Investigation of antibiotic resistance genes in anaerobic bacteria isolated from clinical samples

The isolation, identification, and determination of antibiotic resistance profiles of anaerobic bacteria is challenging and labor-intensive. As a result, empirical treatment, leading to the increase in the antimicrobial resistance among anaerobic bacteria, is commonly applied in clinical practice.In our study, we aimed to identify anaerobic bacteria isolated from clinical samples using Sanger sequencing and investigate resistance genes responsible for beta-lactamase (cepA) production, and metronidazole (nim), carbapenem (cfxA), and clindamycin (ermF) resistance. Between June- November 2024, anaerobic cultures were performed on tissue samples, drain fluids, body fluids, and abscess pus sent to the Medical Microbiology Laboratory of Cerrahpaşa Medical Faculty Hospital. Fifty isolates were identified by Sanger sequencing. Beta-lactamase production and resistance to metronidazole, carbapenem, and clindamycin were investigated by detecting cepA, nim, cfxA, and ermF genes using Real-Time Polymerase Chain Reaction (RT-PCR). Gram-positive were 64% of the isolated anaerobic bacteria, Gram-negative were 36%. Among Gram-positive bacteria, 40% were cocci (5 Peptoniphilus spp., 8 P. anaerobius, 7 F. magna), and 24% were rods (3 Actinomyces spp., 2 Schaalia odontolytica, 3 Schaalia turicensis, 4 Bifidobacterium spp.). Among Gram-negative bacteria, 28% were rods (2 F. nucleatum, 10 B. fragilis, 2 P. melaninogenica), and 8% were cocci (1 Veillonella spp., 3 V. parvula). The nim,cfiA and cfxA genes were not detected in any isolate. The cepA gene was found in 6 B. fragilis isolates, while the ermF gene was detected in 1 Veillonella spp., 2 F. nucleatum, 1 P. melaninogenica, 3 Peptoniphilus spp., 1 Actinomyces spp., and 1 Schaalia turicensis isolate. In conclusion, we found that clindamycin resistance (ermF) is high in both Gram-negative and Gram-positive anaerobes, and beta-lactamase production (cepA) was limited to B. fragilis. We believe that sequencing methods can provide more comprehensive and accurate identification of difficult-to-culture and costly anaerobic bacterial species and strains, which can illuminate the epidemiology of infections