Colistin is extensively used in animal production in many low- and middle-income countries. There is a need to develop methodologies to benchmark and monitor changes in resistance in commensal bacterial populations in farms. We aimed to evaluate the performance of a broth microdilution method based on culturing a pooled Escherichia coli suspension (30-50 organisms) from each sample. In order to confirm the biological basis and sensitivity of the method, we prepared 16 standard suspensions containing variable ratios of colistin-susceptible and mcr-1 encoded colistin-resistant E. coli which were grown in 2mg/L colistin. The optical density (OD_600nm) readings over time were used to generate a growth curve, and were adjusted to the values obtained in the absence of colistin. The median limit of detection of the method was 1 colistin-resistant in 10⁴ susceptible colonies [1^st - 3^rd quartile, 1:10² - 1:10⁵]. We applied this method to 108 pooled faecal samples from 36 chicken flocks in the Mekong Delta (Vietnam) over the production cycle. The correlation between this method and the prevalence of colistin resistance in individual colonies harvested from field samples, determined by the Minimum Inhibitory Concentration (MIC), was established. The overall prevalence of colistin resistance at sample and isolate level was 38.9% and 19.4%, respectively. Increased colistin resistance was associated with recent (2 weeks) use of colistin and other, non-colistin antimicrobials (OR=3.67 and OR=1.84, respectively). Our method is a sensitive and affordable approach to monitor changes in colistin resistance in pooled E. coli populations from faecal samples over time.

中文翻译：

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一种测量鸡群大肠杆菌种群表型大肠菌素抗性的新方法

Colistin在许多中低收入国家中广泛用于动物生产。需要开发一种方法来对农场中共生细菌种群的耐药性进行基准测试和监测。我们旨在基于培养每个样品的合并大肠杆菌悬浮液（30-50个生物体）来评估肉汤微稀释法的性能。为了证实该方法的生物学基础和敏感性，我们制备了16种标准悬浮液，其中含有可变比例的大肠菌素敏感性和mcr-1编码的大肠菌素抗性大肠杆菌，并在2mg / L大肠菌素中生长。光密度（OD _600nm）随时间的读数用于生成生长曲线，并调整为在没有粘菌素的情况下获得的值。检测的方法的中位数限制在10个为1个粘菌素抗性⁴敏感菌落[1^日3 -^第三四分位数，1:10 ² - 1:10 ⁵]。在整个生产周期中，我们将这种方法应用于来自湄公河三角洲（越南）的36个鸡群的108个粪便样本中。建立了该方法与从田间样品中收获的单个菌落中大肠菌素抗性的患病率之间的相关性，并通过最小抑制浓度（MIC）进行了确定。样品和分离株水平上大肠菌素抗性的总体患病率分别为38.9％和19.4％。大肠菌素抗性增加与大肠菌素和其他非colistin抗菌药物的近期使用（2周）有关（分别为OR = 3.67和OR = 1.84）。我们的方法是一种灵敏且负担得起的方法，可以随时间监测粪便样本中合并的大肠杆菌群体中大肠菌素抗性的变化。