Acquired resistome and plasmid sequencing of mcr-1 carrying MDR Enterobacteriaceae from poultry and their relationship to STs associated with humans Antoine Abou Fayad 1,2,3 †, Maria El Azzi 1,2,3 †, Ahmad Sleiman 1,2,3 , Issmat I. Kassem 4,5 , Reema A. Bawazeer 6,7 , Liliane Okdah 6,7 , Michel Doumith 6,7 , Majed F. Alghoribi 6,7 and Ghassan M. Matar 1,2,3 * 1 Department of Experimental Pathology, Immunology and Microbiology, Faculty of Medicine, American University of Beirut, Beirut, Lebanon; 2 Center for Infectious Diseases Research, American University of Beirut, Beirut, Lebanon; 3 World Health Organization (WHO) Collaborating Center for Reference and Research on Bacterial Pathogens, Beirut, Lebanon; 4 Department of Nutrition & Food Science, American University of Beirut, Beirut, Lebanon; 5 Center for Food Safety and Department of Food Science and Technology, University of Georgia, 1109 Experiment Street, Griffin, GA 30223-1797, USA; 6 Infectious Diseases Research Department, King Abdullah International Medical Research Center, Riyadh, Saudi Arabia; 7 King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia *Corresponding author. E-mail: gmatar@aub.edu.lb †These authors contributed equally. Received 1 June 2021; accepted 17 December 2021 Objectives: To investigate the acquired resistome in 18 colistin-resistant Escherichia coli isolated from different poultry farms in Lebanon, analyse Inc plasmids associated with mcr and assess potential transmission to humans. Methods: A total of 18 E. coli were recovered from poultry faeces collected from different poultry farms in Lebanon. Broth microdilution (BMD) assay was performed to determine the antimicrobial resistance profiles. WGS was used to identify the genetic determinants behind the resistance in these isolates. Results: BMD results showed that all of the 18 isolates were colistin resistant. Furthermore, resistance to tri- methoprim/sulfamethoxazole was the most recorded among the isolates and only one isolate was resistant to cefepime. Sequencing results showed that the isolates were distributed into seven different STs and that the most abundant was ST1140. The number of antimicrobial resistant determinants ranged from 4 to 21 among the 18 isolates, with tet(A) and floR being the most frequent. Moreover, a total of 15 different plasmid replicon types were identified. The mcr-1 gene was shown to be predominantly located on IncX4 plasmids. Additionally, two isolates harboured the IncI2-type self-conjugative plasmid. Conclusions: The findings show that mcr and other important resistance determinants occur in MDR E. coli isolated poultry farms in Lebanon. The occurrence of mcr on mobile plasmids and the zoonotic potential and clinical relevance of some strains highlight a risk of transmission to humans. Introduction The emergence of MDR bacteria has resulted in the use of colistin (polymyxin E) as a last resort for treatment of severe Gram-negative bacterial infections. 1 This induced a reliance on this antibiotic and the likely selection of colistin-resistant strains. 2 Initially, colistin resistance was believed to be solely caused by chromosomal mutations. However, the discovery of the plasmid-borne mobile colistin resistance gene, mcr-1, in 2015 in China indicated that resistance can also be transmitted laterally. Today, mcr is spreading globally and colistin use in ani- mal farming is thought to be a major driver in this dissemin- ation. 3 The mcr-1 gene has been reported in approximately all food-producing animal species in 57 countries distributed over five continents. 4 Therefore, this study aimed to investigate the acquired resistome, Inc plasmid types, and STs of 18 colistin- resistant Escherichia coli isolates from different poultry farms in Lebanon. © The Author(s) 2022. Published by Oxford University Press on behalf of British Society for Antimicrobial Chemotherapy. This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial License (https:// creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com 1 of 5 JAC Antimicrob Resist https://doi.org/10.1093/jacamr/dlab198 JAC- Antimicrobial Resistance Downloaded from https://academic.oup.com/jacamr/article/4/1/dlab198/6523942 by guest on 20 July 2022