Utilizing NGS in AMR Surveillance in North Lebanon - A One Health Approach

Abstract

Background: The global rates of antimicrobial resistance (AMR) are rising at an alarming rate with dreadful circumstances of more than 10 million deaths per year by 2050. In the Eastern Mediterranean Region (EMR), reported rates of resistance have reached dangerous levels both in healthcare settings and the community, threatening the hard-won gains in health and development, and the sustainability of public health response to many communicable diseases. AMR surveillance systems are the core component of infectious disease management and the foundation for a better understanding of the spread of antimicrobial resistance. In Lebanon, data on AMR surveillance is fragmented and lack representativeness. To this, we propose using Next-Generation Sequencing (NGS) in a One Health Approach to determine the spread of AMR and identify the threats in North Lebanon.

Methods: A total of 83 samples was received from wild animals, sewage, water, and soil samples. Samples were streaked on MacConkey agar plates supplemented with meropenem. Identification of bacterial spp. was primarily done by API20E for all isolated bacteria. Antimicrobial Susceptibility profile was determined by disk diffusion against 5 different antimicrobial agents. Carbapenem resistant Gram- negative bacteria were further characterized by Whole genome sequencing. Bacterial type, international clone, sequence type, resistance genes, and plasmids were detected using sequence data.

Results: We successfully isolated 76 bacterial isolates from different samples. The most common were E. coli (14 %), Pseudomonas spp. (33 %), and Acinetobacter baumanii (8.7 %). Disk diffusion results showed high resistance to meropenem among identified bacterial organisms which is about 75.5 %. Sequence results detected the presence of E. coli strains harboring NDM-5 along with IncFIA, IncFIB (AP001918), IncFII, IncI2(Delta), Incl (Gamma), IncY plasmids. E. coli strains were of ST 405 (n=1), ST361 (n=2), and ST648 (n=1). Acinetobacter baumanii detected by sequencing all belongs to ST2 in IC2. Some of these strains harbored both OXA-23 and OXA-66. A key finding in this study was the isolation of MDR E. coli strain harboring both NDM-5 and OXA-1 from wild animal (Otter).

Conclusion: This project effectively isolated Carbapenem resistant Enterobacteriaceae, Acinetobacter baumanii, and Pseudomonas spp. from animals and environmental samples (sewage, soil, water). The detection of similar clones in both environmental and clinical samples explain the possible transmission of ARG among species and across ecosystem which was further validated by the presence of plasmids that are common plasmids to humans.