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Bivand JM, Dyrhovden R, Sivertsen A, Tellevik MG, Patel R, Kommedal Ø. Broad-range amplification and sequencing of the rpoB gene: a novel assay for bacterial identification in clinical microbiology. J Clin Microbiol 2024; 62:e0026624. [PMID: 38884485 PMCID: PMC11324016 DOI: 10.1128/jcm.00266-24] [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: 02/15/2024] [Accepted: 05/21/2024] [Indexed: 06/18/2024] Open
Abstract
The rpoB gene has been proposed as a promising phylogenetic marker for bacterial identification, providing theoretically improved species-level resolution compared to the 16S rRNA gene for a range of clinically important taxa. However, its utility in diagnostic microbiology has been limited by the lack of broad-range primers allowing for its amplification from most species with a single PCR assay. Here, we present an assay for broad-range partial amplification and Sanger sequencing of the rpoB gene. To reduce cross-reactivity and allow for rpoB amplification directly from patient samples, primers were based on the dual priming oligonucleotide principle. The resulting amplicon is ~550 base pairs in length and appropriate for species-level identification. Systematic in silico evaluation of a wide selection of taxa demonstrated improved resolution within multiple important genera, including Enterococcus, Fusobacterium, Mycobacterium, Streptococcus, and Staphylococcus species and several genera within the Enterobacteriaceae family. Broad-range rpoB amplification and Sanger sequencing of 115 bacterial isolates provided unambiguous species-level identification for 97 (84%) isolates, as compared to 57 (50%) using a clinical 16S rRNA gene assay. Several unresolved taxonomic matters disguised by the low resolution of the 16S rRNA gene were revealed using the rpoB gene. Using a collection of 33 clinical specimens harboring bacteria and assumed to contain high concentrations of human DNA, the rpoB assay identified the pathogen in 29 specimens (88%). Broad-range rpoB amplification and sequencing provides a promising tool for bacterial identification, improving discrimination between closely related species and making it amenable for use in culture-based and culture-independent diagnostic approaches.
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Affiliation(s)
- Joanna Małgorzata Bivand
- Department of
Microbiology, Haukeland University
Hospital, Bergen,
Norway
- Department of Clinical
Science, University of Bergen,
Bergen, Norway
| | - Ruben Dyrhovden
- Department of
Microbiology, Haukeland University
Hospital, Bergen,
Norway
| | - Audun Sivertsen
- Department of
Microbiology, Haukeland University
Hospital, Bergen,
Norway
| | | | - Robin Patel
- Division of Clinical
Microbiology, Department of Laboratory Medicine and Pathology, Mayo
Clinic, Rochester,
Minnesota, USA
- Division of Public
Health, Infectious Diseases, and Occupational Medicine, Department of
Medicine, Mayo Clinic,
Rochester, Minnesota,
USA
| | - Øyvind Kommedal
- Department of
Microbiology, Haukeland University
Hospital, Bergen,
Norway
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Singh V, West G, Fiocchi C, Good CE, Katz J, Jacobs MR, Dichosa AEK, Flask C, Wesolowski M, McColl C, Grubb B, Ahmed S, Bank NC, Thamma K, Bederman I, Erokwu B, Yang X, Sundrud MS, Menghini P, Basson AR, Ezeji J, Viswanath SE, Veloo A, Sykes DB, Cominelli F, Rodriguez-Palacios A. Clonal Parabacteroides from Gut Microfistulous Tracts as Transmissible Cytotoxic Succinate-Commensal Model of Crohn's Disease Complications. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.09.574896. [PMID: 38260564 PMCID: PMC10802508 DOI: 10.1101/2024.01.09.574896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Crohn's disease (CD) has been traditionally viewed as a chronic inflammatory disease that cause gut wall thickening and complications, including fistulas, by mechanisms not understood. By focusing on Parabacteroides distasonis (presumed modern succinate-producing commensal probiotic), recovered from intestinal microfistulous tracts (cavernous fistulous micropathologies CavFT proposed as intermediate between 'mucosal fissures' and 'fistulas') in two patients that required surgery to remove CD-damaged ilea, we demonstrate that such isolates exert pathogenic/pathobiont roles in mouse models of CD. Our isolates are clonally-related; potentially emerging as transmissible in the community and mice; proinflammatory and adapted to the ileum of germ-free mice prone to CD-like ileitis (SAMP1/YitFc) but not healthy mice (C57BL/6J), and cytotoxic/ATP-depleting to HoxB8-immortalized bone marrow derived myeloid cells from SAMP1/YitFc mice when concurrently exposed to succinate and extracts from CavFT-derived E. coli , but not to cells from healthy mice. With unique genomic features supporting recent genetic exchange with Bacteroides fragilis -BGF539, evidence of international presence in primarily human metagenome databases, these CavFT Pdis isolates could represent to a new opportunistic Parabacteroides species, or subspecies (' cavitamuralis' ) adapted to microfistulous niches in CD.
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Stubhaug TT, Giske CG, Justesen US, Kahlmeter G, Matuschek E, Sundsfjord A, Skaare D. Antimicrobial susceptibility testing of Bacteroides species by disk diffusion: The NordicAST Bacteroides study. Anaerobe 2023:102743. [PMID: 37253399 DOI: 10.1016/j.anaerobe.2023.102743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 05/16/2023] [Accepted: 05/22/2023] [Indexed: 06/01/2023]
Abstract
OBJECTIVES - Antimicrobial susceptibility testing (AST) of anaerobic bacteria has until recently been done by MIC methods. We have carried out a multi-centre evaluation of the newly validated EUCAST disk diffusion method for AST of Bacteroides spp. METHODS - A panel of 30 Bacteroides strains was assembled based on reference agar dilution MICs, resistance gene detection and quantification of cfiA carbapenemase gene expression. Nordic clinical microbiology laboratories (n = 45) performed disk diffusion on Fastidious Anaerobe Agar with 5% mechanically defibrinated horse blood (FAA-HB) for piperacillin-tazobactam, meropenem and metronidazole. RESULTS - A total of 43/45 (95.6%) laboratories carried out disk diffusion per protocol. Intraclass correlation coefficients were 0.87 (0.80-0.93) for piperacillin-tazobactam, 0.95 (0.91-0.97) for meropenem and 0.89 (0.83-0.94) for metronidazole. For metronidazole, one media lot yielded smaller zones and higher variability than another. Piperacillin-tazobactam and meropenem zone diameters correlated negatively with cfiA expression. A meropenem zone diameter of <28 mm in B. fragilis indicated presence of cfiA. Piperacillin-tazobactam had the most false susceptible results. Categorical errors for this antimicrobial were particularly prevalent in cfiA-positive strains, and piperacillin-tazobactam had the highest number of comments describing zone reading difficulties. CONCLUSIONS - Inter-laboratory agreement by disk diffusion was good or very good. The main challenges were media-related variability for metronidazole and categorical disagreement with the reference method for piperacillin-tazobactam in some cfiA-positive strains. An area of technical uncertainty specific for such strains may be warranted.
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Affiliation(s)
- Tore Taksdal Stubhaug
- Vestfold Hospital Trust, Department of Microbiology, Tønsberg, Norway; University of Oslo, Institute of Clinical Medicine, Oslo, Norway.
| | - Christian G Giske
- Karolinska University Hospital, Department of Clinical Microbiology, Stockholm, Sweden; Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Ulrik S Justesen
- Odense University Hospital, Department of Clinical Microbiology, Odense, Denmark
| | | | | | - Arnfinn Sundsfjord
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance (K-res), University Hospital of North Norway, Tromsø, Norway; UiT the Arctic University of Norway, Department of Medical Biology, Tromsø, Norway
| | - Dagfinn Skaare
- Vestfold Hospital Trust, Department of Microbiology, Tønsberg, Norway
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Comparative genomics reveals the evolution of antimicrobial resistance in Bacteroides nordii. Microb Pathog 2022; 173:105811. [PMID: 36183960 DOI: 10.1016/j.micpath.2022.105811] [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: 06/15/2022] [Revised: 09/24/2022] [Accepted: 09/26/2022] [Indexed: 11/22/2022]
Abstract
Bacteroides nordii, is an understudied member of the pathogenic B. fragilis group which comprises several multidrug-resistant (MDR) strains. Thus, it is of great interest to study the genome biology of Bacteroides nordii. However, no detailed study is available that characterized B. nordii at the genetic level and explored its role as a potential pathogen. We isolated an MDR strain viz., B. nordii PGMM4098 from the pus sample and subjected it to whole genome sequencing using Illumina technology. The draft genome was de-novo assembled and annotated, followed by comprehensive comparative genomics analyses using the publicly available genome dataset of B. nordii. The pan-genome analysis revealed the open nature of B. nordii, indicating the continuous accumulation of novel genes in non-core components leading to the emergence of new strains of this species. The thirteen antimicrobial resistance (AMR) genes identified in the genomes of all B. nordii strains were part of the non-core component of the pan-genome. Of these, four AMR genes, nimE, aadS, mef(En2), and ermB/F/G were found to be acquired via the process of horizontal gene transfer (HGT) from anaerobic Bacteroidetes. Importantly, the nimE gene conferring metronidazole resistance was found to be present only in B. nordii PGMM4098, which harbors five other AMR genes encoded in its genome. Of these, nimE (metronidazole resistance), ermB/F/G (macrolide-lincosamide-streptogramin B resistance), and cfxA2/A3 (class A β-lactam resistance) genes were further validated using targeted polymerase chain reaction assay. Notably, these three genes were also found to be under the operation of positive selective pressure suggesting the diversification of these genes, which might lead to the emergence of new MDR strains of B. nordii in the near future. Our study reported and characterized the genome of the first MDR strain of B. nordii and revealed the AMR evolution in this species using a comprehensive comparative genomics approach.
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Antimicrobial-resistant Bacteroides fragilis in Thailand and their inhibitory effect in vitro on the growth of Clostridioides difficile. Anaerobe 2022; 73:102505. [DOI: 10.1016/j.anaerobe.2021.102505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 12/19/2021] [Accepted: 12/23/2021] [Indexed: 11/21/2022]
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Valdezate S, Cobo F, Monzón S, Medina-Pascual MJ, Zaballos Á, Cuesta I, Pino-Rosa S, Villalón P. Genomic Background and Phylogeny of cfiA-Positive Bacteroides fragilis Strains Resistant to Meropenem-EDTA. Antibiotics (Basel) 2021; 10:antibiotics10030304. [PMID: 33809460 PMCID: PMC8001070 DOI: 10.3390/antibiotics10030304] [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: 02/10/2021] [Revised: 03/09/2021] [Accepted: 03/13/2021] [Indexed: 12/31/2022] Open
Abstract
Background: Bacteroides fragilis shows high antimicrobial resistance (AMR) rates and possesses numerous AMR mechanisms. Its carbapenem-resistant strains (metallo-β-lactamase cfiA-positive) appear as an emergent, evolving clade. Methods: This work examines the genomes, taxonomy, and phylogenetic relationships with respect to other B. fragilis genomes of two B. fragilis strains (CNM20180471 and CNM20200206) resistant to meropenem+EDTA and other antimicrobial agents. Results: Both strains possessed cfiA genes (cfiA14b and the new cfiA28), along with other AMR mechanisms. The presence of other efflux-pump genes, mexAB/mexJK/mexXY-oprM, acrEF/mdtEF-tolC, and especially cusR, which reduces the entry of carbapenem via the repression of porin OprD, may be related to meropenem–EDTA resistance. None of the detected insertion sequences were located upstream of cfiA. The genomes of these and other B. fragilis strains that clustered together in phylogenetic analyses did not meet the condition of >95% average nucleotide/amino acid identity, or >70% in silico genome-to-genome hybridization similarity, to be deemed members of the same species, although <1% difference in the genomic G+C content was seen with respect to the reference genome B. fragilis NCTC 9343T. Conclusions: Carbapenem-resistant strains may be considered a distinct clonal entity, and their surveillance is recommended given the ease with which they appear to acquire AMR.
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Affiliation(s)
- Sylvia Valdezate
- National Centre of Microbiology, Reference and Research Laboratory for Taxonomy, Instituto de Salud Carlos III, Majadahonda, 280220 Madrid, Spain; (M.J.M.-P.); (S.P.-R.); (P.V.)
- Correspondence: ; Tel.: +34-91-822-3734; Fax: +34-91-509-7966
| | - Fernando Cobo
- Department of Microbiology, Instituto Biosanitario de Granada, University Hospital of Virgen de las Nieves, Avda. Fuerzas Armadas s/n, 18014 Granada, Spain; (F.C.); (S.M.); (I.C.)
| | - Sara Monzón
- Department of Microbiology, Instituto Biosanitario de Granada, University Hospital of Virgen de las Nieves, Avda. Fuerzas Armadas s/n, 18014 Granada, Spain; (F.C.); (S.M.); (I.C.)
| | - María J. Medina-Pascual
- National Centre of Microbiology, Reference and Research Laboratory for Taxonomy, Instituto de Salud Carlos III, Majadahonda, 280220 Madrid, Spain; (M.J.M.-P.); (S.P.-R.); (P.V.)
| | - Ángel Zaballos
- Bionformatics Unit, Applied Services, Training and Research, Instituto de Salud Carlos III, Majadahonda, 280220 Madrid, Spain;
- Genomics Unit, Applied Services, Training and Research, Instituto de Salud Carlos III, Majadahonda, 280220 Madrid, Spain
| | - Isabel Cuesta
- Department of Microbiology, Instituto Biosanitario de Granada, University Hospital of Virgen de las Nieves, Avda. Fuerzas Armadas s/n, 18014 Granada, Spain; (F.C.); (S.M.); (I.C.)
| | - Silvia Pino-Rosa
- National Centre of Microbiology, Reference and Research Laboratory for Taxonomy, Instituto de Salud Carlos III, Majadahonda, 280220 Madrid, Spain; (M.J.M.-P.); (S.P.-R.); (P.V.)
| | - Pilar Villalón
- National Centre of Microbiology, Reference and Research Laboratory for Taxonomy, Instituto de Salud Carlos III, Majadahonda, 280220 Madrid, Spain; (M.J.M.-P.); (S.P.-R.); (P.V.)
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Kozhakhmetova S, Zholdybayeva E, Tarlykov P, Atavliyeva S, Syzdykov T, Daniyarov A, Mukhtarova K, Ramankulov Y. Determinants of resistance in Bacteroides fragilis strain BFR_KZ01 isolated from a patient with peritonitis in Kazakhstan. J Glob Antimicrob Resist 2021; 25:1-4. [PMID: 33667704 DOI: 10.1016/j.jgar.2021.02.022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 01/28/2021] [Accepted: 02/19/2021] [Indexed: 11/18/2022] Open
Abstract
OBJECTIVES Bacteroides fragilis is one of the most important human anaerobic pathogens often found in various clinical infections. The purpose of this study was to determine the susceptibility of a B. fragilis clinical strain (BFR_KZ01) from Kazakhstan to the most commonly used anti-anaerobic drugs at the local level and to detect genes associated with resistance to these antibiotics. METHODS Species identification of the bacterial isolate was performed by matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF/MS) and 16S rRNA gene sequencing. Susceptibility to broad-spectrum antibiotics (metronidazole, meropenem, ciprofloxacin, clindamycin and tetracycline) most commonly used for the treatment of intra-abdominal infections (IAIs) was determined. Mass spectra groups essential for identifying cfiA-positive strains among clinical isolates were studied using ClinProTools 3.0.22 software. An Ion Torrent PGM™ platform was used for whole-genome sequencing (WGS) of the studied isolate. RESULTS The resulting WGS data of strain BFR_KZ01 was submitted to GenBank. In total, 5300 coding sequences (CDSs) and 69 RNA genes were determined. Analysis of the whole-genome data revealed that the studied strain harbours cfiA, nimB, tetQ and gyrA genes conferring resistance to key drugs used in treatment of the IAIs. MALDI-TOF/MS analysis assigned strain BFR_KZ01 to Group II (cfiA-positive); however, BFR_KZ01 was phenotypically sensitive to meropenem (mean MIC, 1.3 mg/L). CONCLUSION Determinants of drug resistance in strain BFR_KZ01 were identified. It was revealed that B. fragilis strain BFR_KZ01 from Kazakhstan is multidrug-resistant since it carries nimB, tetQ and gyrA genes conferring resistance to metronidazole, tetracycline and ciprofloxacin.
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Affiliation(s)
| | | | - Pavel Tarlykov
- RSE National Center for Biotechnology, Nur-Sultan, Z05K8D5, Kazakhstan
| | - Sabina Atavliyeva
- RSE National Center for Biotechnology, Nur-Sultan, Z05K8D5, Kazakhstan
| | | | - Asset Daniyarov
- RSE National Center for Biotechnology, Nur-Sultan, Z05K8D5, Kazakhstan; Laboratory of Bioinformatics and Systems Biology, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, 53 Kabanbay Batyr Ave, Nur-Sultan, 010000, Kazakhstan
| | - Kymbat Mukhtarova
- RSE National Center for Biotechnology, Nur-Sultan, Z05K8D5, Kazakhstan
| | - Yerlan Ramankulov
- RSE National Center for Biotechnology, Nur-Sultan, Z05K8D5, Kazakhstan; School of Science and Technology, Nazarbayev University, 53 Kabanbay Batyr Ave., Nur-Sultan, 010000, Kazakhstan
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Wang Y, Han Y, Shen H, Lv Y, Zheng W, Wang J. Higher Prevalence of Multi-Antimicrobial Resistant Bacteroides spp. Strains Isolated at a Tertiary Teaching Hospital in China. Infect Drug Resist 2020; 13:1537-1546. [PMID: 32547123 PMCID: PMC7266338 DOI: 10.2147/idr.s246318] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Purpose The study investigates the molecular epidemiology of multi-drug resistant (MDR) Bacteroides spp. isolates and the clinical characteristics of the patients. Materials and Methods Bacteroides spp. clinical strains were identified through MALDI-TOF MS and VITEK-2 anaerobes and corynebacterium (ANC) cards. A broth microdilution method was employed to detect the antimicrobial sensitivities of Bacteroides spp. isolates. PCR was used to detect the resistance genes, including cfxA, cepA, cfiA, ermF, nim, as well as the upstream insertion sequence (IS) element of the cfiA gene. The effects of broad-spectrum efflux pump inhibitors (EPIs) on the minimal inhibitory concentration (MICs) of cefoxitin, moxifloxacin, and imipenem for MDR Bacteroides spp. were investigated. Results The total resistance rates of 115 Bacteroides spp. isolates to cefoxitin, moxifloxacin, clindamycin, metronidazole, imipenem and meropenem were 4.3%, 16.5%, 80.0%, 5.2%, 13.9% and 13.9%, respectively. The positive rates of carbapenem resistance gene cfiA were 38.9% and 8.6% for B. fragilis and non-B. fragilis isolates, respectively. The isolation rate of MDR isolates reached up to 18.26% (21/115), and the isolation rate among the gastrointestinal cancer patients was significantly higher when compared to the non-gastrointestinal cancer patients (52.38%/26.08%, P = 0.006). Furthermore, MDR isolates were more likely to be isolated from the patients exposed to cephalosporins 3 months before Bacteroides spp. isolation (76.19%/31.52%, P = 0.000). Conclusion The overall resistance rates of Bacteroides spp. isolates against multiple antimicrobials were at a high level, especially for B. fragilis. The CfiA gene carrying rate among B. fragilis isolates was as high as 38.9%, and its mediated carbapenem resistance was the major resistance mechanism for B. fragilis. The findings of this study imply that the real resistance tendency of Bacteroides spp. may be underestimated and need to be given more attention.
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Affiliation(s)
- Yanyan Wang
- Department of Clinical Laboratory, Affiliated Hospital of Inner Mongolian Medical University, Hohhot 010050, People's Republic of China
| | - Yanqiu Han
- Department of Clinical Laboratory, Affiliated Hospital of Inner Mongolian Medical University, Hohhot 010050, People's Republic of China
| | - Huimin Shen
- Department of Clinical Laboratory, Affiliated Hospital of Inner Mongolian Medical University, Hohhot 010050, People's Republic of China
| | - Yingying Lv
- Department of Clinical Laboratory, Affiliated Hospital of Inner Mongolian Medical University, Hohhot 010050, People's Republic of China
| | - Wenqi Zheng
- Department of Clinical Laboratory, Affiliated Hospital of Inner Mongolian Medical University, Hohhot 010050, People's Republic of China
| | - Junrui Wang
- Department of Clinical Laboratory, Affiliated Hospital of Inner Mongolian Medical University, Hohhot 010050, People's Republic of China
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Archambault M, Rubin JE. Antimicrobial Resistance in Clostridium and Brachyspira spp. and Other Anaerobes. Microbiol Spectr 2020; 8:10.1128/microbiolspec.arba-0020-2017. [PMID: 31971162 PMCID: PMC10773235 DOI: 10.1128/microbiolspec.arba-0020-2017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Indexed: 01/26/2023] Open
Abstract
This article describes the antimicrobial resistance to date of the most frequently encountered anaerobic bacterial pathogens of animals. The different sections show that antimicrobial resistance can vary depending on the antimicrobial, the anaerobe, and the resistance mechanism. The variability in antimicrobial resistance patterns is also associated with other factors such as geographic region and local antimicrobial usage. On occasion, the same resistance gene was observed in many anaerobes, whereas some were limited to certain anaerobes. This article focuses on antimicrobial resistance data of veterinary origin.
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Affiliation(s)
- Marie Archambault
- Département de Pathologie et Microbiologie, Faculté de Médecine Vétérinaire, Université de Montréal, Saint-Hyacinthe, Québec J2S 2M2, Canada
| | - Joseph E Rubin
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatchewan S7N 5B4, Canada
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Sárvári KP, Schoblocher D. The antibiotic susceptibility pattern of gas gangrene-forming Clostridium spp. clinical isolates from South-Eastern Hungary. Infect Dis (Lond) 2019; 52:196-201. [DOI: 10.1080/23744235.2019.1696472] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
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Feucherolles M, Cauchie HM, Penny C. MALDI-TOF Mass Spectrometry and Specific Biomarkers: Potential New Key for Swift Identification of Antimicrobial Resistance in Foodborne Pathogens. Microorganisms 2019; 7:E593. [PMID: 31766422 PMCID: PMC6955786 DOI: 10.3390/microorganisms7120593] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 11/18/2019] [Accepted: 11/19/2019] [Indexed: 01/16/2023] Open
Abstract
Matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS) is today the reference method for direct identification of microorganisms in diagnostic laboratories, as it is notably time- and cost-efficient. In the context of increasing cases of enteric diseases with emerging multi-drug resistance patterns, there is an urgent need to adopt an efficient workflow to characterize antimicrobial resistance (AMR). Current approaches, such as antibiograms, are time-consuming and directly impact the "patient-physician" workflow. Through this mini-review, we summarize how the detection of specific patterns by MALDI-TOF MS, as well as bioinformatics, become more and more essential in research, and how these approaches will help diagnostics in the future. Along the same lines, the idea to export more precise biomarker identification steps by MALDI-TOF(/TOF) MS data towards AMR identification pipelines is discussed. The study also critically points out that there is currently still a lack of research data and knowledge on different foodborne pathogens as well as several antibiotics families such as macrolides and quinolones, and many questions are still remaining. Finally, the innovative combination of whole-genome sequencing and MALDI-TOF MS could be soon the future for diagnosis of antimicrobial resistance in foodborne pathogens.
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Affiliation(s)
- Maureen Feucherolles
- Luxembourg Institute of Science and Technology (LIST), Environmental Research and Innovation (ERIN) Department, 41 rue du Brill, 4422 Belvaux, Luxembourg;
- Faculté des Sciences, de la Technologie et de la Communication (FSTC), Doctoral School in Science and Engineering (DSSE), University of Luxembourg, 2 avenue de l’Université, 4365 Esch-sur-Alzette, Luxembourg
| | - Henry-Michel Cauchie
- Luxembourg Institute of Science and Technology (LIST), Environmental Research and Innovation (ERIN) Department, 41 rue du Brill, 4422 Belvaux, Luxembourg;
| | - Christian Penny
- Luxembourg Institute of Science and Technology (LIST), Environmental Research and Innovation (ERIN) Department, 41 rue du Brill, 4422 Belvaux, Luxembourg;
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Sydenham TV, Overballe-Petersen S, Hasman H, Wexler H, Kemp M, Justesen US. Complete hybrid genome assembly of clinical multidrug-resistant Bacteroides fragilis isolates enables comprehensive identification of antimicrobial-resistance genes and plasmids. Microb Genom 2019; 5:e000312. [PMID: 31697231 PMCID: PMC6927303 DOI: 10.1099/mgen.0.000312] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 10/17/2019] [Indexed: 02/06/2023] Open
Abstract
Bacteroides fragilis constitutes a significant part of the normal human gut microbiota and can also act as an opportunistic pathogen. Antimicrobial resistance (AMR) and the prevalence of AMR genes are increasing, and prediction of antimicrobial susceptibility based on sequence information could support targeted antimicrobial therapy in a clinical setting. Complete identification of insertion sequence (IS) elements carrying promoter sequences upstream of resistance genes is necessary for prediction of AMR. However, de novo assemblies from short reads alone are often fractured due to repeat regions and the presence of multiple copies of identical IS elements. Identification of plasmids in clinical isolates can aid in the surveillance of the dissemination of AMR, and comprehensive sequence databases support microbiome and metagenomic studies. We tested several short-read, hybrid and long-lead assembly pipelines by assembling the type strain B. fragilis CCUG4856T (=ATCC25285=NCTC9343) with Illumina short reads and long reads generated by Oxford Nanopore Technologies (ONT) MinION sequencing. Hybrid assembly with Unicycler, using quality filtered Illumina reads and Filtlong filtered and Canu-corrected ONT reads, produced the assembly of highest quality. This approach was then applied to six clinical multidrug-resistant B. fragilis isolates and, with minimal manual finishing of chromosomal assemblies of three isolates, complete, circular assemblies of all isolates were produced. Eleven circular, putative plasmids were identified in the six assemblies, of which only three corresponded to a known cultured Bacteroides plasmid. Complete IS elements could be identified upstream of AMR genes; however, there was not complete correlation between the absence of IS elements and antimicrobial susceptibility. As our knowledge on factors that increase expression of resistance genes in the absence of IS elements is limited, further research is needed prior to implementing AMR prediction for B. fragilis from whole-genome sequencing.
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Affiliation(s)
- Thomas V. Sydenham
- Research Unit of Clinical Microbiology, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
- Department of Clinical Microbiology, Odense University Hospital, Odense, Denmark
- Department of Clinical Microbiology, Lillebaelt Hospital, Vejle, Denmark
| | | | - Henrik Hasman
- Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Hannah Wexler
- GLAVA Health Care System and David Geffen School of Medicine, UCLA (University of California, Los Angeles), Los Angeles, CA, USA
| | - Michael Kemp
- Research Unit of Clinical Microbiology, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
- Department of Clinical Microbiology, Odense University Hospital, Odense, Denmark
| | - Ulrik S. Justesen
- Research Unit of Clinical Microbiology, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
- Department of Clinical Microbiology, Odense University Hospital, Odense, Denmark
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13
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Horizontal Gene Transfer and Acquired Antibiotic Resistance in Salmonella enterica Serovar Heidelberg following In Vitro Incubation in Broiler Ceca. Appl Environ Microbiol 2019; 85:AEM.01903-19. [PMID: 31471306 DOI: 10.1128/aem.01903-19] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 08/28/2019] [Indexed: 12/13/2022] Open
Abstract
The chicken gastrointestinal tract harbors microorganisms that play a role in the health and disease status of the host. The cecum is the part of the gut that carries the highest microbial densities, has the longest residence time of digesta, and is a vital site for urea recycling and water regulation. Therefore, the cecum provides a rich environment for bacteria to horizontally transfer genes between one another via mobile genetic elements such as plasmids and bacteriophages. In this study, we used broiler chicken cecum as a model to investigate antibiotic resistance genes that can be transferred in vitro from cecal flora to Salmonella enterica serovar Heidelberg. We used whole-genome sequencing and resistome enrichment to decipher the interactions between S Heidelberg, the gut microbiome, and acquired antibiotic resistance. After 48 h of incubation of ceca under microaerophilic conditions, we recovered one S Heidelberg isolate with an acquired IncK2 plasmid (88 kb) carrying an extended-spectrum-β-lactamase gene (bla CMY-2). In vitro, this plasmid was transferable between Escherichia coli and S Heidelberg strains but transfer was unsuccessful between S Heidelberg strains. An in-depth genetic characterization of transferred plasmids suggests that they share significant homology with P1-like phages. This study contributes to our understanding of horizontal gene transfer between an important foodborne pathogen and the chicken gut microbiome.IMPORTANCE S. Heidelberg is a clinically important serovar, linked to foodborne illness and among the top 5 serovars isolated from poultry in the United States and Canada. Acquisition of new genetic material from the microbial flora in the gastrointestinal tract of food animals, including broilers, may contribute to increased fitness of pathogens like S. Heidelberg and may increase their level of antibiotic tolerance. Therefore, it is critical to gain a better understanding of the interactions that occur between important pathogens and the commensals present in the animal gut and other agroecosystems. In this report, we show that the native flora in broiler ceca were capable of transferring mobile genetic elements carrying the AmpC β-lactamase (bla CMY-2) gene to an important foodborne pathogen, S Heidelberg. The potential role for bacteriophage transduction is also discussed.
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14
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Vich Vila A, Imhann F, Collij V, Jankipersadsing SA, Gurry T, Mujagic Z, Kurilshikov A, Bonder MJ, Jiang X, Tigchelaar EF, Dekens J, Peters V, Voskuil MD, Visschedijk MC, van Dullemen HM, Keszthelyi D, Swertz MA, Franke L, Alberts R, Festen EAM, Dijkstra G, Masclee AAM, Hofker MH, Xavier RJ, Alm EJ, Fu J, Wijmenga C, Jonkers DMAE, Zhernakova A, Weersma RK. Gut microbiota composition and functional changes in inflammatory bowel disease and irritable bowel syndrome. Sci Transl Med 2019; 10:10/472/eaap8914. [PMID: 30567928 DOI: 10.1126/scitranslmed.aap8914] [Citation(s) in RCA: 307] [Impact Index Per Article: 61.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Revised: 04/06/2018] [Accepted: 07/16/2018] [Indexed: 12/15/2022]
Abstract
Changes in the gut microbiota have been associated with two of the most common gastrointestinal diseases, inflammatory bowel disease (IBD) and irritable bowel syndrome (IBS). Here, we performed a case-control analysis using shotgun metagenomic sequencing of stool samples from 1792 individuals with IBD and IBS compared with control individuals in the general population. Despite substantial overlap between the gut microbiome of patients with IBD and IBS compared with control individuals, we were able to use gut microbiota composition differences to distinguish patients with IBD from those with IBS. By combining species-level profiles and strain-level profiles with bacterial growth rates, metabolic functions, antibiotic resistance, and virulence factor analyses, we identified key bacterial species that may be involved in two common gastrointestinal diseases.
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Affiliation(s)
- Arnau Vich Vila
- University of Groningen and University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, Netherlands.,University of Groningen and University Medical Center Groningen, Department of Genetics, Groningen, Netherlands
| | - Floris Imhann
- University of Groningen and University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, Netherlands.,University of Groningen and University Medical Center Groningen, Department of Genetics, Groningen, Netherlands
| | - Valerie Collij
- University of Groningen and University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, Netherlands.,University of Groningen and University Medical Center Groningen, Department of Genetics, Groningen, Netherlands
| | - Soesma A Jankipersadsing
- University of Groningen and University Medical Center Groningen, Department of Genetics, Groningen, Netherlands
| | - Thomas Gurry
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA.,Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Zlatan Mujagic
- Maastricht University Medical Center+, Division Gastroenterology-Hepatology, NUTRIM School for Nutrition, and Translational Research in Metabolism, Maastricht, Netherlands
| | - Alexander Kurilshikov
- University of Groningen and University Medical Center Groningen, Department of Genetics, Groningen, Netherlands
| | - Marc Jan Bonder
- University of Groningen and University Medical Center Groningen, Department of Genetics, Groningen, Netherlands
| | - Xiaofang Jiang
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA.,Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Ettje F Tigchelaar
- University of Groningen and University Medical Center Groningen, Department of Genetics, Groningen, Netherlands
| | - Jackie Dekens
- University of Groningen and University Medical Center Groningen, Department of Genetics, Groningen, Netherlands
| | - Vera Peters
- University of Groningen and University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, Netherlands
| | - Michiel D Voskuil
- University of Groningen and University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, Netherlands.,University of Groningen and University Medical Center Groningen, Department of Genetics, Groningen, Netherlands
| | - Marijn C Visschedijk
- University of Groningen and University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, Netherlands.,University of Groningen and University Medical Center Groningen, Department of Genetics, Groningen, Netherlands
| | - Hendrik M van Dullemen
- University of Groningen and University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, Netherlands
| | - Daniel Keszthelyi
- Maastricht University Medical Center+, Division Gastroenterology-Hepatology, NUTRIM School for Nutrition, and Translational Research in Metabolism, Maastricht, Netherlands
| | - Morris A Swertz
- University of Groningen and University Medical Center Groningen, Department of Genetics, Groningen, Netherlands
| | - Lude Franke
- University of Groningen and University Medical Center Groningen, Department of Genetics, Groningen, Netherlands
| | - Rudi Alberts
- University of Groningen and University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, Netherlands.,University of Groningen and University Medical Center Groningen, Department of Genetics, Groningen, Netherlands
| | - Eleonora A M Festen
- University of Groningen and University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, Netherlands.,University of Groningen and University Medical Center Groningen, Department of Genetics, Groningen, Netherlands
| | - Gerard Dijkstra
- University of Groningen and University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, Netherlands
| | - Ad A M Masclee
- Maastricht University Medical Center+, Division Gastroenterology-Hepatology, NUTRIM School for Nutrition, and Translational Research in Metabolism, Maastricht, Netherlands
| | - Marten H Hofker
- University of Groningen and University Medical Center Groningen, Department of Pediatrics, Groningen, Netherlands
| | - Ramnik J Xavier
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA.,Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Eric J Alm
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA.,Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Jingyuan Fu
- University of Groningen and University Medical Center Groningen, Department of Genetics, Groningen, Netherlands.,University of Groningen and University Medical Center Groningen, Department of Pediatrics, Groningen, Netherlands
| | - Cisca Wijmenga
- University of Groningen and University Medical Center Groningen, Department of Genetics, Groningen, Netherlands
| | - Daisy M A E Jonkers
- Maastricht University Medical Center+, Division Gastroenterology-Hepatology, NUTRIM School for Nutrition, and Translational Research in Metabolism, Maastricht, Netherlands
| | - Alexandra Zhernakova
- University of Groningen and University Medical Center Groningen, Department of Genetics, Groningen, Netherlands
| | - Rinse K Weersma
- University of Groningen and University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, Netherlands.
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15
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Sethi S, Shukla R, Bala K, Gautam V, Angrup A, Ray P. Emerging metronidazole resistance in Bacteroides spp. and its association with the nim gene: a study from North India. J Glob Antimicrob Resist 2019; 16:210-214. [DOI: 10.1016/j.jgar.2018.10.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 10/09/2018] [Accepted: 10/10/2018] [Indexed: 11/25/2022] Open
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16
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Dingsdag SA, Hunter N. Metronidazole: an update on metabolism, structure-cytotoxicity and resistance mechanisms. J Antimicrob Chemother 2019; 73:265-279. [PMID: 29077920 DOI: 10.1093/jac/dkx351] [Citation(s) in RCA: 174] [Impact Index Per Article: 34.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Metronidazole, a nitroimidazole, remains a front-line choice for treatment of infections related to inflammatory disorders of the gastrointestinal tract including colitis linked to Clostridium difficile. Despite >60 years of research, the metabolism of metronidazole and associated cytotoxicity is not definitively characterized. Nitroimidazoles are prodrugs that are reductively activated (the nitro group is reduced) under low oxygen tension, leading to imidazole fragmentation and cytotoxicity. It remains unclear if nitroimidazole reduction (activation) contributes to the cytotoxicity profile, or whether subsequent fragmentation of the imidazole ring and formed metabolites alone mediate cytotoxicity. A molecular mechanism underpinning high level (>256 mg/L) bacterial resistance to metronidazole also remains elusive. Considering the widespread use of metronidazole and other nitroimidazoles, this review was undertaken to emphasize the structure-cytotoxicity profile of the numerous metabolites of metronidazole in human and murine models and to examine conflicting reports regarding metabolite-DNA interactions. An alternative hypothesis, that DNA synthesis and repair of existing DNA is indirectly inhibited by metronidazole is proposed. Prokaryotic metabolism of metronidazole is detailed to discuss new resistance mechanisms. Additionally, the review contextualizes the history and current use of metronidazole, rates of metronidazole resistance including metronidazole MDR as well as the biosynthesis of azomycin, the natural precursor of metronidazole. Changes in the gastrointestinal microbiome and the host after metronidazole administration are also reviewed. Finally, novel nitroimidazoles and new antibiotic strategies are discussed.
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Affiliation(s)
- Simon A Dingsdag
- Institute of Dental Research and Westmead Centre for Oral Health, Westmead, NSW 2145, Australia.,Department of Life Sciences Faculty of Dentistry, The University of Sydney, NSW 2006, Australia.,The Westmead Institute for Medical Research, The University of Sydney, NSW 2145, Australia
| | - Neil Hunter
- Institute of Dental Research and Westmead Centre for Oral Health, Westmead, NSW 2145, Australia.,Department of Life Sciences Faculty of Dentistry, The University of Sydney, NSW 2006, Australia.,The Westmead Institute for Medical Research, The University of Sydney, NSW 2145, Australia
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17
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Metronidazole resistance and nim genes in anaerobes: A review. Anaerobe 2019; 55:40-53. [DOI: 10.1016/j.anaerobe.2018.10.004] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Revised: 10/01/2018] [Accepted: 10/05/2018] [Indexed: 01/06/2023]
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18
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Cordovana M, Kostrzewa M, Sóki J, Witt E, Ambretti S, Pranada A. Bacteroides fragilis: A whole MALDI-based workflow from identification to confirmation of carbapenemase production for routine laboratories. Anaerobe 2018; 54:246-253. [DOI: 10.1016/j.anaerobe.2018.04.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 03/30/2018] [Accepted: 04/03/2018] [Indexed: 10/17/2022]
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19
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Bogdan M, Perić L, Ördög K, Vuković D, Urbán E, Sóki J. The first characterized carbapenem-resistant Bacteroides fragilis strain from Croatia and the case study for it. Acta Microbiol Immunol Hung 2018; 65:317-323. [PMID: 29651861 DOI: 10.1556/030.65.2018.024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
An imipenem-resistant Bacteroides fragilis strain was isolated from the blood of a 72-year-old male patient with a urinary bladder tumor in Osijek, Croatia. This strain was also resistant to ampicillin, piperacillin/tazobactam, cefoxitin, clindamycin, tetracycline, and harbored cfiA, ermF, and tetQ genes where the high-level expression of the cfiA carbapenem-resistant gene was driven by an IS1187 element. Interestingly, despite the carbapenem-resistant feature of the B. fragilis from blood, the patient relatively easily recovered from the bacteremia. It was the first characterized imipenem-resistant B. fragilis isolate with its case report from Croatia, which confirmed the appearance of carbapenem-resistant B. fragilis strains, that continues worldwide with low incidence and the molecular characteristics vary temporally and geographically.
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Affiliation(s)
- Maja Bogdan
- 1 Department of Microbiology, Institute of Public Health for Osijek-Baranja County, Osijek, Croatia
- 2 Faculty of Medicine, Department of Microbiology and Parasitology, University of Osijek, Osijek, Croatia
| | - Ljilijana Perić
- 3 Department of Infectious Diseases, Clinical Hospital Centre Osijek, Osijek, Croatia
| | - Katalin Ördög
- 4 Faculty of Medicine, Institute of Clinical Microbiology, University of Szeged, Szeged, Hungary
| | - Dubravka Vuković
- 1 Department of Microbiology, Institute of Public Health for Osijek-Baranja County, Osijek, Croatia
| | - Edit Urbán
- 4 Faculty of Medicine, Institute of Clinical Microbiology, University of Szeged, Szeged, Hungary
| | - József Sóki
- 4 Faculty of Medicine, Institute of Clinical Microbiology, University of Szeged, Szeged, Hungary
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20
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Sárvári KP, Sóki J, Kristóf K, Juhász E, Miszti C, Melegh SZ, Latkóczy K, Urbán E. Molecular characterisation of multidrug-resistant Bacteroides isolates from Hungarian clinical samples. J Glob Antimicrob Resist 2018; 13:65-69. [DOI: 10.1016/j.jgar.2017.10.020] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Revised: 10/21/2017] [Accepted: 10/24/2017] [Indexed: 10/18/2022] Open
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21
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Rashidan M, Azimirad M, Alebouyeh M, Ghobakhlou M, Asadzadeh Aghdaei H, Zali MR. Detection of B. fragilis group and diversity of bft enterotoxin and antibiotic resistance markers cepA , cfiA and nim among intestinal Bacteroides fragilis strains in patients with inflammatory bowel disease. Anaerobe 2018; 50:93-100. [DOI: 10.1016/j.anaerobe.2018.02.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 02/08/2018] [Accepted: 02/12/2018] [Indexed: 01/06/2023]
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22
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Antimicrobial susceptibility testing of Bacteroides fragilis using the MALDI Biotyper antibiotic susceptibility test rapid assay (MBT-ASTRA). Anaerobe 2018; 54:236-239. [PMID: 29501419 DOI: 10.1016/j.anaerobe.2018.02.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Revised: 02/23/2018] [Accepted: 02/27/2018] [Indexed: 11/24/2022]
Abstract
This study evaluated the MBT-ASTRA for antimicrobial susceptibility testing of Bacteroides fragilis with different classes of antibiotics. MALDI-TOF MS peak AUCs from suspensions with B. fragilis with and without an antibiotic were used to calculate the relative growth (AUC "with antibiotic" divided by "without antibiotic"). Antimicrobial susceptibility testing of B. fragilis ATCC 25285 (susceptible) and B. fragilis O18 (resistant) was demonstrated with a clear difference of the relative growth between susceptible and resistant. The MBT-ASTRA needs further development and assessment but could be a relatively easy and inexpensive method for rapid antimicrobial susceptibility testing in specific cases of infection with B. fragilis.
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23
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How to isolate, identify and determine antimicrobial susceptibility of anaerobic bacteria in routine laboratories. Clin Microbiol Infect 2018; 24:1139-1148. [PMID: 29458156 DOI: 10.1016/j.cmi.2018.02.008] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Revised: 02/09/2018] [Accepted: 02/11/2018] [Indexed: 02/04/2023]
Abstract
BACKGROUND There has been increased interest in the study of anaerobic bacteria that cause human infection during the past decade. Many new genera and species have been described using 16S rRNA gene sequencing of clinical isolates obtained from different infection sites with commercially available special culture media to support the growth of anaerobes. Several systems, such as anaerobic pouches, boxes, jars and chambers provide suitable anaerobic culture conditions to isolate even strict anaerobic bacteria successfully from clinical specimens. Beside the classical, time-consuming identification methods and automated biochemical tests, the use of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry has revolutionized identification of even unusual and slow-growing anaerobes directly from culture plates, providing the possibility of providing timely information about anaerobic infections. AIMS The aim of this review article is to present methods for routine laboratories, which carry out anaerobic diagnostics on different levels. SOURCES Relevant data from the literature mostly published during the last 7 years are encompassed and discussed. CONTENT The review involves topics on the anaerobes that are members of the commensal microbiota and their role causing infection, the key requirements for collection and transport of specimens, processing of specimens in the laboratory, incubation techniques, identification and antimicrobial susceptibility testing of anaerobic bacteria. Advantages, drawbacks and specific benefits of the methods are highlighted. IMPLICATIONS The present review aims to update and improve anaerobic microbiology in laboratories with optimal conditions as well as encourage its routine implementation in laboratories with restricted resources.
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24
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Tajkarimi M, Wexler HM. CRISPR-Cas Systems in Bacteroides fragilis, an Important Pathobiont in the Human Gut Microbiome. Front Microbiol 2017; 8:2234. [PMID: 29218031 PMCID: PMC5704556 DOI: 10.3389/fmicb.2017.02234] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2017] [Accepted: 10/31/2017] [Indexed: 12/29/2022] Open
Abstract
Background: While CRISPR-Cas systems have been identified in bacteria from a wide variety of ecological niches, there are no studies to describe CRISPR-Cas elements in Bacteroides species, the most prevalent anaerobic bacteria in the lower intestinal tract. Microbes of the genus Bacteroides make up ~25% of the total gut microbiome. Bacteroides fragilis comprises only 2% of the total Bacteroides in the gut, yet causes of >70% of Bacteroides infections. The factors causing it to transition from benign resident of the gut microbiome to virulent pathogen are not well understood, but a combination of horizontal gene transfer (HGT) of virulence genes and differential transcription of endogenous genes are clearly involved. The CRISPR-Cas system is a multi-functional system described in prokaryotes that may be involved in control both of HGT and of gene regulation. Results: Clustered regularly interspaced short palindromic repeats (CRISPR) elements in all strains of B. fragilis (n = 109) with publically available genomes were identified. Three different CRISPR-Cas types, corresponding most closely to Type IB, Type IIIB, and Type IIC, were identified. Thirty-five strains had two CRISPR-Cas types, and three strains included all three CRISPR-Cas types in their respective genomes. The cas1 gene in the Type IIIB system encoded a reverse-transcriptase/Cas1 fusion protein rarely found in prokaryotes. We identified a short CRISPR (3 DR) with no associated cas genes present in most of the isolates; these CRISPRs were found immediately upstream of a hipA/hipB operon and we speculate that this element may be involved in regulation of this operon related to formation of persister cells during antimicrobial exposure. Also, blood isolates of B. fragilis did not have Type IIC CRISPR-Cas systems and had atypical Type IIIB CRISPR-Cas systems that were lacking adjacent cas genes. Conclusions: This is the first systematic report of CRISPR-Cas systems in a wide range of B. fragilis strains from a variety of sources. There are four apparent CRISPR-Cas systems in B. fragilis-three systems have adjacent cas genes. Understanding CRISPR/Cas function in B. fragilis will elucidate their role in gene expression, DNA repair and ability to survive exposure to antibiotics. Also, based on their unique CRISPR-Cas arrays, their phylogenetic clustering and their virulence potential, we are proposing that blood isolates of B. fragilis be viewed a separate subgroup.
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Affiliation(s)
- Mehrdad Tajkarimi
- Brentwood Biomedical Research Institute, Los Angeles, CA, United States
| | - Hannah M Wexler
- Brentwood Biomedical Research Institute, Los Angeles, CA, United States.,University of California, Los Angeles, Los Angeles, CA, United States.,GLAVA Health Care System, Los Angeles, CA, United States
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25
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Gajdács M, Spengler G, Urbán E. Identification and Antimicrobial Susceptibility Testing of Anaerobic Bacteria: Rubik's Cube of Clinical Microbiology? Antibiotics (Basel) 2017; 6:E25. [PMID: 29112122 PMCID: PMC5745468 DOI: 10.3390/antibiotics6040025] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Revised: 10/30/2017] [Accepted: 11/03/2017] [Indexed: 12/26/2022] Open
Abstract
Anaerobic bacteria have pivotal roles in the microbiota of humans and they are significant infectious agents involved in many pathological processes, both in immunocompetent and immunocompromised individuals. Their isolation, cultivation and correct identification differs significantly from the workup of aerobic species, although the use of new technologies (e.g., matrix-assisted laser desorption/ionization time-of-flight mass spectrometry, whole genome sequencing) changed anaerobic diagnostics dramatically. In the past, antimicrobial susceptibility of these microorganisms showed predictable patterns and empirical therapy could be safely administered but recently a steady and clear increase in the resistance for several important drugs (β-lactams, clindamycin) has been observed worldwide. For this reason, antimicrobial susceptibility testing of anaerobic isolates for surveillance purposes or otherwise is of paramount importance but the availability of these testing methods is usually limited. In this present review, our aim was to give an overview of the methods currently available for the identification (using phenotypic characteristics, biochemical testing, gas-liquid chromatography, MALDI-TOF MS and WGS) and antimicrobial susceptibility testing (agar dilution, broth microdilution, disk diffusion, gradient tests, automated systems, phenotypic and molecular resistance detection techniques) of anaerobes, when should these methods be used and what are the recent developments in resistance patterns of anaerobic bacteria.
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Affiliation(s)
- Márió Gajdács
- Department of Medical Microbiology and Immunobiology, Faculty of Medicine, University of Szeged, 6720 Szeged, Hungary.
| | - Gabriella Spengler
- Department of Medical Microbiology and Immunobiology, Faculty of Medicine, University of Szeged, 6720 Szeged, Hungary.
| | - Edit Urbán
- Institute of Clinical Microbiology, Faculty of Medicine, University of Szeged, 6725 Szeged, Hungary.
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26
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Silva CMG, Silva DNDS, Costa SBD, Almeida JSDS, Boente RF, Teixeira FL, Domingues RMCP, Lobo LA. Inactivation of MarR gene homologs increases susceptibility to antimicrobials in Bacteroides fragilis. Braz J Microbiol 2017; 49:200-206. [PMID: 28847541 PMCID: PMC5790583 DOI: 10.1016/j.bjm.2017.05.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Revised: 04/18/2017] [Accepted: 05/06/2017] [Indexed: 01/05/2023] Open
Abstract
Bacteroides fragilis is the strict anaerobic bacteria most commonly found in human infections, and has a high mortality rate. Among other virulence factors, the remarkable ability to acquire resistance to a variety of antimicrobial agents and to tolerate nanomolar concentrations of oxygen explains in part their success in causing infection and colonizing the mucosa. Much attention has been given to genes related to multiple drug resistance derived from plasmids, integrons or transposon, but such genes are also detected in chromosomal systems, like the mar (multiple antibiotic resistance) locus, that confer resistance to a range of drugs. Regulators like MarR, that control expression of the locus mar, also regulate resistance to organic solvents, disinfectants and oxygen reactive species are important players in these events. Strains derived from the parental strain 638R, with mutations in the genes hereby known as marRI (BF638R_3159) and marRII (BF638R_3706) were constructed by gene disruption using a suicide plasmid. Phenotypic response of the mutant strains to hydrogen peroxide, cell survival assay against exposure to oxygen, biofilm formation, resistance to bile salts and resistance to antibiotics was evaluated. The results showed that the mutant strains exhibit statistically significant differences in their response to oxygen stress, but no changes were observed in survival when exposed to bile salts. Biofilm formation was not affected by either gene disruption. Both mutant strains however, became more sensitive to multiple antimicrobial drugs tested. This indicates that as observed in other bacterial species, MarR are an important resistance mechanism in B. fragilis.
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Affiliation(s)
| | | | | | | | - Renata Ferreira Boente
- Universidade Federal do Rio de Janeiro, Medical Microbiology Department, Rio de Janeiro, RJ, Brazil
| | - Felipe Lopes Teixeira
- Universidade Federal do Rio de Janeiro, Medical Microbiology Department, Rio de Janeiro, RJ, Brazil
| | | | - Leandro Araujo Lobo
- Universidade Federal do Rio de Janeiro, Medical Microbiology Department, Rio de Janeiro, RJ, Brazil.
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27
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Ferløv-Schwensen SA, Sydenham TV, Hansen KCM, Hoegh SV, Justesen US. Prevalence of antimicrobial resistance and the cfiA resistance gene in Danish Bacteroides fragilis group isolates since 1973. Int J Antimicrob Agents 2017; 50:552-556. [PMID: 28666749 DOI: 10.1016/j.ijantimicag.2017.05.007] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Revised: 05/13/2017] [Accepted: 05/25/2017] [Indexed: 11/16/2022]
Abstract
OBJECTIVES The purpose of this study was to determine the prevalence of resistance and the cfiA carbapenemase-producing gene in historical Bacteroides fragilis group isolates. METHODS Danish clinical B. fragilis group isolates (n = 444) from 1973 to 2015 were identified with Matrix-Assisted Laser Desorption/Ionization Time-Of-Flight Mass Spectrometry (MALDI-TOF MS) on the Biotyper platform. Antimicrobial resistance was determined using a disk diffusion screening method and commercial antibiotic gradient strips. Division I (cfiA-negative) and division II (cfiA-positive) B. fragilis strains were differentiated using MALDI-TOF MS and real-time polymerase chain reaction (PCR). RESULTS From 1973-1980 to 2010-2015 the prevalence of antimicrobial resistance rose from 0% to 21.2%, 2.5%, and 1% for clindamycin, meropenem, and metronidazole, respectively. MALDI-TOF MS and real-time PCR identified 16 of 266 (6.0%) B. fragilis strains as division II, of which 4 strains, isolated between 2010 and 2015, were resistant to meropenem. CONCLUSIONS Substantial increases in resistance were found throughout this study. This supports the general perception that antimicrobial resistance in the B. fragilis group has been established in the recent decades in Europe. Resistance to meropenem, facilitated by expression of the cfiA resistance gene, seems to be increasing; therefore, it is imperative to monitor the occurrence of this gene, e.g. using MALDI-TOF MS.
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Affiliation(s)
| | | | | | - Silje Vermedal Hoegh
- Department of Clinical Microbiology, Odense University Hospital, Odense, Denmark
| | - Ulrik Stenz Justesen
- Department of Clinical Microbiology, Odense University Hospital, Odense, Denmark
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Ho PL, Yau CY, Ho LY, Chen JHK, Lai ELY, Lo SWU, Tse CWS, Chow KH. Rapid detection ofcfiAmetallo-β-lactamase-producingBacteroides fragilisby the combination of MALDI-TOF MS and CarbaNP. J Clin Pathol 2017; 70:868-873. [DOI: 10.1136/jclinpath-2017-204335] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Revised: 02/24/2017] [Accepted: 03/11/2017] [Indexed: 12/31/2022]
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Decousser JW, Poirel L, Nordmann P. Recent advances in biochemical and molecular diagnostics for the rapid detection of antibiotic-resistant Enterobacteriaceae: a focus on ß-lactam resistance. Expert Rev Mol Diagn 2017; 17:327-350. [DOI: 10.1080/14737159.2017.1289087] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Jean-Winoc Decousser
- Department of Virology, Bacteriology - Infection Control, Parasitology - Mycology, Assistance Publique - Hôpitaux de Paris, University Hospital Henri Mondor, Créteil, France
- IAME, UMR 1137, INSERM, Paris, France
| | - Laurent Poirel
- Emerging Antibiotic Resistance Unit, Medical and Molecular Microbiology, Department of Medicine, University of Fribourg, Fribourg, Switzerland
- French INSERM European Unit, University of Fribourg (LEA-IAME), Fribourg, Switzerland
- National Reference Center for Emerging Antibiotic Resistance, University of fribourg, fribourg, switzerland
| | - Patrice Nordmann
- Emerging Antibiotic Resistance Unit, Medical and Molecular Microbiology, Department of Medicine, University of Fribourg, Fribourg, Switzerland
- French INSERM European Unit, University of Fribourg (LEA-IAME), Fribourg, Switzerland
- National Reference Center for Emerging Antibiotic Resistance, University of fribourg, fribourg, switzerland
- Institute for Microbiology, University of Lausanne and University hospital Center, Lausanne, Switzerland
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Dunne Jr WM, Jaillard M, Rochas O, Van Belkum A. Microbial genomics and antimicrobial susceptibility testing. Expert Rev Mol Diagn 2017; 17:257-269. [DOI: 10.1080/14737159.2017.1283220] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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31
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Otte E, Nielsen HL, Hasman H, Fuglsang-Damgaard D. First report of metronidazole resistant, nimD-positive, Bacteroides stercoris isolated from an abdominal abscess in a 70-year-old woman. Anaerobe 2016; 43:91-93. [PMID: 28011371 DOI: 10.1016/j.anaerobe.2016.12.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Revised: 12/14/2016] [Accepted: 12/19/2016] [Indexed: 11/30/2022]
Abstract
We here present the first case of a metronidazole resistant nimD positive Bacteroides stercoris. The isolate originated from a polymicrobial intra-abdominal abscess in a 70-year-old woman. The nimD gene was detected by use of whole-genome shotgun sequencing and the subsequent use of the ResFinder 2.1 web service.
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Affiliation(s)
- Erik Otte
- Department of Clinical Microbiology, Aalborg University Hospital, Aalborg, Denmark; Department of Clinical Microbiology, Aarhus University Hospital, Aarhus, Denmark.
| | - Hans Linde Nielsen
- Department of Clinical Microbiology, Aalborg University Hospital, Aalborg, Denmark
| | - Henrik Hasman
- The Microbial Genomics and Antimicrobial Resistance Group, National Food Institute, Technical University of Denmark, Lyngby, Denmark; Antimicrobial Resistance Reference Laboratory and Surveillance Unit, Statens Serum Institut, Copenhagen, Denmark
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Schwensen SA, Acar Z, Sydenham TV, Johansson ÅC, Justesen US. Phenotypic detection of the cfiA metallo-β-lactamase in Bacteroides fragilis with the meropenem-EDTA double-ended Etest and the ROSCO KPC/MBL Confirm Kit. J Antimicrob Chemother 2016; 72:437-440. [PMID: 27798215 DOI: 10.1093/jac/dkw436] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Revised: 09/15/2016] [Accepted: 09/16/2016] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVES To investigate the performance of the meropenem and imipenem double-ended Etest ± EDTA and the tablet-based (meropenem and meropenem + dipicolinic acid) KPC/MBL Confirm Kit to detect cfiA metallo-β-lactamase (MBL) in Bacteroides fragilis. METHODS Well-characterized B. fragilis isolates, most from previously published studies, harbouring the cfiA gene and covering a wide range of meropenem MICs were included (n = 21). RESULTS The imipenem double-ended Etest showed an indeterminate result in 95% of the included isolates with the cfiA gene (20 of 21), whereas the meropenem double-ended Etest gave an MIC ratio ≥8 (positive test) with all the isolates. All isolates that were meropenem intermediate or resistant had a zone diameter difference ≥6 mm with the KPC/MBL Confirm Kit. CONCLUSIONS The meropenem double-ended Etest and not imipenem should be preferred for phenotypic detection of MBLs in B. fragilis. The KPC/MBL Confirm Kit could be an alternative with isolates that are meropenem intermediate or resistant (MIC >2 mg/L).
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Affiliation(s)
- Simon A Schwensen
- Department of Clinical Microbiology, Odense University Hospital, Odense, Denmark
| | - Ziyap Acar
- Department of Clinical Microbiology, Odense University Hospital, Odense, Denmark
| | - Thomas V Sydenham
- Department of Clinical Microbiology, Odense University Hospital, Odense, Denmark
| | - Åsa C Johansson
- Department of Clinical Microbiology, Central Hospital, Växjo, Sweden
| | - Ulrik S Justesen
- Department of Clinical Microbiology, Odense University Hospital, Odense, Denmark
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Abstract
Alteration in the host microbiome at skin and mucosal surfaces plays a role in the function of the immune system, and may predispose immunocompromised patients to infection. Because obligate anaerobes are the predominant type of bacteria present in humans at skin and mucosal surfaces, immunocompromised patients are at increased risk for serious invasive infection due to anaerobes. Laboratory approaches to the diagnosis of anaerobe infections that occur due to pyogenic, polymicrobial, or toxin-producing organisms are described. The clinical interpretation and limitations of anaerobe recovery from specimens, anaerobe-identification procedures, and antibiotic-susceptibility testing are outlined. Bacteriotherapy following analysis of disruption of the host microbiome has been effective for treatment of refractory or recurrent Clostridium difficile infection, and may become feasible for other conditions in the future.
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Affiliation(s)
- Deirdre L Church
- Departments of Pathology & Laboratory Medicine and Medicine, University of Calgary, and Division of Microbiology, Calgary Laboratory Services, Calgary, Alberta, Canada T2N 1N4
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Ricker N, Shen SY, Goordial J, Jin S, Fulthorpe RR. PacBio SMRT assembly of a complex multi-replicon genome reveals chlorocatechol degradative operon in a region of genome plasticity. Gene 2016; 586:239-47. [PMID: 27063562 DOI: 10.1016/j.gene.2016.04.018] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Revised: 03/14/2016] [Accepted: 04/05/2016] [Indexed: 01/03/2023]
Abstract
We have sequenced a Burkholderia genome that contains multiple replicons and large repetitive elements that would make it inherently difficult to assemble by short read sequencing technologies. We illustrate how the integrated long read correction algorithms implemented through the PacBio Single Molecule Real-Time (SMRT) sequencing technology successfully provided a de novo assembly that is a reasonable estimate of both the gene content and genome organization without making any further modifications. This assembly is comparable to related organisms assembled by more labour intensive methods. Our assembled genome revealed regions of genome plasticity for further investigation, one of which harbours a chlorocatechol degradative operon highly homologous to those previously identified on globally ubiquitous plasmids. In an ideal world, this assembly would still require experimental validation to confirm gene order and copy number of repeated elements. However, we submit that particularly in instances where a polished genome is not the primary goal of the sequencing project, PacBio SMRT sequencing provides a financially viable option for generating a biologically relevant genome estimate that can be utilized by other researchers for comparative studies.
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Affiliation(s)
- N Ricker
- Department of Physical and Environmental Sciences, University of Toronto Scarborough, 1095 Military Trail, Scarborough, Ontario M1C 1A4, Canada
| | - S Y Shen
- Department of Physical and Environmental Sciences, University of Toronto Scarborough, 1095 Military Trail, Scarborough, Ontario M1C 1A4, Canada
| | - J Goordial
- Department of Natural Resource Sciences, McGill University, Macdonald Campus, 21111 Lakeshore Rd., Sainte Anne de Bellevue, Quebec H9X 3V9, Canada
| | - S Jin
- Department of Physical and Environmental Sciences, University of Toronto Scarborough, 1095 Military Trail, Scarborough, Ontario M1C 1A4, Canada
| | - R R Fulthorpe
- Department of Physical and Environmental Sciences, University of Toronto Scarborough, 1095 Military Trail, Scarborough, Ontario M1C 1A4, Canada.
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35
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Abstract
Whole-genome sequencing has opened the way for investigating the dynamics and genomic evolution of bacterial pathogens during the colonization and infection of humans. The application of this technology to the longitudinal study of adaptation in an infected host--in particular, the evolution of drug resistance and host adaptation in patients who are chronically infected with opportunistic pathogens--has revealed remarkable patterns of convergent evolution, suggestive of an inherent repeatability of evolution. In this Review, we describe how these studies have advanced our understanding of the mechanisms and principles of within-host genome evolution, and we consider the consequences of findings such as a potent adaptive potential for pathogenicity. Finally, we discuss the possibility that genomics may be used in the future to predict the clinical progression of bacterial infections and to suggest the best option for treatment.
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Metronidazole- and carbapenem-resistant bacteroides thetaiotaomicron isolated in Rochester, Minnesota, in 2014. Antimicrob Agents Chemother 2015; 59:4157-61. [PMID: 25941219 DOI: 10.1128/aac.00677-15] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Accepted: 04/26/2015] [Indexed: 11/20/2022] Open
Abstract
Emerging antimicrobial resistance in members of the Bacteroides fragilis group is a concern in clinical medicine. Although metronidazole and carbapenem resistance have been reported in Bacteroides thetaiotaomicron, a member of the B. fragilis group, they have not, to the best of our knowledge, been reported together in the same B. thetaiotaomicron isolate. Herein, we report isolation of piperacillin-tazobactam-, metronidazole-, clindamycin-, ertapenem-, and meropenem-resistant B. thetaiotaomicron from a patient with postoperative intra-abdominal abscess and empyema. Whole-genome sequencing demonstrated the presence of nimD with at least a portion of IS1169 upstream, a second putative nim gene, two β-lactamase genes (one of which has not been previously reported), two tetX genes, tetQ, ermF, two cat genes, and a number of efflux pumps. This report highlights emerging antimicrobial resistance in B. thetaiotaomicron and the importance of identification and antimicrobial susceptibility testing of selected anaerobic bacteria.
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37
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Ngo A, Fong KT, Cox DL, Chen X, Fisher AJ. Structures of Bacteroides fragilis uridine 5'-diphosphate-N-acetylglucosamine (UDP-GlcNAc) acyltransferase (BfLpxA). ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2015; 71:1068-76. [PMID: 25945572 PMCID: PMC4427197 DOI: 10.1107/s1399004715003326] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2015] [Accepted: 02/16/2015] [Indexed: 11/11/2022]
Abstract
Uridine 5'-diphosphate-N-acetylglucosamine (UDP-GlcNAc) acyltransferase (LpxA) catalyzes a reversible reaction for adding an O-acyl group to the GlcNAc in UDP-GlcNAc in the first step of lipid A biosynthesis. Lipid A constitutes a major component of lipopolysaccharides, also referred to as endotoxins, which form the outer monolayer of the outer membrane of Gram-negative bacteria. Ligand-free and UDP-GlcNAc-bound crystal structures of LpxA from Bacteroides fragilis NCTC 9343, the most common pathogenic bacteria found in abdominal abscesses, have been determined and are presented here. The enzyme crystallizes in a cubic space group, with the crystallographic threefold axis generating the biological functional homotrimer and with each monomer forming a nine-rung left-handed β-helical (LβH) fold in the N-terminus followed by an α-helical motif in the C-terminus. The structure is highly similar to LpxA from other organisms. Yet, despite sharing a similar LβH structure with LpxAs from Escherichia coli and others, previously unseen calcium ions are observed on the threefold axis in B. fragilis LpxA to help stabilize the trimeric assembly.
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Affiliation(s)
- Alice Ngo
- Department of Chemistry, University of California, One Shields Avenue, Davis, CA 95616, USA
| | - Kai T. Fong
- Department of Chemistry, University of California, One Shields Avenue, Davis, CA 95616, USA
| | - Daniel L. Cox
- Department of Physics, University of California, One Shields Avenue, Davis, CA 95616, USA
| | - Xi Chen
- Department of Chemistry, University of California, One Shields Avenue, Davis, CA 95616, USA
| | - Andrew J. Fisher
- Department of Chemistry, University of California, One Shields Avenue, Davis, CA 95616, USA
- Department of Molecular and Cellular Biology, University of California, One Shields Avenue, Davis, CA 95616, USA
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