Jensen Emilie Egholm Bruun, Otani Saria, Liachko Ivan, Auch Benjamin, Aarestrup Frank M
National Food Institute, Technical University of Denmark, Kgs Lyngby, Ghana.
Phase Genomics, Seattle, Washington, USA.
Microbiol Spectr. 2025 Jan 7;13(1):e0148924. doi: 10.1128/spectrum.01489-24. Epub 2024 Dec 10.
-mediated glycopeptide resistance has been consistently high in one of the three main sewer systems in Copenhagen, Lynetten, for +20 years. To explore this for other glycopeptide resistance genes, and whether the colonization has resulted in establishment of multiple bacterial taxa, we mapped 505 shotgun metagenomic data sets from the inlet of three sewage treatment plants to 831 different glycopeptide resistance genes. Only and genes were differentially abundant in Lynetten. Analyses of eight contigs suggested limited variations in the flanking regions. Proximity ligation metagenomic analysis of 12 samples from Lynetten identified 441 and 5 paired reads mapping to and , respectively. The other end of these reads was mapped to generated metagenomic-assembled genomes and NCBI using BLAST. could only be linked to the phylum level (Bacillota). Plasmid analysis of Hi-C contigs showed that these were mainly located on plasmids reported found in enterococci species. Most -linked reads could only be linked to phylum and class level, but some reads were assigned to (7 reads), (4 reads), (2 reads), and (27 reads). Ten of the 20 Hi-C contigs-containing were annotated as plasmid, all reported found in species. This study shows that while Hi-C technology is valuable for linking antimicrobial resistance genes to bacterial taxa, it suffers from challenges in reliably mapping the linked read to a genomic region with sufficient taxonomic information. Our results also suggest that over the +20 years of colonizing a sewer system, has not become widespread across multiple taxa, remaining primarily in and , with the exception of .IMPORTANCELong-term colonization of microbial communities with antimicrobial-resistant bacteria is expected to result in sharing of the resistance genes between several different bacterial taxa of the communities. We investigated microbiomes from a sewer, which have been colonized with glycopeptide-resistant bacteria harboring the mobile gene cluster for a minimum of 20 years, using metagenomics sequencing and Hi-C. We found that despite the long-term presence in the sewer, the genes have seemingly not disseminated widely.
在哥本哈根的三大主要下水道系统之一——利内滕（Lynetten），介导的糖肽抗性持续20多年一直很高。为了探究其他糖肽抗性基因的情况，以及这种定殖是否导致了多种细菌类群的建立，我们将来自三个污水处理厂进水口的505个鸟枪法宏基因组数据集映射到831个不同的糖肽抗性基因上。只有 和 基因在利内滕的丰度存在差异。对8个重叠群的分析表明侧翼区域的变异有限。对来自利内滕的12个样本进行邻近连接宏基因组分析，分别鉴定出441个和5个配对读段映射到 和 。这些读段的另一端使用BLAST映射到生成的宏基因组组装基因组和NCBI上。 只能与门水平（芽孢杆菌门）相关联。对Hi-C重叠群的质粒分析表明，它们主要位于在肠球菌属物种中发现的质粒上。大多数与 相关的读段只能与门和纲水平相关联，但一些读段被归类到 （7个读段）、 （4个读段）、 （2个读段）和 （27个读段）。20个含有 的Hi-C重叠群中有10个被注释为质粒，所有这些质粒都在 物种中被发现。这项研究表明，虽然Hi-C技术对于将抗微生物抗性基因与细菌类群联系起来很有价值，但它在将连接的读段可靠地映射到具有足够分类信息的基因组区域方面存在挑战。我们的结果还表明，在对一个下水道系统进行20多年的定殖过程中， 并没有在多个类群中广泛传播，主要仍存在于 和 中， 除外。
重要性
预计抗微生物细菌对微生物群落的长期定殖会导致群落中几种不同细菌类群之间共享抗性基因。我们使用宏基因组测序和Hi-C技术研究了一个下水道的微生物群落，该下水道已被携带移动 基因簇的糖肽抗性细菌定殖至少20年。我们发现，尽管 基因在下水道中长期存在，但它们似乎并没有广泛传播。
