MOLECULAR INVESTIGATION OF EXTREMELY DRUG RESISTANT ACINETOBACTER BAUMANNII OUTBREAK IN THE ICU OF A TERTIARY HEALTHCARE CENTER IN LEBANON

Abstract

Antimicrobial resistance (AMR) represents one of the major global health issues today. Infections with extensively drug-resistant (XDR) and pan drug-resistant (PDR) bacteria are associated with prolonged treatment periods and high lethality, owing to the limited and sometimes absent therapeutic options. Due to the misuse of antibiotics by means of over-prescription and their abuse in agriculture, AMR is continuously spreading and causing dangerous outbreaks that prompt establishing persistent and accurate surveillance. Hospitals and other healthcare establishments are fertile ground for drug-resistant bacteria to flourish, especially biofilm-forming bacteria such as the WHO top priority pathogen Acinetobacter baumannii. In this study, we utilize next-generation sequencing (NGS) as a fast and effective diagnostic tool to gain insight into the genomic diversity and clonality of an A. baumannii outbreak at a tertiary care center in Beirut, Lebanon. Methods: A total of 54 A. baumannii isolates from ICU patients and from the hospital environment collected from AUBMC Clinical Microbiology Laboratory were screened for their susceptibility using the Broth Micro-dilution assay (BMD) against 12 different antimicrobials from different antimicrobial classes. For the purpose of determining AMR genes, sequence type (ST) and international clones (IC), whole-genome sequencing (WGS) using Illumina sequencing was performed on all these isolates. Results: According to CLSI guidelines, two A. baumannii isolates were found to be resistant to colistin. All isolates showed resistance to Bactrim. Resistance rates were 98% for imipenem, meropenem, tazocin, ciprofloxacin, levofloxacin, ceftazidime, and cefepime, while resistance to gentamicin and amikacin accounted for 93% and 94%, respectively. Furthermore, 96% of tested A. baumannii isolates can be categorized as XDR, 2% as PDR while 2% were susceptible to antibiotics. Additionally, many antimicrobial resistance genes were detected, including the carbapenem resistance gene OXA-23. All our isolates were of ST 2, with 93% of them belonging to IC 2. Conclusion: The study focused on A. baumannii isolates and found that those belonging to ST-2 and IC-2 were the most prevalent. These isolates were clustered together and had similar antimicrobial resistance genes. WGS was crucial in identifying these differences and highlighting the importance of advanced techniques in tracking and identifying outbreaks accurately. The finding that most isolates detected belongs to IC-2 and ST-2 carrying blaOXA-23 suggests that the current outbreak strain might have originated from older isolates dating back to 2014-2020. This study emphasizes the importance of 3 utilizing NGS in monitoring the antibiotic-resistant pathogens as a way to prevent and control outbreaks.