High resolution parallel sequencing reveals multi-strain Campylobacter in broiler chicken flocks testing 'negative' by conventional culture methods: implications for control of Campylobacter infection
High resolution parallel sequencing reveals multi-strain Campylobacter in broiler chicken flocks testing 'negative' by conventional culture methods: implications for control of Campylobacter infection
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高分辨率并行测序揭示肉鸡群中的多菌株弯曲杆菌通过传统培养方法检测为“阴性”：对控制弯曲杆菌感染的影响
DOI：
10.1101/2022.03.28.485779
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发表时间：
2022
期刊：
影响因子：
--
通讯作者：
Colles F
中科院分区：
文献类型：
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作者：
Colles F
受污染的鸡肉是人类弯曲杆菌病的主要来源，尽管努力限制农场肉鸡群的定植，但感染率仍然很高。使用传统的培养或qPCR检测方法，弯曲杆菌通常在3周龄的肉鸡群中检测到，导致假设感染是在这个时候横向引入鸡舍的。在这项研究中，我们对由poragene编码的弯曲菌外膜蛋白片段进行平行测序，在23至28岁肉鸡群的新鲜粪便样本中检测弯曲菌dna的存在。使用poratart测试的290个样本中都检测到了弯曲菌dna，使用16S细菌谱分析的样本中有48%的样本检测到了弯曲菌dna，无论是否可以用传统的qPCR阈值检测到弯曲菌。在通过常规方法确定为弯曲杆菌“阳性”的鸡群中，单一的poraf2变体占主导地位，但在弯曲杆菌“阴性”的鸡群中，可以看到不同的模式。与传统方法相比，要在更早年龄的肉鸡群中常规检测出低水平的弯曲杆菌，就需要重新检查如何以及何时对活禽采取最佳的生物安全措施。此外，这可能有助于研究为什么单弯曲杆菌变异在某些肉鸡群中而不是其他肉鸡群中增殖。
Contaminated chicken meat is a major source of human Campylobacteriosis and rates of infection remain high, despite efforts to limit the colonisation of broiler (meat) chicken flocks on farms. Using conventional testing methods of culture or qPCR,Campylobacteris typically detected amongst broiler flocks from 3 wk of age, leading to the assumption that infection is introduced horizontally into chicken rearing houses at this time. In this study, we use parallel sequencing of a fragment of theCampylobacterouter membrane protein, encoded by theporAgene, to test for presence ofCampylobacterDNA amongst fresh fecal samples collected from broiler flocks aged 23 to 28 d.CampylobacterDNA was detected in all of the 290 samples tested using theporAtarget, and in 48% of samples using 16S bacterial profiling, irrespective of whether or notCampylobactercould be detected using conventional qPCR thresholds. A singleporAf2variant was predominant among flocks that would be determined to beCampylobacter ‘positive’ by conventional means, but a diverse pattern was seen among flocks that wereCampylobacter‘negative’. The ability to routinely detect low levels ofCampylobacteramongst broiler flocks at a much earlier age than would conventionally be identified requires a re-examination of how and when biosecurity measures are best applied for live birds. In addition, it may be useful to investigate why singleCampylobactervariants proliferate in some broiler flocks and not others.