cfiA Gene Research Articles

Co-occurrence of the cephalosporinase cepA and carbapenemase cfiA genes in a Bacteroides fragilis division II strain, an unexpected finding.

Bacteroides fragilis, an anaerobic gut bacterium and opportunistic pathogen, comprises two genetically divergent groups (or divisions) at the species level. Differences exist both in the core and accessory genomes and the beta-lactamase genes, with the cephalosporinase gene cepA represented only in division I and the carbapenemase gene cfiA only in division II. Multidrug resistance in a clinical B. fragilis strain was examined by whole-genome sequencing. Strain CNM20200260 carried the antimicrobial resistance genes cepA, cfiA2, ant(6'), erm(F), mef(En2), est(T), tet(Q) and cat(A), along with 82-Phe mutation in gyrA (together with 47 amino acid changes in gyrA/B and parC/parE). bexA/B and other efflux pump genes were also observed. None of the detected insertion sequences was located upstream of cfiA2. The genome-based taxonomy coefficients (average nucleotide identity, DNA-DNA hybridization similarity and difference in genomic G + C%) with respect to genomes of the strains of B. fragilis division II and the novel species Bacteroides hominis (both cfiA-positive) met the criteria for CNM20200260 to belong to either species (>95%, >70% and <1%, respectively). No such similarity was seen with type strain NCTC 9343 or the representative genome FDAARGOS 1225 of B. fragilis (division I, cfiA-negative). Strain CNM20200260 harboured four out of nine Kyoto Encyclopedia of Genes and Genomes orthologues defined for division I and one of two defined for division II. This is the first description of the co-occurrence of cepA and cfiA in a Bacteroides strain, confirming the complexity of the taxonomy of this species.

Antimicrobial susceptibility profile of clinically relevant Bacteroides, Phocaeicola, Parabacteroides and Prevotella species, isolated by eight laboratories in the Netherlands.

Recently, reports on antimicrobial-resistant Bacteroides and Prevotella isolates have increased in the Netherlands. This urged the need for a surveillance study on the antimicrobial susceptibility profile of Bacteroides, Phocaeicola, Parabacteroides and Prevotella isolates consecutively isolated from human clinical specimens at eight different Dutch laboratories. Each laboratory collected 20-25 Bacteroides (including Phocaeicola and Parabacteroides) and 10-15 Prevotella isolates for 3 months. At the national reference laboratory, the MICs of amoxicillin, amoxicillin/clavulanic acid, piperacillin/tazobactam, meropenem, imipenem, metronidazole, clindamycin, tetracycline and moxifloxacin were determined using agar dilution. Isolates with a high MIC of metronidazole or a carbapenem, or harbouring cfiA, were subjected to WGS. Bacteroides thetaiotaomicron/faecis isolates had the highest MIC90 values, whereas Bacteroides fragilis had the lowest MIC90 values for amoxicillin/clavulanic acid, piperacillin/tazobactam, meropenem, imipenem and moxifloxacin. The antimicrobial profiles of the different Prevotella species were similar, except for amoxicillin, for which the MIC50 ranged from 0.125 to 16 mg/L for Prevotella bivia and Prevotella buccae, respectively. Three isolates with high metronidazole MICs were sequenced, of which one Bacteroides thetaiotaomicron isolate harboured a plasmid-located nimE gene and a Prevotella melaninogenica isolate harboured a nimA gene chromosomally.Five Bacteroides isolates harboured a cfiA gene and three had an IS element upstream, resulting in high MICs of carbapenems. The other two isolates harboured no IS element upstream of the cfiA gene and had low MICs of carbapenems. Variations in resistance between species were observed. To combat emerging resistance in anaerobes, monitoring resistance and conducting surveillance are essential.

Bacteroides fragilis бактериясының карбапенемге төзімділіктің молекулалық механизмдер

Carbapenems are generally the most successful group of antibacterial drugs due to the combination of a wide spectrum of activity, rapid bactericidal effect, greater potential for the selection of resistant strains and resistance compared to other classes of antibacterial drugs. Carbapenems are potent antimicrobial agents that effective against a wide range of bacteria, including both gram-positive and gram-negative types. Bacteroides fragilis is one of the important and frequently isolated bacteria in clinical laboratories for mono- and polymicrobial infections. Bacteroides fragilis is also resistant to macrolides, beta-lactams, metronidazole, and some newer fluoroquinolones. Carbapenem resistance is considered a rapidly growing problem due to overuse of the drug in therapy. Molecular mechanisms of carbapenem resistance in bacteria involve several factors. The first mechanism is associated with the development of multidrug resistance in microorganisms through the export of drugs via efflux systems. This process enables bacteria to avoid the negative effects of antibiotics. The second mechanism involves the synthesis of beta-lactamases, which is a key factor in the resistance of Bacteroides fragilis to beta-lactam compounds, including carbapenems. These enzymes are capable of hydrolyzing the beta-lactam ring of antibiotics, rendering them inactive. The third mechanism involves changes in the structure of penicillin-binding proteins (PBPs), which are the target sites for carbapenems. Mutations in genes encoding PBPs can lead to decreased affinity of carbapenems to these proteins, making them less sensitive to the antibiotic. The cfiA gene plays an important role in carbapenem resistance, especially in B. fragilis. It encodes a protein that confers resistance to carbapenems and other beta-lactam antibiotics. This gene can be horizontally transferred between different bacteria, increasing the risk of resistance spreading. Understanding the mechanism of antimicrobial resistance is important to avoid pitfalls when selecting alternative antimicrobials for the treatment and prevention of severe infections. This article examines several mechanisms that influence the resistance of B. fragilis strains to carbapenems.

First Report of Antibiotic Resistance Markers cfiA and nim Among Bacteroides fragilis Group Strains in Ecuadorian Patients.

In recent years, increasing resistance of Bacteroides fragilis to several antibiotics has been reported in different countries. The aim of this study was to evaluate the antibiotic resistance profiles of Bacteroides spp. isolated from clinical samples by phenotypic and molecular methods. A total of 40 nonrepetitive isolates of the B. fragilis group were studied from 2018 to 2019. The species was identified by API 20A system. The minimum inhibitory concentrations (MICs) were determined by Sensititre anaerobe MIC plate. The presence of the nim and cfiA genes was checked by conventional PCR. The association between genes and insertion sequence (IS) was performed by whole genome sequencing. Eleven isolates were categorized as metronidazole-resistant and only 2 isolates harbored the nim gene. Five isolates were imipenem-resistant, but cfiA gene was detected in two isolates. cfiA gene was closely related to the cfiA-4 allele and associated with IS614B. The nim gene was not related to any nim gene type and was considered a new variant named nimL. IS612 was found upstream of nimL gene. In view of the scarcity of data on B. fragilis, there is a need to surveil antibiotic resistance levels and molecular mechanisms to implement better antimicrobial therapies against this important group of bacteria.

Phenotypic and genotypic identification of carbapenem resistance in Bacteroides fragilis clinical strains

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.

Can beta-lactamase resistance genes in anaerobic Gram-negative gut bacteria transfer to gut aerobes?

The study was conceived with the hypothesis that human aerobic gut flora could act as a reservoir of ß-lactamases and contribute to the emergence of ß-lactam resistance by transferring ß-lactamase genes to resident anaerobes. Thus, we studied the repertoire of ß-lactam resistance determinants (ß-lactamases associated with aerobes and anaerobes) in Gram-negative anaerobes. The phenotypic resistance against ß-lactams and the presence of aerobic and anaerobic ß-lactamases were tested in Gram-negative anaerobic isolates (n = 200) by agar dilution method and targeted PCR, respectively. In addition, whole-genome sequencing (WGS) was used to study the ß-lactam resistance determinants in 4/200 multi-drug resistant (MDR) strains. The resistance to ß-lactams was as follows: imipenem (0.5%), cefoxitin (26.5%), and piperacillin-tazobactam (27.5%). None of the isolates showed the presence of ß-lactamases found in aerobic microorganisms. The presence of anaerobic ß-lactamase genes viz. cfiA, cepA, cfxA, cfiAIS [the intact segment containing cfiA gene (350 bp) and upstream IS elements (1.6-1.7 kb)] was detected in 10%, 9.5%, 21.5%, and 0% isolates, respectively. The WGS data showed the presence of cfiA, cfiA4, cfxA, cfxA2, cfxA3, cfxA4, cfxA5 in MDR strains. The study showed a distinct dichotomy in repertoires of ß-lactamases between aerobes and anaerobes.

Phenotypic and Genotypic Correlation of Antimicrobial Susceptibility of Bacteroides fragilis: Lessons Learnt.

Background Bacteroides fragilis is an opportunistic pathogen causing severe infections, including bacteremia. There have been increased reports of antimicrobial resistance in B. fragilis. However, phenotypic testing of susceptibility is time consuming and not cost effective for anaerobes. The present study investigates the correlation of phenotypic susceptibility with genotypic markers; to determine if these could be considered for deciding empirical therapy for B. fragilis. Material and methods Bacteroides fragilis isolates from various clinical samples including exudates, tissue, and body fluids were collected between November 2018 and January 2020 in the Department of Clinical Microbiology, Christian Medical College (CMC) Vellore. Species identification was done by MatrixAssistedLaserDesorptionIonization time of flight mass spectrometry (MALDI TOF) according to the manufacturer's instructions. A total number of 51 B. fragilis isolates were tested against metronidazole, clindamycin, piperacillin/tazobactam, and meropenem phenotypically by agar dilution method using Clinical & Laboratory Standards Institute (CLSI) 2019 guidelines and minimum inhibitory concentrations (MIC) were interpretated. The genotypic markers for antimicrobial resistance genes (nim, emrF, and cfiA) were studied by polymerase chain reaction (PCR) assay as per the standard protocol on all isolates to detect resistance genes. Results B. fragilis isolates in this study expressed 45%, 41%, and 16% phenotypic resistance to clindamycin, metronidazole, and meropenem, respectively, with least resistance topiperacillin/tazobactam (6%). Among the metronidazole resistant isolates, 52% harbored nim gene. Nim gene was also present in 76% (23/30) of the metronidazole susceptible isolates. Similarly, cfiA was present in all eight meropenem resistant isolates in addition to 22% (9/41) of the susceptible isolates. All cfiA negative isolates were phenotypically susceptible. Interestingly, 74% (17/23) of the clindamycin resistant isolates were positive for ermF. Conclusions Detection of a limited set of genes does not always correlate with phenotypic resistance to metronidazole and clindamycindue to the reported influence of insertion sequence (IS) elements, efflux, and other genetic determinants. Certainly, the absence of the cfiA gene can be employed to rule out meropenem resistance. However, redundant use of antibiotics such as meropenem along with metronidazole could be avoided for B. fragilis, which might otherwise elevate meropenem resistance. Recommendation of metronidazole requires prior phenotypic testing due to the reported 41% resistance.

High prevalence of cfiA positive Bacteroides fragilis isolates collected at a teaching hospital in Hohhot, China

Objectives: Carbapenem-resistant Bacteroides fragilis has emerged globally and cfiA is the key underlying factor. However, the prevalence of cfiA-positive carbapenem-resistant B. fragilis varies among countries. Therefore, we investigated the prevalence of cfiA-positive B. fragilis clinical isolates in a tertiary hospital in China.Methods: Carbapenem-resistant cfiA-positive B. fragilis isolates were identified using polymerase chain reaction. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI–TOF MS) was used to identify the characteristic mass spectra of cfiA-positive B. fragilis.Results: The prevalence of cfiA among 153 B. fragilis isolates was 22.2% (34/153), when 20.6% (7/34) cfiA-positive B. fragilis strains were isolated from pediatric patients. Twenty-one carbapenem-resistant B. fragilis isolates were identified and were all positive with cfiA gene. Two characteristic peaks (4825 and 9642 Da) were identified using MALDI–TOF MS, and the sensitivity, specificity, and both the positive and negative predictive values of these two peaks were 100%. A new peak shift from 9627 Da for cfiA-negative isolates to 9642 Da for cfiA-positive isolates was observed.Conclusions: A high prevalence of cfiA was observed among B.fragilis isolates in this study, especially those isolated from pediatric patients. Characteristic MS spectra can accurately discriminate cfiA-positive and -negative B. fragilis isolates and can contribute to the rapid screening of cfiA-positive B. fragilis isolates in clinical laboratories.

Prevalence of antimicrobial resistant genes in Bacteroides spp. isolated in Oita Prefecture, Japan

IntroductionBacteroides 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. MethodsWe 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. ResultsThe 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. ConclusionIt 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.

An upgraded version of carbapenem inactivation method to detect Bacteroides fragilis carbapenemase

An increase of carbapenemase-producing Bacteroides fragilis infections is observed. To detect such a resistance in B. fragilis, several tests exist that are expensive or show poor sensitivity and specificity. Therefore, we upgraded the Anaerobic Carbapenem Inactivation Method (Ana-CIM) to easily screen for carbapenemase-producing B. fragilis. The presence of carbapenemase cfiA gene was identified in 50 B. fragilis isolates by PCR. We modified the Ana-CIM by (1) increasing the bacterial inoculum, and (2) measuring the differences in diameter between the negative control and the testing disc. We correctly classified the cfiA-negative and positive isolates and could define a cut-off of positivity at 2 mm. Our modified Ana-CIM allowed to correctly discriminate the 31 cfiA-positive with meropenem MICs ranging from 1 to > 32 µg/mL. We anticipate that our modified Ana-CIM could be used in most clinical laboratories to easily screen for carbapenemase-producing B. fragilis, even at low levels.

Comprehensive investigation of antibiotic resistance gene content in cfiA-harboring Bacteroides fragilis isolates of human and animal origins by whole genome sequencing

IntroductionThe emergence of multidrug resistance in Bacteroides fragilis, especially the phylogenetic lineage carrying the carbapenemase gene cfiA, represents an increasing threat to human health. However, knowledge on the diversity of the multidrug-resistant strains and the genetic elements carrying the antibiotic resistance genes (ARGs) remains limited. AimThe objective of the study was to describe the resistome in cfiA-positive B. fragilis. MethodsA collection of cfiA-positive B. fragilis from diverse human (8 bacteremias, 15 wound infections) and animal (2 chickens, 2 pigs, 6 dogs, 3 cats) sources in Hong Kong, 2015–2017 was analysed by whole genome sequencing. ResultsIn the 36 isolates, 13 distinct ARGs (total number 83, median 2, range 0–7 per isolate) other than cfiA were detected. ARGs encoding resistance to aminoglycosides, β-lactams, macrolides, sulphonamides and tetracyclines were carried by CTn341-like, CTnHyb-like, Tn5220-like, Tn4555-like and Tn613-like transposons and were detected in phylogenetically diverse isolates of different host sources. Only few ARGs encoding resistance to metronidazole and tetracyclines were localized on plasmids. In two chicken isolates, a novel transposon (designated as Tn6994) was found to be involved in the dissemination of multiple ARGs mediating resistance to multiple antibiotics, including metronidazole and linezolid that are critically important for treatment of anaerobic infections. In mating experiments, Tn6994 and the associated phenotypic resistance could be transferred to Bacteroides nordii recipient. ConclusionThis study illustrates the importance of transposons in the dissemination of ARGs in the cfiA-positive division of B. fragilis. One Health approach is necessary to track the dissemination of ARGs.

Rapid detection and surveillance of cfiA-positive Bacteroides fragilis using matrix-assisted laser desorption ionization time-of-flight mass spectrometry

ObjectivesTo perform surveillance of cfiA-positive Bacteroides fragilis using new subtyping software module, MALDI Biotyper Subtyping Module (MBT Subtyping Module), on MALDI-TOF MS system, and to evaluate the detection ability of the module. MethodscfiA-positive strains were presumed using the module against B. fragilis isolated between 2006 and 2019. The cfiA gene was confirmed using PCR. In cfiA-positive B. fragilis, the insertion sequence (IS) elements were examined and the MBT STAR-BL assay was performed to examine meropenem hydrolysis activity. ResultsOf the 396 B. fragilis strains included, the MBT Subtyping Module detected 33 presumptive cfiA-positive strains (8.3%), of which 32 harbored the cfiA gene. The sensitivity and specificity of the MBT Subtyping Module for detecting cfiA-positive B. fragilis were 100.0% and 99.7%, respectively. Of the 32 strains harboring the cfiA gene, seven strains possessed IS elements, which were thought to induce high cfiA expression. Meropenem hydrolysis was detected in all seven strains that were positive for both cfiA and IS elements, and they exhibited resistance to meropenem and imipenem. The overall non-susceptibility rates to meropenem and imipenem were 84.8% and 36.4%, respectively, in the 33 presumptive cfiA-positive strains. ConclusionThe MBT Subtyping Module can detect cfiA-positive B. fragilis rapidly and accurately, supporting its use for surveillance of cfiA-positive B. fragilis in clinical settings.

Phenotypic and genotypic antimicrobial resistance in clinical anaerobic isolates from India.

BackgroundAntimicrobial resistance (AMR) in anaerobes remains a neglected field. The laborious procedures, non-compliance with the standard methodology and differences in interpretive breakpoints add variation in resistance data.ObjectivesTo assess the phenotypic and genotypic resistance among clinically important anaerobes to six antibiotics frequently used as empirical therapy for anaerobic infections.MethodsA total of 150 anaerobic isolates were recovered from clinical specimens. The antimicrobial susceptibility was determined by the breakpoint agar dilution method as per CLSI guidelines. The presence of genes encoding resistance to metronidazole (nim gene), imipenem (cfiA gene) and mobilizable insertion sequence (IS) elements was detected to comprehend their association with phenotypic resistance.ResultsThis is a first study of its kind from the Indian subcontinent looking at the AMR and associated genes in anaerobes. Resistance to metronidazole, clindamycin, imipenem, piperacillin/tazobactam and cefoxitin was 32.6%, 42.6%, 0.6%, 38% and 35.3%, respectively. No resistance was observed to chloramphenicol. The nim gene was detected in 24.6% of isolates, of which 70.2% were resistant by phenotype. On sequencing, the PCR products of six random nim genes showed a close similarity to nimE of Bacteroides fragilis with 99% nucleotide and 100% amino acid sequence similarity. The cfiA gene, associated with imipenem resistance, was detected in 16% of isolates.ConclusionsThe possibility of isolates carrying AMR genes to become resistant to antibiotics by acquisition of IS elements mandates attention to periodically monitor the resistance patterns and geographic distribution of these genes and IS elements to understand the trends of AMR in anaerobes.

Frequency and associated factors for carbapenem-non-susceptible Bacteroides fragilis group bacteria colonization in hospitalized patients: Case control study in a university hospital in Turkey

PurpuseThe carbapenem-resistant Bacteroides fragilis group (CR-BFG) bacteria have been reported in several countries recently with increasing global attention. The high incidence of CR-BFG isolated from our hospitalized patients has become an important problem. Therefore, we aimed to determine the frequency and associated factors for intestinal colonization by carbapenem-non-susceptible BFG (CNS-BFG) among adult patients hospitalized at intensive care units, neurosurgery and internal medicine wards in our hospital. MethodsRectal swabs (n = 1200), collected from 766 patients between February 2014 and March 2015, were inoculated onto kanamycin-vancomycin-leaked blood agar containing 0.125 mg/L meropenem. The isolates were identified by MALDI-TOF MS. Susceptibility testing was performed by agar dilution method. The carbapenemase gene (cfiA) was detected by PCR. Logistic regression analysis was used to evaluate the associated factors for intestinal colonization by CNS-BFG. ResultsA total 180 non-duplicate BFG isolates were obtained from 164 patients.Ten different species, including Parabacteroides distasonis (n = 46, 25.6%), and Bacteroides fragilis (n = 30; 16.6%), were identified. Twenty-five percent of the isolates were non-susceptible to meropenem (MIC >2 mg/L). The highest prevalence of meropenem resistant strains (MIC >8 mg/L) was detected among B. fragilis (n = 12), followed by Parabacteroides spp. (n = 4). All but one B. fragilis strains were cfiA gene positive. Hospital admission, increasing Charlson score, use of antibiotics; including carbapenems in past three months, colonization with other accompanying carbapenem-resistant Gram negative bacteria (Enterobacteriaceae, Acinetobacter baumannii and Pseudomonas aeruginosa), and having undergone surgical operations were significantly associated with RCS- BFG colonization. ConclusionsThe high carriage rate of CNS-BFG in hospitalized patients may lead to worse clinical outcomes, such as serious infections and mortality, and deserves attention.

Genomic Background and Phylogeny of cfiA-Positive Bacteroides fragilis Strains Resistant to Meropenem-EDTA.

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.

Diversity of antimicrobial resistance genes in Bacteroides and Parabacteroides strains isolated in Germany

ObjectivesBacteroides spp. are normal constituents of the human intestinal microflora, but they are also able to cause severe diseases. The aim of this study was to determine the diversity of antibiotic resistance genes found in phenotypically resistant Bacteroides and Parabacteroides strains. MethodsA total of 71 phenotypically resistant Bacteroides spp. from human clinical specimens were screened for the antibiotic resistance genes cfiA, tetQ, tetM, tet36, cepA, cfxA, nim, ermG, ermF, bexA, blaVIM, blaNDM, blaKPC, blaOXA-48 and blaGES. The presence of these genes was compared with phenotypic resistance to ampicillin/sulbactam, cefoxitin, ceftolozane/tazobactam, piperacillin/tazobactam, imipenem, meropenem, meropenem/vaborbactam, clindamycin, moxifloxacin, tigecycline, eravacycline and metronidazole. ResultstetQ was the most frequently detected gene, followed by cfiA, ermF, cfxA, ermG, cepA, nim and bexA. None of the strains were positive for tetM, tet36, blaVIM, blaNDM, blaKPC, blaOXA-48 or blaGES. Resistance to the tested β-lactams was mainly linked to the presence of the cfiA gene. Clindamycin resistance correlated with the presence of the genes ermG and ermF. The bexA gene was found in six strains, but only two of them were resistant to moxifloxacin. Tigecycline and eravacycline showed good activities despite the frequent occurrence of tetQ. The nim gene was detected in six isolates, five of which were resistant to metronidazole. ConclusionThe findings of our study support the general belief that antimicrobial resistance within Bacteroides should be taken into consideration. This underlines the necessity of reliable routine antimicrobial susceptibility test methods for anaerobic bacteria and the implementation of antimicrobial surveillance programmes worldwide.

Clinico-microbiological profile of Bacteroides fragilis with focus on molecular detection of emerging resistance.

Background & objective:Bacteroides fragilis is a Gram-negative anaerobic opportunistic pathogen which is managed by empirical anaerobic coverage as a hospital norm. However, with rising reports of resistance among B. fragilis strains, antibiotic susceptibility testing for this pathogen may be the only way to understand the magnitude of the problem. This study aimed to characterize resistance patterns among clinical isolates and identify resistance genes.Methods:A prospective observational study was conducted which included all samples requesting anaerobic cultures within the study period. Minimum inhibitory concentration (MIC) was detected for metronidazole, clindamycin and chloramphenicol by agar dilution. E-test strips were used for imipenem and piperacillin, followed by polymerase chain reaction to detect nim and cfiA genes.Results:Among a total of 50 isolates, 94 per cent (47/50) were susceptible and six per cent (3/50) showed intermediate resistance to metronidazole. Susceptibility to clindamycin and piperacillin was noted in 70 and 50 per cent of strains; intermediate resistance in 14 and 2 per cent and resistance in 16 and 48 per cent, respectively. No resistance was observed for chloramphenicol and imipenem. Nim gene was found in 26 per cent (13/50) and cfiA gene was found in 52 per cent (26/50) of isolates. Isolates with high metronidazole MIC of 8-16 μg/ml were found to carry nim gene (χ2 test, P<0.001).Interpretation & conclusions:Rising resistance among B. fragilis is evident and there is a significant association between nim gene and metronidazole resistance. Improving awareness among clinicians is paramount in tackling AMR among these pathogens, as empirical anaerobic coverage may not be effective in all cases.

Emerging resistance among clinical Bacteroides fragilis isolates in association with nim and cfiA gene

Emerging resistance among clinical Bacteroides fragilis isolates in association with nim and cfiA gene

Higher Prevalence of Multi-Antimicrobial Resistant Bacteroides spp. Strains Isolated at a Tertiary Teaching Hospital in China.

PurposeThe study investigates the molecular epidemiology of multi-drug resistant (MDR) Bacteroides spp. isolates and the clinical characteristics of the patients.Materials and MethodsBacteroides 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.ResultsThe 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).ConclusionThe 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.

Prevalence and antimicrobial susceptibility of enterotoxigenic extra-intestinal Bacteroides fragilis among 13-year collection of isolates in Kuwait

BackgroundSome strains of Bacteroides fragilis species are associated with diarrhea as a result of enterotoxin production (bft or fragilysin). Fragilysin is activated by C11 protease (fpn) and together with C10 protease (bfp) play a significant role in its invasiveness. The objectives of this study were to investigate the proportion of clinical isolates from extra-intestinal sources that are toxin producers and characterize the genes mediating toxin production. Clinical isolates submitted to our reference laboratory over the last 13 years were screened for toxin production using PCR technique. All stool isolates were excluded. The isolates were tested for their susceptibility to 8 antimicrobial agents by E test. Carbapenem resistance gene cfiA was detected by PCR.ResultsA total of 421 B. fragilis isolates were viable. Out of these, bft was detected in 210 (49.9%) isolates. Of the 210 bft-positive isolates, 171 (81.4%), 33 (15.7%) and 6 (2.8%) harbored bft-1, bft-2, and bft-3 genes, respectively. Twenty (9.5%) of the bft-positive strains originated from bloodstream infections. Twenty-five, 20 and 9 strains harbored bfp-1, bfp-2 and bfp-3 gene, respectively. Two, 3, 4 bfp isotypes were detected simultaneously in some of strains. The resistance rates against amoxicillin-clavulanic acid was 32%, clindamycin 62%, cefoxitin 26%, imipenem 11%, meropenem 17%, metronidazole 4%, piperacillin 61% and tigecycline 14%. A chromosomally located cfiA gene that encode metallo-β-lactamase was identified in only 34 isolates (16.2%).ConclusionsThe prevalence of enterotoxin-producing B. fragilis was high among the extra-intestinal isolates. Metronidazole was the most active agent against all isolates. There was no statistically significance difference between resistance rates among bft-positive and bft-negative isolates except for clindamycin.