Table 1_Mapping the spread of fluoroquinolone resistance: continued presence of non-susceptible Escherichia coli in broilers.docx

IntroductionSustained resistance against fluoroquinolones (FQ), without the use of FQ in broilers, raises important questions about other possible factors contributing to the persistence in farms. Therefore, the current study investigates the prevalence of FQ non-susceptibility in Escherichia coli on broiler farms and examines the roles of day-old chicks, the farm environment, and the antimicrobial use (AMU) in the dynamics of the within-flock spread.
MethodsOn 29 Belgian broiler farms, AMU was monitored, while environmental and day-old chick intestinal samples (day 0) were collected before their arrival. On days 3 and 36 of the production round, 30 cloacal swabs were taken per farm. In all samples, total E. coli and FQ non susceptible E. coli isolates were quantified by non-selective and FQ selective isolation. A selection of the isolates was analyzed using whole-genome sequencing to characterize their resistance and virulence-associated determinants and to investigate their phylogenetic relatedness using core-genome multi-locus sequence typing (cgMLST) and whole-genome single-nucleotide polymorphism (SNP) analysis.
ResultsBefore entering the stable, day-old chicks carried FQ non-susceptible E. coli on 79.3% of the farms, while FQ non-susceptible E. coli were found in 48.3% of the sampled environments. According to cgMLST, identical FQ non-susceptible isolates were found on day 0 and 36, suggesting that FQ non-susceptible isolates present in the environment at the start of a production round or in day-old chicks, can remain present until slaughter, even when no FQs were used. Total AMU was positively correlated with the proportion of FQ non-susceptible E. coli [r = 0.42, 95% CI (0.06, 0.68), p = 0.03], often also multidrug-resistant, at the end of the production cycle.
ConclusionThe continued presence of FQ non-susceptible E. coli in broiler farms is likely the result of both a historical contamination at the farm level and a continuous influx along the production chain. AMU contributes to the continued presence of FQ non-susceptible E. coli in broiler farms, but accounted for only a small proportion of the variability in FQ non-susceptibility in currently investigated farms. The role of certain virulence-associated genes in the persistence of FQ non-susceptible E. coli in broiler farms deserves more in-depth research.

引言：在肉仔鸡未使用氟喹诺酮类（fluoroquinolones, FQ）的情况下，其对氟喹诺酮类的持续耐药性引发了关键问题：究竟有哪些其他因素推动了该类耐药菌在养殖场中的持续存在。为此，本研究针对肉仔鸡养殖场中大肠埃希菌（Escherichia coli）对氟喹诺酮类的不敏感流行率展开调查，并解析1日龄雏鸡、养殖场环境以及抗菌药物使用（antimicrobial use, AMU）在鸡群内传播动态中的作用。

材料与方法：本研究对29家比利时肉仔鸡养殖场的抗菌药物使用情况进行监测，并在雏鸡入场前采集其环境样本与1日龄雏鸡肠道样本（第0天）。在养殖周期的第3天与第36天，每个养殖场采集30份泄殖腔拭子。通过非选择性培养基与氟喹诺酮类选择性培养基分离培养，对所有样本中的总大肠埃希菌与氟喹诺酮类不敏感大肠埃希菌分离株进行定量。选取部分分离株开展全基因组测序，以明确其耐药与毒力相关决定簇；同时采用核心基因组多位点序列分型（core-genome multi-locus sequence typing, cgMLST）与全基因组单核苷酸多态性（single-nucleotide polymorphism, SNP）分析，探究分离株的系统发育相关性。

结果：在雏鸡进入鸡舍前，79.3%的养殖场的1日龄雏鸡体内即可检出氟喹诺酮类不敏感大肠埃希菌，而48.3%的采样环境中也存在此类菌株。核心基因组多位点序列分型结果显示，第0天与第36天检出的氟喹诺酮类不敏感分离株基因型完全一致，这表明即使养殖周期内未使用氟喹诺酮类，在养殖初期环境或1日龄雏鸡中存在的此类菌株，可持续存活至屠宰阶段。总抗菌药物使用量与养殖周期末期的氟喹诺酮类不敏感大肠埃希菌占比呈正相关[r=0.42, 95%置信区间(0.06, 0.68), p=0.03]，此类菌株通常同时具有多重耐药性。

结论：肉仔鸡养殖场中氟喹诺酮类不敏感大肠埃希菌的持续存在，可能源于养殖场层面的既往污染与养殖链中的持续传入两个途径。抗菌药物使用虽会推动此类菌株在养殖场中的持续留存，但在本次研究涉及的养殖场中，其仅能解释氟喹诺酮类不感性变异中的一小部分。部分毒力相关基因在氟喹诺酮类不敏感大肠埃希菌于肉仔鸡养殖场持续存活过程中所发挥的作用，仍有待进一步深入研究。