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Valdezate S, Medina-Pascual MJ, Villalón P, Garrido N, Monzón S, Cuesta I, Cobo F. Co-occurrence of the cephalosporinase cepA and carbapenemase cfiA genes in a Bacteroides fragilis division II strain, an unexpected finding. J Antimicrob Chemother 2024; 79:1683-1687. [PMID: 38814812 DOI: 10.1093/jac/dkae166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Accepted: 05/07/2024] [Indexed: 06/01/2024] Open
Abstract
BACKGROUND Bacteroides fragilis, an anaerobic gut bacterium and opportunistic pathogen, comprises two genetically divergent groups (or divisions) at the species level. Differences exist both in the core and accessory genomes and the beta-lactamase genes, with the cephalosporinase gene cepA represented only in division I and the carbapenemase gene cfiA only in division II. METHODS Multidrug resistance in a clinical B. fragilis strain was examined by whole-genome sequencing. RESULTS Strain CNM20200260 carried the antimicrobial resistance genes cepA, cfiA2, ant(6'), erm(F), mef(En2), est(T), tet(Q) and cat(A), along with 82-Phe mutation in gyrA (together with 47 amino acid changes in gyrA/B and parC/parE). bexA/B and other efflux pump genes were also observed. None of the detected insertion sequences was located upstream of cfiA2. The genome-based taxonomy coefficients (average nucleotide identity, DNA-DNA hybridization similarity and difference in genomic G + C%) with respect to genomes of the strains of B. fragilis division II and the novel species Bacteroides hominis (both cfiA-positive) met the criteria for CNM20200260 to belong to either species (>95%, >70% and <1%, respectively). No such similarity was seen with type strain NCTC 9343 or the representative genome FDAARGOS 1225 of B. fragilis (division I, cfiA-negative). Strain CNM20200260 harboured four out of nine Kyoto Encyclopedia of Genes and Genomes orthologues defined for division I and one of two defined for division II. CONCLUSIONS This is the first description of the co-occurrence of cepA and cfiA in a Bacteroides strain, confirming the complexity of the taxonomy of this species.
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Affiliation(s)
- S Valdezate
- Reference and Research Laboratory for Taxonomy, National Centre of Microbiology, Instituto de Salud Carlos III, Majadahonda, Carretera Pozuelo-Majadahonda km 2.2, 28220, Madrid, Spain
| | - M J Medina-Pascual
- Reference and Research Laboratory for Taxonomy, National Centre of Microbiology, Instituto de Salud Carlos III, Majadahonda, Carretera Pozuelo-Majadahonda km 2.2, 28220, Madrid, Spain
| | - P Villalón
- Reference and Research Laboratory for Taxonomy, National Centre of Microbiology, Instituto de Salud Carlos III, Majadahonda, Carretera Pozuelo-Majadahonda km 2.2, 28220, Madrid, Spain
| | - N Garrido
- Reference and Research Laboratory for Taxonomy, National Centre of Microbiology, Instituto de Salud Carlos III, Majadahonda, Carretera Pozuelo-Majadahonda km 2.2, 28220, Madrid, Spain
| | - S Monzón
- Bioinformatics Unit, Applied Services, Training and Research, Instituto de Salud Carlos III, Majadahonda, Carretera Pozuelo-Majadahonda km 2.2, 28220, Madrid, Spain
| | - I Cuesta
- Bioinformatics Unit, Applied Services, Training and Research, Instituto de Salud Carlos III, Majadahonda, Carretera Pozuelo-Majadahonda km 2.2, 28220, Madrid, Spain
| | - F Cobo
- Department of Microbiology and Instituto Biosanitario de Granada, University Hospital of Virgen de las Nieves, Avda. Fuerzas Armadas s/n, 18014 Granada, Spain
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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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Kierzkowska M, Majewska A, Karłowicz K, Pituch H. Phenotypic and genotypic identification of carbapenem resistance in Bacteroides fragilis clinical strains. Med Microbiol Immunol 2023:10.1007/s00430-023-00765-w. [PMID: 37178261 DOI: 10.1007/s00430-023-00765-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 04/26/2023] [Indexed: 05/15/2023]
Abstract
Bacteroides fragilis is an important etiological agent of serious infections in humans. Rapid methods, readily adaptable to use in medical laboratories, are needed to detect antibiotic resistance and decrease the likelihood of therapy failure. The aim of this study was to determine the prevalence of B. fragilis cfiA-positive isolates. The second purpose was to investigate the carbapenemase activity in B. fragilis strains by Carba NP test. In the study, 5.2% of B. fragilis isolates are phenotypically resistant to meropenem. The cfiA gene was identified in 6.1% of B. fragilis isolates. The MICs of meropenem were significantly higher in cfiA-positive strains. The presence of the cfiA gene along with the IS1186 was detected in one B. fragilis strain which was resistant to meropenem (MIC 1.5 mg/L). The Carba NP test results were positive for all the cfiA-positive strains, including those susceptible to carbapenems based on their MIC values. A review of the literature revealed that the rate of B. fragilis with the cfiA gene varies from 7.6 to 38.9% worldwide. Presented results are in line with the other European studies. Phenotypic testing with the Carba NP test, it seems to be a viable alternative for the cfiA gene detection in B. fragilis isolates. The positive result obtained is of greater clinical importance than the detection of the gene cfiA.
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Affiliation(s)
- Marta Kierzkowska
- Department of Medical Microbiology, Medical University of Warsaw, Warsaw, Poland
| | - Anna Majewska
- Department of Medical Microbiology, Medical University of Warsaw, Warsaw, Poland.
| | - Konrad Karłowicz
- Department of Medical Microbiology, Medical University of Warsaw, Warsaw, Poland
| | - Hanna Pituch
- Department of Medical Microbiology, Medical University of Warsaw, Warsaw, Poland
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Nielsen FD, Skov MN, Sydenham TV, Justesen US. Development and Clinical Application of a Multilocus Sequence Typing Scheme for Bacteroides fragilis Based on Whole-Genome Sequencing Data. Microbiol Spectr 2023:e0511122. [PMID: 36943061 PMCID: PMC10101032 DOI: 10.1128/spectrum.05111-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2023] Open
Abstract
Bacteroides fragilis is among the most abundant and pathogenic bacterial species in the gut microbiota and is associated with diarrheal disease in children, inflammatory bowel disease, and the development of colorectal cancer. It is increasingly resistant to potent antimicrobial agents such as carbapenems and metronidazole, making it among the most resistant anaerobic bacteria. These factors combined call for increased monitoring of B. fragilis and its population structure on a worldwide scale. Here, we present a possible solution through the development of a multilocus sequence typing scheme (MLST). The scheme is based on seven core gene fragments: groL (hsp60), rpoB, recA, dnaJ, rprX, prfA, and fusA. These gene fragments possess high discriminatory power while retaining concordance with whole core genome-based phylogenetic analysis. The scheme proved capable of differentiating B. fragilis isolates at the strain level. It offers a standardized method for molecular typing and can be applied to isolates from various sampling backgrounds, such as patient isolates, environmental samples, and strains obtained from food and animal sources. In total, 567 B. fragilis genomes were sequence typed and their isolate data collected. The MLST scheme clearly divided the B. fragilis population into two divisions based on the presence of the cfiA and cepA resistance genes. However, no other specific subpopulations within the analyzed genomes were found to be associated with any specific diseases or geographical location. With this MLST scheme, we hope to provide a powerful tool for the study and monitoring of B. fragilis on an international scale. IMPORTANCE Here, we present the first MLST scheme for Bacteroides fragilis, one of the most abundant pathogenic bacteria in the human gut microbiota. The scheme enables standard classification and monitoring of B. fragilis on a worldwide scale and groups the majority of current isolate data in one place. A more unified approach to the collection and analysis of B. fragilis data could provide crucial insights into how the pathogen operates and develops as a species. Close monitoring of B. fragilis is especially relevant, as it is increasingly resistant to potent antimicrobial agents and engages in horizontal gene transfer with other bacteria. Hopefully, this approach will guide new discoveries into how B. fragilis evolves and interacts with its human host. Additionally, the scheme could potentially be applied to other species of the genus Bacteroides.
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Affiliation(s)
- Flemming D Nielsen
- Department of Clinical Microbiology, Odense University Hospital, Odense, Denmark
- Research Unit of Clinical Microbiology, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Marianne N Skov
- Department of Clinical Microbiology, Odense University Hospital, Odense, Denmark
- Research Unit of Clinical Microbiology, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Thomas V Sydenham
- Department of Clinical Microbiology, Odense University Hospital, Odense, Denmark
- Research Unit of Clinical Microbiology, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Ulrik S Justesen
- Department of Clinical Microbiology, Odense University Hospital, Odense, Denmark
- Research Unit of Clinical Microbiology, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
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Time for Some Group Therapy: Update on Identification, Antimicrobial Resistance, Taxonomy, and Clinical Significance of the Bacteroides fragilis Group. J Clin Microbiol 2022; 60:e0236120. [PMID: 35700139 DOI: 10.1128/jcm.02361-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacteroides fragilis group (BFG) species are common members of the human microbiota that provide several benefits to healthy hosts, yet BFG are also the most common anaerobes isolated from human infections, including intra-abdominal infections, abscesses, and bloodstream infection. Compared to many other anaerobes associated with disease, members of the BFG are more likely to be resistant to commonly used antimicrobials, including penicillin (>90% resistant), carbapenems (2 to 20% resistant), and metronidazole (0.2 to 4% resistant). As a result, infection with BFG bacteria can be associated with poor clinical outcomes. Here, we discuss the role of BFG in human health and disease, proposed taxonomic reclassifications within the BFG, and updates in methods for species-level identification. The increasing availability of whole-genome sequencing (WGS) supports recent proposals that the BFG now span two families (Bacteroidaceae and "Tannerellaceae") and multiple genera (Bacteroides, Parabacteroides, and Phocaeicola) within the phylum Bacteroidota. While members of the BFG are often reported to "group" rather than "species" level in many clinical settings, new reports of species-specific trends in antimicrobial resistance profiles and improved resolution of identification tools support routine species-level reporting in clinical practice. Empirical therapy may not be adequate for treatment of serious infections with BFG, warranting susceptibility testing for serious infections. We summarize methods for antimicrobial susceptibility testing and resistance prediction for BFG, including broth microdilution, agar dilution, WGS, and matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). We examine global trends in BFG antimicrobial resistance and review genomics of BFG, revealing insights into rapid activation and dissemination of numerous antimicrobial resistance mechanisms.
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Antimicrobial Susceptibility and Clinical Findings of Anaerobic Bacteria. Antibiotics (Basel) 2022; 11:antibiotics11030351. [PMID: 35326814 PMCID: PMC8944802 DOI: 10.3390/antibiotics11030351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 03/01/2022] [Indexed: 11/16/2022] Open
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