犬中的急性出血性腹泻综合征(AHDS)是一种病因不明的病症。Providenciaalcalifaciens被怀疑在这种疾病中起作用,因为它通常在2019年挪威爆发期间在患有AHDS的狗中发现。这种细菌作为犬肠道微生物群的组成部分的作用是未知的,因此,本研究开始使用宏基因组学研究其在健康狗中的发生。
■为了降低错误检测的可能性,我们通过在培养阴性的粪便样本中添加一系列细菌稀释液,并通过qPCR和shot弹枪宏基因组学进行分析,建立了巴氏疟原虫的宏基因组阈值。测定了半乳杆菌的检测极限并用于建立宏基因组阈值。在具有已知培养状态的巴氏疟原虫的自然污染的粪便样品上验证阈值。最后,在HUNTOneHealth项目中收集的犬粪便样本(n=362)的猎枪宏基因组数据集中,使用宏基因组阈值来确定产碱假单胞菌的发生.
■宏基因组测定和qPCR的检出限为每个粪便样品1.1x103CFU。通过shot弹枪宏基因组学,其对应于Cq值为31.4和569个独特的k-mer计数。将这个宏基因组阈值应用于来自健康狗的362个粪便宏基因组数据集,仅在1.1%(95%CI[0.0,6.8])的样品中发现了产碱假单胞菌,然后处于较低的相对丰度(中位数:0.04%;范围:0.00至0.81%)。qPCR和鸟枪宏基因组学检测的灵敏度较低,因为只有40%的培养阳性样本通过qPCR和宏基因组学也是阳性的。
■使用我们的检出限,健康犬的粪便样本中的巴氏疟原虫的发生率很低。鉴于宏基因组检测的灵敏度低,这些结果并不排除这种细菌在较低丰度下的发生率明显较高。
UNASSIGNED: Acute haemorrhagic diarrhoea syndrome (AHDS) in dogs is a condition of unknown aetiology. Providencia alcalifaciens is suspected to play a role in the disease as it was commonly found in dogs suffering from AHDS during a Norwegian outbreak in 2019. The role of this bacterium as a constituent of the canine gut microbiota is unknown, hence this study set out to investigate its occurrence in healthy dogs using metagenomics.
UNASSIGNED: To decrease the likelihood of false detection, we established a metagenomic threshold for P. alcalifaciens by spiking culture-negative stool samples with a range of bacterial dilutions and analysing these by qPCR and shotgun metagenomics. The detection limit for P. alcalifaciens was determined and used to establish a metagenomic threshold. The threshold was validated on naturally contaminated faecal samples with known cultivation status for P. alcalifaciens. Finally, the metagenomic threshold was used to determine the occurrence of P. alcalifaciens in shotgun metagenomic datasets from canine faecal samples (n=362) collected in the HUNT One Health project.
UNASSIGNED: The metagenomic assay and qPCR had a detection limit of 1.1x103 CFU P. alcalifaciens per faecal sample, which corresponded to a Cq value of 31.4 and 569 unique k-mer counts by shotgun metagenomics. Applying this metagenomic threshold to 362 faecal metagenomic datasets from healthy dogs, P. alcalifaciens was found in only 1.1% (95% CI [0.0, 6.8]) of the samples, and then in low relative abundances (median: 0.04%; range: 0.00 to 0.81%). The sensitivity of the qPCR and shotgun metagenomics assay was low, as only 40% of culture-positive samples were also positive by qPCR and metagenomics.
UNASSIGNED: Using our detection limit, the occurrence of P. alcalifaciens in faecal samples from healthy dogs was low. Given the low sensitivity of the metagenomic assay, these results do not rule out a significantly higher occurrence of this bacterium at a lower abundance.