Antibiotic resistance genes prediction via whole genome sequence analysis of Stenotrophomonas maltophilia
Background: Stenotrophomonas maltophilia (S. maltophilia) is the first dominant ubiquitous bacterial species identified from the genus Stenotrophomonas in 1943 from a human source. S. maltophilia clinical strains are resistance to several therapies, this study is designed to investigate the whole ge...
| Main Authors: | , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Elsevier
2024-02-01
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| Series: | Journal of Infection and Public Health |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S187603412300446X |
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| author | Sara Shahid Rameesha Abid Wajya Ajmal Mansour Almuqbil Moneer E. Almadani Yasir Khan Adnan Ahmad Ansari Rehana Rani Ahmed Alshehri Adel Alghamdi Syed Mohammad Basheeruddin Asdaq Shakira Ghazanfar |
| author_facet | Sara Shahid Rameesha Abid Wajya Ajmal Mansour Almuqbil Moneer E. Almadani Yasir Khan Adnan Ahmad Ansari Rehana Rani Ahmed Alshehri Adel Alghamdi Syed Mohammad Basheeruddin Asdaq Shakira Ghazanfar |
| author_sort | Sara Shahid |
| collection | DOAJ |
| description | Background: Stenotrophomonas maltophilia (S. maltophilia) is the first dominant ubiquitous bacterial species identified from the genus Stenotrophomonas in 1943 from a human source. S. maltophilia clinical strains are resistance to several therapies, this study is designed to investigate the whole genome sequence and antimicrobial resistance genes prediction in Stenotrophomonas maltophilia (S. maltophilia) SARC-5 and SARC-6 strains, isolated from the nasopharyngeal samples of an immunocompromised patient. Methods: These bacterial strains were obtained from Pakistan Institute of Medical Sciences (PIMS) Hospital, Pakistan. The bacterial genome was sequenced using a whole-genome shotgun via a commercial service that used an NGS (Next Generation Sequencing) technology called as Illumina Hiseq 2000 system for genomic sequencing. Moreover, detailed in-silico analyses were done to predict the presence of antibiotic resistance genes in S. maltophilia. Results: Results showed that S. maltophilia is a rare gram negative, rod-shaped, non sporulating bacteria. The genome assembly results in 24 contigs (>500 bp) having a size of 4668,850 bp with 65.8% GC contents. Phylogenetic analysis showed that SARC-5 and SARC-6 were closely related to S. maltophilia B111, S. maltophilia BAB-5317, S. maltophilia AHL, S. maltophilia BAB-5307, S. maltophilia RD-AZPVI_04, S. maltophilia JFZ2, S. maltophilia RD_MAAMIB_06 and lastly with S. maltophilia sp ROi7. Moreover, the whole genome sequence analysis of both SARC-5 and SARC-6 revealed the presence of four resistance genes adeF, qacG, adeF, and smeR. Conclusion: Our study confirmed that S. maltophilia SARC-5 and SARC-6 are one of the leading causes of nosocomial infection which carry multiple antibiotic resistance genes. |
| first_indexed | 2024-03-08T12:47:27Z |
| format | Article |
| id | doaj.art-8c7b5773cb0b44f687f698e33f44eb30 |
| institution | Directory Open Access Journal |
| issn | 1876-0341 |
| language | English |
| last_indexed | 2024-03-08T12:47:27Z |
| publishDate | 2024-02-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Journal of Infection and Public Health |
| spelling | doaj.art-8c7b5773cb0b44f687f698e33f44eb302024-01-21T05:06:29ZengElsevierJournal of Infection and Public Health1876-03412024-02-01172236244Antibiotic resistance genes prediction via whole genome sequence analysis of Stenotrophomonas maltophiliaSara Shahid0Rameesha Abid1Wajya Ajmal2Mansour Almuqbil3Moneer E. Almadani4Yasir Khan5Adnan Ahmad Ansari6Rehana Rani7Ahmed Alshehri8Adel Alghamdi9Syed Mohammad Basheeruddin Asdaq10Shakira Ghazanfar11Department of Life Sciences, Abasyn University Islamabad Campus Pakistan, PakistanNational Institute for Genomics and Advanced Biotechnology, National Agricultural Research Centre (NARC), Park Road, Islamabad 45500, Pakistan; Department of Microbiology, Quaid-i-Azam University, Islamabad 44100, PakistanNational Institute for Genomics and Advanced Biotechnology, National Agricultural Research Centre (NARC), Park Road, Islamabad 45500, Pakistan; Corresponding authors.Department of Clinical Pharmacy, College of Pharmacy, King Saud University, Riyadh 11451, Saudi ArabiaDepartment of Clinical Medicine, College of Medicine, AlMaarefa University, Dariyah, 13713 Riyadh, Saudi ArabiaNational Institute for Genomics and Advanced Biotechnology, National Agricultural Research Centre (NARC), Park Road, Islamabad 45500, PakistanNational Center for Bioinformatics, Quaid-i-Azam University, Islamabad 44100, PakistanDepartment of Life Sciences, Abasyn University Islamabad Campus Pakistan, Pakistan; Corresponding authors.Department of Pharmacology, College of Clinical Pharmacy, Imam Abdulrahman Bin Faisal University, King Faisal Road, Dammam 31441, Saudi ArabiaDepartment of Pharmaceutical Chemistry, Faculty of Pharmacy, Al-Baha University, P.O. Box 1988, Al-Baha, Saudi ArabiaDepartment of Pharmacy Practice, College of Pharmacy, AlMaarefa University, Dariyah, 13713 Riyadh, Saudi Arabia; Corresponding authors.National Institute for Genomics and Advanced Biotechnology, National Agricultural Research Centre (NARC), Park Road, Islamabad 45500, Pakistan; Corresponding authors.Background: Stenotrophomonas maltophilia (S. maltophilia) is the first dominant ubiquitous bacterial species identified from the genus Stenotrophomonas in 1943 from a human source. S. maltophilia clinical strains are resistance to several therapies, this study is designed to investigate the whole genome sequence and antimicrobial resistance genes prediction in Stenotrophomonas maltophilia (S. maltophilia) SARC-5 and SARC-6 strains, isolated from the nasopharyngeal samples of an immunocompromised patient. Methods: These bacterial strains were obtained from Pakistan Institute of Medical Sciences (PIMS) Hospital, Pakistan. The bacterial genome was sequenced using a whole-genome shotgun via a commercial service that used an NGS (Next Generation Sequencing) technology called as Illumina Hiseq 2000 system for genomic sequencing. Moreover, detailed in-silico analyses were done to predict the presence of antibiotic resistance genes in S. maltophilia. Results: Results showed that S. maltophilia is a rare gram negative, rod-shaped, non sporulating bacteria. The genome assembly results in 24 contigs (>500 bp) having a size of 4668,850 bp with 65.8% GC contents. Phylogenetic analysis showed that SARC-5 and SARC-6 were closely related to S. maltophilia B111, S. maltophilia BAB-5317, S. maltophilia AHL, S. maltophilia BAB-5307, S. maltophilia RD-AZPVI_04, S. maltophilia JFZ2, S. maltophilia RD_MAAMIB_06 and lastly with S. maltophilia sp ROi7. Moreover, the whole genome sequence analysis of both SARC-5 and SARC-6 revealed the presence of four resistance genes adeF, qacG, adeF, and smeR. Conclusion: Our study confirmed that S. maltophilia SARC-5 and SARC-6 are one of the leading causes of nosocomial infection which carry multiple antibiotic resistance genes.http://www.sciencedirect.com/science/article/pii/S187603412300446XStenotrophomonas maltophiliaWhole Genome Sequencing (WGS)Next Generation Sequencing (NGS)Antibiotic Resistance Genes |
| spellingShingle | Sara Shahid Rameesha Abid Wajya Ajmal Mansour Almuqbil Moneer E. Almadani Yasir Khan Adnan Ahmad Ansari Rehana Rani Ahmed Alshehri Adel Alghamdi Syed Mohammad Basheeruddin Asdaq Shakira Ghazanfar Antibiotic resistance genes prediction via whole genome sequence analysis of Stenotrophomonas maltophilia Journal of Infection and Public Health Stenotrophomonas maltophilia Whole Genome Sequencing (WGS) Next Generation Sequencing (NGS) Antibiotic Resistance Genes |
| title | Antibiotic resistance genes prediction via whole genome sequence analysis of Stenotrophomonas maltophilia |
| title_full | Antibiotic resistance genes prediction via whole genome sequence analysis of Stenotrophomonas maltophilia |
| title_fullStr | Antibiotic resistance genes prediction via whole genome sequence analysis of Stenotrophomonas maltophilia |
| title_full_unstemmed | Antibiotic resistance genes prediction via whole genome sequence analysis of Stenotrophomonas maltophilia |
| title_short | Antibiotic resistance genes prediction via whole genome sequence analysis of Stenotrophomonas maltophilia |
| title_sort | antibiotic resistance genes prediction via whole genome sequence analysis of stenotrophomonas maltophilia |
| topic | Stenotrophomonas maltophilia Whole Genome Sequencing (WGS) Next Generation Sequencing (NGS) Antibiotic Resistance Genes |
| url | http://www.sciencedirect.com/science/article/pii/S187603412300446X |
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