Genome-Based Characterization of Bacterial Pathogens Causing Bloodstream Infection

Abstract

Bloodstream infections (BSIs) caused by multi-drug resistant (MDR) bacterial pathogens are considered among the risk factors that pose a severe threat to public health, leading to increased morbidity and mortality. Our understanding of BSIs has changed with the emergence of next-generation platforms and their applications in epidemiological monitoring and resistance detection. The global rise in extended-spectrum β-lactamase producing (ESBL) and carbapenem-resistant Enterobacteriaceae (CRE) worldwide is alarming. This study aimed to assess antimicrobial resistance (AMR) and virulence determinants among 24 clinical, BSI-causing bacteria recovered from a healthcare setting in Lebanon. Whole-genome sequencing, Replicon Typing, and the Kirby-Bauer disk diffusion test were used for in-depth resistance and virulence characterization. All the isolates were resistant to amoxicillin, 83% to cefotaxime, 46% to cefoxitin, 29% to imipenem, 25% to meropenem, and 12.5% to colistin. Carbapenem resistance and ESBLs were linked to several factors, including variants of NDM such as blaNDM-5 (3/24) and blaNDM-1 (3/24), variants of OXA including blaOXA-1 (9/24) and blaOXA-48 (2/24), and different β-lactamases such as blaCTX-M-15 and blaSHV-11. IncFIA, IncFIB, IncFII, IncA/C, IncX1, and IncU were among the detected replicons. This study highlights the critical public health threat posed by MDR pathogens in bloodstream infections, emphasizing the urgent need for effective and comprehensive infection control measures. The findings highlight the significance of continuous genomic surveillance and epidemiological monitoring to better understand the mechanisms driving antimicrobial resistance and to develop targeted strategies for managing MDR infections.