Department of Medical Microbiology, UMC Utrecht, Utrecht University, Utrecht, The Netherlands.
Centre for Infectious Disease Control Netherlands, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands.
Microbiol Spectr. 2023 Aug 17;11(4):e0006323. doi: 10.1128/spectrum.00063-23. Epub 2023 Jul 5.
The gut microbiome of humans and animals acts as a reservoir of extended-spectrum beta-lactamase-producing Escherichia coli (ESBL-EC). Dogs are known for having a high prevalence of ESBL-EC in their gut microbiota, although their ESBL-EC carrier status often shifts over time. We hypothesized that the gut microbiome composition of dogs is implicated in ESBL-EC colonization status. Therefore, we assessed whether ESBL-EC carriage in dogs is associated with changes in the gut microbiome and resistome. Fecal samples were collected longitudinally from 57 companion dogs in the Netherlands every 2 weeks for a total of 6 weeks ( = 4 samples/dog). Carriage of ESBL-EC was determined through selective culturing and PCR and in line with previous studies, we observed a high prevalence of ESBL-EC carriage in dogs. Using 16s rRNA gene profiling we found significant associations between detected ESBL-EC carriage and an increased abundance of , , , and the shared genera of Escherichia in the dog microbiome. A resistome capture sequencing approach (ResCap) furthermore, revealed associations between detected ESBL-EC carriage and the increased abundance of the antimicrobial resistance genes: , , , , and . In summary, our study showed that ESBL-EC carriage is associated with a distinct microbiome and resistome composition. The gut microbiome of humans and animals is an important source of multidrug resistant pathogens, including beta-lactamase-producing Escherichia coli (ESBL-EC). In this study, we assessed if the carriage of ESBL-EC in dogs was associated with changes in gut composition of bacteria and antimicrobial resistant genes (ARGs). Therefore, stool samples from 57 dogs were collected every 2 weeks for a total of 6 weeks. Sixty eight percent of the dogs carried ESBL-EC during at least one of the time points analyzed. By investigating the gut microbiome and resistome composition, we observed specific changes at time points when dogs were colonized with ESBL-EC compared to time points whenESBL-EC were not detected. In conclusion, our study highlights the importance to study the microbial diversity in companion animals, as gut colonization of particular antimicrobial resistant bacteria might be an indication of a changed microbial composition that is associated with the selection of particular ARGs.
人类和动物的肠道微生物群是产生超广谱β-内酰胺酶的大肠杆菌（ESBL-EC）的储库。众所周知，狗的肠道微生物群中 ESBL-EC 的患病率很高，尽管它们的 ESBL-EC 携带者状态经常随时间而变化。我们假设狗的肠道微生物群组成与 ESBL-EC 定植状态有关。因此，我们评估了狗的 ESBL-EC 携带是否与肠道微生物群和耐药组的变化有关。从荷兰的 57 只伴侣犬中每隔两周收集一次粪便样本，总共 6 周（=每只狗 4 个样本）。通过选择性培养和 PCR 确定 ESBL-EC 的携带情况，与之前的研究一致，我们观察到狗的 ESBL-EC 携带率很高。使用 16s rRNA 基因谱分析，我们发现检测到的 ESBL-EC 携带与狗微生物群中 、 、 、 和 Escherichia 的共享属的丰度增加之间存在显著关联。此外，使用耐药组捕获测序方法（ResCap）还揭示了检测到的 ESBL-EC 携带与抗菌药物耐药基因： 、 、 、 和 的丰度增加之间的关联。总之，我们的研究表明，ESBL-EC 的携带与独特的微生物群和耐药组组成有关。人类和动物的肠道微生物群是包括产超广谱β-内酰胺酶的大肠杆菌（ESBL-EC）在内的多种耐药病原体的重要来源。在这项研究中，我们评估了狗是否携带 ESBL-EC 与肠道细菌组成和抗菌药物耐药基因（ARGs）的变化有关。因此，每隔两周收集 57 只狗的粪便样本，总共 6 周。在分析的至少一个时间点，68%的狗携带 ESBL-EC。通过研究肠道微生物群和耐药组组成，我们观察到与未检测到 ESBL-EC 相比，当狗定植 ESBL-EC 时，特定时间点的肠道微生物群和耐药组组成发生了变化。总之，我们的研究强调了研究伴侣动物微生物多样性的重要性，因为特定抗菌药物耐药细菌的肠道定植可能是微生物组成发生变化的一个迹象，这种变化与特定 ARGs 的选择有关。
