The Role of Neonatal Ward Environment as a Reservoir for the Dissemination of Multidrug-Resistant Klebsiella pneumoniae in Algeria.

Abstract

Klebsiella pneumoniae is a major cause of hospital-acquired infections and contributes to high mortality. We examined the molecular epidemiology, antibiotic resistance, and virulence features of K. pneumoniae from the neonatal ward environment of a hospital in Chlef, Algeria, using whole-genome sequencing (WGS). Antibiotic susceptibility was assessed with the Vitek 2 automated system (AST-N365 card). Genomic DNA was extracted with the GF-1 kit, and WGS was performed by GENEWIZ Europe using the NEBNext Ultra II DNA Library Prep Kit. Species identification and virulence genes were determined using Kleborate, antimicrobial resistance genes were detected with AMRfinder Plus. From 9790 publicly available K. pneumoniae genomes, the 112 closest matches were selected, and core-genome MLST and a minimum-spanning tree were generated in SeqSphere + v10.5.04 using a MLST and cgMLST scheme. All isolates were multidrug-resistant, and WGS identified 22 resistance genes. Core genes detected across all samples included the bla_CTX-M-15, bla_TEM-1, oqxA, oqxB, aph(6)-Id, aph(3")-Ib, sul2, fosA5, emrD and kdeA. Other genes, including bla_SHV-1, bla_SHV-11, bla_DHA-1, bla_OXA-1, qnrB4, qnrS1 and aac(6')-Ib-cr5 were also observed. Yersiniabactin-associated virulence genes ybt and irp were detected in KP32, KP37 and KP57 (high risk clone ST13) while qacE was present only in KP55 (novel strain ST8932). This study highlights the persistence of bla_CTX-M-15, qnr, and bla_DHA-1 in K. pneumoniae from the neonatal ward environment. The presence of the high-risk strain ST13 is particularly concerning, as its identical allelic profiles indicate likely clonal spread within the hospital. These results suggest the hospital environment may act as a reservoir for multidrug-resistant K. pneumoniae.