Abstract
Poultry and poultry meat are important contributors to the global antimicrobial burden. Unregulated and illegal use of extended-spectrum cephalosporins (ESC) in this sector has long been identified as a major cause of massive spread of ESC-resistant Escherichia coli, and colistin usage is considered a main driver of plasmid-mediated mcr genes dissemination. In Lebanon, the first mcr-1-positive E. coli found in poultry dates back to 2015, followed by a few reports of mcr-1-positive E. coli in poultry, swine, humans, and the environment. On the contrary, a comprehensive picture of the population structure of mcr-1-positive E. coli and mcr-1-bearing plasmids carrying the mcr-1 gene using whole-genome analysis is largely lacking. This study reports the prevalence of mcr-1-positive E. coli in poultry originating from 32 farms across three Lebanese governorates and slaughtered in the same place. We report 27/32 (84.4%) mcr-1 positive farms, leading to a total of 84 non-duplicate E. coli collected, of which 62 presented the mcr-1 gene. Numerous associated resistances were identified, including to ESC through the presence of blaCTX–M or blaCMY genes. The mcr-1 gene was mostly carried by IncX4 (n = 36) and IncI2 (n = 24) plasmids, which are both known for their efficient transfer capacities. A high genetic diversity was detected, arguing for the lack of contamination during the slaughter process. ST744 and ST1011 were the most widely identified clones, which have been both regularly associated to mcr-1-carrying E. coli and to the poultry sector. The wide dissemination of colistin-resistance, coupled to resistances to ESC and numerous other molecules, should urge authorities to implement efficient guidelines for the use of antibiotics in the poultry sector in Lebanon.
Highlights
Since the discovery of the plasmid-mediated colistin-resistance gene mcr-1 in 2015 (Liu et al, 2016), this gene has been extensively described in numerous animal settings, and notably in the poultry sector worldwide (Apostolakos and Piccirillo, 2018)
This study first reveals a massive spread of colistin-resistance in poultry farms in Lebanon (27/32, 84.4%), with the wide dissemination of the mcr-1 gene (21/27 positive farms)
The poultry sector is the very first one where mcr-1 was detected in Lebanon (Dandachi et al, 2018), and a recent study in three poultry farms reported high mcr-1 prevalence in broilers (Hmede and Kassem, 2018)
Summary
Since the discovery of the plasmid-mediated colistin-resistance gene mcr-1 in 2015 (Liu et al, 2016), this gene has been extensively described in numerous animal settings, and notably in the poultry sector worldwide (Apostolakos and Piccirillo, 2018). The mcr-1 gene has been detected in retail meat, suggesting a possible transfer to humans through under-cooked meat or cross-contamination (Nishino et al, 2017; Budel et al, 2020). Mcr-1 gene has mostly been found located on IncX4 and IncI2 plasmids, and to a lesser extent on IncHI2 plasmids (Perreten et al, 2016). The usually high transfer capacity of both IncX4 and IncI2 most probably explains their wide geographical dissemination and their occurrence in a large variety of hosts, both human and animals. Colistin-resistance has often been studied under the prism of plasmid-mediated resistance, so that only a few studies reported the characterization of mcrnegative but colistin-resistant isolates and the role of PmrAB and PhoPQ mutations (Quesada et al, 2015)
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