Genetic Characteristics, Virulence Factors, and Clonality of ESBL-Producing E. coli and K. pneumoniae: a Comparative Study During and After National Action Plan on Antimicrobial Resistance in Mwanza, Tanzania.

Introduction: Antimicrobial resistance (AMR) poses a significant global health threat, necessitating regional-specific continuous surveillance to understand its dynamics and implications.

Goals: To respond to the changing landscape of AMR, a cross-sectional hospital-based study was conducted in two periods: June 2019 – June 2020, during the first Tanzania National Action Plan on AMR (NAP-AMR), and March – July 2023, after its completion.

Materials and Methods: Patients" sociodemographic and clinical data were collected by pre-tested structured questionnaires. A total of 2648 and 1929 samples (blood, urine, and pus) collected during and after NAP-AMR respectively, were cultured to isolate bacterial pathogens; identification was based on VITEK MS and 16S rDNA Sanger sequencing, and VITEK 2 was used to determine susceptibility towards antibiotic agents. Next-generation sequencing on the Illumina NextSeq 550 platform was used for sequencing ESBL E. coli (n=22) and ESBL K. pneumoniae (n=23) out of 64 and 79 ESBL strains, respectively isolated during NAP-AMR.

Results: ESBL-producing E. coli and K. pneumoniae phenotypes increased significantly after NAP-AMR [53.4%(134/268) vs. 73.8%(175/237), p<0.0001]. Specific increase for ESBL-E. coli [41.3%(64/155) vs. 61.7%(74/120), p=0.0084] and ESBL-K. pneumoniae [69.9%(79/113) vs. 85.5%(100/117), p=0.0057] was remarkable. E. coli ST 648 (40.9%, 9/22) and K. pneumoniae ST 280 (23.1%, 6/23) were predominant. The IncFII plasmid-replicon was predominantly found in both E. coli (68.2%, 15/22) and K. pneumoniae (65.2%, 15/23). The bla_CTX-M-15 gene was found in 81.5% (18/22) E. coli and all 23 K. pneumoniae. The virulence genes yfcV, fyuA, sitA, and traT were found in 68.2%, 72.7%, 72.7%, and 77.3% of E. coli respectively while the virulence genes acrA/B, entA/B/C/E, fepA-D/G, fimA-I/K, and mrkA-D/F/H-J were found in all K. pneumoniae.

Summary: This study underscores the escalating threat of highly virulent strains of ESBL-producing E. coli and K. pneumoniae causing infections. The study advocates for the stringent implementation of IPC measures to curb the spread of antibiotic-resistant pathogens and associated public health risks.