Antimicrobial Resistance to First-Line Therapy in Clinical Anaerobic Isolates from Southern Croatia

This study analyzed phenotypic and genotypic antimicrobial resistance (AMR) among commonly isolated anaerobes from southern Croatia. Over two years, 176 isolates (Bacteroides spp., Prevotella spp. and Finegoldia magna) were tested for antimicrobial susceptibility by the European Committee on Antimicrobial Susceptibility Testing (EUCAST) disk diffusion method. A subset of twenty-four of clindamycin- and/or metronidazole-resistant isolates (22 Bacteroides, along with one Prevotella bivia and one Finegoldia magna) underwent real-time PCR for resistance genes. Resistance of Bacteroides spp. in the total cohort to piperacillin/tazobactam, meropenem, clindamycin and metronidazole was 2.3%, 6.3%, 49.2%, and 10.2%, respectively. Among Prevotella spp. resistance to penicillin, piperacillin/tazobactam and clindamycin were 54.8%, 6.5%, and 67.7%, respectively. Of all Finegoldia magna isolates, 11.8%, 47.1% and 11.8% were resistant to penicillin, clindamycin and metronidazole. Non-fragilis Bacteroides spp. showed significantly higher resistance rates for clindamycin in comparison to B. fragilis, (36/52; 69.2% vs. 27/76; 35.5%, Fisher’s exact test p = 0.000282). For 22 selected clindamycin- and/or metronidazole-resistant Bacteroides spp., the prevalence of the cepA, cfxA, cfiA, ermF and ermG genes was 54.6%, 45.5%, 4.5%, 63.6% and 4.5%. None of the screened isolates carried the crxA, blaOXA-347, or nim genes. The cfiA gene was detected in one meropenem-resistant B. fragilis isolate, but lacked an associated insertion sequence. Prevotella bivia harbored both cfxA and ermF, while Finegoldia magna carried only ermF. These findings demonstrate substantial resistance rates to first-line antibiotics, emphasizing the urgency of ongoing AMR surveillance with a renewed focus on neglected anaerobic pathogens and the expansion of routine susceptibility testing to additional antimicrobials.