Abstract

Background:

There is a significant gap in our understanding of the sources of multidrug-resistant bacteria and resistance genes in community settings where human–animal interfaces exist.

Objectives:

This study characterized the relationship of third-generation cephalosporin-resistant Escherichia coli (3GCR-EC) isolated from animal feces in the environment and child feces based on phenotypic antimicrobial resistance (AMR) and whole genome sequencing (WGS).

Methods:

We examined 3GCR-EC isolated from environmental fecal samples of domestic animals and child fecal samples in Ecuador. We analyzed phenotypic and genotypic AMR, as well as clonal relationships (CRs) based on pairwise single-nucleotide polymorphisms (SNPs) analysis of 3GCR-EC core genomes. CRs were defined as isolates with fewer than 100 different SNPs.

Results:

A total of 264 3GCR-EC isolates from children ($n=21$), dogs ($n=20$), and chickens ($n=18$) living in the same region of Quito, Ecuador, were identified. We detected 16 CRs total, which were found between 7 children and 5 domestic animals (5 CRs) and between 19 domestic animals (11 CRs). We observed that several clonally related 3GCR-EC isolates had acquired different plasmids and AMR genes. Most CRs were observed in different homes ($n=14$) at relatively large distances. Isolates from children and domestic animals shared the same $bl{a}_{\text{CTX}\text{-M}}$ allelic variants, and the most prevalent were $bl{a}_{\text{CTX}\text{-M-}55}$ and $bl{a}_{\text{CTX}\text{-M-}65}$, which were found in isolates from children, dogs, and chickens.

Discussion:

This study provides evidence of highly dynamic horizontal transfer of AMR genes and mobile genetic elements (MGEs) in the E. coli community and shows that some 3GCR-EC and (extended-spectrum $\mathrm{\beta }\text{-lactamase}$) ESBL genes may have moved relatively large distances among domestic animals and children in semirural communities near Quito, Ecuador. Child–animal contact and the presence of domestic animal feces in the environment potentially serve as important sources of drug-resistant bacteria and ESBL genes. https://doi.org/10.1289/EHP7729

中文翻译：

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产大肠杆菌和 ESBL 基因的超广谱 β-内酰胺酶 (ESBL) 在厄瓜多尔儿童和家畜中的环境传播

摘要

背景：

在存在人与动物界面的社区环境中，我们对多重耐药菌和耐药基因的来源的理解存在重大差距。

目标：

本研究基于表型抗菌素耐药性 (AMR) 和全基因组测序 (WGS)，表征了从环境中的动物粪便中分离出的第三代头孢菌素耐药性大肠杆菌(3GCR-EC) 与儿童粪便之间的关系。

方法：

我们检查了从厄瓜多尔的家畜环境粪便样本和儿童粪便样本中分离的 3GCR-EC。我们分析了表型和基因型 AMR，以及基于 3GCR-EC 核心基因组的成对单核苷酸多态性 (SNP) 分析的克隆关系 (CR)。CR 被定义为具有少于 100 个不同 SNP 的分离株。

结果：

共有 264 株 3GCR-EC 分离株来自儿童（$n=21$）， 小狗 （$n=20$) 和鸡 ($n=18$) 居住在厄瓜多尔基多的同一地区，被确定。我们总共检测到 16 个 CR，分别在 7 个儿童和 5 只家畜（5 个 CR）之间以及 19 个家畜（11 个 CR）之间发现。我们观察到几个克隆相关的 3GCR-EC 分离株获得了不同的质粒和 AMR 基因。大多数 CR 是在不同的家庭中观察到的（$n=14$) 在相对较大的距离。儿童和家畜的隔离物共享相同$乙升{\mathrm{一种}}_{\text{CTX}\text{-M}}$ 等位基因变异，最普遍的是 $乙升{\mathrm{一种}}_{\text{CTX}\text{-M-}55}$ 和 $乙升{\mathrm{一种}}_{\text{CTX}\text{-M-}65}$，这是在儿童、狗和鸡的分离物中发现的。

讨论：

这项研究提供了大肠杆菌群落中 AMR 基因和移动遗传元件 (MGE) 的高度动态水平转移的证据，并表明一些 3GCR-EC 和（扩展谱$\mathrm{\beta }\text{-内酰胺酶}$) ESBL 基因可能在厄瓜多尔基多附近的半农村社区的家畜和儿童之间移动了相对较大的距离。儿童与动物的接触和环境中家畜粪便的存在可能是耐药细菌和 ESBL 基因的重要来源。https://doi.org/10.1289/EHP7729