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.