Molecular and phenotypic profiles of carbapenem- and third-generation cephalosporin-resistant Klebsiella pneumoniae isolates from the fecal microbiota of pediatric patients with COVID-19

Abstract Background Gut colonization with multidrug-resistant (MDR) Klebsiella pneumoniae is commonly associated with an increased risk of extraintestinal infections among hospitalized patients. Extensive antibiotic exposure during the COVID-19 pandemic, is a critical contributing factor for the emergence of resistant strains. This investigation sought to elucidate the phenotypic and molecular resistance traits of carbapenem-resistant K. pneumoniae (CRKP) and extended-spectrum β-lactamase–producing K. pneumoniae (ESBL-KP) colonizing the gut of pediatric patients with confirmed COVID-19. Methods A cross-sectional study was conducted from October 2020 to March 2022 at a tertiary pediatric hospital in Fayoum, Egypt. Fecal samples were collected from hospitalized pediatric COVID-19 patients. K. pneumoniae isolates were identified using standard microbiological methods. Antimicrobial susceptibility testing was carried out in accordance with the CLSI guidelines. ESBL and carbapenemase production were assessed phenotypically, while resistance genes were detected by multiplex and uniplex PCR. Microtiter plate method was used to assess biofilm formation. Results K. pneumoniae was detected in 36 of 71 patients (50.7%) using antibiotic-supplemented selective culture. The isolated strains were exclusively resistant, including 22 CRKP and 14 ESBL-KP. Colistin susceptibility was maintained in all isolates. CRKP strains showed significantly increased rate of resistance to fluoroquinolones and amikacin compared with ESBL-KP. Bla NDM gene (54.5%) and bla KPC (45.5%) were detected among CRKP isolates. ESBL-associated genes bla CTX-M , bla TEM , and bla SHV were prevalent in both groups. Biofilm formation was common and comparable between CRKP and ESBL-KP isolates. Conclusion A high prevalence of fecal carriage of MDR K. pneumoniae , driven by carbapenemase-producing strains, was observed among hospitalized pediatric COVID-19 patients. These outcomes highlight the necessity for routine colonization surveillance, optimized antimicrobial stewardship, and strengthened infection control strategies in pediatric settings.