Influence of age, socioeconomic status, and location on the infant gut resistome across populations
ABSTRACTAntibiotic resistance is a growing global concern, with many ecological niches showing a high abundance of antibiotic resistance genes (ARGs), including the human gut. With increasing indications of ARGs in infants, this study aims to investigate the gut resistome profile during early life a...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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Taylor & Francis Group
2024-12-01
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| Series: | Gut Microbes |
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| Online Access: | https://www.tandfonline.com/doi/10.1080/19490976.2023.2297837 |
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| author | Dhrati V. Patangia Ghjuvan Grimaud Shaopu Wang R. Paul Ross Catherine Stanton |
| author_facet | Dhrati V. Patangia Ghjuvan Grimaud Shaopu Wang R. Paul Ross Catherine Stanton |
| author_sort | Dhrati V. Patangia |
| collection | DOAJ |
| description | ABSTRACTAntibiotic resistance is a growing global concern, with many ecological niches showing a high abundance of antibiotic resistance genes (ARGs), including the human gut. With increasing indications of ARGs in infants, this study aims to investigate the gut resistome profile during early life at a wider geographic level. To achieve this objective, we utilized stool samples data from 26 studies involving subjects aged up to 3 years from different geographical locations. The 32,277 Metagenome Assembled Genomes (MAGs) previously generated from shotgun sequencing reads from these studies were used for resistome analysis using RGI with the CARD database. This analysis showed that the distribution of ARGs across the countries in our study differed in alpha diversity and compositionally. In particular, the abundance of ARGs was found to vary by socioeconomic status and healthcare access and quality (HAQ) index. Surprisingly, countries having lower socioeconomic status and HAQ indices showed lower ARG abundance, which was contradictory to previous reports. Gram-negative genera, including Escherichia, Enterobacter, Citrobacter, and Klebsiella harbored a particularly rich set of ARGs, which included antibiotics that belong to the Reserve, Access or Watch category, such as glycopeptides, fluoroquinolones, sulfonamides, macrolides, and tetracyclines. We showed that ARG abundance exponentially decreased with time during the first 3 years of life. Many highly ARG-abundant species including Escherichia, Klebsiella, Citrobacter species that we observed are well-known pathobionts found in the infant gut in early life. High abundance of these species and a diverse range of ARGs in their genomes point toward the infant gut, acting as an ARG reservoir. This is a concern and further studies are needed to examine the causal effect and its consequences on long-term health. |
| first_indexed | 2024-03-08T14:22:58Z |
| format | Article |
| id | doaj.art-3122368f41874abdb70b3578e77c42a0 |
| institution | Directory Open Access Journal |
| issn | 1949-0976 1949-0984 |
| language | English |
| last_indexed | 2024-03-08T14:22:58Z |
| publishDate | 2024-12-01 |
| publisher | Taylor & Francis Group |
| record_format | Article |
| series | Gut Microbes |
| spelling | doaj.art-3122368f41874abdb70b3578e77c42a02024-01-13T13:03:39ZengTaylor & Francis GroupGut Microbes1949-09761949-09842024-12-0116110.1080/19490976.2023.2297837Influence of age, socioeconomic status, and location on the infant gut resistome across populationsDhrati V. Patangia0Ghjuvan Grimaud1Shaopu Wang2R. Paul Ross3Catherine Stanton4School of Microbiology, University College Cork, Cork, IrelandTeagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, IrelandKey Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, ChinaSchool of Microbiology, University College Cork, Cork, IrelandTeagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, IrelandABSTRACTAntibiotic resistance is a growing global concern, with many ecological niches showing a high abundance of antibiotic resistance genes (ARGs), including the human gut. With increasing indications of ARGs in infants, this study aims to investigate the gut resistome profile during early life at a wider geographic level. To achieve this objective, we utilized stool samples data from 26 studies involving subjects aged up to 3 years from different geographical locations. The 32,277 Metagenome Assembled Genomes (MAGs) previously generated from shotgun sequencing reads from these studies were used for resistome analysis using RGI with the CARD database. This analysis showed that the distribution of ARGs across the countries in our study differed in alpha diversity and compositionally. In particular, the abundance of ARGs was found to vary by socioeconomic status and healthcare access and quality (HAQ) index. Surprisingly, countries having lower socioeconomic status and HAQ indices showed lower ARG abundance, which was contradictory to previous reports. Gram-negative genera, including Escherichia, Enterobacter, Citrobacter, and Klebsiella harbored a particularly rich set of ARGs, which included antibiotics that belong to the Reserve, Access or Watch category, such as glycopeptides, fluoroquinolones, sulfonamides, macrolides, and tetracyclines. We showed that ARG abundance exponentially decreased with time during the first 3 years of life. Many highly ARG-abundant species including Escherichia, Klebsiella, Citrobacter species that we observed are well-known pathobionts found in the infant gut in early life. High abundance of these species and a diverse range of ARGs in their genomes point toward the infant gut, acting as an ARG reservoir. This is a concern and further studies are needed to examine the causal effect and its consequences on long-term health.https://www.tandfonline.com/doi/10.1080/19490976.2023.2297837Infant gut resistancemeta-analysisshotgun sequencingresistome |
| spellingShingle | Dhrati V. Patangia Ghjuvan Grimaud Shaopu Wang R. Paul Ross Catherine Stanton Influence of age, socioeconomic status, and location on the infant gut resistome across populations Gut Microbes Infant gut resistance meta-analysis shotgun sequencing resistome |
| title | Influence of age, socioeconomic status, and location on the infant gut resistome across populations |
| title_full | Influence of age, socioeconomic status, and location on the infant gut resistome across populations |
| title_fullStr | Influence of age, socioeconomic status, and location on the infant gut resistome across populations |
| title_full_unstemmed | Influence of age, socioeconomic status, and location on the infant gut resistome across populations |
| title_short | Influence of age, socioeconomic status, and location on the infant gut resistome across populations |
| title_sort | influence of age socioeconomic status and location on the infant gut resistome across populations |
| topic | Infant gut resistance meta-analysis shotgun sequencing resistome |
| url | https://www.tandfonline.com/doi/10.1080/19490976.2023.2297837 |
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