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Shahid S, Abid R, Ajmal W, Almuqbil M, Almadani ME, Khan Y, Ansari AA, Rani R, Alshehri A, Alghamdi A, Asdaq SMB, Ghazanfar S. Antibiotic resistance genes prediction via whole genome sequence analysis of Stenotrophomonas maltophilia. J Infect Public Health 2024; 17:236-244. [PMID: 38128408 DOI: 10.1016/j.jiph.2023.12.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 12/06/2023] [Accepted: 12/13/2023] [Indexed: 12/23/2023] Open
Abstract
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.
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Affiliation(s)
- Sara Shahid
- Department of Life Sciences, Abasyn University Islamabad Campus Pakistan, Pakistan
| | - Rameesha Abid
- National 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, Pakistan
| | - Wajya Ajmal
- National Institute for Genomics and Advanced Biotechnology, National Agricultural Research Centre (NARC), Park Road, Islamabad 45500, Pakistan.
| | - Mansour Almuqbil
- Department of Clinical Pharmacy, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Moneer E Almadani
- Department of Clinical Medicine, College of Medicine, AlMaarefa University, Dariyah, 13713 Riyadh, Saudi Arabia
| | - Yasir Khan
- National Institute for Genomics and Advanced Biotechnology, National Agricultural Research Centre (NARC), Park Road, Islamabad 45500, Pakistan
| | - Adnan Ahmad Ansari
- National Center for Bioinformatics, Quaid-i-Azam University, Islamabad 44100, Pakistan
| | - Rehana Rani
- Department of Life Sciences, Abasyn University Islamabad Campus Pakistan, Pakistan.
| | - Ahmed Alshehri
- Department of Pharmacology, College of Clinical Pharmacy, Imam Abdulrahman Bin Faisal University, King Faisal Road, Dammam 31441, Saudi Arabia
| | - Adel Alghamdi
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Al-Baha University, P.O. Box 1988, Al-Baha, Saudi Arabia
| | | | - Shakira Ghazanfar
- National Institute for Genomics and Advanced Biotechnology, National Agricultural Research Centre (NARC), Park Road, Islamabad 45500, Pakistan.
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Lyu T, Cheung KS, Deng Z, Ni L, Chen C, Wu J, Leung WK, Seto WK. Whole genome sequencing reveals novel genetic mutations of Helicobacter pylori associating with resistance to clarithromycin and levofloxacin. Helicobacter 2023:e12972. [PMID: 36965192 DOI: 10.1111/hel.12972] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 02/16/2023] [Accepted: 03/07/2023] [Indexed: 03/27/2023]
Abstract
BACKGROUND Detection of mutations in one or a couple of genes may not provide enough data or cover all the genomic DNA variance related to antibiotic resistance of Helicobacter pylori to clarithromycin (CLA) and levofloxacin (LVX). We aimed to perform whole genome sequencing to explore novel antibiotic resistance-related genes to increase predictive accuracy for future targeted sequencing tests. METHODS Gastric mucosal biopsies were taken during upper endoscopy in 27 H. pylori-infected patients. According to culture-based antibacterial susceptibility test, H. pylori strains were divided into three groups, with nine strains in each group: CLA single-drug resistance (group C), LVX single-drug resistance (group L), and strains sensitive to all antibacterial drugs (group S). Based on whole genome sequencing with group S being the control, group C and group L group-specific single nucleotide variants and amino acid mutations were screened, and potential candidate genes related to CLA and LVX resistance were identified. RESULTS The median age of study subjects was 35 years (IQR: 31-40), and 17 (63.0%) were male. All nine CLA-resistant strains had A2143G mutations in 23S rRNA, while none of nine sensitive strains had the mutation. Six of nine strains in group L and six of nine strains in group S had 87th or 91st mutation in gyrA. After comparing sequencing data of strains among the three groups, we identified five mutated positions belonging to four genes related to CLA resistance, and 31 mutated positions belonging to 20 genes related to LVX resistance. Novel genetic mutations were detected for CLA resistance (including fliJ and clpX) and LVX resistance (including fliJ, cheA, hemE, Val360Ile, and HP0568). Missense mutations in fliJ and cheA gene were mainly involved in chemotaxis and flagellar motility to facilitate bacterial escape of antibiotics, while the functions of other novel gene mutations underpinning antibiotic resistance remain to be investigated. CONCLUSION Whole genome sequencing detected potential novel genetic mutations conferring resistance of H. pylori to CLA and LVX including fliJ and cheA. Further studies to correlate these findings with treatment outcome should be performed.
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Affiliation(s)
- Tao Lyu
- Department of Medicine, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China
| | - Ka Shing Cheung
- Department of Medicine, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China
- Department of Medicine, School of Clinical Medicine, The University of Hong Kong, Queen Mary Hospital, Hong Kong, China
| | - Zijie Deng
- Department of Medicine, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China
| | - Li Ni
- Department of Medicine, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China
| | - Chuan Chen
- Department of Medicine, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China
| | - Juan Wu
- Department of Medicine, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China
| | - Wai K Leung
- Department of Medicine, School of Clinical Medicine, The University of Hong Kong, Queen Mary Hospital, Hong Kong, China
| | - Wai Kay Seto
- Department of Medicine, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China
- Department of Medicine, School of Clinical Medicine, The University of Hong Kong, Queen Mary Hospital, Hong Kong, China
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Analysis of Genetic Relatedness between Gastric and Oral Helicobacter pylori in Patients with Early Gastric Cancer Using Multilocus Sequence Typing. Int J Mol Sci 2023; 24:ijms24032211. [PMID: 36768541 PMCID: PMC9917182 DOI: 10.3390/ijms24032211] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 01/13/2023] [Accepted: 01/19/2023] [Indexed: 01/24/2023] Open
Abstract
The oral cavity is the second most colonized site of Helicobacter pylori after the stomach. This study aimed to compare the genetic relatedness between gastric and oral H. pylori in Japanese patients with early gastric cancer through multilocus sequence typing (MLST) analysis using eight housekeeping genes. Gastric biopsy specimens and oral samples were collected from 21 patients with a fecal antigen test positive for H. pylori. The number of H. pylori allelic profiles ranged from zero to eight since the yield of DNA was small even when the nested PCR was performed. MLST analysis revealed that only one patient had a matching oral and gastric H. pylori genotype, suggesting that different genotypes of H. pylori inhabit the oral cavity and gastric mucosa. The phylogenetic analysis showed that oral H. pylori in six patients was similar to gastric H. pylori, implying that the two strains are related but not of the same origin, and those strains may be infected on separate occasions. It is necessary to establish a culture method for oral H. pylori to elucidate whether the oral cavity acts as the source of gastric infection, as our analysis was based on a limited number of allele sequences.
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Vital JS, Tanoeiro L, Lopes-Oliveira R, Vale FF. Biomarker Characterization and Prediction of Virulence and Antibiotic Resistance from Helicobacter pylori Next Generation Sequencing Data. Biomolecules 2022; 12:691. [PMID: 35625618 PMCID: PMC9138241 DOI: 10.3390/biom12050691] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 05/02/2022] [Accepted: 05/07/2022] [Indexed: 02/06/2023] Open
Abstract
The Gram-negative bacterium Helicobacter pylori colonizes c.a. 50% of human stomachs worldwide and is the major risk factor for gastric adenocarcinoma. Its high genetic variability makes it difficult to identify biomarkers of early stages of infection that can reliably predict its outcome. Moreover, the increasing antibiotic resistance found in H. pylori defies therapy, constituting a major human health problem. Here, we review H. pylori virulence factors and genes involved in antibiotic resistance, as well as the technologies currently used for their detection. Furthermore, we show that next generation sequencing may lead to faster characterization of virulence factors and prediction of the antibiotic resistance profile, thus contributing to personalized treatment and management of H. pylori-associated infections. With this new approach, more and permanent data will be generated at a lower cost, opening the future to new applications for H. pylori biomarker identification and antibiotic resistance prediction.
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Affiliation(s)
- Joana S. Vital
- Pathogen Genome Bioinformatics and Computational Biology, Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, 1649-003 Lisboa, Portugal; (J.S.V.); (L.T.); (R.L.-O.)
| | - Luís Tanoeiro
- Pathogen Genome Bioinformatics and Computational Biology, Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, 1649-003 Lisboa, Portugal; (J.S.V.); (L.T.); (R.L.-O.)
| | - Ricardo Lopes-Oliveira
- Pathogen Genome Bioinformatics and Computational Biology, Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, 1649-003 Lisboa, Portugal; (J.S.V.); (L.T.); (R.L.-O.)
| | - Filipa F. Vale
- Pathogen Genome Bioinformatics and Computational Biology, Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, 1649-003 Lisboa, Portugal; (J.S.V.); (L.T.); (R.L.-O.)
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Brasil-Costa I, Souza CDO, Monteiro LCR, Santos MES, Oliveira EHCD, Burbano RMR. H. pylori Infection and Virulence Factors cagA and vacA (s and m Regions) in Gastric Adenocarcinoma from Pará State, Brazil. Pathogens 2022; 11:pathogens11040414. [PMID: 35456089 PMCID: PMC9028951 DOI: 10.3390/pathogens11040414] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 03/17/2022] [Accepted: 03/21/2022] [Indexed: 12/23/2022] Open
Abstract
H. pylori shows a great variability in genes associated with virulence, which may influence properties related to gastric adenocarcinoma initiation and progression. Among them, cagA and vacA show a strong positive association with the disease. Therefore, a cross-sectional study was carried out with 281 samples of gastric adenocarcinoma, collected at a cancer reference center in the Brazilian Amazon. Detection of H. pylori was proceeded by PCR of the ureA and 16S genes. Positive samples were subjected to the cagA detection and vacA typing. The bacteria were observed in 32.03% of the samples. Positivity for H. pylori was associated with advanced age (p = 0.0093) and metastases (p = 0.0073). Among the positive cases, 80% (72/90) had the cagA gene. For the “s” position of the vacA gene, 98.8% (83/84) of the bacteria had genotype s1 and 1.2% (1/84) were genotyped as s2. For the “m” position, the results were: 63.6% (56/88) with m1 genotype, 2.3% (2/88) genotyped as m2 and 34.1% (30/88) m1/m2. Virulence factors did not impact an increase in the association with age or metastases. In conclusion, H. pylori infection is associated with malignant phenotype cases of gastric adenocarcinoma, involving metastases. The virulence factors related to the cagA and vacA genes showed a high prevalence in the Brazilian Amazon.
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Affiliation(s)
- Igor Brasil-Costa
- Laboratório de Imunologia, Seção de Virologia, Instituto Evandro Chagas, Ananindeua 67030-000, PA, Brazil
- Correspondence: ; Tel.: +55-91-3214-2005
| | - Cintya de Oliveira Souza
- Laboratório de Enteroinfecções Bacterianas, Seção de Bacteriologia e Micologia, Instituto Evandro Chagas, Ananindeua 67030-000, PA, Brazil; (C.d.O.S.); (L.C.R.M.)
| | - Leni Célia Reis Monteiro
- Laboratório de Enteroinfecções Bacterianas, Seção de Bacteriologia e Micologia, Instituto Evandro Chagas, Ananindeua 67030-000, PA, Brazil; (C.d.O.S.); (L.C.R.M.)
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