BackgroundBacteroides 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 methodsBacteroides 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 Matrix Assisted Laser Desorption Ionization 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. ResultsB. fragilis isolates in this study expressed 45%, 41%, and 16% phenotypic resistance to clindamycin, metronidazole, and meropenem, respectively, with least resistance to piperacillin/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. ConclusionsDetection of a limited set of genes does not always correlate with phenotypic resistance to metronidazole and clindamycin due 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.
BackgroundBacteroides fragilis are opportunistic pathogens causing severe infections with increasing antimicrobial resistance. Since, phenotypic susceptibility testing is time-consuming and uneconomical, this necessitates a need for genotypic screening for deciding empirical therapy for B. fragilis.MethodsB. fragilis was isolated from clinical samples, exudates, tissue and body fluids collected between November 2018 and January 2020 in a tertiary care hospital. Samples were cultured in anaerobic blood agar and neomycin blood agar using the Anoxomat Mark system and species identified by MALDI-TOF-MS. Brucella agar supplemented with hemin, Vit K1 and 5% v/v laked sheep blood was used to determine the minimum inhibitory concentration by agar dilution. Genomic DNA was extracted and nim, ermF and cfiA genes were amplified, and visualized in a 2% agarose gel.ResultsOut of 51 non-duplicate B. fragilis, majority (74.5%) were recovered from exudates followed by body fluids. Isolates (n=51) expressed 45%, 41%, 16% resistance for clindamycin, metronidazole, and meropenem, respectively with least resistance to piperacillin/tazobactam (6%). Among metronidazole resistant isolates, 52% harboured nim genes in addition to 76% (23/30) of susceptible isolates. Similarly, cfiA was present in all eight meropenem resistant isolates in addition to 22% (9/41) susceptible ones. ConclusionsAll cfiA negative were phenotypically susceptible that can be employed to rule out meropenem resistance. Detecting limited genes for B. fragilis does not always correlate with phenotypic resistance, due to IS elements, efflux and other genetic determinants. Redundant use of meropenem with metronidazole should be avoided, as recommendation of metronidazole requires prior phenotypic testing due to the reported 41% resistance.
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