Hospital epidemiology of Acinetobacter baumannii in Lebanon

Although A. baumannii appears to be endemic in the Lebanese clinical settings with the description of many outbreaks, its true burden is still not adequately captured despite the increasing number of publications in the last few years (Dandachi et al., 2019). For instance, A. baumannii was the most predominant pathogen of ventilator-associated pneumonia among adult ICU patients between 2008 and 2017 at a Lebanese tertiary referral center (Kanafani et al., 2019). It was also responsible for 4% of all recorded bacterial bloodstream infections over 10 years among patients with hematological malignancies (Haddad et al., 2021). It was also the third pathogen isolated after Staphylococcus aureus and Pseudomonas aeruginosa among patients admitted to a Burn care center between 2014 and 2018 (Bourgi et al., 2020). The majority of the Lebanese isolates were multi-drug resistant with high percentages of carbapenem-resistant A. baumannii (CRAB) varying between 60% and 100% (Nawfal Dagher et al., 2019; Chamoun et al., 2016; Rafei et al., 2015; Dahdouh et al., 2016; Al Atrouni et al., 2016; Hammoudi et al., 2015; Hajjar Soudeiha et al., 2018; Moghnieh et al., 2019). Even with the increasing trend of CRAB, many hopeful interventions such as carbapenem sparing regimens and appropriate infection prevention and control measures showed success in containing the outbreaks and reducing CRAB (Chamieh et al., 2019; Osman et al., 2020; Chamieh et al., 2021; Rizk et al., 2022; Moussally et al., 2021; Moghnieh et al., 2020).

OXA-58 was the unique carbapenemase described in the earliest epidemiological studies (published in or before 2011) and was harbored by the global clones 1 (sequence type 20 “ST20”^IP, a single locus variant of ST1^IP), 2 (ST2^IP), and 3 (ST3^IP) (Zarrilli et al., 2008; Di Popolo et al., 2011). In global clone 1 strains incriminated in an outbreak that occurred between 2004 and 2005 in a university hospital in Beirut, bla_OXA-58 was carried by a pABIR plasmid and bounded by 2 insertion sequences (IS18 and ISAba3) explaining thus its dissemination (Zarrilli et al., 2008). However, in agreement with worldwide observations, a marked shift from OXA-58 to OXA-23 was witnessed in the following studies with ST2^IP (a main ST in the global clone 2) being the main OXA-23 producing clone (Nawfal Dagher et al., 2019; Rafei et al., 2015; Dahdouh et al., 2016; Al Atrouni et al., 2016; Hajjar Soudeiha et al., 2018; Osman et al., 2020; Rafei et al., 2014). Despite the predominance of OXA-23-producing ST2 strains, other mechanisms and clones were also detected but to a lesser degree. Isolates belonging to ST636^IP and carrying bla_OXA-72 (bla_OXA-24 variant) on pMAL-1 plasmid were responsible for a nosocomial outbreak along with other ST2^IP and ST2-like^IP carrying bla_OXA-23 on Tn2006 (Makke et al., 2020). NDM-1, produced by ST85^IP strains, was firstly detected in Syrian refugees and then in Lebanese patients (Al Atrouni et al., 2016; Rafei et al., 2014). Other STs positive for bla_NDM-1 were also identified as ST25^IP and ST708^IP (Rafei et al., 2015; Al Atrouni et al., 2016). In another multi-regional study, the beta-lactamase gene bla_GES-11 was associated with bla_OXA-23 isolates in 90% of CRAB collected in 2012 (Hammoudi et al., 2015). Generally, the genomic context of resistance genes was sparingly addressed in Lebanon. In one of the sequenced bla_NDM-1 carrying ST85^IP isolates, bla_NDM-1 along with 14 copies of the aphA6 amikacin resistance genes were enclosed within a novel transposon Tn7 named Tn6924 (Mann et al., 2022). In another ST2^IP strain, each of the four bla_OXA-23 copies was located in an AbaR4 copy, and bla_TEM and aphA1 genes were present in a novel variant of AbGRI2 known as AbGRI2-15 (Liepa et al., 2022).

^IP: sequence types (ST) defined according to the MLST scheme of the Pasteur Institute.

Extra-hospital epidemiology of Acinetobacter baumannii in Lebanon

Nationwide and regional studies investigating the extra hospital epidemiology of A. baumannii in Lebanon, isolated it from several environmental (soil, water, sewage), animal (pets, livestock), and food (milk, vegetables, meat, cheese) samples (Rafei et al., 2015; Al Atrouni et al., 2016; Al Bayssari et al., 2015). These isolates were generally susceptible to the tested antimicrobial agents including beta-lactams and non-beta-lactam antibiotics (Rafei et al., 2015; Al Atrouni et al., 2016). However, some isolates from the livestock and poultry animals (horse, cattle, pig, and fowl) showed resistance to carbapenems and harbored enzymes like the bla_OXA-23, bla_OXA-58, and bla_OXA-143 (Rafei et al., 2015; Al Bayssari et al., 2015).

Concerning clonality, they were so diverse belonging to different STs, generally, novel ones, which were different from the STs found among hospital isolates. However, some identified STs are common in health care settings as ST1^IP, ST2^IP, and ST10^IP (Rafei et al., 2015; Al Atrouni et al., 2016; Al Bayssari et al., 2015). Studying two susceptible environmental isolates belonging to global clone 1 helped to better redraw the population structure of this clone, which now encompasses 2 major clades including 5 main antibiotic-resistant lineages and 4 single-isolate antibiotic-susceptible lineages outside of the 2 clades (Koong et al., 2021).

   

^IP: sequence types (ST) defined according to the MLST scheme of the Pasteur Institute.

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