Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School of Sciences and Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon.
Université de Lyon-ANSES laboratoire de Lyon, Unité Antibiorésistance et Virulence Bactériennes, Lyon, France.
J Antimicrob Chemother. 2021 Nov 12;76(12):3135-3143. doi: 10.1093/jac/dkab327.
Knowledge on the dynamic of MDR Escherichia coli in the human community is still limited, especially in low- and middle-income countries. Our goal was to decipher the dynamics of E. coli lineages and plasmids resistant to ESC, carbapenem and colistin within and between food workers in Lebanon using genomic-based approaches.
Eighty-four healthy adults working in three bakeries were sampled twice at a 6 monthly interval. E. coli resistant to ESC (ESC-E), carbapenem (CP-E) and colistin (CO-E) were collected on selective plates. Non-duplicate isolates were whole-genome sequenced using the Illumina technology and plasmid transmission was assessed by long-read sequencing. Data were analysed using bioinformatics tools and SNP-based phylogeny.
ESC-E carriage rate reached 34.5% (t0) and 52.9% (t6), and 15 workers were positive at both t0 and t6. Carbapenem resistance (blaOXA-181, blaOXA-204, blaNDM-5) was found in five workers at t0 and two at t6, while colistin resistance (mcr-1.1) was found in five workers at t0 and one at t6. Forty-seven different STs were identified, of which three STs were predominant (ST131, n = 9; ST10, n = 5; ST69, n = 5). One worker presented the same ESC-E clone at t0 and t6. Twelve different events of clonal transmission among individuals were exemplified while plasmid transmission was only shown once.
Our study revealed a high carriage rate of MDR E. coli (60.7%) and the emergence of CP and colistin resistance in the Lebanese community. Incidental and long-term ESC-E carriage was observed in 41.7% and 17.9% of the workers, respectively. The high clonal diversity suggests an important dynamic of acquisition and loss of MDR E. coli and limited plasmid spread.
人类社区中对多重耐药大肠杆菌（MDR Escherichia coli）动态的了解仍然有限，特别是在中低收入国家。我们的目标是使用基于基因组的方法，解析黎巴嫩食品工人内部和之间对 ESC、碳青霉烯和黏菌素具有耐药性的大肠杆菌谱系和质粒的动态。
84 名在三家面包店工作的健康成年人每隔 6 个月接受两次采样。在选择性平板上收集对 ESC（ESC-E）、碳青霉烯（CP-E）和黏菌素（CO-E）具有耐药性的大肠杆菌。使用 Illumina 技术对非重复分离株进行全基因组测序，并通过长读测序评估质粒传播。使用生物信息学工具和 SNP 系统发育分析数据。
ESC-E 的携带率在 t0 时达到 34.5%，在 t6 时达到 52.9%，有 15 名工人在 t0 和 t6 时均呈阳性。在 t0 时发现五名工人具有碳青霉烯耐药性（blaOXA-181、blaOXA-204、blaNDM-5），两名工人在 t6 时具有碳青霉烯耐药性，而在 t0 时发现五名工人具有黏菌素耐药性（mcr-1.1），一名工人在 t6 时具有黏菌素耐药性。共鉴定出 47 种不同的 ST 型，其中三种 ST 型占主导地位（ST131，n=9；ST10，n=5；ST69，n=5）。一名工人在 t0 和 t6 时携带相同的 ESC-E 克隆。在个体之间例证了 12 个不同的克隆传播事件，而质粒传播仅显示了一次。
本研究揭示了黎巴嫩社区中 MDR 大肠杆菌（60.7%）的高携带率以及碳青霉烯和黏菌素耐药性的出现。在 41.7%和 17.9%的工人中分别观察到偶然和长期携带 ESC-E。高克隆多样性表明 MDR 大肠杆菌的获得和丧失具有重要的动态性，且质粒传播有限。
