Clinical Significance of cfiA Positivity Detected by Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry in Bacteroides fragilis Infections

The MALDI-TOF MS Bruker Biotyper MBT subtyping IVD module enables the early detection of <i>cfiA</i>-positive <i>Bacteroides fragilis</i> (<i>cfiA</i>+ BF) during bacterial identification. However, the relationship between genetic positivity, phenotypic resistance, and clinical outcomes has not been fully elucidated. This retrospective study analyzed <i>B. fragilis</i> isolates from three Hong Kong hospitals between 2021 and 2025 to examine their prevalence and the clinical utility of MALDI-TOF MS in rapid <i>cfiA</i> detection. Antibiotic susceptibility testing, <i>cfiA</i> gene detection using MALDI-TOF MS, and Oxford Nanopore sequencing were performed. Medical records were reviewed, and univariate analyses and multivariate logistic regression were used to identify factors associated with <i>cfiA</i> positivity and 30-day all-cause mortality. Overall, <i>B. fragilis</i> exhibited a high rate of antibiotic resistance. Concomitant resistance to carbapenems and metronidazole was identified in three isolates. Among the 166 isolates, 40 (24.1%) were <i>cfiA</i>-positive. <i>cfiA</i> detection by MALDI-TOF MS showed 100% concordance with the gene sequencing results and correlated strongly with phenotypic carbapenem resistance (Φ = 0.82, <i>p</i> < 0.001 for meropenem; Φ = 0.70, <i>p</i> < 0.001 for ertapenem; Φ = 0.63, <i>p</i> < 0.001 for imipenem). Phylogenetic analysis revealed two distinct clusters corresponding to <i>cfiA</i> status, each exhibiting genetic diversity based on multi-locus sequence typing (MLST). The <i>cfiA</i>+ BF isolates demonstrated high-level phenotypic carbapenem resistance in the presence of upstream insertion sequences. The predominant sequence type (ST) among <i>cfiA</i>+ BF isolates was ST157, and 70% of ST157 isolates harbored IS<i>1187</i> in the upstream region of <i>cfiA</i>. Gene sequencing also identified other emerging beta-lactamase genes <i>bla</i>_OXA-347 and <i>bla</i>_MUN. The 30-day all-cause mortality following <i>B. fragilis</i> infection was 13.3%, with independent predictors including a high Charlson Comorbidity Index (OR = 1.30; <i>p</i> = 0.02) and the absence of early source control (OR = 4.84; <i>p</i> = 0.03). This study highlights the widespread occurrence of <i>cfiA</i>+ BF in Hong Kong and the clinical significance of rapid <i>cfiA</i> detection. Continuous surveillance is essential to monitor the ongoing threat of antibiotic resistance in <i>B. fragilis</i>.