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

TL;DR

This study shows that MALDI-TOF MS can rapidly detect cfiA-positive Bacteroides fragilis, which is linked to carbapenem resistance and poor clinical outcomes.

Contribution

The study establishes the clinical relevance of MALDI-TOF MS for detecting cfiA-positive B. fragilis and its association with antibiotic resistance and mortality.

Findings

cfiA positivity detected by MALDI-TOF MS strongly correlates with carbapenem resistance in B. fragilis isolates.

cfiA+ isolates are predominantly of sequence type ST157 and often carry IS1187 insertion sequences upstream of cfiA.

High 30-day mortality (13.3%) is associated with comorbidities and lack of early source control in B. fragilis infections.

Abstract

The MALDI-TOF MS Bruker Biotyper MBT subtyping IVD module enables the early detection of cfiA-positive Bacteroides fragilis (cfiA+ BF) during bacterial identification. However, the relationship between genetic positivity, phenotypic resistance, and clinical outcomes has not been fully elucidated. This retrospective study analyzed B. fragilis isolates from three Hong Kong hospitals between 2021 and 2025 to examine their prevalence and the clinical utility of MALDI-TOF MS in rapid cfiA detection. Antibiotic susceptibility testing, cfiA 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 cfiA positivity and 30-day all-cause mortality. Overall, B. fragilis 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 cfiA-positive. cfiA detection by MALDI-TOF MS showed 100% concordance with the gene sequencing results and correlated strongly with phenotypic carbapenem resistance (Φ = 0.82, p < 0.001 for meropenem; Φ = 0.70, p < 0.001 for ertapenem; Φ = 0.63, p < 0.001 for imipenem). Phylogenetic analysis revealed two distinct clusters corresponding to cfiA status, each exhibiting genetic diversity based on multi-locus sequence typing (MLST). The cfiA+ BF isolates demonstrated high-level phenotypic carbapenem resistance in the presence of upstream insertion sequences. The predominant sequence type (ST) among cfiA+ BF isolates was ST157, and 70% of ST157 isolates harbored IS1187 in the upstream region of cfiA. Gene sequencing also identified other emerging beta-lactamase genes blaOXA-347 and blaMUN. The 30-day all-cause mortality following B. fragilis infection was 13.3%, with independent predictors including a high Charlson Comorbidity Index (OR = 1.30; p = 0.02) and the absence of early source control (OR = 4.84; p = 0.03). This study highlights the widespread occurrence of cfiA+ BF in Hong Kong and the clinical significance of rapid cfiA detection. Continuous surveillance is essential to monitor the ongoing threat of antibiotic resistance in B. fragilis.

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