Saeed Muhammad Hassan, Kujawska Magdalena, Ellen Kristiana, Acuna-Gonzalez Antia, Bernabeu Lorenzo Manuel, Carmen Collado Maria, Mommers Monique, van Best Niels, Hall Lindsay J, Neuhaus Klaus
Core Facility Microbiome, ZIEL - Institute for Food & Health, Freising, Germany.
Intestinal Microbiome, TUM School of Life Sciences, Freising, Germany.
Gut Microbes. 2025 Dec;17(1):2516699. doi: 10.1080/19490976.2025.2516699. Epub 2025 Jun 16.
spp. some of which are pathogenic, are common gut microbiota members, including also infants. Infants may be more susceptible to due to their developing gut ecosystems. It is unclear whether antibiotic resistance genes (ARGs) and certain genomic traits in enterococci are restricted to the human subpopulation or more widespread. Furthermore, the correlation between these traits and geographic variation is poorly understood. Therefore, we sequenced 100 strains isolated from full-term healthy infants' fecal samples from two geographically distant European cohorts (MAMI in Spain and LucKi from the Netherlands) to explore the diversity of spp. within the infant's gut microbiome and assess cohort-specific traits such as ARGs. Most isolates were and , with a total of 11 species identified. We found a rich reservoir of ARGs, plasmids, prophages and virulence factors in the infant strains, with minimal cohort-specific differences in resistome profiles. In addition, Epx, a pore-forming toxin associated with pathogenicity, was found in strains. While metabolic profiles were similar across cohorts, strains harbored more virulence genes and prophages compared to other species. An analysis of public genomes revealed that multi-drug resistant (MDR) strains exist without any significant geographic or temporal pattern. Phenotypic resistance analysis indicated that 28% of MAMI strains were gentamicin resistant, compared to 5% of the strains from the LucKi cohort, though LucKi isolates were also resistant to other antibiotics. We also selected ten isolates with varying virulence gene repertoires for phenotypic virulence testing in and found them killing at various rates, however no clear pattern emerged in correlation with any specific genetic determinant. Overall, our results suggest that spp. including ARGs, are highly mobile across Europe and beyond. Their adaptability likely facilitates long-distance dissemination, with strains being acquired early in life from community environments.
肠球菌属（Enterococcus spp.）中的一些具有致病性，是常见的肠道微生物群成员，包括婴儿。由于婴儿肠道生态系统正在发育，他们可能更容易受到影响。目前尚不清楚肠球菌中的抗生素抗性基因（ARGs）和某些基因组特征是仅限于人类亚群还是更为广泛。此外，人们对这些特征与地理变异之间的相关性了解甚少。因此，我们对从两个地理上相距遥远的欧洲队列（西班牙的MAMI和荷兰的LucKi）中足月健康婴儿粪便样本中分离出的100株菌株进行了测序，以探索婴儿肠道微生物群中肠球菌属的多样性，并评估特定队列特征，如ARGs。大多数分离株为粪肠球菌（E. faecalis）和屎肠球菌（E. faecium），共鉴定出11个物种。我们在婴儿菌株中发现了丰富的ARGs、质粒、前噬菌体和毒力因子库，耐药组谱中特定队列的差异极小。此外，在粪肠球菌菌株中发现了与致病性相关的成孔毒素Epx。虽然各队列的代谢谱相似，但粪肠球菌菌株与其他物种相比含有更多的毒力基因和前噬菌体。对公开的肠球菌基因组分析表明，多药耐药（MDR）菌株的存在没有任何明显的地理或时间模式。表型抗性分析表明，MAMI队列中28%的菌株对庆大霉素耐药，而LucKi队列中这一比例为5%，不过LucKi分离株也对其他抗生素耐药。我们还选择了十株具有不同毒力基因库的肠球菌分离株，在秀丽隐杆线虫（Caenorhabditis elegans）中进行表型毒力测试，发现它们以不同的速率致死，然而与任何特定遗传决定因素均未出现明显的相关性模式。总体而言，我们的结果表明，包括ARGs在内的肠球菌属在欧洲及其他地区具有高度的流动性。它们的适应性可能促进了远距离传播，菌株在生命早期从社区环境中获得。
