Departament of Biotechnology, Institute of Agrochemistry and Food Technology- National Spanish Research Council (IATA-CSIC), Paterna, Valencia, Spain.
Department of Pediatrics, School of Medicine, University of Valencia, Valencia, Spain.
Ann Clin Microbiol Antimicrob. 2024 Aug 13;23(1):72. doi: 10.1186/s12941-024-00725-z.
Alongside microbiota development, the evolution of the resistome is crucial in understanding the early-life acquisition and persistence of Antibiotic Resistance Genes (ARGs). Therefore, the aim of this study is to provide a comprehensive view of the evolution and dynamics of the neonatal resistome from 7 days to 4 months of age using a high-throughput qPCR platform.
In the initial phase, a massive screening of 384 ARGs using a high-throughput qPCR in pooled healthy mother-infant pairs feces from the MAMI cohort was carried out to identify the most abundant and prevalent ARGs in infants and in mothers. This pre-analysis allowed for later targeted profiling in a large number of infants in a longitudinal manner during the first 4 months of life. 16S rRNA V3-V4 amplicon sequencing was performed to asses microbial composition longitudinally. Potential factors influencing the microbiota and ARGs in this period were also considered, such as mode of birth and breastfeeding type.
Following the massive screening, the top 45 abundant ARGs and mobile genetic elements were identified and studied in 72 infants during their first months of life (7 days, 1, 2, and 4 months). These genes were associated with resistance to aminoglycosides, beta-lactams and tetracyclines, among others, as well as integrons, and other mobile genetic elements. Changes in both ARG composition and quantity were observed during the first 4 months of life: most ARGs abundance increased over time, but mobile genetic elements decreased significantly. Further exploration of modulating factors highlighted the effect on ARG composition of specific microbial genus, and the impact of mode of birth at 7 days and 4 months. The influence of infant formula feeding was observed at 4-month-old infants, who exhibited a distinctive resistome composition.
This study illustrates the ARG evolution and dynamics in the infant gut by use of a targeted, high-throughput, quantitative PCR-based method. An increase in antibiotic resistance over the first months of life were observed with a fundamental role of delivery mode in shaping resistance profiles. Further, we highlighted the influence of feeding methods on the resistome development. These findings offer pivotal insights into dynamics of and factors influencing early-life resistome, with potential avenues for intervention strategies.
除了微生物组的发展外，抗性组的进化在理解抗生素耐药基因（ARGs）的早期获得和持久性方面至关重要。因此，本研究旨在使用高通量 qPCR 平台提供新生儿抗性组从 7 天到 4 个月大的演变和动态的全面视图。
在初始阶段，对来自 MAMI 队列的健康母婴粪便混合样本使用高通量 qPCR 进行了 384 个 ARG 的大规模筛选，以确定婴儿和母亲中最丰富和最常见的 ARGs。这种预分析允许在生命的头 4 个月以纵向方式对大量婴儿进行靶向分析。16S rRNA V3-V4 扩增子测序用于纵向评估微生物组成。还考虑了影响该时期微生物群和 ARGs 的潜在因素，例如分娩方式和母乳喂养类型。
在大规模筛选之后，在 72 名婴儿的第一个月生命中鉴定并研究了前 45 个丰富的 ARG 和移动遗传元件（7 天、1、2 和 4 个月）。这些基因与对氨基糖苷类、β-内酰胺类和四环素类的耐药性有关，以及整合子和其他移动遗传元件。在生命的头 4 个月中观察到 ARG 组成和数量的变化：大多数 ARG 丰度随时间增加，但移动遗传元件显著减少。对调节因子的进一步探索突出了特定微生物属对 ARG 组成的影响，以及出生方式在 7 天和 4 个月时的影响。在 4 个月大的婴儿中观察到婴儿配方奶喂养的影响，他们表现出独特的抗性组组成。
本研究通过使用靶向、高通量、基于定量 PCR 的方法说明了婴儿肠道中 ARG 的演变和动态。在生命的头几个月中观察到抗生素耐药性增加，分娩方式在塑造耐药谱方面起着重要作用。此外，我们强调了喂养方法对抗性组发展的影响。这些发现提供了对早期生命抗性组的动态和影响因素的重要见解，为干预策略提供了潜在途径。
