High Prevalence of Multidrug-Resistant Clostridioides difficile Following Extensive Use of Antimicrobials in Hospitalized Patients in Kenya

Abstract

Introduction: Clostridioides difficile is a neglected pathogen in many African countries as it is generally not regarded as one of the major contributors toward the diarrheal disease burden in the continent. However, several studies have suggested that C. difficile infection (CDI) may be underreported in many African settings. The aim of this study was to determine the prevalence of CDI in hospitalized patients, evaluate antimicrobial exposure, and detect toxin and antimicrobial resistance profiles of the isolated C. difficile strains.

Methods: In this cross-sectional study, 333 hospitalized patients with hospital-onset diarrhoea were selected. The stool samples were collected and cultured on cycloserine-cefoxitin egg yolk agar (CCEY). Isolates were presumptively identified by phenotypic characteristics and Gram stain and confirmed by singleplex real-time PCR (qPCR) assays detecting the species-specific tpi gene, toxin A (tcdA) gene, toxin B (tcdB) gene, and the binary toxin (cdtA/cdtB) genes. Confirmed C. difficile isolates were tested against a panel of eight antimicrobials (vancomycin, metronidazole, rifampicin, ciprofloxacin, tetracycline, clindamycin, erythromycin, and ceftriaxone) using E-test strips.

Results: C. difficile was detected in 57 (25%) of diarrheal patients over the age of two, 56 (98.2%) of whom received antimicrobials before the diarrheal episode. Amongst the 71 confirmed isolates, 69 (97.1%) harbored at least one toxin gene. More than half of the toxigenic isolates harbored a truncated tcdA gene. All isolates were sensitive to vancomycin, while three isolates (2.1%) were resistant to metronidazole (MIC >32 mg/L). High levels of resistance were observed to rifampicin (65/71, 91.5%), erythromycin (63/71, 88.7%), ciprofloxacin (59/71, 83.1%), clindamycin (57/71, 80.3%), and ceftriaxone (36/71, 50.7.8%). Among the resistant isolates, 61 (85.9%) were multidrug-resistant.

Conclusion: Multidrug-resistant C. difficile strains were a significant cause of healthcare facility-onset C. difficile infections in patients with prior antimicrobial exposure in this Kenyan hospital.

Keywords: Africa; Clostridioides difficile; antimicrobial use; multidrug resistance; toxin types.

Figure 1

Distribution of the toxin types of the 71 C. difficile isolates. A⁻ *: isolates in which the tcdA gene had a 110 bp deletion compared to the wildtype tcdA gene. CDT⁺: isolates harboured both cdtA and cdtB gene of the binary toxin. CDTA⁺B⁻: isolates only harboured the A component of the binary toxin. CDT^– isolates lacked either of the binary toxin genes.

Figure 2

Gel electrophoresis of qPCR amplicon products; lanes 1, 7, and 15 represent 100 bp molecular weight marker, lanes 2–4 tpi positive (230 bp) clinical isolates, lane 5 tpi positive control (C. difficile DSM 27147), lane 6 no template control. Lane 8 clinical isolate with truncated tcdA (110 bp) amplicon, lane 9–12 clinical isolates with full length tcdA gene (369 bp), lane 13 positive control (C. difficile DSM 27147), and lane 14 no template control. Lane 16–18 clinical samples with tcdB gene (160 bp), lane 19 positive control (C. difficile DSM 27147), and lane 20 no template control.