1
|
Tiwari A, Krolicka A, Tran TT, Räisänen K, Ásmundsdóttir ÁM, Wikmark OG, Lood R, Pitkänen T. Antibiotic resistance monitoring in wastewater in the Nordic countries: A systematic review. ENVIRONMENTAL RESEARCH 2024; 246:118052. [PMID: 38163547 DOI: 10.1016/j.envres.2023.118052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 12/23/2023] [Accepted: 12/25/2023] [Indexed: 01/03/2024]
Abstract
The Nordic countries (Denmark, Finland, Iceland, Norway, and Sweden) have effectively kept lower antibiotic-resistant bacterial (ARB) pathogen rates than many other countries. However, in recent years, these five countries have encountered a rise in ARB cases and challenges in treating infections due to the growing prevalence of ARB pathogens. Wastewater-based surveillance (WBS) is a valuable supplement to clinical methods for ARB surveillance, but there is a lack of comprehensive understanding of WBS application for ARB in the Nordic countries. This review aims to compile the latest state-of-the-art developments in WBS for ARB monitoring in the Nordic countries and compare them with clinical surveillance practices. After reviewing 1480 papers from the primary search, 54 were found relevant, and 15 additional WBS-related papers were included. Among 69 studies analyzed, 42 dedicated clinical epidemiology, while 27 focused on wastewater monitoring. The PRISMA review of the literature revealed that Nordic countries focus on four major WBS objectives of ARB: assessing ARB in the human population, identifying ARB evading wastewater treatment, quantifying removal rates, and evaluating potential ARB evolution during the treatment process. In both clinical and wastewater contexts, the most studied targets were pathogens producing carbapenemase and extended-spectrum beta-lactamase (ESBL), primarily Escherichia coli and Klebsiella spp. However, vancomycin-resistant Enterococcus (VRE) and methicillin-resistant Staphylococcus aureus (MRSA) have received more attention in clinical epidemiology than in wastewater studies, probably due to their lower detection rates in wastewater. Clinical surveillance has mostly used culturing, antibiotic susceptibility testing, and genotyping, but WBS employed PCR-based and metagenomics alongside culture-based techniques. Imported cases resulting from international travel and hospitalization abroad appear to have frequently contributed to the rise in ARB pathogen cases in these countries. The many similarities between the Nordic countries (e.g., knowledge exchange practices, antibiotic usage patterns, and the current ARB landscape) could facilitate collaborative efforts in developing and implementing WBS for ARB in population-level screening.
Collapse
Affiliation(s)
- Ananda Tiwari
- Expert Microbiology Unit, Finnish Institute for Health and Welfare, 70701, Kuopio, Finland.
| | - Adriana Krolicka
- Norwegian Research Centre AS (NORCE), Nygårdstangen, 5838, Bergen, Norway
| | - Tam T Tran
- Norwegian Research Centre AS (NORCE), Nygårdstangen, 5838, Bergen, Norway
| | - Kati Räisänen
- Expert Microbiology Unit, Finnish Institute for Health and Welfare, Helsinki, Finland
| | | | - Odd-Gunnar Wikmark
- Norwegian Research Centre AS (NORCE), Nygårdstangen, 5838, Bergen, Norway; Unit for Environmental Science and Management, North West University, Potchefstroom Campus, Private Bag X6001, Potchefstroom 2520, South Africa
| | - Rolf Lood
- Department of Clinical Sciences Lund, Division of Infection Medicine, Faculty of Medicine, Lund University, Lund, Sweden
| | - Tarja Pitkänen
- Expert Microbiology Unit, Finnish Institute for Health and Welfare, 70701, Kuopio, Finland; Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Finland.
| |
Collapse
|
2
|
Mahmood B, Sárvári KP, Orosz L, Nagy E, Sóki J. Novel and rare β-lactamase genes of Bacteroides fragilis group species: Detection of the genes and characterization of their genetic backgrounds. Anaerobe 2024; 86:102832. [PMID: 38360202 DOI: 10.1016/j.anaerobe.2024.102832] [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: 10/30/2023] [Revised: 02/09/2024] [Accepted: 02/12/2024] [Indexed: 02/17/2024]
Abstract
OBJECTIVES This study screened the prevalence of rare β-lactamase genes in Bacteroides fragilis group strains from clinical specimens and normal microbiota and examined the genetic properties of the strains carrying these genes. METHODS blaHGD1, blaOXA347, cblA, crxA, and pbbA were detected by real-time polymerase chain reaction in collections of Bacteroides strains from clinical (n = 406) and fecal (n = 184) samples. To examine the genetic backgrounds of the samples, end-point PCR, FT-IR, and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry were used. RESULTS All B. uniformis isolates were positive for cblA in both collections. Although crxA was B. xylanisolvens-specific and associated with carbapenem resistance, it was only found in six fecal and three clinical B. xylanisolvens strains. Moreover, the crxA-positive strains were not clonal among B. xylanisolvens (contrary to cfiA in B. fragilis), implicating a rate of mobility or emergence by independent evolutionary events. The Phocaeicola (B.) vulgatus/P. dorei-specific gene blaHGD1 was detected among all P. vulgatus/P. dorei isolates from fecal (n = 36) and clinical (n = 26) samples. No blaOXA347-carrying isolate was found from European collections, but all US samples (n = 6) were positive. For three clinical isolates belonging to B. thetaiotaomicron (n = 2) and B. ovatus (n = 1), pbbA was detected on mobile genetic elements, and pbbA-positive strains displayed non-susceptibility to piperacillin or piperacillin/tazobactam phenotypically. CONCLUSIONS Based on these observations, β-lactamases produced by rare β-lactamase genes in B. fragilis group strains should not be overlooked because they could encode important resistance phenotypes.
Collapse
Affiliation(s)
- Bakhtiyar Mahmood
- Institute of Medical Microbiology, Albert Szent-Györgyi Health Centre and Medical School, University of Szeged, Szeged, Hungary; Department of Biology, University of Garmian, Kalar, Kurdistan Region, Iraq.
| | - Károly Péter Sárvári
- Institute of Medical Microbiology, Albert Szent-Györgyi Health Centre and Medical School, University of Szeged, Szeged, Hungary
| | - Laszló Orosz
- Institute of Medical Microbiology, Albert Szent-Györgyi Health Centre and Medical School, University of Szeged, Szeged, Hungary
| | - Elisabeth Nagy
- Institute of Medical Microbiology, Albert Szent-Györgyi Health Centre and Medical School, University of Szeged, Szeged, Hungary
| | - József Sóki
- Institute of Medical Microbiology, Albert Szent-Györgyi Health Centre and Medical School, University of Szeged, Szeged, Hungary
| |
Collapse
|
3
|
English J, Newberry F, Hoyles L, Patrick S, Stewart L. Genomic analyses of Bacteroides fragilis: subdivisions I and II represent distinct species. J Med Microbiol 2023; 72. [PMID: 37910167 DOI: 10.1099/jmm.0.001768] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2023] Open
Abstract
Introduction. Bacteroides fragilis is a Gram-negative anaerobe that is a member of the human gastrointestinal microbiota and is frequently found as an extra-intestinal opportunistic pathogen. B. fragilis comprises two distinct groups - divisions I and II - characterized by the presence/absence of genes [cepA and ccrA (cfiA), respectively] that confer resistance to β-lactam antibiotics by either serine or metallo-β-lactamase production. No large-scale analyses of publicly available B. fragilis sequence data have been undertaken, and the resistome of the species remains poorly defined.Hypothesis/Gap Statement. Reclassification of divisions I and II B. fragilis as two distinct species has been proposed but additional evidence is required.Aims. To investigate the genomic diversity of GenBank B. fragilis genomes and establish the prevalence of division I and II strains among publicly available B. fragilis genomes, and to generate further evidence to demonstrate that B. fragilis division I and II strains represent distinct genomospecies.Methodology. High-quality (n=377) genomes listed as B. fragilis in GenBank were included in pangenome and functional analyses. Genome data were also subject to resistome profiling using The Comprehensive Antibiotic Resistance Database.Results. Average nucleotide identity and phylogenetic analyses showed B. fragilis divisions I and II represent distinct species: B. fragilis sensu stricto (n=275 genomes) and B. fragilis A (n=102 genomes; Genome Taxonomy Database designation), respectively. Exploration of the pangenome of B. fragilis sensu stricto and B. fragilis A revealed separation of the two species at the core and accessory gene levels.Conclusion. The findings indicate that B. fragilis A, previously referred to as division II B. fragilis, is an individual species and distinct from B. fragilis sensu stricto. The B. fragilis pangenome analysis supported previous genomic, phylogenetic and resistome screening analyses collectively reinforcing that divisions I and II are two separate species. In addition, it was confirmed that differences in the accessory genes of B. fragilis divisions I and II are primarily associated with carbohydrate metabolism and suggest that differences other than antimicrobial resistance could also be used to distinguish between these two species.
Collapse
Affiliation(s)
- Jamie English
- Institute for Global Food Security, School of Biological Sciences, Queen's University, Belfast, UK
| | - Fiona Newberry
- Department of Biosciences, School of Science and Technology, Nottingham Trent University, Nottingham, UK
| | - Lesley Hoyles
- Department of Biosciences, School of Science and Technology, Nottingham Trent University, Nottingham, UK
| | - Sheila Patrick
- Institute for Global Food Security, School of Biological Sciences, Queen's University, Belfast, UK
- Wellcome Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7BL, UK
| | - Linda Stewart
- Institute for Global Food Security, School of Biological Sciences, Queen's University, Belfast, UK
| |
Collapse
|
4
|
Reissier S, Penven M, Guérin F, Cattoir V. Recent Trends in Antimicrobial Resistance among Anaerobic Clinical Isolates. Microorganisms 2023; 11:1474. [PMID: 37374976 DOI: 10.3390/microorganisms11061474] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 05/26/2023] [Accepted: 05/28/2023] [Indexed: 06/29/2023] Open
Abstract
Anaerobic bacteria are normal inhabitants of the human commensal microbiota and play an important role in various human infections. Tedious and time-consuming, antibiotic susceptibility testing is not routinely performed in all clinical microbiology laboratories, despite the increase in antibiotic resistance among clinically relevant anaerobes since the 1990s. β-lactam and metronidazole are the key molecules in the management of anaerobic infections, to the detriment of clindamycin. β-lactam resistance is usually mediated by the production of β-lactamases. Metronidazole resistance remains uncommon, complex, and not fully elucidated, while metronidazole inactivation appears to be a key mechanism. The use of clindamycin, a broad-spectrum anti-anaerobic agent, is becoming problematic due to the increase in resistance rate in all anaerobic bacteria, mainly mediated by Erm-type rRNA methylases. Second-line anti-anaerobes are fluoroquinolones, tetracyclines, chloramphenicol, and linezolid. This review aims to describe the up-to-date evolution of antibiotic resistance, give an overview, and understand the main mechanisms of resistance in a wide range of anaerobes.
Collapse
Affiliation(s)
- Sophie Reissier
- Rennes University Hospital, Department of Clinical Microbiology, F-35033 Rennes, France
- UMR_S1230 BRM, Inserm, University of Rennes, F-35043 Rennes, France
| | - Malo Penven
- Rennes University Hospital, Department of Clinical Microbiology, F-35033 Rennes, France
- UMR_S1230 BRM, Inserm, University of Rennes, F-35043 Rennes, France
| | - François Guérin
- Rennes University Hospital, Department of Clinical Microbiology, F-35033 Rennes, France
- UMR_S1230 BRM, Inserm, University of Rennes, F-35043 Rennes, France
| | - Vincent Cattoir
- Rennes University Hospital, Department of Clinical Microbiology, F-35033 Rennes, France
- UMR_S1230 BRM, Inserm, University of Rennes, F-35043 Rennes, France
- CHU de Rennes, Service de Bactériologie-Hygiène Hospitalière, 2 Rue Henri Le Guilloux, CEDEX 9, F-35033 Rennes, France
| |
Collapse
|
5
|
Sood A, Ray P, Angrup A. Anaerobic Gram-Negative Bacteria: Role as a Reservoir of Antibiotic Resistance. Antibiotics (Basel) 2023; 12:antibiotics12050942. [PMID: 37237845 DOI: 10.3390/antibiotics12050942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 05/08/2023] [Accepted: 05/11/2023] [Indexed: 05/28/2023] Open
Abstract
BACKGROUND Anaerobic Gram-negative bacteria (AGNB) play a significant role as both pathogens and essential members of the human microbiota. Despite their clinical importance, there remains limited understanding regarding their antimicrobial resistance (AMR) patterns. This knowledge gap poses challenges in effectively managing AGNB-associated infections, as empirical treatment approaches may not adequately address the evolving resistance landscape. To bridge this research gap, we conducted a comprehensive study aimed at exploring the role of human AGNB as a reservoir of AMR. This can provide valuable insights for the prevention and management of anaerobic infections. METHODS We studied the prevalence of AMR and AMR determinants conferring resistance to metronidazole (nimE), imipenem (cfiA), piperacillin-tazobactam (cepA), cefoxitin (cfxA), clindamycin (ermF), chloramphenicol (cat) and mobile genetic elements (MGEs) such as cfiAIS and IS1186 associated with the cfiA and nim gene expression. These parameters were studied in Bacteroides spp., Fusobacterium spp., Prevotella spp., Veillonella spp., Sutterella spp., and other clinical AGNB. RESULTS Resistance to metronidazole, clindamycin, imipenem, piperacillin-tazobactam, cefoxitin and chloramphenicol was 29%, 33.5%, 0.5%, 27.5%, 26.5% and 0%, respectively. The presence of resistance genes, viz., nim, ermF, cfiA, cepA, cfxA, was detected in 24%, 33.5%, 10%, 9.5%, 21.5% isolates, respectively. None of the tested isolates showed the presence of a cat gene and MGEs, viz., cfiAIS and IS1186. The highest resistance to all antimicrobial agents was exhibited by Bacteroides spp. The association between resistant phenotypes and genotypes was complete in clindamycin, as all clindamycin-resistant isolates showed the presence of ermF gene, and none of the susceptible strains harbored this gene; similarly, all isolates were chloramphenicol-susceptible and also lacked the cat gene, whereas the association was low among imipenem and piperacillin-tazobactam. Metronidazole and imipenem resistance was seen to be dependent on insertion sequences for the expression of AMR genes. A constrained co-existence of cepA and cfiA gene in B. fragilis species was seen. Based on the absence and presence of the cfiA gene, we divided B. fragilis into two categories, Division I (72.6%) and Division II (27.3%), respectively. CONCLUSION AGNB acts as a reservoir of specific AMR genes, which may pose a threat to other anaerobes due to functional compatibility and acquisition of these genes. Thus, AST-complying standard guidelines must be performed periodically to monitor the local and institutional susceptibility trends, and rational therapeutic strategies must be adopted to direct empirical management.
Collapse
Affiliation(s)
- Anshul Sood
- Department of Medical Microbiology, Post Graduate Institute of Medical Education and Research (PGIMER), Chandigarh 160012, India
| | - Pallab Ray
- Department of Medical Microbiology, Post Graduate Institute of Medical Education and Research (PGIMER), Chandigarh 160012, India
| | - Archana Angrup
- Department of Medical Microbiology, Post Graduate Institute of Medical Education and Research (PGIMER), Chandigarh 160012, India
| |
Collapse
|
6
|
Kierzkowska M, Majewska A, Karłowicz K, Pituch H. Phenotypic and genotypic identification of carbapenem resistance in Bacteroides fragilis clinical strains. Med Microbiol Immunol 2023:10.1007/s00430-023-00765-w. [PMID: 37178261 DOI: 10.1007/s00430-023-00765-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 04/26/2023] [Indexed: 05/15/2023]
Abstract
Bacteroides fragilis is an important etiological agent of serious infections in humans. Rapid methods, readily adaptable to use in medical laboratories, are needed to detect antibiotic resistance and decrease the likelihood of therapy failure. The aim of this study was to determine the prevalence of B. fragilis cfiA-positive isolates. The second purpose was to investigate the carbapenemase activity in B. fragilis strains by Carba NP test. In the study, 5.2% of B. fragilis isolates are phenotypically resistant to meropenem. The cfiA gene was identified in 6.1% of B. fragilis isolates. The MICs of meropenem were significantly higher in cfiA-positive strains. The presence of the cfiA gene along with the IS1186 was detected in one B. fragilis strain which was resistant to meropenem (MIC 1.5 mg/L). The Carba NP test results were positive for all the cfiA-positive strains, including those susceptible to carbapenems based on their MIC values. A review of the literature revealed that the rate of B. fragilis with the cfiA gene varies from 7.6 to 38.9% worldwide. Presented results are in line with the other European studies. Phenotypic testing with the Carba NP test, it seems to be a viable alternative for the cfiA gene detection in B. fragilis isolates. The positive result obtained is of greater clinical importance than the detection of the gene cfiA.
Collapse
Affiliation(s)
- Marta Kierzkowska
- Department of Medical Microbiology, Medical University of Warsaw, Warsaw, Poland
| | - Anna Majewska
- Department of Medical Microbiology, Medical University of Warsaw, Warsaw, Poland.
| | - Konrad Karłowicz
- Department of Medical Microbiology, Medical University of Warsaw, Warsaw, Poland
| | - Hanna Pituch
- Department of Medical Microbiology, Medical University of Warsaw, Warsaw, Poland
| |
Collapse
|
7
|
Hashimoto T, Hashinaga K, Komiya K, Hiramatsu K. Prevalence of antimicrobial resistant genes in Bacteroides spp. isolated in Oita Prefecture, Japan. J Infect Chemother 2023; 29:284-288. [PMID: 36473684 DOI: 10.1016/j.jiac.2022.11.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 10/31/2022] [Accepted: 11/29/2022] [Indexed: 12/11/2022]
Abstract
INTRODUCTION Bacteroides spp. are the most common anaerobic bacteria isolated from the human gastrointestinal tract. Several resistant genes are present in Bacteroides spp. However, most studies have focused on the prevalence of the cfiA gene in Bacteroides fragilis alone. We assessed the susceptibility to antimicrobial agents and the prevalence of cepA, cfiA, cfxA, ermF, nim, and tetQ genes in Bacteroides strains isolated from clinical specimens in our hospital. METHODS We isolated 86 B. fragilis and 58 non-fragilis Bacteroides strains from human clinical specimens collected from January 2011 to November 2021. Resistance against piperacillin (PIPC), cefotaxime (CTX), cefepime (CFPM), meropenem (MEPM), clindamycin, and minocycline was determined. RESULTS The resistant rates of penicillins and cephalosporins in non-fragilis isolates were significantly higher than those in B. fragilis isolates. In B. fragilis isolates, the resistant rates of PIPC, CTX, and CFPM in cfxA-positive isolates were significantly higher than those in cfxA-negative isolates (71% vs. 16%, 77% vs. 19%, and 77% vs. 30%, respectively). Thirteen B. fragilis isolates harbored the cfiA gene, two of which were resistant to MEPM. Six of the 13 cfiA-positive B. fragilis isolates were heterogeneously resistant to MEPM. CONCLUSION It is important to evaluate the use of MEPM as empirical therapy for Bacteroides spp. infections, considering the emergence of carbapenem resistance during treatment, existence of MEPM-resistant strains, and heterogeneous resistance.
Collapse
Affiliation(s)
| | | | - Kosaku Komiya
- Department of Respiratory Medicine and Infectious Diseases, Oita University Faculty of Medicine, Japan
| | | |
Collapse
|
8
|
Tang H, Zhou H, Zhang R. Antibiotic Resistance and Mechanisms of Pathogenic Bacteria in Tubo-Ovarian Abscess. Front Cell Infect Microbiol 2022; 12:958210. [PMID: 35967860 PMCID: PMC9363611 DOI: 10.3389/fcimb.2022.958210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 06/23/2022] [Indexed: 11/13/2022] Open
Abstract
A tubo-ovarian abscess (TOA) is a common type of inflammatory lump in clinical practice. TOA is an important, life-threatening disease, and it has become more common in recent years, posing a major health risk to women. Broad-spectrum antimicrobial agents are necessary to cover the most likely pathogens because the pathogens that cause TOA are polymicrobial. However, the response rate of antibiotic treatment is about 70%, whereas one-third of patients have poor clinical consequences and they require drainage or surgery. Rising antimicrobial resistance serves as a significant reason for the unsatisfactory medical outcomes. It is important to study the antibiotic resistance mechanism of TOA pathogens in solving the problems of multi-drug resistant strains. This paper focuses on the most common pathogenic bacteria isolated from TOA specimens and discusses the emerging trends and epidemiology of resistant Escherichia coli, Bacteroides fragilis, and gram-positive anaerobic cocci. Besides that, new methods that aim to solve the antibiotic resistance of related pathogens are discussed, such as CRISPR, nanoparticles, bacteriophages, antimicrobial peptides, and pathogen-specific monoclonal antibodies. Through this review, we hope to reveal the current situation of antibiotic resistance of common TOA pathogens, relevant mechanisms, and possible antibacterial strategies, providing references for the clinical treatment of drug-resistant pathogens.
Collapse
Affiliation(s)
- Huanna Tang
- Women’s Reproductive Health Research Key Laboratory of Zhejiang Province and Department of Reproductive Endocrinology, Women’s Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Hui Zhou
- Department of Infectious Disease, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- *Correspondence: Hui Zhou, ; Runju Zhang,
| | - Runju Zhang
- Women’s Reproductive Health Research Key Laboratory of Zhejiang Province and Department of Reproductive Endocrinology, Women’s Hospital, Zhejiang University School of Medicine, Hangzhou, China
- *Correspondence: Hui Zhou, ; Runju Zhang,
| |
Collapse
|
9
|
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.
Collapse
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.
| |
Collapse
|
10
|
Comparative Genomics of Bacteroides fragilis Group Isolates Reveals Species-Dependent Resistance Mechanisms and Validates Clinical Tools for Resistance Prediction. mBio 2022; 13:e0360321. [PMID: 35038926 PMCID: PMC8764542 DOI: 10.1128/mbio.03603-21] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Bacteroides fragilis group (BFG) are the most frequently recovered anaerobic bacteria from human infections, and resistance to frontline antibiotics is emerging. In the absence of routine antimicrobial susceptibility testing (AST) for BFG in most clinical settings, we assessed the utility of clinical and modern genomics tools to determine BFG species-level identification and resistance patterns. A total of 174 BFG clinical isolates supplemented with 20 archived carbapenem-resistant B. fragilis sensu stricto (BFSS) isolates underwent antimicrobial susceptibility testing, MALDI-ToF mass-spectrometry, and whole-genome sequencing (WGS). Bruker BioTyper and VITEK-MS MALDI-ToF systems demonstrated accurate species-level identifications (91% and 90% agreement, respectively) compared to average nucleotide identity (ANI) analysis of WGS data. Distinct β-lactamase gene profiles were observed between BFSS and non-fragilis Bacteroides species, with significantly higher MICs to piperacillin-tazobactam in B. vulgatus and B. thetaiotaomicron relative to BFSS (P ≤ 0.034). We also uncovered phylogenetic diversity at the genomospecies level between division I and division II BFSS (ANI <0.95) and demonstrate that division II BFSS strains harbor an increased capacity to achieve carbapenem resistance through chromosomal activation of the CfiA carbapenemase. Finally, we report that CfiA detection by the Bruker BioTyper Subtyping Module accurately detected carbapenem resistance in BFSS with positive and negative percent agreement of 94%/90% and 95%/95% compared to ertapenem and meropenem susceptibility, respectively. These comparative analyses indicate that resistance mechanisms are distinct at both the phenotypic and genomic level across species within the BFG and that modern MALDI-ToF identification systems can be used for accurate species-level identification and resistance prediction of the BFG. IMPORTANCE Anaerobic infections present unique challenges in terms of detecting and identifying the etiologic agent and selecting the optimal antimicrobial therapy. Antimicrobial resistance is increasing in anaerobic pathogens, and it is critical to understand the prevalence and mechanisms of resistance to commonly prescribed antimicrobial therapies. This study uses comparative genomics to validate clinical tools for species-level identification and phenotypic resistance prediction in 194 isolates of Bacteroides fragilis group (BFG) bacteria, which represent the most commonly isolated organisms among anaerobic infections. We demonstrate species-specific patterns in antimicrobial resistance and validate new strategies for species-level organism identification and phenotypic resistance prediction in a routine clinical laboratory setting. These findings expand our understanding and management of anaerobic infections and justify further investigations into the molecular basis for species-specific resistance patterns observed within this study.
Collapse
|
11
|
Jasemi S, Emaneini M, Ahmadinejad Z, Fazeli MS, Sechi LA, Sadeghpour Heravi F, Feizabadi MM. Antibiotic resistance pattern of Bacteroides fragilis isolated from clinical and colorectal specimens. Ann Clin Microbiol Antimicrob 2021; 20:27. [PMID: 33892721 PMCID: PMC8066845 DOI: 10.1186/s12941-021-00435-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 04/16/2021] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Bacteroides fragilis is a part of the normal gastrointestinal flora, but it is also the most common anaerobic bacteria causing the infection. It is highly resistant to antibiotics and contains abundant antibiotic resistance mechanisms. METHODS The antibiotic resistance pattern of 78 isolates of B. fragilis (22 strains from clinical samples and 56 strains from the colorectal tissue) was investigated using agar dilution method. The gene encoding Bacteroides fargilis toxin bft, and antibiotic resistance genes were targeted by PCR assay. RESULTS The highest rate of resistance was observed for penicillin G (100%) followed by tetracycline (74.4%), clindamycin (41%) and cefoxitin (38.5%). Only a single isolate showed resistance to imipenem which contained cfiA and IS1186 genes. All isolates were susceptible to metronidazole. Accordingly, tetQ (87.2%), cepA (73.1%) and ermF (64.1%) were the most abundant antibiotic-resistant genes identified in this study. MIC values for penicillin, cefoxitin and clindamycin were significantly different among isolates with the cepA, cfxA and ermF in compare with those lacking such genes. In addition, 22.7 and 17.8% of clinical and GIT isolates had the bft gene, respectively. CONCLUSIONS The finding of this study shows that metronidazole is highly in vitro active agent against all of B. fragilis isolates and remain the first-line antimicrobial for empirical therapy.
Collapse
Affiliation(s)
- Seyedesomaye Jasemi
- Department of Microbiology, School of Medicine, Tehran University of Medical Sciences, Poursina Street, Engelab-e-Eslami Avenue, Tehran, Iran
| | - Mohammad Emaneini
- Department of Microbiology, School of Medicine, Tehran University of Medical Sciences, Poursina Street, Engelab-e-Eslami Avenue, Tehran, Iran
| | - Zahra Ahmadinejad
- Department of Infectious Diseases, Imam Khomeini Hospital Complex, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad Sadegh Fazeli
- Department of Surgery, Imam Khomeini Hospital Complex, Tehran University of Medical Sciences, Tehran, Iran
| | - Leonardo A Sechi
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Fatemah Sadeghpour Heravi
- Surgical Infection Research Group, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, Australia
| | - Mohammad Mehdi Feizabadi
- Department of Microbiology, School of Medicine, Tehran University of Medical Sciences, Poursina Street, Engelab-e-Eslami Avenue, Tehran, Iran. .,Department of Biomedical Sciences, University of Sassari, Sassari, Italy.
| |
Collapse
|
12
|
Rentenaar RJ, Bovo-Heijmans B, Diggle J, Fluit AC, Wootton M. False amoxicillin/clavulanic acid susceptibility in Bacteroides fragilis using gradient strip tests. Anaerobe 2021; 69:102358. [PMID: 33741507 DOI: 10.1016/j.anaerobe.2021.102358] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 03/01/2021] [Accepted: 03/12/2021] [Indexed: 12/27/2022]
Abstract
BACKGROUND Repeatedly, too low MIC results were obtained in Bacteroides fragilis quality assessment strains, using gradient strip tests with a ratio of amoxicillin:clavulanic acid of 2:1. We aimed to find the most accurate available gradient strip tests for susceptibility testing of amoxicillin/clavulanic acid in B. fragilis in comparison with agar dilution with EUCAST methodology and breakpoints. METHODS Twenty-seven clinical B. fragilis isolates were investigated using gold standard EUCAST amoxicillin/clavulanic acid agar dilution (fixed clavulanic acid concentration at 2 mg/L, with increasing amoxicillin concentrations) as well as three commercial gradient strip tests: XL (ratio), AUG (ratio) or AMC (fixed concentration). RESULTS Using agar dilution (fixed concentration), 19 isolates were susceptible, 1 isolate was susceptible increased exposure (I) and 7 isolates were resistant. Categorical agreement of the gradient strip tests with agar dilution (fixed concentration) was 70% for XL (ratio), 71% for AUG (ratio) and 89% for AMC (fixed concentration). Very major error rates in comparison with agar dilution (fixed concentration) were 100%, 0%, and 0%, respectively. CONCLUSIONS EUCAST breakpoint usage in amoxicillin/clavulanic acid susceptibility tests for B. fragilis should be accompanied by EUCAST methodology. When using alternative methods such as gradient strip tests, a higher degree of alignment with EUCAST methodology, such as using fixed clavulanic acid concentrations, improves precision.
Collapse
Affiliation(s)
- Rob J Rentenaar
- Department of Medical Microbiology, University Medical Center Utrecht, Internal mail no G.04.614, P.O. Box 85500, 3508 GA, Utrecht, The Netherlands.
| | - Bianca Bovo-Heijmans
- Department of Medical Microbiology, University Medical Center Utrecht, Internal mail no G.04.614, P.O. Box 85500, 3508 GA, Utrecht, The Netherlands
| | - Joanna Diggle
- Specialist Antimicrobial Chemotherapy Unit, Microbiology Cardiff, Public Health Wales, University Hospital of Wales, Heath Park, CARDIFF CF14 4XW, UK
| | - Ad C Fluit
- Department of Medical Microbiology, University Medical Center Utrecht, Internal mail no G.04.614, P.O. Box 85500, 3508 GA, Utrecht, The Netherlands
| | - Mandy Wootton
- Specialist Antimicrobial Chemotherapy Unit, Microbiology Cardiff, Public Health Wales, University Hospital of Wales, Heath Park, CARDIFF CF14 4XW, UK
| |
Collapse
|
13
|
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.
Collapse
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
| |
Collapse
|
14
|
Welker M, van Belkum A. One System for All: Is Mass Spectrometry a Future Alternative for Conventional Antibiotic Susceptibility Testing? Front Microbiol 2019; 10:2711. [PMID: 31849870 PMCID: PMC6901965 DOI: 10.3389/fmicb.2019.02711] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 11/08/2019] [Indexed: 12/20/2022] Open
Abstract
The two main pillars of clinical microbiological diagnostics are the identification of potentially pathogenic microorganisms from patient samples and the testing for antibiotic susceptibility (AST) to allow efficient treatment with active antimicrobial agents. While routine microbial species identification is increasingly performed with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), routine AST still largely relies on conventional and molecular techniques such as broth microdilution or disk and gradient diffusion tests, PCR and automated variants thereof. However, shortly after the introduction of MALDI-TOF MS based routine identification, first attempts to perform AST on the same instruments were reported. Today, a number of different approaches to perform AST with MALDI-TOF MS and other MS techniques have been proposed, some restricted to particular microbial taxa and resistance mechanisms while others being more generic. Further, while some of the methods are in a stage of proof of principles, others are already commercialized. In this review we discuss the different principal approaches of mass spectrometry based AST and evaluate the advantages and disadvantages compared to conventional and molecular techniques. At present, the possibility that MS will soon become a routine tool for AST seems unlikely – still, the same was true for routine microbial identification a mere 15 years ago.
Collapse
Affiliation(s)
- Martin Welker
- Microbiology Research Unit, BioMérieux SA, La Balme-les-Grottes, France
| | - Alex van Belkum
- Microbiology Research Unit, BioMérieux SA, La Balme-les-Grottes, France
| |
Collapse
|
15
|
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.
Collapse
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
| |
Collapse
|
16
|
Veloo A, Baas W, Haan F, Coco J, Rossen J. Prevalence of antimicrobial resistance genes in Bacteroides spp. and Prevotella spp. Dutch clinical isolates. Clin Microbiol Infect 2019; 25:1156.e9-1156.e13. [DOI: 10.1016/j.cmi.2019.02.017] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 02/06/2019] [Accepted: 02/15/2019] [Indexed: 10/27/2022]
|
17
|
Kostrzewa M, Nagy E, Schröttner P, Pranada AB. How MALDI-TOF mass spectrometry can aid the diagnosis of hard-to-identify pathogenic bacteria - the rare and the unknown. Expert Rev Mol Diagn 2019; 19:667-682. [PMID: 31303071 DOI: 10.1080/14737159.2019.1643238] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Introduction: Ten years after its introduction into clinical microbiology, MALDI-TOF mass spectrometry has become the standard routine identification tool for bacteria in most laboratories. The technology has accelerated analyses and improved the quality of results. The greatest significance has been observed for bacteria that were challenging to be identified by traditional methods. Areas covered: We searched in existing literature (Pubmed) for reports how MALDI-TOF MS has contributed to identification of rare and unknown bacteria from different groups. We describe how this has improved the diagnostics in different groups of bacteria. Reference patterns for strains which yet cannot be assigned to a known species even enable the search for related bacteria in studies as well as in routine diagnostics. MALDI-TOF MS can help to discover and investigate new species and their clinical relevance. It is a powerful tool in the elucidation of the bacterial composition of complex microbiota in culturomics studies. Expert opinion: MALDI-TOF MS has improved the diagnosis of bacterial infections. It also enables knowledge generation for prospective diagnostics. The term 'hard-to-identify' might only be rarely attributed to bacteria in the future. Novel applications are being developed, e.g. subspecies differentiation, typing, and antibiotic resistance testing which may further contribute to improved microbial diagnostics.
Collapse
Affiliation(s)
- Markus Kostrzewa
- Bioanalytical Development, Bruker Daltonik GmbH , Bremen , Germany
| | - Elisabeth Nagy
- Institute of Clinical Microbiology, University of Szeged , Szeged , Hungary
| | - Percy Schröttner
- Institut für Medizinische Mikrobiologie und Hygiene, Technische Universität Dresden , Dresden , Germany
| | - Arthur B Pranada
- Department of Medical Microbiology, MVZ Dr. Eberhard & Partner Dortmund (ÜBAG) , Dortmund , Germany
| |
Collapse
|
18
|
Jeverica S, Sóki J, Premru MM, Nagy E, Papst L. High prevalence of division II (cfiA positive) isolates among blood stream Bacteroides fragilis in Slovenia as determined by MALDI-TOF MS. Anaerobe 2019; 58:30-34. [PMID: 30716401 DOI: 10.1016/j.anaerobe.2019.01.011] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 01/31/2019] [Accepted: 01/31/2019] [Indexed: 12/12/2022]
Abstract
Bacteroides fragilis can be classified into division I (cfiA negative) and division II (cfiA positive) isolates. Division II isolates have a silent chromosomal carbapenemase gene (cfiA) that can become overexpressed by an insertion of a mobile genetic element and thus develop a phenotypic resistance to carbapenems. Aims of our study were (i) to determine the prevalence of B. fragilis division II (cfiA positive) isolates among blood stream and non-blood stream isolates from two major Slovenian tertiary-care hospitals and (ii) to assess its influence on phenotypic resistance to imipenem. Consecutive non-duplicate B. fragilis isolates from blood stream and non-blood stream specimens were included in the analysis from 2015 to 2017 period. Data from laboratory information system were matched with mass spectra obtained with Microflex LT instrument and MALDI Biotyper 3.1 software (Bruker Daltonik, Bremen, Germany). All mass spectra were reanalyzed using Bruker taxonomy library. Spectra with a log(score) > 2.0 were further analyzed with cfiA library that separates B. fragilis division I and II isolates based on a log(score) value difference of >0.3. Minimal inhibitory concentrations (MICs) for imipenem were determined with Etest (bioMérieux, Marcy l'Étoile, France), using supplemented Brucella agar and EUCAST breakpoints (S ≤ 2 mg/L, R > 8 mg/L). Altogether 623 consecutive B. fragilis isolates were included in the analysis; 47 (7.5%) were isolated from blood stream and 576 (92.5%) from non-blood stream specimens. Among all study isolates, 51 (8.2%) proved to belong to division II (cfiA positive). The proportions of division II isolates among blood stream and non-blood stream isolates were 14.9% and 7.6%, respectively (p = 0.081, ns). In total, 1.3% (n = 8) were non-susceptible to imipenem (MIC >2 mg/L); 4.3% (n = 2) among blood stream and 1% (n = 6) among non-blood stream isolates. All imipenem resistant isolates belonged to division II. Modal MICs (MIC range) were 0.064 mg/L (0.016 mg/L-2 mg/L) and 0.125 mg/L (0.064 mg/L-≥32 mg/L) for division I and II isolates, respectively.
Collapse
Affiliation(s)
- Samo Jeverica
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia.
| | - József Sóki
- Institute of Clinical Microbiology, University of Szeged, Szeged, Hungary
| | - Manica Mueller Premru
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Elizabeth Nagy
- Institute of Clinical Microbiology, University of Szeged, Szeged, Hungary
| | - Lea Papst
- Department of Infectious Diseases, University Medical Centre Ljubljana, Ljubljana, Slovenia
| |
Collapse
|
19
|
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]
|
20
|
|
21
|
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]
|
22
|
Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry for the Rapid Detection of Antimicrobial Resistance Mechanisms and Beyond. Clin Microbiol Rev 2018; 32:32/1/e00037-18. [PMID: 30487165 DOI: 10.1128/cmr.00037-18] [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] [Indexed: 12/11/2022] Open
Abstract
Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has been successfully applied in recent years for first-line identification of pathogens in clinical microbiology because it is simple to use, rapid, and accurate and has economic benefits in hospital management. The range of clinical applications of MALDI-TOF MS for bacterial isolates is increasing constantly, from species identification to the two most promising applications in the near future: detection of antimicrobial resistance and strain typing for epidemiological studies. The aim of this review is to outline the contribution of previous MALDI-TOF MS studies in relation to detection of antimicrobial resistance and to discuss potential future challenges in this field. Three main approaches are ready (or almost ready) for clinical use, including the detection of antibiotic modifications due to the enzymatic activity of bacteria, the detection of antimicrobial resistance by analysis of the peak patterns of bacteria or mass peak profiles, and the detection of resistance by semiquantification of bacterial growth in the presence of a given antibiotic. This review provides an expert guide for MALDI-TOF MS users to new approaches in the field of antimicrobial resistance detection, especially possible applications as a routine diagnostic tool in microbiology laboratories.
Collapse
|
23
|
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.
Collapse
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
| |
Collapse
|
24
|
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]
|