Investigating an Outbreak of Extensively Drug-Resistant Acinetobacter baumannii in a Tertiary Healthcare Centre in Lebanon Using Next-Generation Sequencing

The frequent occurrence of Acinetobacter baumannii in hospital settings and the elevated rate of antimicrobial resistance in this pathogen represent a serious clinical and public health threat worldwide, and particularly in Lebanon where outbreak surveillance and control are still insufficient. Whole-genome sequencing (WGS) is a fast and reliable tool to study outbreaks at the molecular level and obtain actionable knowledge, leading to better control measures. A total of 59 A. baumannii isolates were collected from intensive care unit (ICU) patients (57 isolates) and from the hospital environment (2 isolates) between August 2022 and May 2023, antimicrobial susceptibility testing (AST) was performed and gDNA was subjected to WGS. Analysis was performed to reveal the sequence types (ST), the relatedness to strains that caused other outbreaks and the arsenal of resistance genes harboured by these bacteria. Of 59 isolates, 85% were categorised as extensively drug-resistant (XDR), 13.6% as multidrug-resistant (MDR) and 1.7% as pan-drug-resistant. All isolates belonged to international clone (IC)2, of which the majority were of ST2 (91.5%). The isolates clustered well with those of a previous outbreak in the same hospital. In addition, isolates from hospitals in Lebanon clustered well together and some clustered with those originating from other countries. The observed genetic relatedness between the current isolates and those from the previous outbreaks underscores the importance of strict surveillance to limit the threat of outbreaks. Moreover, the clustering of isolates from Lebanon with others from distant countries proves the necessity to further investigate the international spread of drug-resistant pathogens and the implementation of control strategies.