genetic Engineering, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, Bangladesh
| | - Abu Nasar M Aminoor Rahman
- Molecular Biology and Bioinformatics Laboratory, Department of Gynaecology, Obstetrics, and Reproductive Health, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, Bangladesh
| |
Collapse
|
19
|
Hoque MN, Moyna Z, Faisal GM, Das ZC, Islam T. Whole-Genome Sequence of Multidrug-Resistant Klebsiella pneumoniae MNH_G2C5, Isolated from Bovine Clinical Mastitis Milk. Microbiol Resour Announc 2023; 12:e0007923. [PMID: 37093061 DOI: 10.1128/mra.00079-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2023] Open
Abstract
Klebsiella pneumoniae is one of the most common and important mastitis-causing bacteria, and strain MNH_G2C5 was isolated from the milk of a cow suffering from clinical mastitis in a dairy farm of the Gazipur district of Bangladesh. The MNH_G2C5 genome was estimated to be 4,589,728 bp, with 65.5% genome coverage.
Collapse
Affiliation(s)
- M Nazmul Hoque
- Molecular Biology and Bioinformatics Laboratory, Department of Gynaecology, Obstetrics and Reproductive Health, Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur, Bangladesh
| | - Zannatara Moyna
- Molecular Biology and Bioinformatics Laboratory, Department of Gynaecology, Obstetrics and Reproductive Health, Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur, Bangladesh
| | - Golam Mahbub Faisal
- Molecular Biology and Bioinformatics Laboratory, Department of Gynaecology, Obstetrics and Reproductive Health, Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur, Bangladesh
| | - Ziban Chandra Das
- Molecular Biology and Bioinformatics Laboratory, Department of Gynaecology, Obstetrics and Reproductive Health, Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur, Bangladesh
| | - Tofazzal Islam
- Institute of Biotechnology and Genetic Engineering, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, Bangladesh
| |
Collapse
|
20
|
Hoque MN, Moyna Z, Faisal GM, Das ZC. Whole-Genome Sequence of the Multidrug-Resistant Staphylococcus warneri Strain G1M1F, Isolated from Mice with Mastitis. Microbiol Resour Announc 2023; 12:e0027523. [PMID: 37093041 DOI: 10.1128/mra.00275-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2023] Open
Abstract
We sequenced the genome of Staphylococcus warneri G1M1F, a multidrug-resistant strain isolated from fecal samples of mice with induced mastitis. The complete genome of G1M1F consists of one chromosome of 2,504,515 bp and two plasmid replicons of 28,679 and 8,615 bp; it comprises 32.7% GC content, with 60× genome coverage.
Collapse
Affiliation(s)
- M Nazmul Hoque
- Molecular Biology and Bioinformatics Laboratory, Department of Gynaecology, Obstetrics and Reproductive Health, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, Bangladesh
| | - Zannatara Moyna
- Molecular Biology and Bioinformatics Laboratory, Department of Gynaecology, Obstetrics and Reproductive Health, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, Bangladesh
| | - Golam Mahbub Faisal
- Molecular Biology and Bioinformatics Laboratory, Department of Gynaecology, Obstetrics and Reproductive Health, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, Bangladesh
| | - Ziban Chandra Das
- Molecular Biology and Bioinformatics Laboratory, Department of Gynaecology, Obstetrics and Reproductive Health, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, Bangladesh
| |
Collapse
|
21
|
Rahman MS, Hoque MN, Chowdhury SR, Siddique MM, Islam OK, Galib SM, Islam MT, Hossain MA. Temporal dynamics and fatality of SARS-CoV-2 variants in Bangladesh. Health Sci Rep 2023; 6:e1209. [PMID: 37077184 PMCID: PMC10108430 DOI: 10.1002/hsr2.1209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 03/15/2023] [Accepted: 03/24/2023] [Indexed: 04/21/2023] Open
Abstract
Background and Aims Since the beginning of the SARS-CoV-2 pandemic, multiple new variants have emerged posing an increased risk to global public health. This study aimed to investigate SARS-CoV-2 variants, their temporal dynamics, infection rate (IFR) and case fatality rate (CFR) in Bangladesh by analyzing the published genomes. Methods We retrieved 6610 complete whole genome sequences of the SARS-CoV-2 from the GISAID (Global Initiative on Sharing all Influenza Data) platform from March 2020 to October 2022, and performed different in-silico bioinformatics analyses. The clade and Pango lineages were assigned by using Nextclade v2.8.1. SARS-CoV-2 infections and fatality data were collected from the Institute of Epidemiology Disease Control and Research (IEDCR), Bangladesh. The average IFR was calculated from the monthly COVID-19 cases and population size while average CFR was calculated from the number of monthly deaths and number of confirmed COVID-19 cases. Results SARS-CoV-2 first emerged in Bangladesh on March 3, 2020 and created three pandemic waves so far. The phylogenetic analysis revealed multiple introductions of SARS-CoV-2 variant(s) into Bangladesh with at least 22 Nextstrain clades and 107 Pangolin lineages with respect to the SARS-CoV-2 reference genome of Wuhan/Hu-1/2019. The Delta variant was detected as the most predominant (48.06%) variant followed by Omicron (27.88%), Beta (7.65%), Alpha (1.56%), Eta (0.33%) and Gamma (0.03%) variant. The overall IFR and CFR from circulating variants were 13.59% and 1.45%, respectively. A time-dependent monthly analysis showed significant variations in the IFR (p = 0.012, Kruskal-Wallis test) and CFR (p = 0.032, Kruskal-Wallis test) throughout the study period. We found the highest IFR (14.35%) in 2020 while Delta (20A) and Beta (20H) variants were circulating in Bangladesh. Remarkably, the highest CFR (1.91%) from SARS-CoV-2 variants was recorded in 2021. Conclusion Our findings highlight the importance of genomic surveillance for careful monitoring of variants of concern emergence to interpret correctly their relative IFR and CFR, and thus, for implementation of strengthened public health and social measures to control the spread of the virus. Furthermore, the results of the present study may provide important context for sequence-based inference in SARS-CoV-2 variant(s) evolution and clinical epidemiology beyond Bangladesh.
Collapse
Affiliation(s)
- M. Shaminur Rahman
- Department of MicrobiologyJashore University of Science and TechnologyJashoreBangladesh
| | - M. Nazmul Hoque
- Department of Gynecology, Obstetrics and Reproductive HealthBangabandhu Sheikh Mujibur Rahman Agricultural UniversityGazipurBangladesh
| | - Susmita Roy Chowdhury
- Department of MicrobiologyJashore University of Science and TechnologyJashoreBangladesh
| | - Md. Moradul Siddique
- Department of Computer Science and EngineeringJashore University of Science and TechnologyJashoreBangladesh
| | - Ovinu Kibria Islam
- Department of MicrobiologyJashore University of Science and TechnologyJashoreBangladesh
| | - Syed Md. Galib
- Department of Computer Science and EngineeringJashore University of Science and TechnologyJashoreBangladesh
| | - Md. Tanvir Islam
- Department of MicrobiologyJashore University of Science and TechnologyJashoreBangladesh
| | - M. Anwar Hossain
- Department of MicrobiologyUniversity of DhakaDhakaBangladesh
- Jashore University of Science and TechnologyJashoreBangladesh
| |
Collapse
|
22
|
Al Mamun Khan MA, Ahsan A, Khan MA, Sanjana JM, Biswas S, Saleh MA, Gupta DR, Hoque MN, Sakif TI, Rahman MM, Islam T. In-silico prediction of highly promising natural fungicides against the destructive blast fungus Magnaporthe oryzae. Heliyon 2023; 9:e15113. [PMID: 37123971 PMCID: PMC10130775 DOI: 10.1016/j.heliyon.2023.e15113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 03/24/2023] [Accepted: 03/27/2023] [Indexed: 05/02/2023] Open
Abstract
Magnaporthe oryzae causes destructive blast disease in more than 50 species of the major cereal crops rice, wheat and maize and destroys food of millions of people worldwide. Application of synthetic chemical fungicides are environmentally hazardous and unreliable in controlling M. oryzae. Conversely, naturally occurring biofungicides with multiple modes of actions are needed to be discovered for combatting the blast fungus. To find the effective biofungicides, we performed molecular docking study of some potential antifungal natural compounds targeting two proteins including a single-stranded DNA binding protein MoSub1 (4AGH), and an effector protein AVR-Pik (5E9G) of M. oryzae that regulates transcription in fungus and/or suppresses the host cell immunity. The thirty-nine natural compounds previously shown to inhibit M. oryzae growth and reproduction were put under molecular docking against these two proteins followed by simulation, free energy, and interaction analysis of protein-ligand complexes. The virtual screening revealed that two alkaloidal metabolites, camptothecin and GKK1032A2 showed excellent binding energy with any of these target proteins compared to reference commercial fungicides, azoxystrobin and strobilurin. Of the detected compounds, GKK1032A2 bound to both target proteins of M. oryzae. Both compounds showed excellent bioactivity scores as compared to the reference fungicides. Results of our computational biological study suggest that both camptothecin and GKK1032A2 are potential fungicides that could also be considered as lead compounds to design novel fungicides against the blast fungus. Furthermore, the GKK1032A2 acted as a multi-site mode of action fungicide against M. oryzae.
Collapse
Affiliation(s)
- Md Abdullah Al Mamun Khan
- Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Tangail 1902, Bangladesh
| | - Asif Ahsan
- Department of Biotechnology, Bangladesh Agricultural University, Mymensingh, 2202, Bangladesh
| | - Md Arif Khan
- Department of Biotechnology and Genetic Engineering, University of Development Alternative, Dhaka 1209, Bangladesh
- Bio-Bio-1 Bioinformatics Research Foundation, Dhaka, Bangladesh
| | - Jannatul Maowa Sanjana
- Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Tangail 1902, Bangladesh
| | - Suvro Biswas
- Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - Md Abu Saleh
- Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - Dipali Rani Gupta
- Institute of Biotechnology and Genetic Engineering (IBGE), Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur 1706, Bangladesh
| | - M. Nazmul Hoque
- Department of Gynecology, Obstetrics and Reproductive Health, BSMRAU, Gazipur 1706, Bangladesh
| | - Tahsin Islam Sakif
- Lane Department of Computer Science and Electrical Engineering, West Virginia University, Morgantown, WV 26506-6109, USA
| | - Md Masuder Rahman
- Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Tangail 1902, Bangladesh
| | - Tofazzal Islam
- Institute of Biotechnology and Genetic Engineering (IBGE), Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur 1706, Bangladesh
- Corresponding author. Institute of Biotechnology and Genetic Engineering (IBGE), Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur 1706, Bangladesh.
| |
Collapse
|
23
|
Mannan A, Hoque MN, Noyon SH, Hamidullah Mehedi HM, Foisal J, Salauddin A, Rafiqul Islam SM, Sharmen F, Tanni AA, Siddiki AZ, Tay A, Siddique M, Shaminur Rahman M, Galib SM, Akter F. SARS-CoV-2 infection alters the gut microbiome in diabetes patients: A cross-sectional study from Bangladesh. J Med Virol 2023; 95:e28691. [PMID: 36946508 DOI: 10.1002/jmv.28691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 03/07/2023] [Accepted: 03/19/2023] [Indexed: 03/23/2023]
Abstract
Populations of different South Asian nations including Bangladesh reportedly have a high risk of developing diabetes in recent years. This study aimed to investigate the differences in the gut microbiome of COVID-19 positive participants with or without T2DM compared with healthy control subjects. Microbiome data of thirty participants with T2DM were compared with twenty-two age-, sex-, and BMI-matched individuals. Clinical features were recorded while fecal samples were collected aseptically from the participants. Amplicon-based (16S rRNA) metagenome analyses were employed to explore the dysbiosis of gut microbiota and its correlation with genomic and functional features in COVID-19 patients with or without T2DM. Comparing the detected bacterial genera across the sample groups, 98 unique genera were identified, of which nine genera had unique association with COVID-19 T2DM patients. Among different bacterial groups, Shigella (25.0%), Bacteroides (23.45%), and Megamonas (15.90%) had higher mean relative abundances in COVID-19 patients with T2DM. An elevated gut microbiota dysbiosis in T2DM patients with COVID-19 was observed while some metabolic functional changes correlated with bidirectional microbiome dysbiosis between diabetes and non-diabetes humans gut. These results further highlight the possible association of COVID-19 infection that might be linked with alteration of gut microbiome among T2DM patients. This article is protected by copyright. All rights reserved.
Collapse
Affiliation(s)
- Adnan Mannan
- Department of Genetic Engineering and Biotechnology, University of Chittagong, Chattogram, Bangladesh
- Next Generation Sequencing, Research and Innovation laboratory Chittagong (NRICh), Biotechnology Research and Innovation Centre (BRIC), Department of Genetic Engineering and Biotechnology, University of Chittagong, Chattogram, Bangladesh
| | - M Nazmul Hoque
- Department of Gynecology, Obstetrics and Reproductive Health, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, Bangladesh
| | - Sajjad Hossain Noyon
- Department of Genetic Engineering and Biotechnology, University of Chittagong, Chattogram, Bangladesh
- Next Generation Sequencing, Research and Innovation laboratory Chittagong (NRICh), Biotechnology Research and Innovation Centre (BRIC), Department of Genetic Engineering and Biotechnology, University of Chittagong, Chattogram, Bangladesh
| | | | - Javed Foisal
- School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia
| | - Asma Salauddin
- Department of Genetic Engineering and Biotechnology, University of Chittagong, Chattogram, Bangladesh
- Next Generation Sequencing, Research and Innovation laboratory Chittagong (NRICh), Biotechnology Research and Innovation Centre (BRIC), Department of Genetic Engineering and Biotechnology, University of Chittagong, Chattogram, Bangladesh
| | - S M Rafiqul Islam
- Department of Genetic Engineering and Biotechnology, University of Chittagong, Chattogram, Bangladesh
- Next Generation Sequencing, Research and Innovation laboratory Chittagong (NRICh), Biotechnology Research and Innovation Centre (BRIC), Department of Genetic Engineering and Biotechnology, University of Chittagong, Chattogram, Bangladesh
| | - Farjana Sharmen
- Department of Genetic Engineering and Biotechnology, University of Chittagong, Chattogram, Bangladesh
- Next Generation Sequencing, Research and Innovation laboratory Chittagong (NRICh), Biotechnology Research and Innovation Centre (BRIC), Department of Genetic Engineering and Biotechnology, University of Chittagong, Chattogram, Bangladesh
| | - Afroza Akter Tanni
- Department of Genetic Engineering and Biotechnology, University of Chittagong, Chattogram, Bangladesh
- Next Generation Sequencing, Research and Innovation laboratory Chittagong (NRICh), Biotechnology Research and Innovation Centre (BRIC), Department of Genetic Engineering and Biotechnology, University of Chittagong, Chattogram, Bangladesh
| | - Amam Zonaed Siddiki
- COVID Diagnostic Lab, Department of Pathology and Parasitology, Chattogram Veterinary and Animal Sciences University, Chattogram, Bangladesh
| | - Alfred Tay
- Helicobacter Research Laboratory, Marshall Centre for Infectious Disease Research and Training, School of Biomedical Sciences, University of Western Australia, Perth, WA, Australia
| | - Moradul Siddique
- Department of Computer Science and Engineering, Jashore University of Science and Technology, Jashore, 7408, Bangladesh
| | - M Shaminur Rahman
- Department of Microbiology, Jashore University of Science and Technology, Bangladesh, Jashore, 7408
| | - Syed Md Galib
- Department of Computer Science and Engineering, Jashore University of Science and Technology, Jashore, 7408, Bangladesh
| | - Farhana Akter
- Department of Endocrinology, Chittagong Medical College, Chattogram, 4203, Bangladesh
| |
Collapse
|
24
|
Islam MA, Shahi S, Marzan AA, Amin MR, Hasan MN, Hoque MN, Ghosh A, Barua A, Khan A, Dhama K, Chakraborty C, Bhattacharya P, Wei DQ. Variant-specific deleterious mutations in the SARS-CoV-2 genome reveal immune responses and potentials for prophylactic vaccine development. Front Pharmacol 2023; 14:1090717. [PMID: 36825152 PMCID: PMC9941545 DOI: 10.3389/fphar.2023.1090717] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Accepted: 01/19/2023] [Indexed: 02/10/2023] Open
Abstract
Introduction: Coronavirus disease 2019 (COVID-19), caused by SARS-CoV-2, has had a disastrous effect worldwide during the previous three years due to widespread infections with SARS-CoV-2 and its emerging variations. More than 674 million confirmed cases and over 6.7 million deaths have been attributed to successive waves of SARS-CoV-2 infections as of 29th January 2023. Similar to other RNA viruses, SARS-CoV-2 is more susceptible to genetic evolution and spontaneous mutations over time, resulting in the continual emergence of variants with distinct characteristics. Spontaneous mutations of SARS-CoV-2 variants increase its transmissibility, virulence, and disease severity and diminish the efficacy of therapeutics and vaccines, resulting in vaccine-breakthrough infections and re-infection, leading to high mortality and morbidity rates. Materials and methods: In this study, we evaluated 10,531 whole genome sequences of all reported variants globally through a computational approach to assess the spread and emergence of the mutations in the SARS-CoV-2 genome. The available data sources of NextCladeCLI 2.3.0 (https://clades.nextstrain.org/) and NextStrain (https://nextstrain.org/) were searched for tracking SARS-CoV-2 mutations, analysed using the PROVEAN, Polyphen-2, and Predict SNP mutational analysis tools and validated by Machine Learning models. Result: Compared to the Wuhan-Hu-1 reference strain NC 045512.2, genome-wide annotations showed 16,954 mutations in the SARS-CoV-2 genome. We determined that the Omicron variant had 6,307 mutations (retrieved sequence:1947), including 67.8% unique mutations, more than any other variant evaluated in this study. The spike protein of the Omicron variant harboured 876 mutations, including 443 deleterious mutations. Among these deleterious mutations, 187 were common and 256 were unique non-synonymous mutations. In contrast, after analysing 1,884 sequences of the Delta variant, we discovered 4,468 mutations, of which 66% were unique, and not previously reported in other variants. Mutations affecting spike proteins are mostly found in RBD regions for Omicron, whereas most of the Delta variant mutations drawn to focus on amino acid regions ranging from 911 to 924 in the context of epitope prediction (B cell & T cell) and mutational stability impact analysis protruding that Omicron is more transmissible. Discussion: The pathogenesis of the Omicron variant could be prevented if the deleterious and persistent unique immunosuppressive mutations can be targeted for vaccination or small-molecule inhibitor designing. Thus, our findings will help researchers monitor and track the continuously evolving nature of SARS-CoV-2 strains, the associated genetic variants, and their implications for developing effective control and prophylaxis strategies.
Collapse
Affiliation(s)
- Md. Aminul Islam
- Advanced Molecular Lab, Department of Microbiology, President Abdul Hamid Medical College, Karimganj, Bangladesh,COVID-19 Diagnostic lab, Department of Microbiology, Noakhali Science and Technology University, Noakhali, Bangladesh,*Correspondence: Md. Aminul Islam, , ; Prosun Bhattacharya,
| | - Shatila Shahi
- Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet, Bangladesh
| | - Abdullah Al Marzan
- Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet, Bangladesh
| | - Mohammad Ruhul Amin
- COVID-19 Diagnostic lab, Department of Microbiology, Noakhali Science and Technology University, Noakhali, Bangladesh
| | - Mohammad Nayeem Hasan
- Department of Statistics, Shahjalal University of Science and Technology, Sylhet, Bangladesh
| | - M. Nazmul Hoque
- Department of Gynecology, Obstetrics and Reproductive Health, Faculty of Veterinary Medicine and Animal Science, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, Bangladesh
| | - Ajit Ghosh
- Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet, Bangladesh
| | - Abanti Barua
- COVID-19 Diagnostic lab, Department of Microbiology, Noakhali Science and Technology University, Noakhali, Bangladesh
| | - Abbas Khan
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China,Zhongjing Research and Industrialization Institute of Chinese Medicine, Zhongguancun Scientific Park, Nayang, Henan, China
| | - Kuldeep Dhama
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Bareilly, Uttar Pradesh, India
| | - Chiranjib Chakraborty
- Department of Biotechnology, School of Life Science and Biotechnology, Adamas University, Kolkata, West Bengal, India
| | - Prosun Bhattacharya
- COVID-19 Research @KTH, Department of Sustainable Development, Environmental Science and Engineering, KTH Royal Institute of Technology, Stockholm, Sweden,*Correspondence: Md. Aminul Islam, , ; Prosun Bhattacharya,
| | - Dong-Qing Wei
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China,Zhongjing Research and Industrialization Institute of Chinese Medicine, Zhongguancun Scientific Park, Nayang, Henan, China,Peng Cheng Laboratory, Shenzhen, Guangdong, China
| |
Collapse
|
25
|
Hoque MN, Rahman MS, Sarkar MMH, Habib MA, Akter S, Banu TA, Goswami B, Jahan I, Hossain MA, Khan MS, Islam T. Transcriptome analysis reveals increased abundance and diversity of opportunistic fungal pathogens in nasopharyngeal tract of COVID-19 patients. PLoS One 2023; 18:e0278134. [PMID: 36656835 PMCID: PMC9851516 DOI: 10.1371/journal.pone.0278134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 11/09/2022] [Indexed: 01/20/2023] Open
Abstract
We previously reported that SARS-CoV-2 infection reduces human nasopharyngeal commensal microbiomes (bacteria, archaea and commensal respiratory viruses) with inclusion of pathobionts. This study aimed to assess the possible changes in the abundance and diversity of resident mycobiome in the nasopharyngeal tract (NT) of humans due to SARS-CoV-2 infections. Twenty-two (n = 22) nasopharyngeal swab samples (including COVID-19 = 8, Recovered = 7, and Healthy = 7) were collected for RNA-sequencing followed by taxonomic profiling of mycobiome. Our analyses indicate that SARS-CoV-2 infection significantly increased (p < 0.05, Wilcoxon test) the population and diversity of fungi in the NT with inclusion of a high proportion of opportunistic pathogens. We detected 863 fungal species including 533, 445, and 188 species in COVID-19, Recovered, and Healthy individuals, respectively that indicate a distinct mycobiome dysbiosis due to the SARS-CoV-2 infection. Remarkably, 37% of the fungal species were exclusively associated with SARS-CoV-2 infection, where S. cerevisiae (88.62%) and Phaffia rhodozyma (10.30%) were two top abundant species. Likewise, Recovered humans NT samples were predominated by Aspergillus penicillioides (36.64%), A. keveii (23.36%), A. oryzae (10.05%) and A. pseudoglaucus (4.42%). Conversely, Nannochloropsis oceanica (47.93%), Saccharomyces pastorianus (34.42%), and S. cerevisiae (2.80%) were the top abundant fungal species in Healthy controls nasal swabs. Importantly, 16% commensal fungal species found in the Healthy controls were not detected in either COVID-19 patients or when they were cured from COVID-19 (Recovered). We also detected several altered metabolic pathways correlated with the dysbiosis of fungal mycobiota in COVID-19 patients. Our results suggest that SARS-CoV-2 infection causes significant dysbiosis of mycobiome and related metabolic functions possibly play a determining role in the progression of SARS-CoV-2 pathogenesis. These findings might be helpful for developing mycobiome-based diagnostics, and also devising appropriate therapeutic regimens including antifungal drugs for prevention and control of concurrent fungal coinfections in COVID-19 patients.
Collapse
Affiliation(s)
- M. Nazmul Hoque
- Department of Gynecology, Obstetrics and Reproductive Health, Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur, Bangladesh
| | - M. Shaminur Rahman
- Department of Microbiology, Jashore University of Science and Technology, Jashore, Bangladesh
| | | | - Md Ahashan Habib
- Bangladesh Council of Scientific & Industrial Research (BCSIR), Dhanmondi, Dhaka, Bangladesh
| | - Shahina Akter
- Bangladesh Council of Scientific & Industrial Research (BCSIR), Dhanmondi, Dhaka, Bangladesh
| | - Tanjina Akhtar Banu
- Bangladesh Council of Scientific & Industrial Research (BCSIR), Dhanmondi, Dhaka, Bangladesh
| | - Barna Goswami
- Bangladesh Council of Scientific & Industrial Research (BCSIR), Dhanmondi, Dhaka, Bangladesh
| | - Iffat Jahan
- Bangladesh Council of Scientific & Industrial Research (BCSIR), Dhanmondi, Dhaka, Bangladesh
| | - M. Anwar Hossain
- Jashore Unive rsity of Science and Technology, Jashore, Bangladesh
| | - M. Salim Khan
- Bangladesh Council of Scientific & Industrial Research (BCSIR), Dhanmondi, Dhaka, Bangladesh
| | - Tofazzal Islam
- Institute of Biotechnology and Genetic Engineering (IBGE), BSMRAU, Gazipur, Bangladesh
| |
Collapse
|
26
|
Islam T, Afroz N, Koh C, Hoque MN, Rahman MJ, Gupta DR, Mahmud NU, Nahid AA, Islam R, Bhowmik PK, Sharpe AG. Whole-genome sequencing of a year-round fruiting jackfruit ( Artocarpus heterophyllus Lam.) reveals high levels of single nucleotide variation. Front Plant Sci 2022; 13:1044420. [PMID: 36605965 PMCID: PMC9809283 DOI: 10.3389/fpls.2022.1044420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 11/28/2022] [Indexed: 06/17/2023]
Abstract
Jackfruit (Artocarpus heterophyllus Lam.) is the national fruit of Bangladesh and produces fruit in the summer season only. However, jackfruit is not commercially grown in Bangladesh because of an extremely high variation in fruit quality, short seasonal fruiting (June-August) and susceptibility to abiotic stresses. Conversely, a year-round high yielding (ca. 4-fold higher than the seasonal variety) jackfruit variety, BARI Kanthal-3 developed by the Bangladesh Agricultural Research Institute (BARI) derived from a wild accession found in Ramgarh of Chattogram Hiltracts of Bangladesh, provides fruits from September to June. This study aimed to generate a draft whole-genome sequence (WGS) of BARI Kanthal-3 to obtain molecular insights including genes associated with year-round fruiting trait of this important unique variety. The estimated genome size of BARI Kanthal-3 was 1.04-gigabase-pair (Gbp) with a heterozygosity rate of 1.62%. De novo assembly yielded a scaffolded 817.7 Mb genome while a reference-guided approach, yielded 843 Mb of genome sequence. The estimated GC content was 34.10%. Variant analysis revealed that BARI Kanthal-3 included 5.7 M (35%) and 10.4 M (65%) simple and heterozygous single nucleotide polymorphisms (SNPs), and about 90% of all these polymorphisms are in inter-genic regions. Through BUSCO assessment, 97.2% of the core genes were represented in the assembly with 1.3% and 1.5% either fragmented or missing, respectively. By comparing identified orthologous gene groups in BARI Kanthal-3 with five closely and one distantly related species of 10,092 common orthogroups were found across the genomes of the six species. The phylogenetic analysis of the shared orthogroups showed that A. heterophyllus was the closest species to BARI Kanthal-3 and orthogroups related to flowering time were found to be more highly prevalent in BARI Kanthal-3 compared to the other Arctocarpus spp. The findings of this study will help better understanding the evolution, domestication, phylogenetic relationships, year-round fruiting of this highly nutritious fruit crop as well as providing a resource for molecular breeding.
Collapse
Affiliation(s)
- Tofazzal Islam
- Institute of Biotechnology and Genetic Engineering (IBGE), Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur, Bangladesh
| | - Nadia Afroz
- Institute of Biotechnology and Genetic Engineering (IBGE), Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur, Bangladesh
| | - ChuShin Koh
- Global Institute for Food Security (GIFS), University of Saskatchewan, Saskatoon, SK, Canada
| | - M. Nazmul Hoque
- Department of Gynecology, Obstetrics and Reproductive Health, Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur, Bangladesh
| | - Md. Jillur Rahman
- Pomology Division, Horticultural Research Center, Bangladesh Agricultural Research Institute, Gazipur, Bangladesh
| | - Dipali Rani Gupta
- Institute of Biotechnology and Genetic Engineering (IBGE), Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur, Bangladesh
| | - Nur Uddin Mahmud
- Institute of Biotechnology and Genetic Engineering (IBGE), Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur, Bangladesh
| | - Abdullah Al Nahid
- Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet, Bangladesh
| | - Rashedul Islam
- Bioinformatics Graduate Program, University of British Columbia, Vancouver, BC, Canada
| | - Pankaj K. Bhowmik
- Cell Technologies and Trait Development, National Research Council of Canada, Saskatoon, SK, Canada
| | - Andrew G. Sharpe
- Global Institute for Food Security (GIFS), University of Saskatchewan, Saskatoon, SK, Canada
| |
Collapse
|
27
|
Hoque MN, Jahan MI, Hossain MA, Sultana M. Genomic diversity and molecular epidemiology of a multidrug-resistant Pseudomonas aeruginosa DMC30b isolated from a hospitalized burn patient in Bangladesh. J Glob Antimicrob Resist 2022; 31:110-118. [PMID: 36058512 DOI: 10.1016/j.jgar.2022.08.023] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 08/02/2022] [Accepted: 08/29/2022] [Indexed: 12/30/2022] Open
Abstract
OBJECTIVES Pseudomonas aeruginosa is a key opportunistic pathogen causing a wide range of community- and hospital-acquired infections in immunocompromised or catheterized patients. Here, we report the complete genome sequence of a multidrug-resistant (MDR) P. aeruginosa DMC30b to elucidate the genetic diversity, molecular epidemiology, and underlying mechanisms for antimicrobial resistance and virulence. METHODS P. aeruginosa DMC30b was isolated from septic wound swab of a severe burn patient. Whole-genome sequencing was performed under Ion Torrent platform. The genome was assembled using the SPAdes v. 3.12.01 in an integrated Genome Analysis Platform for Ion Torrent sequence data. The genome was annotated using the National Center for Biotechnology Information (NCBI) Prokaryotic Genome Annotation Pipeline. In-silico predictions of antimicrobial resistance genes, virulence factor genes, and metabolic functional potentials were performed using different curated bioinformatics tools. RESULTS P. aeruginosa DMC30b was found as a MDR strain and belonged to sequence type 244 (ST244). The complete genome size is 6 994 756 bp with a coverage of 76.76x, guanine-cytosine content of 65.7% and a Benchmarking Universal Single-Copy Orthologs score of 100. The genome of P. aeruginosa DMC30b harboured two predicted plasmid replicons (e,g. IncP-6; 78 007 bp and ColRNAI; 9359 bp), 35 resistomes (antimicrobial resistance genes) conferring resistance to 18 different antibiotics (including four beta-lactam classes), and 214 virulence factor genes. It was identified as the 167th ST244 strain among ∼ 5800 whole-genome sequences of P. aeruginosa available in the NCBI database. CONCLUSION The MDR P. aeruginosa DMC30b was identified as the 167th ST244 complete genome to be submitted to the NCBI, and the first ST244 isolate sequenced from Bangladesh. The complete genome data with high genetic diversity and underlying mechanisms for antimicrobial resistance and virulence of P. aeruginosa DMC30b will aid in understanding the evolution and phylogeny of such high-risk clones and provide a solid basis for further research on MDR or extensively drug resistant strains.
Collapse
Affiliation(s)
- M Nazmul Hoque
- Department of Gynaecology, Obstetrics and Reproductive Health, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, Bangladesh
| | - M Ishrat Jahan
- Department of Microbiology, University of Dhaka, Dhaka, Bangladesh
| | - M Anwar Hossain
- Department of Microbiology, University of Dhaka, Dhaka, Bangladesh
| | - Munawar Sultana
- Department of Microbiology, University of Dhaka, Dhaka, Bangladesh.
| |
Collapse
|
28
|
Khan MA, Al Mamun Khan MA, Mahfuz AMUB, Sanjana JM, Ahsan A, Gupta DR, Hoque MN, Islam T. Highly potent natural fungicides identified in silico against the cereal killer fungus Magnaporthe oryzae. Sci Rep 2022; 12:20232. [PMID: 36418863 PMCID: PMC9684433 DOI: 10.1038/s41598-022-22217-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Accepted: 10/11/2022] [Indexed: 11/25/2022] Open
Abstract
Magnaporthe oryzae is one of the most notorious fungal pathogens that causes blast disease in cereals, and results in enormous loss of grain production. Many chemical fungicides are being used to control the pathogen but none of them are fully effective in controlling blast disease. Therefore, there is a demand for the discovery of a new natural biofungicide to manage the blast disease efficiently. A large number of new natural products showed inhibitory activities against M. oryzae in vitro. To find out effective biofungicides, we performed in silico molecular docking analysis of some of the potent natural compounds targeting four enzymes namely, scytalone dehydratase, SDH1 (PDB ID:1STD), trihydroxynaphthalene reductase, 3HNR (PDB ID:1YBV), trehalose-6-phosphate synthase, Tps1 (PDB ID:6JBI) and isocitrate lyase, ICL1 (PDB ID:5E9G) of M. oryzae fungus that regulate melanin biosynthesis and/or appresorium formation. Thirty-nine natural compounds that were previously reported to inhibit the growth of M. oryzae were subjected to rigid and flexible molecular docking against aforementioned enzymes followed by molecular dynamic simulation. The results of virtual screening showed that out of 39, eight compounds showed good binding energy with any one of the target enzymes as compared to reference commercial fungicides, azoxystrobin and strobilurin. Among the compounds, camptothecin, GKK1032A2 and chaetoviridin-A bind with more than one target enzymes of M. oryzae. All of the compounds except tricyclazole showed good bioactivity score. Taken together, our results suggest that all of the eight compounds have the potential to develop new fungicides, and remarkably, camptothecin, GKK1032A2 and chaetoviridin-A could act as multi-site mode of action fungicides against the blast fungus M. oryzae.
Collapse
Affiliation(s)
- Md. Arif Khan
- grid.443057.10000 0004 4683 7084Department of Biotechnology and Genetic Engineering, University of Development Alternative, Dhaka, 1209 Bangladesh
| | - Md. Abdullah Al Mamun Khan
- grid.443019.b0000 0004 0479 1356Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Tangail, 1902 Bangladesh
| | - A. M. U. B. Mahfuz
- grid.443057.10000 0004 4683 7084Department of Biotechnology and Genetic Engineering, University of Development Alternative, Dhaka, 1209 Bangladesh
| | - Jannatul Maowa Sanjana
- grid.443019.b0000 0004 0479 1356Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Tangail, 1902 Bangladesh
| | - Asif Ahsan
- grid.411511.10000 0001 2179 3896Department of Biotechnology, Bangladesh Agricultural University, Mymensingh, 2202 Bangladesh
| | - Dipali Rani Gupta
- grid.443108.a0000 0000 8550 5526Institute of Biotechnology and Genetic Engineering (IBGE), Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur, 1706 Bangladesh
| | - M. Nazmul Hoque
- grid.443108.a0000 0000 8550 5526Department of Gynecology, Obstetrics and Reproductive Health, BSMRAU, Gazipur, 1706 Bangladesh
| | - Tofazzal Islam
- grid.443108.a0000 0000 8550 5526Institute of Biotechnology and Genetic Engineering (IBGE), Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur, 1706 Bangladesh
| |
Collapse
|
29
|
Hoque MN, Talukder AK, Saha O, Hasan MM, Sultana M, Rahman ANMA, Das ZC. Antibiogram and virulence profiling reveals multidrug resistant
Staphylococcus aureus
as the predominant aetiology of subclinical mastitis in riverine buffaloes. Vet Med Sci 2022; 8:2631-2645. [DOI: 10.1002/vms3.942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Affiliation(s)
- M. Nazmul Hoque
- Department of Gynecology Obstetrics and Reproductive Health Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU) Gazipur Bangladesh
| | - Anup Kumar Talukder
- Department of Gynecology Obstetrics and Reproductive Health Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU) Gazipur Bangladesh
| | - Otun Saha
- Department of Microbiology Noakhali Science and Technology University Noakhali Bangladesh
- Department of Microbiology University of Dhaka Dhaka Bangladesh
| | - Mehedi Mahmudul Hasan
- Department of Fisheries and Marine Science Noakhali Science and Technology University Noakhali Bangladesh
| | - Munawar Sultana
- Department of Microbiology University of Dhaka Dhaka Bangladesh
| | - ANM Aminoor Rahman
- Department of Gynecology Obstetrics and Reproductive Health Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU) Gazipur Bangladesh
| | - Ziban Chandra Das
- Department of Gynecology Obstetrics and Reproductive Health Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU) Gazipur Bangladesh
| |
Collapse
|
30
|
Hoque MN, Sarkar MMH, Khan MA, Hossain MA, Hasan MI, Rahman MH, Habib MA, Akter S, Banu TA, Goswami B, Jahan I, Nafisa T, Molla MMA, Soliman ME, Araf Y, Khan MS, Zheng C, Islam T. Differential gene expression profiling reveals potential biomarkers and pharmacological compounds against SARS-CoV-2: Insights from machine learning and bioinformatics approaches. Front Immunol 2022; 13:918692. [PMID: 36059456 PMCID: PMC9429819 DOI: 10.3389/fimmu.2022.918692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 06/27/2022] [Indexed: 12/02/2022] Open
Abstract
The COVID-19 pandemic, caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), has created an urgent global situation. Therefore, it is necessary to identify the differentially expressed genes (DEGs) in COVID-19 patients to understand disease pathogenesis and the genetic factor(s) responsible for inter-individual variability and disease comorbidities. The pandemic continues to spread worldwide, despite intense efforts to develop multiple vaccines and therapeutic options against COVID-19. However, the precise role of SARS-CoV-2 in the pathophysiology of the nasopharyngeal tract (NT) is still unfathomable. This study utilized machine learning approaches to analyze 22 RNA-seq data from COVID-19 patients (n = 8), recovered individuals (n = 7), and healthy individuals (n = 7) to find disease-related differentially expressed genes (DEGs). We compared dysregulated DEGs to detect critical pathways and gene ontology (GO) connected to COVID-19 comorbidities. We found 1960 and 153 DEG signatures in COVID-19 patients and recovered individuals compared to healthy controls. In COVID-19 patients, the DEG–miRNA, and DEG–transcription factors (TFs) interactions network analysis revealed that E2F1, MAX, EGR1, YY1, and SRF were the highly expressed TFs, whereas hsa-miR-19b, hsa-miR-495, hsa-miR-340, hsa-miR-101, and hsa-miR-19a were the overexpressed miRNAs. Three chemical agents (Valproic Acid, Alfatoxin B1, and Cyclosporine) were abundant in COVID-19 patients and recovered individuals. Mental retardation, mental deficit, intellectual disability, muscle hypotonia, micrognathism, and cleft palate were the significant diseases associated with COVID-19 by sharing DEGs. Finally, the detected DEGs mediated by TFs and miRNA expression indicated that SARS-CoV-2 infection might contribute to various comorbidities. Our results provide the common DEGs between COVID-19 patients and recovered humans, which suggests some crucial insights into the complex interplay between COVID-19 progression and the recovery stage, and offer some suggestions on therapeutic target identification in COVID-19 caused by the SARS-CoV-2.
Collapse
Affiliation(s)
- M. Nazmul Hoque
- Department of Gynecology, Obstetrics and Reproductive Health, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, Bangladesh
| | | | - Md. Arif Khan
- Department of Biotechnology and Genetic Engineering, University of Development Alternative, Dhaka, Bangladesh
- Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Tangail, Bangladesh
| | - Md. Arju Hossain
- Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Tangail, Bangladesh
| | - Md. Imran Hasan
- Department of Computer Science and Engineering, Islamic University, Kushtia, Bangladesh
| | - Md. Habibur Rahman
- Department of Computer Science and Engineering, Islamic University, Kushtia, Bangladesh
| | - Md. Ahashan Habib
- Bangladesh Council of Scientific & Industrial Research (BCSIR), Dhaka, Bangladesh
| | - Shahina Akter
- Bangladesh Council of Scientific & Industrial Research (BCSIR), Dhaka, Bangladesh
| | - Tanjina Akhtar Banu
- Bangladesh Council of Scientific & Industrial Research (BCSIR), Dhaka, Bangladesh
| | - Barna Goswami
- Bangladesh Council of Scientific & Industrial Research (BCSIR), Dhaka, Bangladesh
| | - Iffat Jahan
- Bangladesh Council of Scientific & Industrial Research (BCSIR), Dhaka, Bangladesh
| | - Tasnim Nafisa
- National Institute of Laboratory Medicine and Referral Center, Dhaka, Bangladesh
| | | | - Mahmoud E. Soliman
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Yusha Araf
- Department of Genetic Engineering and Biotechnology, School of Life Sciences, Shahjalal University of Science and Technology, Sylhet, Bangladesh
- Department of Immunology, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - M. Salim Khan
- Bangladesh Council of Scientific & Industrial Research (BCSIR), Dhaka, Bangladesh
- *Correspondence: Tofazzal Islam, ; Chunfu Zheng, ; Md. Salim Khan,
| | - Chunfu Zheng
- Department of Immunology, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, AB, Canada
- *Correspondence: Tofazzal Islam, ; Chunfu Zheng, ; Md. Salim Khan,
| | - Tofazzal Islam
- Institute of Biotechnology and Genetic Engineering (IBGE), Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur, Bangladesh
- *Correspondence: Tofazzal Islam, ; Chunfu Zheng, ; Md. Salim Khan,
| |
Collapse
|
31
|
Tanzina AY, Hoque MN, Mannan A, Foysal MJ, Rumi MH, Biswas S, Bhuiyan JJ, Siddiki AZ, Islam MS, Chin-Yen Tay A, Islam SR. Investigating the nutritional profile and bacteriome diversity in Bangladeshi sour yogurt. Biocatalysis and Agricultural Biotechnology 2022. [DOI: 10.1016/j.bcab.2022.102451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
32
|
Hoque MN, Rahman MS, Islam T, Sultana M, Crandall KA, Hossain MA. Induction of mastitis by cow-to-mouse fecal and milk microbiota transplantation causes microbiome dysbiosis and genomic functional perturbation in mice. Anim Microbiome 2022; 4:43. [PMID: 35794639 PMCID: PMC9258091 DOI: 10.1186/s42523-022-00193-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 06/28/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Mastitis pathogenesis involves a wide range of opportunistic and apparently resident microorganims including bacteria, viruses and archaea. In dairy animals, microbes reside in the host, interact with environment and evade the host immune system, providing a potential for host-tropism to favor mastitis pathogenesis. To understand the host-tropism phenomena of bovine-tropic mastitis microbiomes, we developed a cow-to-mouse mastitis model. METHODS A cow-to-mouse mastitis model was established by fecal microbiota transplantation (FMT) and milk microbiota transplantation (MMT) to pregnant mice to assess microbiome dysbiosis and genomic functional perturbations through shotgun whole metagenome sequencing (WMS) along with histopathological changes in mice mammary gland and colon tissues. RESULTS The cow-to-mouse FMT and MMT from clinical mastitis (CM) cows induced mastitis syndromes in mice as evidenced by histopathological changes in mammary gland and colon tissues. The WMS of 24 samples including six milk (CM = 3, healthy; H = 3), six fecal (CM = 4, H = 2) samples from cows, and six fecal (CM = 4, H = 2) and six mammary tissue (CM = 3, H = 3) samples from mice generating 517.14 million reads (average: 21.55 million reads/sample) mapped to 2191 bacterial, 94 viral and 54 archaeal genomes. The Kruskal-Wallis test revealed significant differences (p = 0.009) in diversity, composition, and relative abundances in microbiomes between CM- and H-metagenomes. These differences in microbiome composition were mostly represented by Pseudomonas aeruginosa, Lactobacillus crispatus, Klebsiella oxytoca, Enterococcus faecalis, Pantoea dispersa in CM-cows (feces and milk), and Muribaculum spp., Duncaniella spp., Muribaculum intestinale, Bifidobacterium animalis, Escherichia coli, Staphylococcus aureus, Massilia oculi, Ralstonia pickettii in CM-mice (feces and mammary tissues). Different species of Clostridia, Bacteroida, Actinobacteria, Flavobacteriia and Betaproteobacteria had a strong co-occurrence and positive correlation as the indicator species of murine mastitis. However, both CM cows and mice shared few mastitis-associated microbial taxa (1.14%) and functional pathways regardless of conservation of mastitis syndromes, indicating the higher discrepancy in mastitis-associated microbiomes among lactating mammals. CONCLUSIONS We successfully induced mastitis by FMT and MMT that resulted in microbiome dysbiosis and genomic functional perturbations in mice. This study induced mastitis in a mouse model through FMT and MMT, which might be useful for further studies- focused on pathogen(s) involved in mastitis, their cross-talk among themselves and the host.
Collapse
Affiliation(s)
- M Nazmul Hoque
- Department of Gynecology, Obstetrics and Reproductive Health, Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur, 1706, Bangladesh
| | - M Shaminur Rahman
- Department of Microbiology, Jashore University of Science and Technology, Jashore, 7408, Bangladesh
| | - Tofazzal Islam
- Institute of Biotechnology and Genetic Engineering (IBGE), BSMRAU, Gazipur, 1706, Bangladesh
| | - Munawar Sultana
- Department of Microbiology, University of Dhaka, Dhaka, 1000, Bangladesh
| | - Keith A Crandall
- Computational Biology Institute and Department of Biostatistics and Bioinformatics, Milken Institute School of Public Health, The George Washington University, Washington, DC, 20052, USA
| | - M Anwar Hossain
- Department of Microbiology, University of Dhaka, Dhaka, 1000, Bangladesh.
- Jashore University of Science and Technology, Jashore, 7408, Bangladesh.
| |
Collapse
|
33
|
Ievy S, Hoque MN, Islam MS, Sobur MA, Ballah FM, Rahman MS, Rahman MB, Hassan J, Khan MFR, Rahman MT. Genomic characteristics, virulence and antimicrobial resistance in avian pathogenic Escherichia coli MTR_BAU02 strain isolated from layer farms in Bangladesh. J Glob Antimicrob Resist 2022; 30:155-162. [PMID: 35671989 DOI: 10.1016/j.jgar.2022.06.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 05/29/2022] [Accepted: 06/01/2022] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND Colibacillosis, caused by avian pathogenic Escherichia coli (APEC), is one of the most significant infectious diseases affecting poultry worldwide. OBJECTIVE This study was aimed to determine the genomic diversity, virulence factor genes (VFGs) and antimicrobial resistance genes (ARGs) in the APEC MTR_BAU02 strain isolated from layer chickens using whole-genome sequencing (WGS). METHOD Paired-end (2 × 250) WGS was performed using Illumina MiSeq sequencer and de novo assembly was performed using SPAdes. Core genome MLST (cgMLST) analysis between APEC MTR_BAU02 and all of the ST1196 E. coli strains retrieved from the NCBI GenBank database was performed using BacWGSTdb 2.0 server. We further utilized different databases to detect ARGs, VFGs and genomic functional features of the APEC MTR_BAU02 strain. RESULTS The complete genome of APEC MTR_BAU02 consists of 94 contigs comprising 4,924,680 bp (51.1% GC content) including 4,681 protein-coding sequences, one chromosome, one plasmid, and was assigned to ST1196. The closest relatives of APEC MTR_BAU02 were another four isolates originating from human clinical (diarrhoeic stool) specimens in Bangladesh and two clinical isolates originating from chicken in India, which differed by 694 cgMLST alleles. One hundred twenty-two ARGs and 92 VFGs were identified in APEC MTR_BAU02 genome. Metabolic functional annotations detected 380 SEED subsystems including genes coding for carbohydrate metabolism, protein metabolism, cofactors, vitamins, prosthetic groups and pigments, respiration, membrane transport, stress response, motility and chemotaxis, and virulence, disease and defense. CONCLUSION This study reports the genome sequence of a multidrug resistant APEC strain isolated from layer birds in Bangladesh. The ARGs and VFGs, widespread in APEC MTR_BAU02, are similar to those found in human isolates, and highlight the growing threat of antimicrobial resistance in both poultry and humans.
Collapse
Affiliation(s)
- Samina Ievy
- Department of Microbiology and Hygiene, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh, 2202, Bangladesh
| | - M Nazmul Hoque
- Department of Gynaecology, Obstetrics and Reproductive Health, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, 1706, Bangladesh
| | - Md Saiful Islam
- Department of Microbiology and Hygiene, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh, 2202, Bangladesh
| | - Md Abdus Sobur
- Department of Microbiology and Hygiene, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh, 2202, Bangladesh
| | - Fatimah Muhammad Ballah
- Department of Microbiology and Hygiene, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh, 2202, Bangladesh
| | - M Shaminur Rahman
- Department of Microbiology, Jashore University of Science and Technology, Jashore, 7408, Bangladesh
| | - Md Bahanur Rahman
- Department of Microbiology and Hygiene, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh, 2202, Bangladesh
| | - Jayedul Hassan
- Department of Microbiology and Hygiene, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh, 2202, Bangladesh
| | - Mohammad Ferdousur Rahman Khan
- Department of Microbiology and Hygiene, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh, 2202, Bangladesh
| | - Md Tanvir Rahman
- Department of Microbiology and Hygiene, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh, 2202, Bangladesh.
| |
Collapse
|
34
|
Al Amin M, Pasha MH, Hoque MN, Siddiki AZ, Saha S, Kamal MM. Methodology for laboratory-based antimicrobial resistance surveillance in animals. Vet World 2022; 15:1066-1079. [PMID: 35698528 PMCID: PMC9178567 DOI: 10.14202/vetworld.2022.1066-1079] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Accepted: 03/22/2022] [Indexed: 11/20/2022] Open
Abstract
Antimicrobial resistance (AMR) is a crucial and emerging multifactorial “One Health” problem involving human and animal health, agriculture, aquaculture, and environment; and posing a potential public health hazard globally. The containment of AMR justifies effective surveillance programs to explicate the magnitude of the problem across the contributing sectors. Laboratory-based AMR testing and characterization is the key component of an AMR surveillance program. An AMR surveillance program should have a “top management” for fund mobilization, planning, formulating, and multilateral coordinating of the surveillance activities. The top management should identify competent participating laboratories to form a network comprising a reference laboratory and an adequate number of sentinel laboratories. The responsibilities of the reference laboratory include the development of standardized test methods for ensuring quality and homogeneity of surveillance activities, providing training to the laboratory personnel, and in-depth AMR characterization. The sentinel laboratories will take the responsibilities of receiving samples, isolation and identification of microbes, and initial AMR characterization. The sentinel laboratories will use simple antimicrobial susceptibility test (AST) methods such as disk diffusion tests, whereas the reference laboratories should use automated quantitative AST methods as well as advanced molecular methods to explicit AMR emergence mechanisms. Standard guidelines set by Clinical Laboratory Standards Institute or the European Committee on Antimicrobial Susceptibility Testing, should be followed to bring about conformity and harmonization in the AST procedures. AMR surveillance program in animals is eventually similar to that in human health with the exception is that veterinary antibiotics and veterinary pathogens should be given preference here. Hence, the review study was envisaged to look deep into the structure of the AMR surveillance program with significance on laboratory-based AMR testing and characterization methods.
Collapse
Affiliation(s)
- Md. Al Amin
- Quality Control Laboratory, Department of Livestock Services, Savar, Dhaka-1341, Bangladesh
| | | | - M. Nazmul Hoque
- Department of Gynecology, Obstetrics and Reproductive Health, Faculty of Veterinary Medicine and Animal Science, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur-1706, Bangladesh
| | - Amam Zonaed Siddiki
- Department of Pathology and Parasitology, Chittagong Veterinary and Animal Sciences University, Chittagong, Bangladesh
| | - Sukumar Saha
- Department of Microbiology and Hygiene, Bangladesh Agricultural University, Mymensingh-2202, Bangladesh
| | - Md. Mostofa Kamal
- Quality Control Laboratory, Department of Livestock Services, Savar, Dhaka-1341, Bangladesh
| |
Collapse
|
35
|
Hoque MN, Faisal GM, Chowdhury FR, Haque A, Islam T. The urgency of wider adoption of one health approach for the prevention of a future pandemic. Int J One Health 2022. [DOI: 10.14202/ijoh.2022.20-33] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Recurring outbreaks of emerging and re-emerging zoonoses serve as a reminder that the health of humans, animals, and the environment are interconnected. Therefore, multisectoral, transdisciplinary, and collaborative approaches are required at local, regional, and global levels to tackle the ever-increasing zoonotic threat. The ongoing pandemic of COVID-19 zoonosis has been posing tremendous threats to global human health and economies. The devastation caused by the COVID-19 pandemic teaches us to adopt a "One Health Approach (OHA)" to tackle a possible future pandemic through a concerted effort of the global scientific community, human health professionals, public health experts, veterinarians and policymakers through open science and open data sharing practices. The OHA is an integrated, holistic, collaborative, multisectoral, and transdisciplinary approach to tackle potential pandemic zoonotic diseases. It includes expanding scientific inquiry into zoonotic infections; monitoring, and regulating traditional food markets, transforming existing food systems, and incentivizing animal husbandry and legal wildlife trade to adopt effective zoonotic control measures. To adopt an OHA globally, research and academic institutions, governments and non-government sectors at the local, regional, and international levels must work together. This review aimed to provide an overview of the major pandemics in human history including the COVID-19, anthropogenic drivers of zoonoses, Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) reverse zoonoses, the concept of OHA and how an OHA could be utilized to prevent future pandemic threats to the human-animal-ecosystem interfaces. In addition, this review article discusses the strategic framework of OHA and possible challenges to implement OHA in practice to prevent any future pandemics. The practices of open data sharing, open science, and international collaboration should be included in the OHA to prevent and/or rapidly tackle any health emergencies in the future.
Collapse
Affiliation(s)
- M. Nazmul Hoque
- Department of Gynecology, Obstetrics and Reproductive Health, Faculty of Veterinary Medicine and Animal Science, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, Bangladesh; Faculty of Veterinary Medicine and Animal Science, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, Bangladesh
| | - Golam Mahbub Faisal
- Faculty of Veterinary Medicine and Animal Science, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, Bangladesh
| | - Farhan Rahman Chowdhury
- Institute of Biotechnology and Genetic Engineering, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, Bangladesh
| | - Amlan Haque
- School of Business and Law, CQUniversity, Sydney Campus, Australia
| | - Tofazzal Islam
- Institute of Biotechnology and Genetic Engineering, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, Bangladesh
| |
Collapse
|
36
|
Rafiqul Islam SM, Foysal MJ, Hoque MN, Mehedi HMH, Rob MA, Salauddin A, Tanzina AY, Biswas S, Noyon SH, Siddiki AMAMZ, Tay A, Mannan A. Dysbiosis of Oral and Gut Microbiomes in SARS-CoV-2 Infected Patients in Bangladesh: Elucidating the Role of Opportunistic Gut Microbes. Front Med (Lausanne) 2022; 9:821777. [PMID: 35237631 PMCID: PMC8882723 DOI: 10.3389/fmed.2022.821777] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 01/14/2022] [Indexed: 12/16/2022] Open
Abstract
Coronavirus disease-2019 (COVID-19) is an infectious disease caused by SARS-CoV-2 virus. The microbes inhabiting the oral cavity and gut might play crucial roles in maintaining a favorable gut environment, and their relationship with SARS-CoV-2 infection susceptibility and severity is yet to be fully explored. This study investigates the diversity and species richness of gut and oral microbiota of patients with COVID-19, and their possible implications toward the severity of the patient's illness and clinical outcomes. Seventy-four (n = 74) clinical samples (gut and oral) were collected from 22 hospitalized patients with COVID-19 with various clinical conditions and 15 apparently healthy people (served as controls). This amplicon-based metagenomic sequencing study yielded 1,866,306 paired-end reads that were mapped to 21 phyla and 231 classified genera of bacteria. Alpha and beta diversity analyses revealed a distinct dysbiosis of the gut and oral microbial communities in patients with COVID-19, compared to healthy controls. We report that SARS-CoV-2 infection significantly reduced richness and evenness in the gut and oral microbiomes despite showing higher unique operational taxonomic units in the gut. The gut samples of the patients with COVID-19 included 46 opportunistic bacterial genera. Escherichia, Shigella, and Bacteroides were detected as the signature genera in the gut of patients with COVID-19 with diarrhea, whereas a relatively higher abundance of Streptococcus was found in patients with COVID-19 having breathing difficulties and sore throat (BDST). The patients with COVID-19 had a significantly lower abundance of Prevotella in the oral cavity, compared to healthy controls and patients with COVID-19 without diabetes, respectively. The altered metabolic pathways, including a reduction in biosynthesis capabilities of the gut and oral microbial consortia after SARS-CoV-2 infection, were also observed. The present study may, therefore, shed light on interactions of SARS-CoV-2 with resilient oral and gut microbes which might contribute toward developing microbiome-based diagnostics and therapeutics for this deadly pandemic disease.
Collapse
Affiliation(s)
- S. M. Rafiqul Islam
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chattogram, Bangladesh
| | - Md. Javed Foysal
- School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia
| | - M. Nazmul Hoque
- Department of Gynecology, Obstetrics and Reproductive Health, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, Bangladesh
| | | | - Md. Abdur Rob
- Department of Medicine, 250 Bedded General Hospital, Chattogram, Bangladesh
| | - Asma Salauddin
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chattogram, Bangladesh
| | - Afsana Yeasmin Tanzina
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chattogram, Bangladesh
| | - Sabuj Biswas
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chattogram, Bangladesh
| | - Sajjad Hossain Noyon
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chattogram, Bangladesh
| | - A. M. A. M. Zonaed Siddiki
- Department of Pathology and Parasitology, Chattogram Veterinary and Animal Sciences University, Chattogram, Bangladesh
| | - Alfred Tay
- Helicobacter Research Laboratory, Marshall Centre for Infectious Disease Research and Training, School of Biomedical Sciences, University of Western Australia, Perth, WA, Australia
| | - Adnan Mannan
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chattogram, Bangladesh
- *Correspondence: Adnan Mannan
| |
Collapse
|
37
|
Hoque MN, Sarkar MMH, Rahman MS, Akter S, Banu TA, Goswami B, Jahan I, Hossain MS, Shamsuzzaman AKM, Nafisa T, Molla MMA, Yeasmin M, Ghosh AK, Osman E, Alam SKS, Uzzaman MS, Habib MA, Mahmud ASM, Crandall KA, Islam T, Khan MS. SARS-CoV-2 infection reduces human nasopharyngeal commensal microbiome with inclusion of pathobionts. Sci Rep 2021; 11:24042. [PMID: 34911967 PMCID: PMC8674272 DOI: 10.1038/s41598-021-03245-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Accepted: 11/08/2021] [Indexed: 01/02/2023] Open
Abstract
The microbiota of the nasopharyngeal tract (NT) play a role in host immunity against respiratory infectious diseases. However, scant information is available on interactions of SARS-CoV-2 with the nasopharyngeal microbiome. This study characterizes the effects of SARS-CoV-2 infection on human nasopharyngeal microbiomes and their relevant metabolic functions. Twenty-two (n = 22) nasopharyngeal swab samples (including COVID-19 patients = 8, recovered humans = 7, and healthy people = 7) were collected, and underwent to RNAseq-based metagenomic investigation. Our RNAseq data mapped to 2281 bacterial species (including 1477, 919 and 676 in healthy, COVID-19 and recovered metagenomes, respectively) indicating a distinct microbiome dysbiosis. The COVID-19 and recovered samples included 67% and 77% opportunistic bacterial species, respectively compared to healthy controls. Notably, 79% commensal bacterial species found in healthy controls were not detected in COVID-19 and recovered people. Similar dysbiosis was also found in viral and archaeal fraction of the nasopharyngeal microbiomes. We also detected several altered metabolic pathways and functional genes in the progression and pathophysiology of COVID-19. The nasopharyngeal microbiome dysbiosis and their genomic features determined by our RNAseq analyses shed light on early interactions of SARS-CoV-2 with the nasopharyngeal resident microbiota that might be helpful for developing microbiome-based diagnostics and therapeutics for this novel pandemic disease.
Collapse
Affiliation(s)
- M Nazmul Hoque
- Department of Gynecology, Obstetrics and Reproductive Health, Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur, 1706, Bangladesh
- Bangladesh Council of Scientific and Industrial Research (BCSIR), Dhanmondi, Dhaka, 1205, Bangladesh
| | - Md Murshed Hasan Sarkar
- Bangladesh Council of Scientific and Industrial Research (BCSIR), Dhanmondi, Dhaka, 1205, Bangladesh
| | - M Shaminur Rahman
- Department of Microbiology, Jashore University of Science Technology, Jashore, 7408, Bangladesh
| | - Shahina Akter
- Bangladesh Council of Scientific and Industrial Research (BCSIR), Dhanmondi, Dhaka, 1205, Bangladesh
| | - Tanjina Akhtar Banu
- Bangladesh Council of Scientific and Industrial Research (BCSIR), Dhanmondi, Dhaka, 1205, Bangladesh
| | - Barna Goswami
- Bangladesh Council of Scientific and Industrial Research (BCSIR), Dhanmondi, Dhaka, 1205, Bangladesh
| | - Iffat Jahan
- Bangladesh Council of Scientific and Industrial Research (BCSIR), Dhanmondi, Dhaka, 1205, Bangladesh
| | - M Saddam Hossain
- Bangladesh Council of Scientific and Industrial Research (BCSIR), Dhanmondi, Dhaka, 1205, Bangladesh
| | | | - Tasnim Nafisa
- National Institute of Laboratory Medicine and Referral Center, Dhaka, 1207, Bangladesh
| | - M Maruf Ahmed Molla
- National Institute of Laboratory Medicine and Referral Center, Dhaka, 1207, Bangladesh
| | - Mahmuda Yeasmin
- National Institute of Laboratory Medicine and Referral Center, Dhaka, 1207, Bangladesh
| | - Asish Kumar Ghosh
- National Institute of Laboratory Medicine and Referral Center, Dhaka, 1207, Bangladesh
| | - Eshrar Osman
- SciTech Consulting and Solutions, Dhaka, 1213, Bangladesh
| | - S K Saiful Alam
- Shaheed Tajuddin Ahmad Medical College, Gazipur, 1700, Bangladesh
| | | | - Md Ahashan Habib
- Bangladesh Council of Scientific and Industrial Research (BCSIR), Dhanmondi, Dhaka, 1205, Bangladesh
| | | | - Keith A Crandall
- Computational Biology Institute and Department of Biostatistics and Bioinformatics, Milken Institute School of Public Health, The George Washington University, Washington, DC, USA
| | - Tofazzal Islam
- Institute of Biotechnology and Genetic Engineering (IBGE), BSMRAU, Gazipur, 1706, Bangladesh.
| | - Md Salim Khan
- Bangladesh Council of Scientific and Industrial Research (BCSIR), Dhanmondi, Dhaka, 1205, Bangladesh.
| |
Collapse
|
38
|
Saha O, Islam MR, Rahman MS, Hoque MN, Hossain MA, Sultana M. First report from Bangladesh on genetic diversity of multidrug-resistant Pasteurella multocida type B:2 in fowl cholera. Vet World 2021; 14:2527-2542. [PMID: 34840474 PMCID: PMC8613801 DOI: 10.14202/vetworld.2021.2527-2542] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 08/13/2021] [Indexed: 01/05/2023] Open
Abstract
Background and Aim: Fowl cholera (FC) caused by Pasteurella multocida is a highly contagious bacterial disease of global importance for poultry production. The severity and incidence of FC caused by P. multocida may vary considerably depending on several factors associated with the host (including species and age of infected birds), the environment, and the bacterial strain. This study aimed to investigate the genetic diversity of multidrug-resistant P. multocida strains isolated from FC outbreaks in laying hens from commercial farms of Bangladesh. Materials and Methods: We collected 57 samples of suspected FC, including 36 live and 21 dead laying hens. P. multocida isolates were characterized by biochemical and molecular-biological methods. Results: Twenty-two strains of P. multocida were isolated from these samples through phenotypic and genotypic characterization. The strains were grouped into two distinct random amplification of polymorphic DNA (RAPD) biotypes harboring a range of pathogenic genes; exbB, ompH, ptfA, nanB, sodC, and hgbA. In this study, 90.90% and 81.82% P. multocida strains were multidrug-resistant and biofilm formers, respectively. Whole-genome sequencing of the two representative RAPD phylotypes confirmed as P. multocida type B: L2:ST122, harboring a number of virulence factors-associated genes (VFGs), and antimicrobial resistance (AMR) genes (ARGs). In addition, pan-genome analysis revealed 90 unique genes in the genomes of P. multocida predicted to be associated with versatile metabolic functions, pathogenicity, virulence, and AMR. Conclusion: This is first-ever report on the association of P. multocida genotype B: L2:ST122 and related VFGs and ARGs in the pathogenesis of FC in laying hens. This study also provides a genetic context for future researches on the evolutionary diversity of P. multocida strains and their host adaptation.
Collapse
Affiliation(s)
- Otun Saha
- Department of Microbiology, University of Dhaka, Dhaka-1000, Bangladesh
| | - M Rafiul Islam
- Department of Microbiology, University of Dhaka, Dhaka-1000, Bangladesh
| | - M Shaminur Rahman
- Department of Microbiology, University of Dhaka, Dhaka-1000, Bangladesh
| | - M Nazmul Hoque
- Department of Microbiology, University of Dhaka, Dhaka-1000, Bangladesh.,Department of Gynecology, Obstetrics and Reproductive Health, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur-1706, Bangladesh
| | - M Anwar Hossain
- Department of Microbiology, University of Dhaka, Dhaka-1000, Bangladesh.,Vice-Chancellor, Jashore University of Science and Technology, Jashore-7408, Bangladesh
| | - Munawar Sultana
- Department of Microbiology, University of Dhaka, Dhaka-1000, Bangladesh
| |
Collapse
|
39
|
Islam SMR, Tanzina AY, Foysal MJ, Hoque MN, Rumi MH, Siddiki AMAMZ, Tay ACY, Hossain MJ, Bakar MA, Mostafa M, Mannan A. Insights into the nutritional properties and microbiome diversity in sweet and sour yogurt manufactured in Bangladesh. Sci Rep 2021; 11:22667. [PMID: 34811394 PMCID: PMC8608820 DOI: 10.1038/s41598-021-01852-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Accepted: 10/27/2021] [Indexed: 11/09/2022] Open
Abstract
Yogurt is one of the most frequently consumed dairy products for nutritional benefits. Although yogurt is enriched with probiotics, it is susceptible to spoilage because of the presence of pathogenic microbes. Spoiled yogurt if consumed can cause food-borne diseases. This study aimed to assess the nutritional composition and microbiome diversity in yogurt manufactured in Bangladesh. Microbial diversity was analyzed through high-throughput sequencing of bacterial 16S rRNA gene and fungal internal transcribed spacer (ITS) region. From nutritional analysis, significantly (P < 0.05) higher pH, fat, moisture, total solid and solid-non-fat contents (%) were observed in sweet yogurt. Following the classification of Illumina sequences, 84.86% and 72.14% of reads were assigned to bacterial and fungal genera, respectively, with significantly higher taxonomic richness in sour yogurt prepared from buffalo. A significant difference in bacterial (Ppermanova = 0.001) and fungal (Ppermanova = 0.013) diversity between sweet and sour yogurt was recorded. A total of 76 bacterial and 70 fungal genera were detected across these samples which were mostly represented by Firmicutes (92.89%) and Ascomycota (98%) phyla, respectively. This is the first study that accentuates nutritional profiles and microbiome diversity of Bangladeshi yogurt which are crucial in determining both active and passive health effects of yogurt consumption in individuals.
Collapse
Affiliation(s)
- S M Rafiqul Islam
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chattogram, 4331, Bangladesh.
| | - Afsana Yeasmin Tanzina
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chattogram, 4331, Bangladesh
| | - Md Javed Foysal
- School of Molecular and Life Sciences, Curtin University, Bentley, WA, 6102, Australia
- Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet, 3114, Bangladesh
| | - M Nazmul Hoque
- Department of Gynecology, Obstetrics and Reproductive Health, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, 1706, Bangladesh
| | - Meheadi Hasan Rumi
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chattogram, 4331, Bangladesh
| | - A M A M Zonaed Siddiki
- Department of Pathology and Parasitology, Chattogram Veterinary and Animal Sciences University, Chattogram, 4225, Bangladesh
| | - Alfred Chin-Yen Tay
- Helicobacter Research Laboratory, The Marshall Centre, University of Western Australia, Perth, WA, 6009, Australia
| | - M Jakir Hossain
- Forest Chemistry Division, Bangladesh Forest Research Institute, Chattogram, 4211, Bangladesh
| | - Muhammad Abu Bakar
- Bangladesh Council of Scientific and Industrial Research (BCSIR) Laboratories, Chattogram, 4220, Bangladesh
| | - Mohammad Mostafa
- Bangladesh Council of Scientific and Industrial Research (BCSIR) Laboratories, Chattogram, 4220, Bangladesh
| | - Adnan Mannan
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chattogram, 4331, Bangladesh.
| |
Collapse
|
40
|
Islam MR, Hoque MN, Rahman MS, Alam ASMRU, Akther M, Puspo JA, Akter S, Sultana M, Crandall KA, Hossain MA. Author Correction: Genome-wide analysis of SARS-CoV-2 virus strains circulating worldwide implicates heterogeneity. Sci Rep 2021; 11:20568. [PMID: 34642347 PMCID: PMC8506079 DOI: 10.1038/s41598-021-00133-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Affiliation(s)
- M Rafiul Islam
- Department of Microbiology, University of Dhaka, Dhaka, 1000, Bangladesh
| | - M Nazmul Hoque
- Department of Microbiology, University of Dhaka, Dhaka, 1000, Bangladesh.,Department of Gynecology, Obstetrics and Reproductive Health, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, 1706, Bangladesh
| | - M Shaminur Rahman
- Department of Microbiology, University of Dhaka, Dhaka, 1000, Bangladesh
| | - A S M Rubayet Ul Alam
- Department of Microbiology, Jashore University of Science and Technology, Jashore, 7408, Bangladesh
| | - Masuda Akther
- Department of Microbiology, University of Dhaka, Dhaka, 1000, Bangladesh
| | - J Akter Puspo
- Department of Microbiology, University of Dhaka, Dhaka, 1000, Bangladesh
| | - Salma Akter
- Department of Microbiology, University of Dhaka, Dhaka, 1000, Bangladesh.,Department of Microbiology, Jahangirnagar University, Savar, Dhaka, 1342, Bangladesh
| | - Munawar Sultana
- Department of Microbiology, University of Dhaka, Dhaka, 1000, Bangladesh
| | - Keith A Crandall
- Computational Biology Institute, Milken Institute School of Public Health, The George Washington University, Washington, USA
| | - M Anwar Hossain
- Department of Microbiology, University of Dhaka, Dhaka, 1000, Bangladesh. .,Jashore University of Science and Technology, Jashore, 7408, Bangladesh.
| |
Collapse
|
41
|
Rahman MS, Hoque MN, Puspo JA, Islam MR, Das N, Siddique MA, Hossain MA, Sultana M. Microbiome signature and diversity regulates the level of energy production under anaerobic condition. Sci Rep 2021; 11:19777. [PMID: 34611238 PMCID: PMC8492712 DOI: 10.1038/s41598-021-99104-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 09/13/2021] [Indexed: 02/08/2023] Open
Abstract
The microbiome of the anaerobic digester (AD) regulates the level of energy production. To assess the microbiome diversity and composition in different stages of anaerobic digestion, we collected 16 samples from the AD of cow dung (CD) origin. The samples were categorized into four groups (Group-I, Group-II, Group-III and Group-IV) based on the level of energy production (CH4%), and sequenced through whole metagenome sequencing (WMS). Group-I (n = 2) belonged to initial time of energy production whereas Group-II (n = 5), Group-III (n = 5), and Group-IV (n = 4) had 21-34%, 47-58% and 71-74% of CH4, respectively. The physicochemical analysis revealed that level of energy production (CH4%) had significant positive correlation with digester pH (r = 0.92, p < 0.001), O2 level (%) (r = 0.54, p < 0.05), and environmental temperature (°C) (r = 0.57, p < 0.05). The WMS data mapped to 2800 distinct bacterial, archaeal and viral genomes through PathoScope (PS) and MG-RAST (MR) analyses. We detected 768, 1421, 1819 and 1774 bacterial strains in Group-I, Group-II, Group-III and Group-IV, respectively through PS analysis which were represented by Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria, Spirochaetes and Fibrobacteres phyla (> 93.0% of the total abundances). Simultaneously, 343 archaeal strains were detected, of which 95.90% strains shared across four metagenomes. We identified 43 dominant species including 31 bacterial and 12 archaeal species in AD microbiomes, of which only archaea showed positive correlation with digester pH, CH4 concentration, pressure and temperature (Spearman correlation; r > 0.6, p < 0.01). The indicator species analysis showed that the species Methanosarcina vacuolate, Dehalococcoides mccartyi, Methanosarcina sp. Kolksee and Methanosarcina barkeri were highly specific for energy production. The correlation network analysis showed that different strains of Euryarcheota and Firmicutes phyla exhibited significant correlation (p = 0.021, Kruskal-Wallis test; with a cutoff of 1.0) with the highest level (74.1%) of energy production (Group-IV). In addition, top CH4 producing microbiomes showed increased genomic functional activities related to one carbon and biotin metabolism, oxidative stress, proteolytic pathways, membrane-type-1-matrix-metalloproteinase (MT1-MMP) pericellular network, acetyl-CoA production, motility and chemotaxis. Importantly, the physicochemical properties of the AD including pH, CH4 concentration (%), pressure, temperature and environmental temperature were found to be positively correlated with these genomic functional potentials and distribution of ARGs and metal resistance pathways (Spearman correlation; r > 0.5, p < 0.01). This study reveals distinct changes in composition and diversity of the AD microbiomes including different indicator species, and their genomic features that are highly specific for energy production.
Collapse
Affiliation(s)
- M. Shaminur Rahman
- grid.8198.80000 0001 1498 6059Department of Microbiology, University of Dhaka, Dhaka, 1000 Bangladesh
| | - M. Nazmul Hoque
- grid.8198.80000 0001 1498 6059Department of Microbiology, University of Dhaka, Dhaka, 1000 Bangladesh ,grid.443108.a0000 0000 8550 5526Department of Gynecology, Obstetrics and Reproductive Health, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, 1706 Bangladesh
| | - Joynob Akter Puspo
- grid.8198.80000 0001 1498 6059Department of Microbiology, University of Dhaka, Dhaka, 1000 Bangladesh
| | - M. Rafiul Islam
- grid.8198.80000 0001 1498 6059Department of Microbiology, University of Dhaka, Dhaka, 1000 Bangladesh
| | - Niloy Das
- grid.8198.80000 0001 1498 6059Department of Microbiology, University of Dhaka, Dhaka, 1000 Bangladesh ,Surge Engineering (www.surgeengineering.com), Dhaka, 1205 Bangladesh
| | - Mohammad Anwar Siddique
- grid.8198.80000 0001 1498 6059Department of Microbiology, University of Dhaka, Dhaka, 1000 Bangladesh
| | - M. Anwar Hossain
- grid.8198.80000 0001 1498 6059Department of Microbiology, University of Dhaka, Dhaka, 1000 Bangladesh ,Present Address: Jashore University of Science and Technology, Jashore, 7408 Bangladesh
| | - Munawar Sultana
- grid.8198.80000 0001 1498 6059Department of Microbiology, University of Dhaka, Dhaka, 1000 Bangladesh
| |
Collapse
|
42
|
Sultana KF, Saha O, Hoque MN, Sultana M, Hossain MA. Multilocus sequence typing of multidrug-resistant Salmonella strains circulating in poultry farms of Bangladesh. Braz J Microbiol 2021; 52:2385-2399. [PMID: 34297327 DOI: 10.1007/s42770-021-00577-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 07/11/2021] [Indexed: 11/28/2022] Open
Abstract
Salmonella is one of the most important foodborne zoonotic pathogens, and becoming multidrug-resistant (MDR), which represents a serious public health concern worldwide. This study aimed to identify the circulating MDR strains of Salmonella through cutting edge molecular techniques including gene specific PCR, RAPD-PCR, ribosomal gene sequencing, and multilocus sequence types (MLST) in the poultry industry of Bangladesh. Two hundred Salmonella isolates were retrieved from 154 samples comprising droppings (n = 60), cloacal swabs (n = 60), feeds (n = 14), feeding water (n = 14), and handler's swab (n = 6) from 14 commercial layer farms of Bangladesh. The isolates were confirmed as Salmonella through invA gene specific PCR, and further genotyping was done by RAPD-PCR, and 16S rRNA sequencing. The isolates were distributed into 18 different genotypes according to RAPD typing. The phylogenetic analysis identified three diverging phylogroups such as S. enterica Litchfield, S. enterica Enteritidis and S. enterica Kentucky with 11, 8, and 6 strains, respectively. The in vitro antibiogram profiling the Salmonella isolates through disc diffusion method using 13 commercially available antibiotics revealed highest resistance against doxycycline (91.5%) followed by tetracycline and ampicillin (86.0%, in each), and 72.0% isolates as MDR, being resistant to ≥ 5 antibiotics. The MLST typing was carried out based on the PCR amplification of seven housekeeping genes (aroC, hisD, hemD, purE, secA, thrA, and dnaN). MLST typing also revealed three sequence types (STs) such as ST11, ST198, and ST214 in these isolates, and eBURST analysis showed ST11 as the founder genotype. The three STs were highly resistant to tetracyclines and quinolone group of antibiotics, and all of the isolates harboring S. enterica Litchfield showed the highest resistance. Circulating common MLSTs with MDR properties in different farms confirmed the possibility of a common route of intra-farm transmission. We report for the first time of the association serovar Litchfield (ST11) in avian salmonellosis with MDR properties which is an urgent public health concern in Bangladesh.
Collapse
Affiliation(s)
- Khandokar Fahmida Sultana
- Department of Microbiology, University of Dhaka, Dhaka, Bangladesh.,Department of Microbiology, Noakhali Science and Technology University, Noakhali, Bangladesh
| | - Otun Saha
- Department of Microbiology, University of Dhaka, Dhaka, Bangladesh
| | - M Nazmul Hoque
- Department of Microbiology, University of Dhaka, Dhaka, Bangladesh.,Department of Gynecology, Obstetrics and Reproductive Health, Bangabandhu Sheikh Muibur Rahman Agricultural University, Gazipur, 1706, Bangladesh
| | - Munawar Sultana
- Department of Microbiology, University of Dhaka, Dhaka, Bangladesh.
| | - M Anwar Hossain
- Department of Microbiology, University of Dhaka, Dhaka, Bangladesh. .,Jashore Science and Technology University, Jessore, Bangladesh.
| |
Collapse
|
43
|
Hoque MN, Akter S, Mishu ID, Islam MR, Rahman MS, Akhter M, Islam I, Hasan MM, Rahaman MM, Sultana M, Islam T, Hossain MA. Microbial co-infections in COVID-19: Associated microbiota and underlying mechanisms of pathogenesis. Microb Pathog 2021; 156:104941. [PMID: 33962007 PMCID: PMC8095020 DOI: 10.1016/j.micpath.2021.104941] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Revised: 04/08/2021] [Accepted: 04/08/2021] [Indexed: 01/08/2023]
Abstract
The novel coronavirus infectious disease-2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has traumatized the whole world with the ongoing devastating pandemic. A plethora of microbial domains including viruses (other than SARS-CoV-2), bacteria, archaea and fungi have evolved together, and interact in complex molecular pathogenesis along with SARS-CoV-2. However, the involvement of other microbial co-pathogens and underlying molecular mechanisms leading to extortionate ailment in critically ill COVID-19 patients has yet not been extensively reviewed. Although, the incidence of co-infections could be up to 94.2% in laboratory-confirmed COVID-19 cases, the fate of co-infections among SARS-CoV-2 infected hosts often depends on the balance between the host's protective immunity and immunopathology. Predominantly identified co-pathogens of SARS-CoV-2 are bacteria such as Streptococcus pneumoniae, Staphylococcus aureus, Klebsiella pneumoniae, Haemophilus influenzae, Mycoplasma pneumoniae, Acinetobacter baumannii, Legionella pneumophila and Clamydia pneumoniae followed by viruses including influenza, coronavirus, rhinovirus/enterovirus, parainfluenza, metapneumovirus, influenza B virus, and human immunodeficiency virus. The cross-talk between co-pathogens (especially lung microbiomes), SARS-CoV-2 and host is an important factor that ultimately increases the difficulty of diagnosis, treatment, and prognosis of COVID-19. Simultaneously, co-infecting microbiotas may use new strategies to escape host defense mechanisms by altering both innate and adaptive immune responses to further aggravate SARS-CoV-2 pathogenesis. Better understanding of co-infections in COVID-19 is critical for the effective patient management, treatment and containment of SARS-CoV-2. This review therefore necessitates the comprehensive investigation of commonly reported microbial co-pathogens amid COVID-19, their transmission pattern along with the possible mechanism of co-infections and outcomes. Thus, identifying the possible co-pathogens and their underlying molecular mechanisms during SARS-CoV-2 pathogenesis may shed light in developing diagnostics, appropriate curative and preventive interventions for suspected SARS-CoV-2 respiratory infections in the current pandemic.
Collapse
Affiliation(s)
- M Nazmul Hoque
- Department of Microbiology, University of Dhaka, Dhaka, 1000, Bangladesh; Department of Gynecology, Obstetrics and Reproductive Health, Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur, 1706, Bangladesh
| | - Salma Akter
- Department of Microbiology, University of Dhaka, Dhaka, 1000, Bangladesh; Department of Microbiology, Jahangirnagar University, Savar, Dhaka, 1342, Bangladesh
| | | | - M Rafiul Islam
- Department of Microbiology, University of Dhaka, Dhaka, 1000, Bangladesh
| | - M Shaminur Rahman
- Department of Microbiology, University of Dhaka, Dhaka, 1000, Bangladesh
| | - Masuda Akhter
- Department of Microbiology, University of Dhaka, Dhaka, 1000, Bangladesh
| | - Israt Islam
- Department of Microbiology, University of Dhaka, Dhaka, 1000, Bangladesh
| | - Mehedi Mahmudul Hasan
- Department of Microbiology, University of Dhaka, Dhaka, 1000, Bangladesh; Department of Fisheries and Marine Science, Noakhali Science and Technology University, Noakhali, 3814, Bangladesh
| | - Md Mizanur Rahaman
- Department of Microbiology, University of Dhaka, Dhaka, 1000, Bangladesh
| | - Munawar Sultana
- Department of Microbiology, University of Dhaka, Dhaka, 1000, Bangladesh
| | - Tofazzal Islam
- Institute of Biotechnology and Genetic Engineering (IBGE), BSMRAU, Gazipur, 1706, Bangladesh
| | - M Anwar Hossain
- Department of Microbiology, University of Dhaka, Dhaka, 1000, Bangladesh; Jashore University of Science and Technology, Jashore, 7408, Bangladesh.
| |
Collapse
|
44
|
Hoque MN, Rahman MS, Ahmed R, Hossain MS, Islam MS, Islam T, Hossain MA, Siddiki AZ. Diversity and genomic determinants of the microbiomes associated with COVID-19 and non-COVID respiratory diseases. Gene Rep 2021; 23:101200. [PMID: 33977168 PMCID: PMC8102076 DOI: 10.1016/j.genrep.2021.101200] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 05/03/2021] [Indexed: 12/11/2022]
Abstract
The novel coronavirus disease 2019 (COVID-19) is a rapidly emerging and highly transmissible disease caused by the Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2). Understanding the microbiomes associated with the upper respiratory tract infection (URTI), chronic obstructive pulmonary disease (COPD) and COVID-19 diseases has clinical interest. We hypothesize that microbiome diversity and composition, and their genomic features are associated with different pathological conditions of these human respiratory tract diseases. To test this hypothesis, we analyzed 21 RNASeq metagenomic data including eleven COVID-19 (BD = 6 and China = 5), six COPD (UK = 6) and four URTI (USA = 4) samples to unravel the microbiome diversity and related genomic metabolic functions. The metagenomic data mapped to 534 bacterial, 60 archaeal and 61 viral genomes with distinct variation in the microbiome composition across the samples (COVID-19 > COPD > URTI). Notably, 94.57%, 80.0% and 24.59% bacterial, archaeal and viral genera shared between the COVID-19 and non-COVID samples, respectively. However, the COVID-19 related samples had sole association with 16 viral genera other than SARS-CoV-2. Strain-level virome profiling revealed 660 and 729 strains in COVID-19 and non-COVID samples, respectively, and of them 34.50% strains shared between the conditions. Functional annotation of the metagenomic data identified the association of several biochemical pathways related to basic metabolism (amino acid and energy), ABC transporters, membrane transport, virulence, disease and defense, regulation of virulence, programmed cell death, and primary immunodeficiency. We also detected 30 functional gene groups/classes associated with resistance to antibiotics and toxic compounds (RATC) in both COVID-19 and non-COVID microbiomes. Furthermore, we detected comparatively higher abundance of cobalt-zinc-cadmium resistance (CZCR) and multidrug resistance to efflux pumps (MREP) genes in COVID-19 metagenome. The profiles of microbiome diversity and associated microbial genomic features found in both COVID-19 and non-COVID (COPD and URTI) samples might be helpful in developing microbiome-based diagnostics and therapeutics for COVID-19 and non-COVID respiratory diseases. However, future studies might be carried out to explore the microbiome dynamics and the cross-talk between host and microbiomes employing larger volume of samples from different ethnic groups and geoclimatic conditions.
Collapse
Affiliation(s)
- M Nazmul Hoque
- Department of Gynecology, Obstetrics and Reproductive Health, Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur 1706, Bangladesh
| | - M Shaminur Rahman
- Department of Microbiology, University of Dhaka, Dhaka 1000, Bangladesh
| | - Rasel Ahmed
- Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh
| | | | | | - Tofazzal Islam
- Institute of Biotechnology and Genetic Engineering (IBGE), BSMRAU, Gazipur 1706, Bangladesh
| | - M Anwar Hossain
- Department of Microbiology, University of Dhaka, Dhaka 1000, Bangladesh.,Vice-Chancellor, Jashore University of Science and Technology, Jashore 7408, Bangladesh
| | - Amam Zonaed Siddiki
- Department of Pathology and Parasitology, Chattogram Veterinary and Animal Sciences University (CVASU), Chattogram 4202, Bangladesh
| |
Collapse
|
45
|
Saha O, Rakhi NN, Hoque MN, Sultana M, Hossain MA. Genome-wide genetic marker analysis and genotyping of Escherichia fergusonii strain OTSVEF-60. Braz J Microbiol 2021; 52:989-1004. [PMID: 33591555 DOI: 10.1007/s42770-021-00441-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Accepted: 02/02/2021] [Indexed: 10/21/2022] Open
Abstract
Poultry originated Escherichia fergusonii (POEF), an emerging bacterial pathogen, causes a wide range of intestinal and extra-intestinal infections in the poultry industry which incurred significant economic losses worldwide. Chromosomal co-existence of antibiotics and metal resistance genes has recently been the focal point of POEF isolates besides its pathogenic potentials. This study reports the complete genome analysis of POEF strain OTSVEF-60 from the poultry originated samples of Bangladesh. The assembled draft genome of the strain was 4.2 Mbp containing 4503 coding sequences, 120 RNA (rRNA = 34, tRNA = 79, ncRNA = 7), and three intact phage signature regions. Forty-one broad range antibiotic resistance genes (ARGs) including dfrA12, qnrS1, blaTEM-1, aadA2, tet(A), and sul-2 along with multiple efflux pump genes were detected, which translated to phenotypic resistant patterns of the pathogen to trimethoprim, fluoroquinolones, β-lactams, aminoglycoside, tetracycline, and sulfonamides. Moreover, 22 metal resistance genes were found co-existing within the genome of the POEF strain, and numerous virulence genes (VGs) coding for cit (AB), feo (AB), fep (ABCG), csg (ABCDEFG), fliC, ompA, gadA, ecpD, etc. were also identified throughout the genome. In addition, we detected a class I integron gene cassette harboring dfrA12, ant (3″)-I, and qacEΔ-sul2 genes; 42 copies of insertion sequence (IS) elements; and two CRISPR arrays. The genomic functional analysis predicted several metabolic pathways related to motility, flagellar assembly, epithelial cell invasion, quorum sensing, biofilm formation, and biosynthesis of vitamin, co-factors, and secondary metabolites. We herein for the first time detected multiple ARGs, VGs, mobile genetic elements, and some metabolic functional genes in the complete genome of POEF strain OTSVEF-60, which might be associated with the pathogenesis, spreading of ARGs and VGs, and subsequent treatment failure against this emerging avian pathogen with currently available antimicrobials.
Collapse
Affiliation(s)
- Otun Saha
- Department of Microbiology, University of Dhaka, Dhaka, 1000, Bangladesh
| | - Nadira Naznin Rakhi
- Department of Biotechnology and Genetic Engineering, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj, Bangladesh
| | - M Nazmul Hoque
- Department of Microbiology, University of Dhaka, Dhaka, 1000, Bangladesh.,Department of Gynecology, Obstetrics and Reproductive Health, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, 1706, Bangladesh
| | - Munawar Sultana
- Department of Microbiology, University of Dhaka, Dhaka, 1000, Bangladesh.
| | - M Anwar Hossain
- Department of Microbiology, University of Dhaka, Dhaka, 1000, Bangladesh. .,Jashore University of Science and Technology, Jashore, 7408, Bangladesh.
| |
Collapse
|
46
|
Malek MS, Hoque MN, Azam MG, Kabir MA, Islam MS, Mamoon MA, Ahmed S, Siddiqui NI. Prediction of Esophageal Varices in Chronic Liver Disease by Liver Stiffness-Spleen Size-to-Plalelet Ratio Risk Score. Mymensingh Med J 2021; 30:115-122. [PMID: 33397861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Non-invasive tools are needed to rule out the presence of esophageal varices (EV) in patients with chronic liver disease. The aim of this study was to evaluate diagnostic accuracy of Liver stiffness-spleen size-to-platelet ratio (LSPS) for EV detection and identification of high risk EV in patients with CLD. A total of 70 patients with CLD irrespective of the etiology attending at OPD and admitted in Department of Gastrointestinal, Hepatobiliary and Pancreatic Disorders (GHPD) of BIRDEM General Hospital, Dhaka, Bangladesh from January 2016 to October 2017 were enrolled in this observational cross-sectional study. All patients underwent routine laboratory tests, liver function tests, ultrasonography, liver stiffness (LS) measurement and esophagogastroduodenoscopy. Clinical value of LSPS was compared with platelet count, spleen size and LS for detection of esophageal varices. Diagnostic accuracy was assessed by the Area under the receiver operating characteristic (AUROC) curve. The sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) were calculated using ROC curve. LSPS has better diagnostic accuracy for detection of EV in terms of AUROC, showing superiority over each factor alone. LSPS also detect high risk EV but accuracy was lower than detection of EV. The optimal cutoff values of LSPS for EV and high risk EV were 0.879 and 4.132 respectively, at which AUROC, negative predictive value, and accuracy were 0.910 [95% confidence interval (CI) 0.832-0.988], 90.9% and 90.0% and 0.695 (95% CI 0.520-0.870), 62.5% and 69.4% respectively. LSPS represents a useful, noninvasive method to detect EV and a high risk EV in patients with CLD. Clinicians should recommend those patients with CLD who show higher values of LSPS to undergo further endoscopic examination.
Collapse
Affiliation(s)
- M S Malek
- Dr Md Saiful Malek, Junior Consultant Medicine, Upazilla Health Complex, Vhaluka, Mymensingh, Bangladesh; E-mail:
| | | | | | | | | | | | | | | |
Collapse
|
47
|
Al Amin M, Hoque MN, Siddiki AZ, Saha S, Kamal MM. Antimicrobial resistance situation in animal health of Bangladesh. Vet World 2020; 13:2713-2727. [PMID: 33487990 PMCID: PMC7811541 DOI: 10.14202/vetworld.2020.2713-2727] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Accepted: 11/12/2020] [Indexed: 11/16/2022] Open
Abstract
Antimicrobial resistance (AMR) is a crucial multifactorial and complex global problem and Bangladesh poses a regional and global threat with a high degree of antibiotic resistance. Although the routine application of antimicrobials in the livestock industry has largely contributed to the health and productivity, it correspondingly plays a significant role in the evolution of different pathogenic bacterial strains having multidrug resistance (MDR) properties. Bangladesh is implementing the National Action Plan (NAP) for containing AMR in human, animal, and environment sectors through “One Health” approach where the Department of Livestock Services (DLS) is the mandated body to implement NAP strategies in the animal health sector of the country. This review presents a “snapshot” of the predisposing factors, and current situations of AMR along with the weakness and strength of DLS to contain the problem in animal farming practices in Bangladesh. In the present review, resistance monitoring data and risk assessment identified several direct and/or indirect predisposing factors to be potentially associated with AMR development in the animal health sector of Bangladesh. The predisposing factors are inadequate veterinary healthcare, monitoring and regulatory services, intervention of excessive informal animal health service providers, and farmers’ knowledge gap on drugs, and AMR which have resulted in the misuse and overuse of antibiotics, ultimate in the evolution of antibiotic-resistant bacteria and genes in all types of animal farming settings of Bangladesh. MDR bacteria with extreme resistance against antibiotics recommended to use in both animals and humans have been reported and been being a potential public health hazard in Bangladesh. Execution of extensive AMR surveillance in veterinary practices and awareness-building programs for stakeholders along with the strengthening of the capacity of DLS are recommended for effective containment of AMR emergence and dissemination in the animal health sector of Bangladesh.
Collapse
Affiliation(s)
- Md Al Amin
- Quality Control Laboratory, Department of Livestock Services, Savar, Dhaka-1341, Bangladesh
| | - M Nazmul Hoque
- Department of Gynecology, Obstetrics and Reproductive Health, Faculty of Veterinary Medicine and Animal Science, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur-1706, Bangladesh
| | - Amam Zonaed Siddiki
- Department of Pathology and Parasitology, Chattogram Veterinary and Animal Sciences University, Chattogram, Bangladesh
| | - Sukumar Saha
- Department of Microbiology and Hygiene, Bangladesh Agricultural University, Mymensingh-2202, Bangladesh
| | - Md Mostofa Kamal
- Quality Control Laboratory, Department of Livestock Services, Savar, Dhaka-1341, Bangladesh
| |
Collapse
|
48
|
Rahman MS, Hoque MN, Islam MR, Islam I, Mishu ID, Rahaman MM, Sultana M, Hossain MA. Mutational insights into the envelope protein of SARS-CoV-2. Gene Rep 2020; 22:100997. [PMID: 33319124 PMCID: PMC7723457 DOI: 10.1016/j.genrep.2020.100997] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 10/23/2020] [Accepted: 12/02/2020] [Indexed: 01/03/2023]
Abstract
The ongoing mutations in the structural proteins of SARS-CoV-2 are the major impediment for prevention and control of the COVID-19 disease. Presently we focused on evolution of the envelope (E) protein, one of the most enigmatic and less studied protein among the four structural proteins (S, E, M and N) associated with multitude of immunopathological functions of SARS-CoV-2. In the present study, we comprehensively analyzed 81,818 high quality E protein sequences of SARS-CoV-2 globally available in the GISAID database as of 20 August 2020. Compared to Wuhan reference strain, our mutational analysis explored only 1.2 % (982/81818) mutant strains undergoing a total of 115 unique amino acid (aa) substitutions in the E protein, highlighting the fact that most (98.8 %) of the E protein of SARS-CoV-2 strains are highly conserved. Moreover, we found 58.77 % (134 of 228) nucleotides (nt) positions of SARS-CoV-2 E gene encountering a total of 176 unique nt-level mutations globally, which may affect the efficacy of real time RT-PCR-based molecular detection of COVID-19. Importantly, higher aa variations observed in the C-terminal domain (CTD) of the E protein, particularly at Ser55-Phe56, Arg69 and the C-terminal end (DLLV: 72–75) may alter the binding of SARS-CoV-2 Envelope protein to tight junction-associated PALS1 and thus could play a key role in COVID-19 pathogenesis. Furthermore, this study revealed the V25A mutation in the transmembrane domain which is a key factor for the homopentameric conformation of E protein. Our analysis also observed a triple cysteine motif harboring mutation (L39M, A41S, A41V, C43F, C43R, C43S, C44Y, N45R) which may hinder the binding of E protein with spike glycoprotein. These results therefore suggest the continuous monitoring of the structural proteins including the envelope protein of SARS-CoV-2 since the number of genome sequences from across the world are continuously increasing.
Collapse
Key Words
- CTD, C-terminal domain
- E, envelope
- Envelope protein
- M, membrane
- Mutations
- N, nucleocapsid
- NC, negatively charged
- NP, non-polar
- PC, positively charged
- S, spike
- SARS-CoV-2
- SARS-CoV-2, Severe Acute Respiratory Syndrome Coronavirus-2
- TMD, transmembrane domain
- Transmembrane domain
- Triple cysteine motif
- aa, amino acid
- nt, nucleotide
Collapse
Affiliation(s)
- M Shaminur Rahman
- Department of Microbiology, University of Dhaka, Dhaka 1000, Bangladesh
| | - M Nazmul Hoque
- Department of Microbiology, University of Dhaka, Dhaka 1000, Bangladesh
- Department of Gynecology, Obstetrics and Reproductive Health, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur 1706, Bangladesh
| | - M Rafiul Islam
- Department of Microbiology, University of Dhaka, Dhaka 1000, Bangladesh
| | - Israt Islam
- Department of Microbiology, University of Dhaka, Dhaka 1000, Bangladesh
| | | | | | - Munawar Sultana
- Department of Microbiology, University of Dhaka, Dhaka 1000, Bangladesh
| | - M Anwar Hossain
- Department of Microbiology, University of Dhaka, Dhaka 1000, Bangladesh
| |
Collapse
|
49
|
Rahman MS, Islam MR, Alam ASMRU, Islam I, Hoque MN, Akter S, Rahaman MM, Sultana M, Hossain MA. Evolutionary dynamics of SARS-CoV-2 nucleocapsid protein and its consequences. J Med Virol 2020; 93:2177-2195. [PMID: 33095454 DOI: 10.1002/jmv.26626] [Citation(s) in RCA: 82] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 10/17/2020] [Accepted: 10/20/2020] [Indexed: 12/21/2022]
Abstract
The emerged novel coronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has created a global health crisis that warrants an accurate and detailed characterization of the rapidly evolving viral genome for understanding its epidemiology, pathogenesis, and containment. Here, we explored 61,485 sequences of the nucleocapsid (N) protein, a potent diagnostic and prophylactic target, for identifying the mutations to review their roles in real-time polymerase chain reaction based diagnosis and observe consequent impacts. Compared to the Wuhan reference strain, a total of 1034 unique nucleotide mutations were identified in the mutant strains (49.15%, n = 30,221) globally. Of these mutations, 367 occupy primer binding sites including the 3'-end mismatch to the primer-pair of 11 well-characterized primer sets. Noteworthily, CDC (USA) recommended the N2 primer set contained a lower mismatch than the other primer sets. Moreover, 684 amino acid (aa) substitutions were located across 317 (75.66% of total aa) unique positions including 82, 21, and 83 of those in the RNA binding N-terminal domain (NTD), SR-rich region, and C-terminal dimerization domain, respectively. Moreover, 11 in-frame deletions, mostly (n = 10) within the highly flexible linker region, were revealed, and the rest was within the NTD region. Furthermore, we predicted the possible consequence of high-frequency mutations (≥20) and deletions on the tertiary structure of the N protein. Remarkably, we observed that a high frequency (67.94% of mutated sequences) co-occuring mutations (R203K and G204R) destabilized and decreased overall structural flexibility. The N protein of SARS-CoV-2 comprises an average of 1.2 mutations per strain compared to 4.4 and 0.4 in Middle East respiratory syndrome-related coronavirus and SARS-CoV, respectively. Despite being proposed as the alternative target to spike protein for vaccine and therapeutics, the ongoing evolution of the N protein may challenge these endeavors, thus needing further immunoinformatics analyses. Therefore, continuous monitoring is required for tracing the ongoing evolution of the SARS-CoV-2 N protein in prophylactic and diagnostic interventions.
Collapse
Affiliation(s)
| | - M Rafiul Islam
- Department of Microbiology, University of Dhaka, Dhaka, Bangladesh
| | - A S M Rubayet Ul Alam
- Department of Microbiology, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Israt Islam
- Department of Microbiology, University of Dhaka, Dhaka, Bangladesh
| | - M Nazmul Hoque
- Department of Microbiology, University of Dhaka, Dhaka, Bangladesh.,Department of Gynecology, Obstetrics and Reproductive Health, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, Bangladesh
| | - Salma Akter
- Department of Microbiology, University of Dhaka, Dhaka, Bangladesh.,Department of Microbiology, Jahangirnagar University, Savar, Dhaka, Bangladesh
| | | | - Munawar Sultana
- Department of Microbiology, University of Dhaka, Dhaka, Bangladesh
| | - M Anwar Hossain
- Department of Microbiology, University of Dhaka, Dhaka, Bangladesh
| |
Collapse
|
50
|
Hoque MN, Chaudhury A, Akanda MAM, Hossain MA, Islam MT. Genomic diversity and evolution, diagnosis, prevention, and therapeutics of the pandemic COVID-19 disease. PeerJ 2020; 8:e9689. [PMID: 33005486 PMCID: PMC7510477 DOI: 10.7717/peerj.9689] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 07/19/2020] [Indexed: 12/14/2022] Open
Abstract
The coronavirus disease 19 (COVID-19) is a highly transmittable and pathogenic viral infection caused by a novel evolutionarily divergent RNA virus, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The virus first emerged in Wuhan, China in December 2019, and subsequently spreaded around the world. Genomic analyses revealed that this zoonotic virus may be evolved naturally but not a purposefully manipulated laboratory construct. However, currently available data are not sufficient to precisely conclude the origin of this fearsome virus. Comprehensive annotations of the whole-genomes revealed hundreds of nucleotides, and amino acids mutations, substitutions and/or deletions at different positions of the ever changing SARS-CoV-2 genome. The spike (S) glycoprotein of SARS-CoV-2 possesses a functional polybasic (furin) cleavage site at the S1-S2 boundary through the insertion of 12 nucleotides. It leads to the predicted acquisition of 3-O-linked glycan around the cleavage site. Although real-time RT-PCR methods targeting specific gene(s) have widely been used to diagnose the COVID-19 patients, however, recently developed more convenient, cheap, rapid, and specific diagnostic tools targeting antigens or CRISPR-Cas-mediated method or a newly developed plug and play method should be available for the resource-poor developing countries. A large number of candidate drugs, vaccines and therapies have shown great promise in early trials, however, these candidates of preventive or therapeutic agents have to pass a long path of trials before being released for the practical application against COVID-19. This review updates current knowledge on origin, genomic evolution, development of the diagnostic tools, and the preventive or therapeutic remedies of the COVID-19. We also discussed the future scopes for research, effective management, and surveillance of the newly emerged COVID-19 disease.
Collapse
Affiliation(s)
- M. Nazmul Hoque
- Department of Gynecology, Obstetrics and Reproductive Health, Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur, Bangladesh
- Department of Microbiology, University of Dhaka, Dhaka, Bangladesh
| | | | - Md Abdul Mannan Akanda
- Department of Plant Pathology, Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur, Bangladesh
| | - M. Anwar Hossain
- Department of Microbiology, University of Dhaka, Dhaka, Bangladesh
- Jashore University of Science and Technology, Jashore, Bangladesh
| | - Md Tofazzal Islam
- Institute of Biotechnology and Genetic Engineering (IBGE), Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur, Bangladesh
| |
Collapse
|