Mixed gastrointestinal nematode (GIN) infections are a common and significant cause of financial loss for small ruminant producers. Morphologic examination of third-stage larvae (L3) can be used to identify species composition in feces but has limitations due to the requirement for specialized expertise and the extensive time (8-15 d depending on method used) and labour involved. Moreover, differential development and survival of larvae during coproculture to the third stage often occurs. Deep amplicon sequencing of the ITS-2 rDNA locus of first-stage larvae (L1) allows for higher throughput with reduced specialist labour and reduces the risk of misidentification. Harvesting of L1 soon after hatching is also faster and further reduces labour as well as biases that can occur due to differential larval development and survival. This study compares the results of morphologic examination of L3 with those of ITS-2 rDNA deep amplicon sequencing of L1 from a set of pooled fecal samples. The proportions of eggs that were successfully recovered as larvae following culture to L3 and L1 were also compared. Larval recovery rate was significantly lower from L3 cultures than from L1 cultures (p < 0.001); eggs were 238.7 times less likely to develop to L3 than to L1 (95 % confidence interval for odds ratio 80.0-712.0). Significantly lower proportions of Teladorsagia circumcincta (odds ratio = 3.1, p = 0.008) and higher proportions of Trichostrongylus spp. (p = 0.009) were identified using morphologic examination of L3 compared with deep amplicon sequencing of L1 on the same samples. This is consistent with previous reports of differential survival of these species in L3 cultures. These results indicate that deep amplicon sequencing of L1 may reduce bias introduced by differential GIN survival to L3 in small ruminants.

中文翻译：

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比较ITS-2 rDNA线虫基因组测序与形态学鉴定以量化小反刍动物粪便中胃肠道线虫群落的种类组成。

混合胃肠道线虫（GIN）感染是小型反刍动物生产者经济损失的常见且重要原因。可以对第三阶段幼虫（L3）进行形态学检查，以鉴定粪便中的物种组成，但由于需要专门的技术知识和较长的时间（取决于使用的方法，时间为8-15 d）和所涉及的劳动而受到限制。而且，在共培养至第三阶段期间，经常发生幼虫的不同发育和存活。第一阶段幼虫（L1）ITS-2 rDNA基因座的深度扩增子测序可实现更高的通量，同时减少专业劳动，并降低误识别的风险。孵化后不久收获L1的速度也更快，并进一步减少了人工以及由于幼虫发育和生存差异而可能产生的偏见。本研究将L3的形态学检查结果与一组粪便样本中L1的ITS-2 rDNA深度扩增子测序结果进行了比较。还比较了培养到L3和L1后成功回收为幼虫的卵的比例。L3培养物的幼虫恢复率显着低于L1培养物（p <0.001）。卵发育到L3的可能性比生长到L1的可能性小238.7倍（优势比80.0-712.0，95％置信区间）。明显的比例是Teladorsagia circumcincta（奇数比= 3.1，p = 0.008）和较高的Trichostrongylus spp。（p = 0.009）是使用L3的形态学检查与相同样品上L1的深度扩增子测序进行比较而确定的。这与以前在L3培养物中这些物种的差异存活率的报道一致。