1
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Yekani M, Rezaee MA, Beheshtirouy S, Baghi HB, Bazmani A, Farzinazar A, Memar MY, Sóki J. Carbapenem resistance in Bacteroides fragilis: A review of molecular mechanisms. Anaerobe 2022; 76:102606. [PMID: 35738484 DOI: 10.1016/j.anaerobe.2022.102606] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 06/10/2022] [Accepted: 06/16/2022] [Indexed: 11/28/2022]
Abstract
Carbapenems are an applicable subclass of β-lactam drugs in the antibiotic therapy of anaerobic infections, especially for poly-microbial cases, due to their broad antimicrobial spectrum on aerobic and anaerobic bacteria. Bacteroides fragilis is the most commonly recovered anaerobic bacteria in the clinical laboratories from mono- and poly-microbial infections. B. fragilis is relatively non-susceptible to different antibiotics, including β-lactams, tetracyclines, fluoroquinolones, and macrolides. Carbapenems are among the most effective drugs against B. fragilis strains with high-level resistance to different antibiotics. Increased antibiotic resistance of B. fragilis strains has been reported following the overuse of an antimicrobial agent. Earlier contact with carbapenems is linked with increased resistance to them that limits the options for treatment of B. fragilis caused infections, especially in cases caused by multidrug-resistant strains. Several molecular mechanisms of resistance to carbapenems have been described for different carbapenem-resistant bacteria. Understanding the mechanisms of resistance to antimicrobial agents is necessary for selecting alternative antimicrobial agents and the application of control strategies. In the present study, we reviewed the mechanisms contributing to resistance to carbapenems in B. fragilis strains.
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Affiliation(s)
- Mina Yekani
- Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Student Research Committee, Kashan University of Medical Sciences, Kashan, Iran
| | | | - Samad Beheshtirouy
- Cardiothoracic Department, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | - Ahad Bazmani
- Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Abbas Farzinazar
- Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mohammad Yousef Memar
- Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
| | - József Sóki
- Institute of Medical Microbiology, Albert Szent-Györgyi Health Centre and School of of Medicine, University of Szeged, Szeged, Hungary.
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2
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Patrick S. A tale of two habitats: Bacteroides fragilis, a lethal pathogen and resident in the human gastrointestinal microbiome. Microbiology (Reading) 2022; 168. [DOI: 10.1099/mic.0.001156] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Bacteroides fragilis
is an obligately anaerobic Gram-negative bacterium and a major colonizer of the human large colon where
Bacteroides
is a predominant genus. During the growth of an individual clonal population, an astonishing number of reversible DNA inversion events occur, driving within-strain diversity. Additionally, the
B. fragilis
pan-genome contains a large pool of diverse polysaccharide biosynthesis loci, DNA restriction/modification systems and polysaccharide utilization loci, which generates remarkable between-strain diversity. Diversity clearly contributes to the success of
B. fragilis
within its normal habitat of the gastrointestinal (GI) tract and during infection in the extra-intestinal host environment. Within the GI tract,
B. fragilis
is usually symbiotic, for example providing localized nutrients for the gut epithelium, but
B. fragilis
within the GI tract may not always be benign. Metalloprotease toxin production is strongly associated with colorectal cancer.
B. fragilis
is unique amongst bacteria; some strains export a protein >99 % structurally similar to human ubiquitin and antigenically cross-reactive, which suggests a link to autoimmune diseases.
B. fragilis
is not a primary invasive enteric pathogen; however, if colonic contents contaminate the extra-intestinal host environment, it successfully adapts to this new habitat and causes infection; classically peritoneal infection arising from rupture of an inflamed appendix or GI surgery, which if untreated, can progress to bacteraemia and death. In this review selected aspects of
B. fragilis
adaptation to the different habitats of the GI tract and the extra-intestinal host environment are considered, along with the considerable challenges faced when studying this highly variable bacterium.
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Affiliation(s)
- Sheila Patrick
- Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences Queen’s University Belfast, 97 Lisburn Rd, Belfast BT9 7BL, UK
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3
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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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4
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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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5
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Yekani M, Baghi HB, Vahed SZ, Ghanbari H, Hosseinpur R, Azargun R, Azimi S, Memar MY. Tightly controlled response to oxidative stress; an important factor in the tolerance of Bacteroides fragilis. Res Microbiol 2021; 172:103798. [PMID: 33485914 DOI: 10.1016/j.resmic.2021.103798] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 01/07/2021] [Accepted: 01/08/2021] [Indexed: 12/01/2022]
Abstract
The exposure of Bacteroides fragilis to highly oxygenated tissues induces an oxidative stress due to a shift from the reduced condition of the gastrointestinal tract to an aerobic environment of host tissues. The potent and effective responses to reactive oxygen species (ROS) make the B. fragilis tolerant to atmospheric oxygen for several days. The response to oxidative stress in B. fragilis is a complicated event that is induced and regulated by different agents. In this review, we will focus on the B. fragilis response to oxidative stress and present an overview of the regulators of responses to oxidative stress in this bacterium.
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Affiliation(s)
- Mina Yekani
- Department of Microbiology, Faculty of Medicine, Kashan University of Medical Sciences, Kashan, Iran; Student Research Committee, Kashan University of Medical Sciences, Kashan, Iran
| | - Hossein Bannazadeh Baghi
- Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | - Hadi Ghanbari
- Department of Pharmacognosy, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Rasul Hosseinpur
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Robab Azargun
- Department of Microbiology, Faculty of Medicine, Maragheh University of Medical Sciences, Maragheh, Iran
| | - Somayeh Azimi
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mohammad Yousef Memar
- Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Microbiology Department, School of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran.
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6
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Yekani M, Baghi HB, Naghili B, Vahed SZ, Sóki J, Memar MY. To resist and persist: Important factors in the pathogenesis of Bacteroides fragilis. Microb Pathog 2020; 149:104506. [PMID: 32950639 DOI: 10.1016/j.micpath.2020.104506] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 07/15/2020] [Accepted: 09/15/2020] [Indexed: 02/07/2023]
Abstract
Bacteroides fragilis is a most frequent anaerobic pathogen isolated from human infections, particularly found in the abdominal cavity. Different factors contribute to the pathogenesis and persistence of B. fragilis at infection sites. The knowledge of the virulence factors can provide applicable information for finding alternative options for the antibiotic therapy and treatment of B. fragilis caused infections. Herein, a comprehensive review of the important B. fragilis virulence factors was prepared. In addition to B. fragilis toxin (BFT) and its potential role in the diarrhea and cancer development, some other important virulence factors and characteristics of B. fragilis are described including capsular polysaccharides, iron acquisition, resistance to antimicrobial agents, and survival during the prolonged oxidative stress, quorum sensing, and secretion systems.
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Affiliation(s)
- Mina Yekani
- Department of Microbiology, Faculty of Medicine, Kashan University of Medical Sciences, Kashan, Iran; Student Research Committee,Kashan University of Medical Sciences, Kashan, Iran
| | - Hossein Bannazadeh Baghi
- Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Behrooz Naghili
- Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | - József Sóki
- Institute of Clinical Microbiology, Faculty of Medicine, University of Szeged, Szeged, Hungary.
| | - Mohammad Yousef Memar
- Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Microbiology Department, School of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran; Students' Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran.
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7
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Xia T, Zhang B, Li Y, Fang B, Zhu X, Xu B, Zhang J, Wang M, Fang J. New insight into 20(S)-ginsenoside Rh2 against T-cell acute lymphoblastic leukemia associated with the gut microbiota and the immune system. Eur J Med Chem 2020; 203:112582. [PMID: 32682197 DOI: 10.1016/j.ejmech.2020.112582] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 06/13/2020] [Accepted: 06/14/2020] [Indexed: 02/07/2023]
Abstract
T-cell acute lymphoblastic leukemia (T-ALL) is a hematopoietic malignancy associated with unfavorable factors including male gender and over nine years of age. Chemotherapy toxicity continues to present a major challenge. There is a need to develop novel natural agents to improve survival and quality of life in patients with T-ALL. 20(S)-ginsenoside Rh2 (GRh2) exhibits immune regulation and anti-tumor effects in both cellular and murine xenograft models. In the present study, the anti-cancer mechanisms of 20(S)-GRh2 involved in the immune system and intestinal microbiota were investigated in T-ALL mice. We revealed that 20(S)-Rh2 suppressed T-ALL by blocking the PI3K/Akt/mTOR signaling pathway, and enhanced immunity in the spleen by regulating immune factors. In addition, 20(S)-GRh2 altered the composition of the gut microbiota, and promoted intestinal homeostasis by elevating the levels of tight junction proteins, antimicrobial peptides and IgA. 20(S)-GRh2 ameliorated the LPS-induced inflammatory response in the intestine of T-ALL mice. Furthermore, Bacteroidetes, Verrucomicrobia, Akkermansia, Lactobacillus, and Lachnospiraceae_NK4A136_group were positively correlated with anti-tumor immune factors, intestinal barrier-related factors, and the anti-inflammatory response. Conversely, Firmicutes, Proteobacteria, Parabacteroides and Alistipes had the opposite correlation. Collectively, these results suggest that 20(S)-GRh2 is a safe and effective natural product, that shows promise for the prevention and treatment of T-ALL.
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Affiliation(s)
- Ting Xia
- State Key Laboratory of Food Nutrition and Safety, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, PR China.
| | - Bo Zhang
- State Key Laboratory of Food Nutrition and Safety, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, PR China
| | - Yu Li
- State Key Laboratory of Food Nutrition and Safety, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, PR China
| | - Bin Fang
- State Key Laboratory of Food Nutrition and Safety, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, PR China
| | - Xiaoxuan Zhu
- State Key Laboratory of Food Nutrition and Safety, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, PR China
| | - Bicheng Xu
- State Key Laboratory of Food Nutrition and Safety, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, PR China
| | - Jin Zhang
- State Key Laboratory of Food Nutrition and Safety, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, PR China
| | - Min Wang
- State Key Laboratory of Food Nutrition and Safety, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, PR China.
| | - Jianpei Fang
- Department of Pediatrics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guang Dong, 510120, PR China; Key Laboratory of Malignant Tumor Gene Regulation and Target Therapy of Guangdong Higher Education Institutes, Sun Yat-sen University, Guangzhou, Guang Dong, 510120, PR China.
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8
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Improved Metagenomic Taxonomic Profiling Using a Curated Core Gene-Based Bacterial Database Reveals Unrecognized Species in the Genus Streptococcus. Pathogens 2020; 9:pathogens9030204. [PMID: 32164338 PMCID: PMC7157611 DOI: 10.3390/pathogens9030204] [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] [Received: 02/17/2020] [Revised: 03/09/2020] [Accepted: 03/09/2020] [Indexed: 12/31/2022] Open
Abstract
Shotgun metagenomics is of great importance in order to understand the composition of the microbial community associated with a sample and the potential impact it may exert on its host. For clinical metagenomics, one of the initial challenges is the accurate identification of a pathogen of interest and ability to single out that pathogen within a complex community of microorganisms. However, in absence of an accurate identification of those microorganisms, any kind of conclusion or diagnosis based on misidentification may lead to erroneous conclusions, especially when comparing distinct groups of individuals. When comparing a shotgun metagenomic sample against a reference genome sequence database, the classification itself is dependent on the contents of the database. Focusing on the genus Streptococcus, we built four synthetic metagenomic samples and demonstrated that shotgun taxonomic profiling using the bacterial core genes as the reference database performed better in both taxonomic profiling and relative abundance prediction than that based on the marker gene reference database included in MetaPhlAn2. Additionally, by classifying sputum samples of patients suffering from chronic obstructive pulmonary disease, we showed that adding genomes of genomospecies to a reference database offers higher taxonomic resolution for taxonomic profiling. Finally, we show how our genomospecies database is able to identify correctly a clinical stool sample from a patient with a streptococcal infection, proving that genomospecies provide better taxonomic coverage for metagenomic analyses.
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9
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Identification and Antimicrobial Susceptibility of Clinically Isolated Anaerobic Bacteria: A Retrospectively Study in a Jiangxi Tertiary-Care Hospital. Jundishapur J Microbiol 2019. [DOI: 10.5812/jjm.95800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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10
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Ha SM, Kim CK, Roh J, Byun JH, Yang SJ, Choi SB, Chun J, Yong D. Application of the Whole Genome-Based Bacterial Identification System, TrueBac ID, Using Clinical Isolates That Were Not Identified With Three Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS) Systems. Ann Lab Med 2019; 39:530-536. [PMID: 31240880 PMCID: PMC6660342 DOI: 10.3343/alm.2019.39.6.530] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Revised: 01/08/2019] [Accepted: 05/22/2019] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Next-generation sequencing is increasingly used for taxonomic identification of pathogenic bacterial isolates. We evaluated the performance of a newly introduced whole genome-based bacterial identification system, TrueBac ID (ChunLab Inc., Seoul, Korea), using clinical isolates that were not identified by three matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) systems and 16S rRNA gene sequencing. METHODS Thirty-six bacterial isolates were selected from a university-affiliated hospital and a commercial clinical laboratory. Species was identified by three MALDI-TOF MS systems: Bruker Biotyper MS (Bruker Daltonics, Billerica, MA, USA), VITEK MS (bioMérieux, Marcy l'Étoile, France), and ASTA MicroIDSys (ASTA Inc., Suwon, Korea). Whole genome sequencing was conducted using the Illumina MiSeq system (Illumina, San Diego, CA, USA), and genome-based identification was performed using the TrueBac ID cloud system (www.truebacid.com). RESULTS TrueBac ID assigned 94% (34/36) of the isolates to known (N=25) or novel (N=4) species, genomospecies (N=3), or species group (N=2). The remaining two were identified at the genus level. CONCLUSIONS TrueBac ID successfully identified the majority of isolates that MALDI-TOF MS failed to identify. Genome-based identification can be a useful tool in clinical laboratories, with its superior accuracy and database-driven operations.
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Affiliation(s)
- Sung Min Ha
- ChunLab, Inc., Seoul, Korea.,School of Biological Sciences & Institute of Molecular Biology and Genetics, Seoul National University, Seoul, Korea
| | - Chang Ki Kim
- Seoul Clinical Laboratories, Yongin, Korea.,Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, Korea
| | - Juhye Roh
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Korea
| | - Jung Hyun Byun
- Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, Korea.,Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Korea.,Department of Laboratory Medicine, Gyeongsang National University Hospital, and Gyeongsang National University College of Medicine, Jinju, Korea
| | | | | | - Jongsik Chun
- ChunLab, Inc., Seoul, Korea.,School of Biological Sciences & Institute of Molecular Biology and Genetics, Seoul National University, Seoul, Korea
| | - Dongeun Yong
- Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, Korea.,Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Korea.,Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, Korea.
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11
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Abstract
Multidrug resistance (MDR) in anaerobes is not a well-known topic. Bacteroides fragilis group isolates have numerous resistance determinants such as multidrug efflux pumps, cfiA and nimB genes and activating insertion sequences, and some isolates exhibited extensive drug-resistant patterns. MDR rates in B. fragilis group were from 1.5 to >18% and up to >71% in cfiA and nimB positive isolates carrying insertion sequences. MDR was present in >1/2 of Clostridioides difficile isolates, most often in epidemic/hypervirulent strains and unusually high metronidazole or vancomycin resistance has been reported in single studies. MDR was found in Prevotella spp. (in ≤10% of isolates), Finegoldia magna, Veillonella spp. and Cutibacterium acnes. Resistance in the anaerobes tends to be less predictable and anaerobic microbiology is required in more laboratories. New hopes may be new antibiotics such as eravacycline, cadazolid, surotomycin, ridinilazol or C. difficile toxoid vaccines; however, more efforts are needed to track the MDR in anaerobes.
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Affiliation(s)
- Lyudmila Boyanova
- Department of Medical Microbiology, Medical University of Sofia, Sofia 1431, Bulgaria
| | - Rumyana Markovska
- Department of Medical Microbiology, Medical University of Sofia, Sofia 1431, Bulgaria
| | - Ivan Mitov
- Department of Medical Microbiology, Medical University of Sofia, Sofia 1431, Bulgaria
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12
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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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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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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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15
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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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16
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A Novel Selective Medium for Isolation of Bacteroides fragilis from Clinical Specimens. J Clin Microbiol 2016; 55:384-390. [PMID: 27852672 DOI: 10.1128/jcm.01988-16] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Accepted: 11/08/2016] [Indexed: 12/20/2022] Open
Abstract
A novel Bacteroides fragilis selective (BFS) medium, consisting of a brain heart infusion agar base supplemented with yeast extract, cysteine hydrochloride, bile salts, vitamin K, hemin, glucose, esculin, ferric ammonium citrate, bromothymol blue, gentamicin, kanamycin, and novobiocin, was evaluated. When BFS agar was tested with a collection of 303 bacteria of different genera, it allowed the growth of B. fragilis as large yellow colonies, with blackening of the medium after 48 h of anaerobic incubation, while the growth of most other anaerobes, facultative anaerobes, and aerobes was inhibited. In a prospective comparison of BFS agar with a routinely used medium (neomycin blood agar) in 1,209 clinical specimens, 60 B. fragilis bacteria were detected on BFS agar while 46 were detected on the routine agar (McNemar's test, P = 0.008). In conclusion, this novel medium may be added to improve the recovery of B. fragilis in clinical specimens and to facilitate surveillance of antimicrobial-resistant strains.
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17
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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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18
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Roach DJ, Burton JN, Lee C, Stackhouse B, Butler-Wu SM, Cookson BT, Shendure J, Salipante SJ. A Year of Infection in the Intensive Care Unit: Prospective Whole Genome Sequencing of Bacterial Clinical Isolates Reveals Cryptic Transmissions and Novel Microbiota. PLoS Genet 2015; 11:e1005413. [PMID: 26230489 PMCID: PMC4521703 DOI: 10.1371/journal.pgen.1005413] [Citation(s) in RCA: 135] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Accepted: 07/02/2015] [Indexed: 01/05/2023] Open
Abstract
Bacterial whole genome sequencing holds promise as a disruptive technology in clinical microbiology, but it has not yet been applied systematically or comprehensively within a clinical context. Here, over the course of one year, we performed prospective collection and whole genome sequencing of nearly all bacterial isolates obtained from a tertiary care hospital's intensive care units (ICUs). This unbiased collection of 1,229 bacterial genomes from 391 patients enables detailed exploration of several features of clinical pathogens. A sizable fraction of isolates identified as clinically relevant corresponded to previously undescribed species: 12% of isolates assigned a species-level classification by conventional methods actually qualified as distinct, novel genomospecies on the basis of genomic similarity. Pan-genome analysis of the most frequently encountered pathogens in the collection revealed substantial variation in pan-genome size (1,420 to 20,432 genes) and the rate of gene discovery (1 to 152 genes per isolate sequenced). Surprisingly, although potential nosocomial transmission of actively surveilled pathogens was rare, 8.7% of isolates belonged to genomically related clonal lineages that were present among multiple patients, usually with overlapping hospital admissions, and were associated with clinically significant infection in 62% of patients from which they were recovered. Multi-patient clonal lineages were particularly evident in the neonatal care unit, where seven separate Staphylococcus epidermidis clonal lineages were identified, including one lineage associated with bacteremia in 5/9 neonates. Our study highlights key differences in the information made available by conventional microbiological practices versus whole genome sequencing, and motivates the further integration of microbial genome sequencing into routine clinical care.
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Affiliation(s)
- David J. Roach
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Joshua N. Burton
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Choli Lee
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Bethany Stackhouse
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Susan M. Butler-Wu
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, United States of America
| | - Brad T. Cookson
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, United States of America
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Stephen J. Salipante
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, United States of America
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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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