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. 2023 Oct 14;22(1):91.
doi: 10.1186/s12941-023-00641-8.

Extended-spectrum β-lactamase- producing gram-negative bacterial infections in severely ill COVID-19 patients admitted in a national referral hospital, Kenya

Jeniffer Munyiva Mutua  1   2 , John Mwaniki Njeru  3 , Abednego Moki Musyoki  4
Affiliations

Extended-spectrum β-lactamase- producing gram-negative bacterial infections in severely ill COVID-19 patients admitted in a national referral hospital, Kenya

Jeniffer Munyiva Mutua et al. Ann Clin Microbiol Antimicrob. .

Abstract

Background: Bacterial infections in COVID-19 patients, especially those caused by multidrug-resistant gram-negative strains, are associated with increased morbidity, hospital stay and mortality. However, there is limited data on the epidemiology of extended-spectrum β-lactamase (ESBL)-producing bacteria in COVID-19 patients. Here, we assessed the prevalence and the factors associated with ESBL-producing gram-negative bacterial (GNB) infections among severely ill COVID-19 patients admitted in Kenyatta National Hospital (KNH), Kenya.

Methods: We adopted a descriptive cross-sectional study design for patients admitted between October 2021 and February 2022, purposively recruiting 120 SARS-CoV- 2 infected participants based on clinical presentation. Demographics and clinical characteristics data were collected using structured questionnaires and case report forms. Clinical samples were collected and analyzed by standard microbiological methods in the KNH Microbiology laboratory and the Centre for Microbiology Research, Kenya Medical Research Institute.

Results: GNB infections prevalence was 40.8%, majorly caused by ESBL-producers (67.3%) predominated by Klebsiella pneumoniae (45.5%). Generally, 73% of the ESBL producers harboured our target ESBL genes, mainly CTX-M-type (59%, 17/29) in K. pneumoniae (76.9%, 20/26). GNB harbouring TEM-type (83%, 10/12) and SHV-type (100%, 7/7) genes showed ESBLs phenotypes and inhibitor resistance, mainly involving clavulanate, but most of them remained susceptible to tazobactam (60%, 6/10). SHV-type genes carrying ESBL producers showed resistance to both cefotaxime (CTX) and ceftazidime (CAZ) (K. pneumoniae), CAZ (E. coli) or CTX (E. cloacae complex and K. pneumoniae). About 87% (20/23) of isolates encoding CTX-M-type β-lactamases displayed CTX/ceftriaxone (CRO) resistance phenotype. About 42% of isolates with CTX-M-type β-lactamases only hydrolyzed ceftazidime (CAZ). Isolates with OXA-type β-lactamases were resistant to CTX, CAZ, CRO, cefepime and aztreonam. Patients with comorbidities were 10 times more likely to have an ESBL-producing GNB infection (aOR = 9.86, 95%CI 1.30 - 74.63, p = 0.003).

Conclusion: We report a high prevalence of ESBL-GNB infections in severely ill COVID-19 patients, predominantly due to Klebsiella pneumoniae harbouring CTX-M type ESBL genes. The patient's underlying comorbidities increased the risk of ESBL-producing GNB infection. In COVID-19 pandemic, enhanced systematic and continuous surveillance of ESBL-producing GNB, strict adherence to infection control measures and antimicrobial stewardship policies are warranted in the current study setting.

Keywords: COVID-19; ESBL-GNB; ESBL-resistance; Gram negative bacteria; Multidrug-resistance; SARS-CoV-2.

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Conflict of interest statement

The authors declare that they have no competing interests.

Figures

Fig. 1
Fig. 1
Spectrum of ESBL-producing GNB isolates in COVID-19 patients admitted in KNH-IDU. ESBL-p extended-spectrum beta-lactamases-producing, non-ESBL-p non-extended-spectrum beta-lactamases-producing
Fig. 2
Fig. 2
Distribution AMR genes among ESBL-producing GNB isolates from COVID-19 patients admitted in KNH-IDU. a Klebsiella pneumoniae. b Enterobacter cloacae complex. c Enterobacter cloacae. d Escherichia coli. e Pseudomonas aeruginosa. f ESBL gene carriage among all isolates. TEM TEM-type β-lactamase genes, CTX-M CTX-M-type β-lactamase genes, SHV SHV-type β-lactamase genes, OXA-1 Oxacillinases -type β-lactamases 1, ESBL Extended Spectrum Beta Lactamase
See this image and copyright information in PMC

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