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Oles RE, Carrillo Terrazas M, Loomis LR, Hsu CY, Tribelhorn C, Belda-Ferre P, Ea AC, Bryant M, Young JA, Carrow HC, Sandborn WJ, Dulai PS, Sivagnanam M, Pride D, Knight R, Chu H. Pangenome comparison of Bacteroides fragilis genomospecies unveils genetic diversity and ecological insights. mSystems 2024; 9:e0051624. [PMID: 38934546 PMCID: PMC11265264 DOI: 10.1128/msystems.00516-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Accepted: 05/31/2024] [Indexed: 06/28/2024] Open
Abstract
Bacteroides fragilis is a Gram-negative commensal bacterium commonly found in the human colon, which differentiates into two genomospecies termed divisions I and II. Through a comprehensive collection of 694 B. fragilis whole genome sequences, we identify novel features distinguishing these divisions. Our study reveals a distinct geographic distribution with division I strains predominantly found in North America and division II strains in Asia. Additionally, division II strains are more frequently associated with bloodstream infections, suggesting a distinct pathogenic potential. We report differences between the two divisions in gene abundance related to metabolism, virulence, stress response, and colonization strategies. Notably, division II strains harbor more antimicrobial resistance (AMR) genes than division I strains. These findings offer new insights into the functional roles of division I and II strains, indicating specialized niches within the intestine and potential pathogenic roles in extraintestinal sites. IMPORTANCE Understanding the distinct functions of microbial species in the gut microbiome is crucial for deciphering their impact on human health. Classifying division II strains as Bacteroides fragilis can lead to erroneous associations, as researchers may mistakenly attribute characteristics observed in division II strains to the more extensively studied division I B. fragilis. Our findings underscore the necessity of recognizing these divisions as separate species with distinct functions. We unveil new findings of differential gene prevalence between division I and II strains in genes associated with intestinal colonization and survival strategies, potentially influencing their role as gut commensals and their pathogenicity in extraintestinal sites. Despite the significant niche overlap and colonization patterns between these groups, our study highlights the complex dynamics that govern strain distribution and behavior, emphasizing the need for a nuanced understanding of these microorganisms.
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Affiliation(s)
- Renee E. Oles
- Department of Pathology, University of California, San Diego, California, USA
- Department of Pediatrics, School of Medicine, University of California, San Diego, California, USA
| | | | - Luke R. Loomis
- Department of Pathology, University of California, San Diego, California, USA
| | - Chia-Yun Hsu
- Department of Pathology, University of California, San Diego, California, USA
| | - Caitlin Tribelhorn
- Department of Pediatrics, School of Medicine, University of California, San Diego, California, USA
| | - Pedro Belda-Ferre
- Department of Pediatrics, School of Medicine, University of California, San Diego, California, USA
| | - Allison C. Ea
- Department of Pathology, University of California, San Diego, California, USA
| | - MacKenzie Bryant
- Department of Pediatrics, School of Medicine, University of California, San Diego, California, USA
| | - Jocelyn A. Young
- Department of Pediatrics, School of Medicine, University of California, San Diego, California, USA
- Rady Children’s Hospital, San Diego, California, USA
| | - Hannah C. Carrow
- Department of Pathology, University of California, San Diego, California, USA
| | - William J. Sandborn
- Division of Gastroenterology, University of California, San Diego, California, USA
- Center for Microbiome Innovation, University of California, San Diego, California, USA
| | - Parambir S. Dulai
- Division of Gastroenterology, University of California, San Diego, California, USA
- Division of Gastroenterology, Northwestern University, Chicago, Illinois, USA
| | - Mamata Sivagnanam
- Department of Pediatrics, School of Medicine, University of California, San Diego, California, USA
- Rady Children’s Hospital, San Diego, California, USA
| | - David Pride
- Department of Pathology, University of California, San Diego, California, USA
- Center for Microbiome Innovation, University of California, San Diego, California, USA
- Center for Innovative Phage Applications and Therapeutics (IPATH), University of California, San Diego, California, USA
- Center of Advanced Laboratory Medicine (CALM), University of California, San Diego, California, USA
| | - Rob Knight
- Department of Pediatrics, School of Medicine, University of California, San Diego, California, USA
- Center for Microbiome Innovation, University of California, San Diego, California, USA
- Shu Chien-Gene Lay Department of Bioengineering, University of California, San Diego, California, USA
- Department of Computer Science & Engineering, University of California, San Diego, California, USA
- Halıcıoğlu Data Science Institute, University of California, San Diego, California, USA
| | - Hiutung Chu
- Department of Pathology, University of California, San Diego, California, USA
- Center for Microbiome Innovation, University of California, San Diego, California, USA
- Chiba University-UC San Diego Center for Mucosal Immunology, Allergy and Vaccines (cMAV), University of California, San Diego, California, USA
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Nazarinejad N, Hajikhani B, Vaezi AA, Firoozeh F, Sameni F, Yaslianifard S, Goudarzi M, Dadashi M. Association between colorectal cancer, the frequency of Bacteroides fragilis, and the level of mismatch repair genes expression in the biopsy samples of Iranian patients. BMC Gastroenterol 2024; 24:82. [PMID: 38395750 PMCID: PMC10885486 DOI: 10.1186/s12876-024-03169-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 02/11/2024] [Indexed: 02/25/2024] Open
Abstract
BACKGROUND Deficient DNA mismatch repair (MMR) can cause microsatellite instability (MSI) and is more common in colorectal cancer (CRC) patients. Understanding the carcinogenic mechanism of bacteria and their impact on cancer cells is crucial. Bacteroides fragilis (B. fragilis) has been identified as a potential promoter of tumorigenesis through the alteration of signaling pathways. This study aims to assess the expression levels of msh2, msh6, mlh1, and the relative frequency of B. fragilis in biopsy samples from CRC patients. MATERIALS AND METHODS Based on the sequence of mlh1, msh2, and msh6 genes, B. fragilis specific 16srRNA and bacterial universal 16srRNA specific primers were selected, and the expression levels of the target genes were analyzed using the Real-Time PCR method. RESULTS Significant increases in the expression levels of mlh1, msh2, and msh6 genes were observed in the cancer group. Additionally, the expression of these MMR genes showed a significant elevation in samples positive for B. fragilis presence. The relative frequency of B. fragilis in the cancer group demonstrated a significant rise compared to the control group. CONCLUSION The findings suggest a potential correlation between the abundance of B. fragilis and alterations in the expression of MMR genes. Since these genes can play a role in modifying colon cancer, investigating microbial characteristics and gene expression changes in CRC could offer a viable solution for CRC diagnosis.
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Affiliation(s)
- Nooshin Nazarinejad
- Department of Microbiology, School of Medicine, Alborz University of Medical Sciences, Karaj, Iran
| | - Bahareh Hajikhani
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Amir Abbas Vaezi
- Department of Internal Medicine, Alborz University of Medical Sciences, Karaj, Iran
| | - Farzaneh Firoozeh
- Department of Microbiology, School of Medicine, Alborz University of Medical Sciences, Karaj, Iran
| | - Fatemeh Sameni
- Department of Microbiology, Faculty of Medicine, Shahed University, Tehran, Iran
| | - Somayeh Yaslianifard
- Department of Microbiology, School of Medicine, Alborz University of Medical Sciences, Karaj, Iran
| | - Mehdi Goudarzi
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Masoud Dadashi
- Department of Microbiology, School of Medicine, Alborz University of Medical Sciences, Karaj, Iran.
- Non-Communicable Diseases Research Center, Alborz University of Medical Sciences, Karaj, Iran.
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Oles RE, Terrazas MC, Loomis LR, Hsu CY, Tribelhorn C, Ferre PB, Ea A, Bryant M, Young J, Carrow HC, Sandborn WJ, Dulai P, Sivagnanam M, Pride D, Knight R, Chu H. Pangenome comparison of Bacteroides fragilis genomospecies unveil genetic diversity and ecological insights. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.20.572674. [PMID: 38187556 PMCID: PMC10769428 DOI: 10.1101/2023.12.20.572674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Bacteroides fragilis is a Gram-negative commensal bacterium commonly found in the human colon that differentiates into two genomospecies termed division I and II. We leverage a comprehensive collection of 694 B. fragilis whole genome sequences and report differential gene abundance to further support the recent proposal that divisions I and II represent separate species. In division I strains, we identify an increased abundance of genes related to complex carbohydrate degradation, colonization, and host niche occupancy, confirming the role of division I strains as gut commensals. In contrast, division II strains display an increased prevalence of plant cell wall degradation genes and exhibit a distinct geographic distribution, primarily originating from Asian countries, suggesting dietary influences. Notably, division II strains have an increased abundance of genes linked to virulence, survival in toxic conditions, and antimicrobial resistance, consistent with a higher incidence of these strains in bloodstream infections. This study provides new evidence supporting a recent proposal for classifying divisions I and II B. fragilis strains as distinct species, and our comparative genomic analysis reveals their niche-specific roles.
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Affiliation(s)
- Renee E Oles
- Department of Pathology, University of California, San Diego, La Jolla, CA
- Department of Pediatrics, School of Medicine, University of California, La Jolla, CA
| | | | - Luke R Loomis
- Department of Pathology, University of California, San Diego, La Jolla, CA
| | - Chia-Yun Hsu
- Department of Pathology, University of California, San Diego, La Jolla, CA
| | - Caitlin Tribelhorn
- Department of Pediatrics, School of Medicine, University of California, La Jolla, CA
| | - Pedro Belda Ferre
- Department of Pediatrics, School of Medicine, University of California, La Jolla, CA
| | - Allison Ea
- Department of Pathology, University of California, San Diego, La Jolla, CA
| | - MacKenzie Bryant
- Department of Pediatrics, School of Medicine, University of California, La Jolla, CA
| | - Jocelyn Young
- Department of Pediatrics, School of Medicine, University of California, La Jolla, CA
- Rady Children's Hospital, San Diego, CA, United States
| | - Hannah C Carrow
- Department of Pathology, University of California, San Diego, La Jolla, CA
| | - William J Sandborn
- Division of Gastroenterology, University of California, San Diego, La Jolla, CA
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA
| | - Parambir Dulai
- Division of Gastroenterology, University of California, San Diego, La Jolla, CA
- Division of Gastroenterology, Northwestern University, Chicago, Illinois
| | - Mamata Sivagnanam
- Department of Pediatrics, School of Medicine, University of California, La Jolla, CA
- Rady Children's Hospital, San Diego, CA, United States
| | - David Pride
- Department of Pathology, University of California, San Diego, La Jolla, CA
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA
- Center for Innovative Phage Applications and Therapeutics (IPATH), University of California, San Diego, La Jolla, CA
- Center of Advanced Laboratory Medicine (CALM), University of California, San Diego, La Jolla, CA
| | - Rob Knight
- Department of Pediatrics, School of Medicine, University of California, La Jolla, CA
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA
- Shu Chien-Gene Lay Department of Bioengineering, University of California San Diego, La Jolla, CA
- Department of Computer Science & Engineering, University of California, San Diego, La Jolla, CA
- Halıcıoğlu Data Science Institute, University of California, San Diego, La Jolla, CA
| | - Hiutung Chu
- Department of Pathology, University of California, San Diego, La Jolla, CA
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA
- Chiba University-UC San Diego Center for Mucosal Immunology, Allergy and Vaccines (cMAV), University of California, San Diego, La Jolla, CA
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English J, Newberry F, Hoyles L, Patrick S, Stewart L. Genomic analyses of Bacteroides fragilis: subdivisions I and II represent distinct species. J Med Microbiol 2023; 72. [PMID: 37910167 DOI: 10.1099/jmm.0.001768] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2023] Open
Abstract
Introduction. Bacteroides fragilis is a Gram-negative anaerobe that is a member of the human gastrointestinal microbiota and is frequently found as an extra-intestinal opportunistic pathogen. B. fragilis comprises two distinct groups - divisions I and II - characterized by the presence/absence of genes [cepA and ccrA (cfiA), respectively] that confer resistance to β-lactam antibiotics by either serine or metallo-β-lactamase production. No large-scale analyses of publicly available B. fragilis sequence data have been undertaken, and the resistome of the species remains poorly defined.Hypothesis/Gap Statement. Reclassification of divisions I and II B. fragilis as two distinct species has been proposed but additional evidence is required.Aims. To investigate the genomic diversity of GenBank B. fragilis genomes and establish the prevalence of division I and II strains among publicly available B. fragilis genomes, and to generate further evidence to demonstrate that B. fragilis division I and II strains represent distinct genomospecies.Methodology. High-quality (n=377) genomes listed as B. fragilis in GenBank were included in pangenome and functional analyses. Genome data were also subject to resistome profiling using The Comprehensive Antibiotic Resistance Database.Results. Average nucleotide identity and phylogenetic analyses showed B. fragilis divisions I and II represent distinct species: B. fragilis sensu stricto (n=275 genomes) and B. fragilis A (n=102 genomes; Genome Taxonomy Database designation), respectively. Exploration of the pangenome of B. fragilis sensu stricto and B. fragilis A revealed separation of the two species at the core and accessory gene levels.Conclusion. The findings indicate that B. fragilis A, previously referred to as division II B. fragilis, is an individual species and distinct from B. fragilis sensu stricto. The B. fragilis pangenome analysis supported previous genomic, phylogenetic and resistome screening analyses collectively reinforcing that divisions I and II are two separate species. In addition, it was confirmed that differences in the accessory genes of B. fragilis divisions I and II are primarily associated with carbohydrate metabolism and suggest that differences other than antimicrobial resistance could also be used to distinguish between these two species.
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Affiliation(s)
- Jamie English
- Institute for Global Food Security, School of Biological Sciences, Queen's University, Belfast, UK
| | - Fiona Newberry
- Department of Biosciences, School of Science and Technology, Nottingham Trent University, Nottingham, UK
| | - Lesley Hoyles
- Department of Biosciences, School of Science and Technology, Nottingham Trent University, Nottingham, UK
| | - Sheila Patrick
- Institute for Global Food Security, School of Biological Sciences, Queen's University, Belfast, UK
- Wellcome Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7BL, UK
| | - Linda Stewart
- Institute for Global Food Security, School of Biological Sciences, Queen's University, Belfast, UK
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Sevillano G, Paz Y Miño A, Solís MB, Vaca JP, Zurita-Salinas C, Zurita J. First Report of Antibiotic Resistance Markers cfiA and nim Among Bacteroides fragilis Group Strains in Ecuadorian Patients. Microb Drug Resist 2023; 29:533-539. [PMID: 37733248 DOI: 10.1089/mdr.2023.0125] [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] [Indexed: 09/22/2023] Open
Abstract
In recent years, increasing resistance of Bacteroides fragilis to several antibiotics has been reported in different countries. The aim of this study was to evaluate the antibiotic resistance profiles of Bacteroides spp. isolated from clinical samples by phenotypic and molecular methods. A total of 40 nonrepetitive isolates of the B. fragilis group were studied from 2018 to 2019. The species was identified by API 20A system. The minimum inhibitory concentrations (MICs) were determined by Sensititre anaerobe MIC plate. The presence of the nim and cfiA genes was checked by conventional PCR. The association between genes and insertion sequence (IS) was performed by whole genome sequencing. Eleven isolates were categorized as metronidazole-resistant and only 2 isolates harbored the nim gene. Five isolates were imipenem-resistant, but cfiA gene was detected in two isolates. cfiA gene was closely related to the cfiA-4 allele and associated with IS614B. The nim gene was not related to any nim gene type and was considered a new variant named nimL. IS612 was found upstream of nimL gene. In view of the scarcity of data on B. fragilis, there is a need to surveil antibiotic resistance levels and molecular mechanisms to implement better antimicrobial therapies against this important group of bacteria.
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Affiliation(s)
- Gabriela Sevillano
- Unidad de Investigaciones en Biomedicina, Zurita & Zurita Laboratorios, Quito, Ecuador
| | - Ariane Paz Y Miño
- Unidad de Investigaciones en Biomedicina, Zurita & Zurita Laboratorios, Quito, Ecuador
| | - María Belén Solís
- Unidad de Investigaciones en Biomedicina, Zurita & Zurita Laboratorios, Quito, Ecuador
| | - Juan Pablo Vaca
- Carrera de Ingeniería en Biotecnología, Departamento de Ciencias de la Vida, Universidad de las Fuerzas Armadas-ESPE, Sangolquí, Ecuador
| | - Camilo Zurita-Salinas
- Unidad de Investigaciones en Biomedicina, Zurita & Zurita Laboratorios, Quito, Ecuador
- Cátedra de Inmunología, Carrera de Medicina, Universidad Central del Ecuador, Quito, Ecuador
| | - Jeannete Zurita
- Unidad de Investigaciones en Biomedicina, Zurita & Zurita Laboratorios, Quito, Ecuador
- Pontificia Universidad Católica del Ecuador, Quito, Ecuador
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Jiang X, Yan C, Zhang H, Chen L, Jiang R, Zheng K, Jin W, Ma H, Liu X, Dong M. Oral Probiotic Expressing Human Ethanol Dehydrogenase Attenuates Damage Caused by Acute Alcohol Consumption in Mice. Microbiol Spectr 2023; 11:e0429422. [PMID: 37039510 PMCID: PMC10269551 DOI: 10.1128/spectrum.04294-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 02/24/2023] [Indexed: 04/12/2023] Open
Abstract
Alcohol is an essential drug in human life with multiple medical functions, but excessive alcohol intake, even a single episode of binge drinking, can cause serious damage. Reducing alcohol consumption or absorption is a direct way to alleviate the related harm. Alcohol is decomposed successively by alcohol dehydrogenase (ADH) and acetaldehyde dehydrogenase (ALDH) in the liver. Here, we produced a human ADH1B (hADH1B)-expressing probiotic, a recombinant Lactococcus lactis, that aimed to enhance alcohol degradation in the intestinal tract after oral administration. Our results showed that the oral hADH1B-expressing probiotic reduced alcohol absorption, prolonged the alcohol tolerance time, and shortened the recovery time after acute alcohol challenge. More importantly, the liver and intestine were protected from acute injury caused by alcohol challenge. Therefore, the engineered probiotic has the potential to protect organ damage from alcohol consumption. Furthermore, this engineered probiotic may have beneficial effects on alcohol-related diseases such as alcoholic fatty liver disease. IMPORTANCE Alcohol plays an important role in medical treatment, culture, and social interaction. However, excessive alcohol consumption or improper alcohol intake patterns can lead to serious damage to health. Aiming to reduce the harm of alcohol consumption, we designed a recombinant probiotic expressing hADH1B. Our results showed that this recombinant probiotic can reduce alcohol absorption and protect the body from alcohol damage, including hangover, liver, and intestinal damage. Reducing alcohol damage is helpful to the health of people with difficulty in abstinence. The engineered probiotic may provide new strategies for treatment and prevention of the negative effects of alcohol, and it also has the potential for widespread application.
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Affiliation(s)
- Xiaoxiao Jiang
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Chunlong Yan
- Agriculture College of Yanbian University, Yanji, Jilin, China
| | - Hanlin Zhang
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Li Chen
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Rui Jiang
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Kexin Zheng
- Institute of Infectious Disease, Ditan Hospital, Capital Medical University, Beijing, China
| | - Wanzhu Jin
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Huijuan Ma
- Department of Internal Medicine, Hebei Medical University, Shijiazhuang, Hebei, China
- Key Laboratory of Metabolic Diseases, Hebei General Hospital, Shijiazhuang, Hebei, China
| | - Xiaomeng Liu
- Department of Nutrition and Food Hygiene, College of Public Health, Xinxiang Medical University, Xinxiang, Henan, China
- Institute of Neuroscience and Translational Medicine, College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, China
| | - Meng Dong
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of the Chinese Academy of Sciences, Beijing, China
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Salarieh N, Emami Meibodi A, Alipour S, Azimirad M, Looha MA, Asadzadeh Aghdaei H, Yadegar A, Shahrokh S, Zali MR. Characterization of the mucosal microbiota in patients with nodular lymphoid hyperplasia with concurrent irritable bowel syndrome compared to healthy controls. Mol Biol Rep 2023; 50:145-155. [PMID: 36315327 DOI: 10.1007/s11033-022-07974-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Accepted: 09/21/2022] [Indexed: 01/29/2023]
Abstract
BACKGROUND Nodular lymphoid hyperplasia (NLH) is known as a lymphoproliferative lesion in which multiple small nodules appear on the intestinal wall. It has been documented that patients who struggle with irritable bowel syndrome (IBS) are at greater risk of developing NLH. Here, we aimed to investigate the previously reported pathogens and the abundance of a selection of mucosal microbiota in IBS + NLH patients compared to IBS, and healthy controls. METHODS AND RESULTS Terminal ileum biopsies were collected from 37 IBS + NLH, 37 IBS, and 29 healthy controls. Bacterial culture and PCR was performed to detect the presence of pathogens in biopsies. A qPCR assay was applied to assess the abundance of a selection of bacterial taxa. Totally, five bacterial isolates including two enteropathogenic and one enteroaggregative Escherichia coli (EPEC, EAEC), one enterotoxigenic Staphylococcus aureus (SEA), and one Yersinia enterocolitica strains were detected among the IBS + NLH cases. The relative abundance of Bacteroidetes and Streptococcus spp. in IBS + NLH patients was significantly less than IBS and healthy controls. Firmicutes, Pseudomonas spp., Haemophilus spp., and Campylobacter spp. were notably more abundant in IBS + NLH than in IBS patients. The abundance of Verrucomicrobia was higher in NLH + IBS than in healthy controls. Actinobacteria was also significantly more abundant among NLH + IBS patients than the controls. CONCLUSION Our results demonstrated that mucosal microbiota composition in NLH + IBS patients slightly differs from that of IBS patients and healthy controls. Further research using large-scale cohorts are needed to enhance current understanding of the contribution of the mucosal microbiota to NLH pathogenesis with concurrent IBS.
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Affiliation(s)
- Naghmeh Salarieh
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Armitasadat Emami Meibodi
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Samira Alipour
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Masoumeh Azimirad
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mehdi Azizmohammad Looha
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hamid Asadzadeh Aghdaei
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Abbas Yadegar
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Shabnam Shahrokh
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Mohammad Reza Zali
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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Diversity of genomic clusters and CfiA/cfiA alleles in Bacteroides fragilis isolates from human and animals. Anaerobe 2022; 75:102567. [DOI: 10.1016/j.anaerobe.2022.102567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 03/28/2022] [Accepted: 04/09/2022] [Indexed: 11/23/2022]
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9
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Amiri R, Norouzbabaei Z, Kalali N, Ghourchian S, Yaseri M, Abdollahi A, Douraghi M. Identification of enterotoxigenic Bacteroides fragilis in patients with diarrhea: A study targeting 16S rRNA, gyrB and nanH genes. Anaerobe 2022; 75:102546. [DOI: 10.1016/j.anaerobe.2022.102546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 03/08/2022] [Accepted: 03/10/2022] [Indexed: 11/25/2022]
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10
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Chandra H, Sharma KK, Tuovinen OH, Sun X, Shukla P. Pathobionts: mechanisms of survival, expansion, and interaction with host with a focus on Clostridioides difficile. Gut Microbes 2022; 13:1979882. [PMID: 34724858 PMCID: PMC8565823 DOI: 10.1080/19490976.2021.1979882] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Pathobionts are opportunistic microbes that emerge as a result of perturbations in the healthy microbiome due to complex interactions of various genetic, exposomal, microbial, and host factors that lead to their selection and expansion. Their proliferations can aggravate inflammatory manifestations, trigger autoimmune diseases, and lead to severe life-threatening conditions. Current surge in microbiome research is unwinding these complex interplays between disease development and protection against pathobionts. This review summarizes the current knowledge of pathobiont emergence with a focus on Clostridioides difficile and the recent findings on the roles of immune cells such as iTreg cells, Th17 cells, innate lymphoid cells, and cytokines in protection against pathobionts. The review calls for adoption of innovative tools and cutting-edge technologies in clinical diagnostics and therapeutics to provide insights in identification and quantification of pathobionts.
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Affiliation(s)
- Harish Chandra
- Department of Environmental Microbiology, School of Earth and Environmental Sciences, Babasaheb Bhimrao Ambedkar University, Lucknow, Uttar Pradesh, India,Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Krishna Kant Sharma
- Laboratory of Enzymology and Recombinant DNA Technology, Department of Microbiology, Maharshi Dayanand University, Rohtak, Haryana, India
| | - Olli H. Tuovinen
- Department of Microbiology, Ohio State University, Columbus, OH, USA
| | - Xingmin Sun
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA,Xingmin Sun Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| | - Pratyoosh Shukla
- School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi, India,Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, Haryana, India,CONTACT Pratyoosh Shukla School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi 221005, India
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Ibragimova S, Ramachandran R, Ali FR, Lipovich L, Ho SB. Dietary Patterns and Associated Microbiome Changes that Promote Oncogenesis. Front Cell Dev Biol 2021; 9:725821. [PMID: 34869313 PMCID: PMC8633417 DOI: 10.3389/fcell.2021.725821] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 10/25/2021] [Indexed: 12/24/2022] Open
Abstract
The recent increases in cancer incidences have been linked to lifestyle changes that result in obesity and metabolic syndrome. It is now evident that these trends are associated with the profound changes that occur in the intestinal microbiome, producing altered microbial population signatures that interact, directly or indirectly, with potentially pro-carcinogenic molecular pathways of transcription, proliferation, and inflammation. The effects of the entire gut microbial population on overall health are complex, but individual bacteria are known to play important and definable roles. Recent detailed examinations of a large number of subjects show a tight correlation between habitual diets, fecal microbiome signatures, and markers of metabolic health. Diets that score higher in healthfulness or diversity such as plant-based diets, have altered ratios of specific bacteria, including an increase in short-chain fatty acid producers, which in turn have been linked to improved metabolic markers and lowered cancer risk. Contrarily, numerous studies have implicated less healthy, lower-scoring diets such as the Western diet with reduced intestinal epithelial defenses and promotion of specific bacteria that affect carcinogenic pathways. In this review, we will describe how different dietary patterns affect microbial populations in the gut and illustrate the subsequent impact of bacterial products and metabolites on molecular pathways of cancer development, both locally in the gut and systemically in distant organs.
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Affiliation(s)
- Shakhzada Ibragimova
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai Healthcare City, Dubai, UAE
| | - Revathy Ramachandran
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai Healthcare City, Dubai, UAE
| | - Fahad R Ali
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai Healthcare City, Dubai, UAE
| | - Leonard Lipovich
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai Healthcare City, Dubai, UAE
| | - Samuel B Ho
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai Healthcare City, Dubai, UAE.,Department of Medicine, Mediclinic City Hospital, Dubai Healthcare City, Dubai, UAE
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12
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Jasemi S, Emaneini M, Ahmadinejad Z, Fazeli MS, Sechi LA, Sadeghpour Heravi F, Feizabadi MM. Antibiotic resistance pattern of Bacteroides fragilis isolated from clinical and colorectal specimens. Ann Clin Microbiol Antimicrob 2021; 20:27. [PMID: 33892721 PMCID: PMC8066845 DOI: 10.1186/s12941-021-00435-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 04/16/2021] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Bacteroides fragilis is a part of the normal gastrointestinal flora, but it is also the most common anaerobic bacteria causing the infection. It is highly resistant to antibiotics and contains abundant antibiotic resistance mechanisms. METHODS The antibiotic resistance pattern of 78 isolates of B. fragilis (22 strains from clinical samples and 56 strains from the colorectal tissue) was investigated using agar dilution method. The gene encoding Bacteroides fargilis toxin bft, and antibiotic resistance genes were targeted by PCR assay. RESULTS The highest rate of resistance was observed for penicillin G (100%) followed by tetracycline (74.4%), clindamycin (41%) and cefoxitin (38.5%). Only a single isolate showed resistance to imipenem which contained cfiA and IS1186 genes. All isolates were susceptible to metronidazole. Accordingly, tetQ (87.2%), cepA (73.1%) and ermF (64.1%) were the most abundant antibiotic-resistant genes identified in this study. MIC values for penicillin, cefoxitin and clindamycin were significantly different among isolates with the cepA, cfxA and ermF in compare with those lacking such genes. In addition, 22.7 and 17.8% of clinical and GIT isolates had the bft gene, respectively. CONCLUSIONS The finding of this study shows that metronidazole is highly in vitro active agent against all of B. fragilis isolates and remain the first-line antimicrobial for empirical therapy.
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Affiliation(s)
- Seyedesomaye Jasemi
- Department of Microbiology, School of Medicine, Tehran University of Medical Sciences, Poursina Street, Engelab-e-Eslami Avenue, Tehran, Iran
| | - Mohammad Emaneini
- Department of Microbiology, School of Medicine, Tehran University of Medical Sciences, Poursina Street, Engelab-e-Eslami Avenue, Tehran, Iran
| | - Zahra Ahmadinejad
- Department of Infectious Diseases, Imam Khomeini Hospital Complex, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad Sadegh Fazeli
- Department of Surgery, Imam Khomeini Hospital Complex, Tehran University of Medical Sciences, Tehran, Iran
| | - Leonardo A Sechi
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Fatemah Sadeghpour Heravi
- Surgical Infection Research Group, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, Australia
| | - Mohammad Mehdi Feizabadi
- Department of Microbiology, School of Medicine, Tehran University of Medical Sciences, Poursina Street, Engelab-e-Eslami Avenue, Tehran, Iran. .,Department of Biomedical Sciences, University of Sassari, Sassari, Italy.
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13
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Herbal medicine WangShiBaoChiWan improves gastrointestinal health in mice via modulation of intestinal tight junctions and gut microbiota and inhibition of inflammation. Biomed Pharmacother 2021; 138:111426. [PMID: 33762124 PMCID: PMC9586841 DOI: 10.1016/j.biopha.2021.111426] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 01/19/2021] [Accepted: 02/21/2021] [Indexed: 11/26/2022] Open
Abstract
WangShiBoChiWan (WSBCW) is a commonly used Chinese herbal medicine for the treatment of functional gastrointestinal disorders. However, its preclinical efficacy and the mechanisms of action have not been adequately studied. The goals of this study were to evaluate the effects of WSBCW on gastrointestinal health and modulation of related biomarkers. Female C57BL mice were randomly assigned into one of the experimental groups consisting of the control, drug controls, and WSBCW at 40, 120, and 360 mg/kg BW. Whole gut transit, small intestinal motility, and intestinal barrier permeability were determined. The castor oil-induced diarrhea mouse model was used to determine the effect of WSBCW on the diarrhea type of irritable bowel syndrome (IBSD). WSBCW increased whole gut transit and intestinal motility, improved intestinal permeability in healthy animals and alleviated diarrhea symptoms in IBS-D mice. WSBCW upregulated intestinal junction proteins, increased the abundance of Bifidobacterium genus, Desulfovibrio genus and inhibited Bacteroides fragillis group in the gut microbiota, increased intestinal villi lengths, and decreased blood levels of inflammatory cytokines. Our study provided preclinical evidence to verify the effectiveness of WSBCW in gastrointestinal health and elucidate mechanistic insights. The results warrant further investigations to evaluate the therapeutic efficacy of WSBCW on gastrointestinal disorders, such as IBS and IBD.
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Genotyping of multi drug resistant Bacteroides fragilis group of clinical isolates from mangalore, south India. Indian J Med Microbiol 2020; 39:19-23. [PMID: 33610251 DOI: 10.1016/j.ijmmb.2020.10.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
INTRODUCTION Bacteroides fragilis group, the most encountered anaerobic bacterium is emerging with resistance to antibiotics. This study explores the antibiogram and occurrence of resistance genes in isolates of B fragilis group from clinical samples. METHOD In this study the antimicrobial susceptibility test was done using commercially available E strip test and the results were recorded according to CLSI guidelines. Genotypic investigations were performed by conventional PCR to detect the target resistant genes. RESULTS Ceftriaxone, cefoxitin, clindamycin and imipenem were found to be the most resistant antimicrobials in E test method. Metronidazole has shown resistance in 7 strains in vitro while resistance nim genes were detected in 12 strains from 62 randomly selected isolates. Other resistance genes (cfiA, ermF and cepA) were expressed at 58%, 62.9% and 48.3% respectively, among these strains. CONCLUSION B fragilis group harbouring the resistant genes may not be fully expressed phenotypically. Hence, detection of these genes by PCR might be necessary for a pertinent conclusion.
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15
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Oral delivery of bacteria: Basic principles and biomedical applications. J Control Release 2020; 327:801-833. [DOI: 10.1016/j.jconrel.2020.09.011] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 09/05/2020] [Indexed: 12/18/2022]
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Salmonella enterica Serovar Typhimurium Temporally Modulates the Enteric Microbiota and Host Responses To Overcome Colonization Resistance in Swine. Appl Environ Microbiol 2020; 86:AEM.01569-20. [PMID: 32859592 DOI: 10.1128/aem.01569-20] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 08/19/2020] [Indexed: 02/07/2023] Open
Abstract
Salmonella enterica serovar Typhimurium is a prevalent incitant of enteritis in human beings and nonhuman animals. It has been proposed that host defense responses incited by Salmonella allow the bacterium to overcome colonization resistance. Piglets (n = 24) were orally inoculated with S. enterica serovar Typhimurium DT104 or buffer alone, and the host and microbial responses were temporally examined at the acute (2 days postinoculation [dpi]), subacute (6 dpi), and recovery (10 dpi) stages of salmonellosis. At the acute stage of disease, body temperatures were elevated, and feed consumption and weight gain were reduced. The densities of Salmonella associated with the gut mucosa decreased over time, with higher densities of the bacterium in the ileum and the large intestine. Moreover, substantive histopathological changes were observed as a function of time, with prominent epithelial injury and neutrophil infiltration observed at 2 dpi. Correspondingly, a variety of host metrics were temporally affected in piglets with salmonellosis (e.g., TNFα, IFNγ, PR39, βD2, iNOS, IL8, REGIIIγ). The enteric microbiota was characterized using culture-independent and -dependent methods in concert, and taxon- and location-specific changes to the microbiota were observed in infected piglets. Bacteroides spp. (e.g., Bacteroides uniformis, Bacteroides fragilis), Streptococcus spp. (e.g., Streptococcus gallolyticus), and various Gammaproteobacteria were highly associated with inflamed tissues, while bacteria within the Ruminococcaceae and Veillonellaceae families were mainly associated with healthy mucosae. In conclusion, the study findings showed that S Typhimurium incited temporal and spatial modifications to the swine autochthonous microbiota, and to host defense responses, that were consistent with overcoming colonization resistance to incite salmonellosis in swine.IMPORTANCE Limited information is available on host and enteric microbiota responses incited by Salmonella enterica serovar Typhimurium in swine and on possible mechanisms by which the bacterium overcomes colonization resistance to incite salmonellosis. Temporal characterization of a variety of host metrics in piglets (e.g., physiological, histopathological, and immunological) showed the importance of studying the progression of salmonellosis. A number of host responses integrally associated with disease development were identified. Utilization of next-generation sequence analysis to characterize the enteric microbiota was found to lack sufficient resolution; however, culture-dependent and -independent methods in combination identified taxon- and location-specific changes to bacterial communities in infected piglets. The study identified bacterial and host responses associated with salmonellosis, which will be beneficial in understanding colonization resistance and in the development of effective alternatives to antibiotics to mitigate salmonellosis.
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Zamani S, Taslimi R, Sarabi A, Jasemi S, Sechi LA, Feizabadi MM. Enterotoxigenic Bacteroides fragilis: A Possible Etiological Candidate for Bacterially-Induced Colorectal Precancerous and Cancerous Lesions. Front Cell Infect Microbiol 2020; 9:449. [PMID: 32010637 PMCID: PMC6978650 DOI: 10.3389/fcimb.2019.00449] [Citation(s) in RCA: 84] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2019] [Accepted: 12/12/2019] [Indexed: 12/21/2022] Open
Abstract
Enterotoxigenic Bacteroides fragilis (ETBF) produces Bacteroides fragilis toxin (BFT), which is associated with acute diarrheal, inflammatory bowel disease, and colorectal cancer (CRC). In experimental models, ETBF has been shown to contribute to colon carcinogenesis. The present study was conducted to investigate mucosal colonization of ETBF in the colon to find a possible association between the presence of ETBF and precancerous and cancerous lesions. The mucosal biopsies of involved sites were obtained from 68 patients with precancerous and cancerous lesions and 52 healthy controls (HC). The samples were cultured on Bacteroides Bile Esculin agar. Then, specific primers were designed to detect B. fragilis and bft gene using quantitative real-time PCR, and the possible links of ETBF with clinicopathological characteristics was evaluated. Also real-time PCR was performed to detect the bft gene subtypes. Bacteroides fragilis was detected in 51% of the patients and 48% of HCs cultures. The 16SrRNA gene was found to be present in 63 and 81% of the patients and HCs' samples, respectively. Moreover, the bft gene was detected in 47 and 3.8% of the patients and HCs, respectively. Also, B. fragilis was significantly more abundant in the patients' samples compared to those of HCs. In the patient group, higher odds ratio (OR) of ETBF was significantly associated with serrated lesions and adenoma with low-grade dysplasia. The bft1 gene was the most prevalent subtype of bft gene, followed by the bft2 gene. This was the first study in Iran to demonstrate increased positivity of ETBF in patients with precancerous and cancerous lesions. In this study, the bft gene was found to be associated with CRC, especially in the patients with precancerous lesions and initial carcinogenic lesions. Moreover, the results suggest that mucosal BFT exposure is common and could be a risk factor and a screening marker for developing CRC.
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Affiliation(s)
- Samin Zamani
- Laboratory Sciences Research Center, Golestan University of Medical Sciences, Gorgan, Iran
- Department of Microbiology, School of Medicine, Golestan University of Medical Sciences, Gorgan, Iran
| | - Reza Taslimi
- Division of Gastroenterology and Hepatology, Imam Khomeini Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Akram Sarabi
- Department of Microbiology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Seyedesomaye Jasemi
- Department of Microbiology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Leonardo A. Sechi
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Mohammad Mehdi Feizabadi
- Department of Microbiology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
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Kouhsari E, Mohammadzadeh N, Kashanizadeh MG, Saghafi MM, Hallajzadeh M, Fattahi A, Ahmadi A, Niknejad F, Ghafouri Z, Asadi A, Boujary Nasrabadi MR. Antimicrobial resistance, prevalence of resistance genes, and molecular characterization in intestinalBacteroides fragilisgroup isolates. APMIS 2019; 127:454-461. [DOI: 10.1111/apm.12943] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 02/21/2019] [Indexed: 12/14/2022]
Affiliation(s)
- Ebrahim Kouhsari
- Department of Microbiology School of Medicine Iran University of Medical Sciences Tehran Iran
- Laboratory Sciences Research Center Golestan University of Medical Sciences Gorgan Iran
| | - Nima Mohammadzadeh
- Department of Microbiology School of Medicine Iran University of Medical Sciences Tehran Iran
| | | | - Mohammad Mehdi Saghafi
- Department of Clinical Pharmacology Firouz Abadi Hospital Iran University of Medical Sciences Tehran Iran
| | - Masoumeh Hallajzadeh
- Department of Microbiology School of Medicine Iran University of Medical Sciences Tehran Iran
| | - Azam Fattahi
- Center for Research and Training in Skin Disease and Leprosy Tehran University of Medical Sciences Tehran Iran
| | - Alireza Ahmadi
- Laboratory Sciences Research Center Golestan University of Medical Sciences Gorgan Iran
| | - Farhad Niknejad
- Laboratory Sciences Research Center Golestan University of Medical Sciences Gorgan Iran
| | - Zahra Ghafouri
- Department of Biochemistry, Biophysics and Genetics Faculty of Medicine Mazandaran University of Medical Sciences Sari Iran
| | - Arezoo Asadi
- Department of Microbiology School of Medicine Iran University of Medical Sciences Tehran Iran
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Kierzkowska M, Majewska A, Szymanek-Majchrzak K, Sawicka-Grzelak A, Mlynarczyk A, Mlynarczyk G. The presence of antibiotic resistance genes and bft genes as well as antibiotic susceptibility testing of Bacteroides fragilis strains isolated from inpatients of the Infant Jesus Teaching Hospital, Warsaw during 2007-2012. Anaerobe 2019; 56:109-115. [PMID: 30844502 DOI: 10.1016/j.anaerobe.2019.03.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 03/01/2019] [Accepted: 03/04/2019] [Indexed: 01/05/2023]
Abstract
The purpose of this study was to assess drug susceptibility of clinical B. fragilis strains and to determine any correlation between drug resistance and the presence of specific genes. Antimicrobial susceptibility was assessed using E-tests. All isolates were analyzed with the PCR technique for the presence of antibiotic resistance genes (cepA, cfxA, cfiA, ermF, ermB, ermG, nim), insertion sequences elements (IS1186, IS1187, IS1188, IS942), and enterotoxin-encoding genes (bft). Susceptibility tests yielded the following rates of resistance to the evaluated antibiotics: penicillin G (100%), clindamycin (22.5%), cefoxitin (6.3%), amoxicillin/clavulanic acid (1.8%). All strain were susceptible to imipenem, and metronidazole. The following antibiotic resistance genes were detected in the evaluated isolates: cepA (in 96.4% of isolates), cfxA (in 12.6%), cfiA (in 1.8%), and ermF (in 25.2%). Genes ermB, ermG, and nim were not found. The presence of the cepA gene showed no correlation with the penicillin G MIC. However, we observed a high correlation between cefoxitin MIC values and the presence of gene cfxA as well as a nearly complete correlation between clindamycin MIC values and the presence of gene ermF. The presence of a bft gene was detected in 14.4% of the analyzed B. fragilis isolates; with the bft-1 allele found in 75%, bft-2 in 25%, and bft-3 in none of the isolates. Antibiotic susceptibility profiles of enterotoxin gene-positive isolates in our study did not differ from those of enterotoxin gene-negative isolates.
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Affiliation(s)
- Marta Kierzkowska
- Chair and Department of Medical Microbiology, Medical University of Warsaw, Chalubinskiego 5 Str., 02-004, Warsaw, Poland; Department of Medical Microbiology, The Infant Jesus Teaching Hospital, Lindleya 4 Str., 02-004, Warsaw, Poland
| | - Anna Majewska
- Chair and Department of Medical Microbiology, Medical University of Warsaw, Chalubinskiego 5 Str., 02-004, Warsaw, Poland; Department of Medical Microbiology, The Infant Jesus Teaching Hospital, Lindleya 4 Str., 02-004, Warsaw, Poland.
| | - Ksenia Szymanek-Majchrzak
- Chair and Department of Medical Microbiology, Medical University of Warsaw, Chalubinskiego 5 Str., 02-004, Warsaw, Poland; Department of Medical Microbiology, The Infant Jesus Teaching Hospital, Lindleya 4 Str., 02-004, Warsaw, Poland
| | - Anna Sawicka-Grzelak
- Chair and Department of Medical Microbiology, Medical University of Warsaw, Chalubinskiego 5 Str., 02-004, Warsaw, Poland; Department of Medical Microbiology, The Infant Jesus Teaching Hospital, Lindleya 4 Str., 02-004, Warsaw, Poland
| | - Andrzej Mlynarczyk
- Department of Medical Microbiology, The Infant Jesus Teaching Hospital, Lindleya 4 Str., 02-004, Warsaw, Poland
| | - Grazyna Mlynarczyk
- Chair and Department of Medical Microbiology, Medical University of Warsaw, Chalubinskiego 5 Str., 02-004, Warsaw, Poland; Department of Medical Microbiology, The Infant Jesus Teaching Hospital, Lindleya 4 Str., 02-004, Warsaw, Poland
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Inhibition of enterohemorrhagic Escherichia coli O157:H7 infection in a gnotobiotic mouse model with pre-colonization by Bacteroides strains. Biomed Rep 2019; 10:175-182. [PMID: 30906546 PMCID: PMC6403472 DOI: 10.3892/br.2019.1193] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 02/04/2019] [Indexed: 12/11/2022] Open
Abstract
Enterohemorrhagic Escherichia coli (EHEC) O157:H7 has been known to cause outbreaks of hemorrhagic colitis and hemolytic uremic syndrome. We previously demonstrated that intestinal flora contribute to the prevention of EHEC infection in a mouse model. However, it has not yet been determined whether Bacteroides, a predominant genus in the human intestine, contributes to the prevention of EHEC infection. The aim of the present study was to investigate the effect of Bacteroides fragilis (B. fragilis) and Bacteroides vulgatus (B. vulgatus) on EHEC O157:H7 infection in vivo using gnotobiotic mice. These strains were inoculated into germ-free mice to create a gnotobiotic mouse model. EHEC was inoculated into the mice, which were then monitored for 7 days for any change in symptoms. The mice that had been pre-colonized with the Bacteroides strains did not develop lethal EHEC infection, although several inflammatory symptoms were observed in the B. vulgatus pre-colonized group. However, no inflammatory symptoms were identified in the B. fragilis pre-colonized group. Moreover, B. fragilis exerted an inhibitory effect on enterocyte-like cell apoptosis. B. fragilis protected HT29 cells from apoptosis caused by Shiga toxin. In conclusion, the findings of the present study demonstrated that colonization by Bacteroides strains can inhibit EHEC infection.
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Abstract
Bacteroides fragilis is Gram-negative obligatory anaerobe which usually resides in the gut of humans and animals. As an important member of the human gut microbiota it plays a vital role in digestion and absorption of nutrients as well as shaping of host immune system. B. fragilis is also infamous for causing serious infections. Treatment of B. fragilis infections caused emergence of multidrug-resistant strains. Molecular biology tools such as transposon mutagenesis help to decipher and understand commensal and pathogenic faces of B. fragilis. Using two mariner transposon vectors we describe the detailed methodology for the transposon mutagenesis of B. fragilis. We also describe two methods for the identification of transposon integration site (TIS) in transposon mutants. Transposon mutagenesis methods described in this chapter serve as a great tool for studying B. fragilis.
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Affiliation(s)
- Yaligara Veeranagouda
- Greater Los Angeles VA Health Care System, Los Angeles, CA, USA.
- David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA.
| | - Fasahath Husain
- Greater Los Angeles VA Health Care System, Los Angeles, CA, USA
| | - Hannah M Wexler
- Greater Los Angeles VA Health Care System, Los Angeles, CA, USA
- David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
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