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This retrospective study analyzed the susceptibility levels of Bacteroides fragilis group (BFG) in a hospital-based laboratory where disk diffusion test (DDT) was routinely performed. Isolates non-susceptible to imipenem and metronidazole by DDT were further investigated using a gradient method. The DDT and MIC susceptibility data of clindamycin, metronidazole, moxifloxacin and imipenem obtained on Brucella blood agar for 1264 non-duplicated isolates during 2020–2021 were analyzed. Species identification was obtained by matrix-assisted laser desorption ionization time-of-flight mass spectrometry and 16S rRNA sequencing. Interpretative agreement of DDT results using the 2015 EUCAST tentative and 2021 CA-SFM breakpoints was compared against MIC as the reference. The dataset included 604 B. fragilis (483 division I, 121 division II isolates), 415 non- fragilis Bacteroides , 177 Phocaeicola and 68 Parabacteroides. Susceptibility rates for clindamycin (22.1–62.1%) and moxifloxacin (59.9–80.9%) were low and many had no inhibition zones. At the EUCAST and CA-SFM breakpoints, 83.0 and 89.4% were imipenem-susceptible, and 89.6% and 97.4 were metronidazole-susceptible. MIC testing confirmed 11.4% and 2.8% isolates as imipenem-non-susceptible and metronidazole-resistant, respectively. Significant numbers of false-susceptibility and/or false-resistance results were observed at the CA-SFM breakpoint but not the EUCAST breakpoint. Higher rates of imipenem and/or metronidazole resistance were detected in B. fragilis division II, B. caccae, B. ovatus, B. salyersiae, B. stercoris and Parabacteroides. Co-resistance to imipenem and metronidazole was detected in 3 B. fragilis division II isolates. The data demonstrated emerging BFG resistance to several important anti-anaerobic antibiotics and highlights the importance of anaerobic susceptibility testing in clinical laboratories to guide therapy. • Antimicrobial resistance in Bacteroides fragilis group is emerging. • Antimicrobial susceptibilities of 1264 B. fragilis group were analyzed. • Clindamycin and moxifloxacin resistance rates were high. • Imipenem resistance rate was 11.4%. • Metronidazole resistance rate was 2.8%. [ABSTRACT FROM AUTHOR]

To compare the phylogeny of cfiA -positive Bacteroides fragilis isolates from diverse human and animal sources. Complete genome sequences were obtained from 42 cfiA -positive B. fragilis isolates (Hong Kong, 2015–2017) and additional 24 genomes deposited in the GenBank (multiple countries, 1985–2019) were included. The genomic clusters were constructed using PopPUNK. The CfiA alleles and polymorphism in the cfiA locus were analyzed in silico. The 66 isolates were grouped into 12 genomic clusters (BFSC-1 to 12). Human infection isolates were distributed in diverse clusters, being many of them common to fecal isolates from both human and animals. Thirteen CfiA alleles including 2 novel ones were identified. CfiA-1 (n = 28) is the predominating allele, following by CfiA-13 (n = 8), CfiA-4 (n = 7) and CfiA-14 (n = 6). The other CfiA alleles were identified in 1–3 isolates. Six patterns of gene context were identified in the regions flanking cfiA locus. No consistent association between genomic clusters and CfiA alleles could be detected. Similarly, markedly elevated imipenem MIC was linked to the integration, immediately upstram of cfiA of an IS element but not the CfiA allele or gene context. The phylogeny of cfiA -positive B. fragilis isolates causing human diseases was diverse and overlaped with those from human and animal carriage. • The genomic phylogeny of 66 cfiA -positive Bacteroides fragilis isolates was analyzed. • The isolates were grouped into 12 PopPUNK-based genomic clusters. • Clinical isolates shared the same genome clusters as carriage isolates from human and animals. • No correlation between CfiA allele and genome cluster was identifed. • The phylogeny of emerging cfiA -positive B. fragilis is diverse. [ABSTRACT FROM AUTHOR]