Saeed, Muhammad Hassan, Kujawska, Magdalena, Ellen, Kristiana, Acuna-Gonzalez, Antia, Bernabeu Lorenzo, Manuel, Carmen Collado, Maria, Mommers, Monique, van Best, Niels, Hall, Lindsay J. and Neuhaus, Klaus (2025) Comprehensive analysis of Enterococcus spp. from two European healthy infant cohorts shows stable genomic traits including antimicrobial resistance (AMR). Gut Microbes, 17 (1). ISSN 1949-0976
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Abstract
Enterococcus spp. some of which are pathogenic, are common gut microbiota members, including also infants. Infants may be more susceptible to Enterococcus 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 Enterococcus spp. within the infant’s gut microbiome and assess cohort-specific traits such as ARGs. Most isolates were E. faecalis and E. gallinarum, 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 E.hirae strains. While metabolic profiles were similar across cohorts, E. faecalis strains harbored more virulence genes and prophages compared to other species. An analysis of public Enterococcus 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 E. faecalis isolates with varying virulence gene repertoires for phenotypic virulence testing in Caenorhabditis elegans and found them killing at various rates, however no clear pattern emerged in correlation with any specific genetic determinant. Overall, our results suggest that Enterococcus 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.
Item Type: | Article |
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Additional Information: | Data availability: Publicly available genomes were downloaded from NCBI (19 Oct 2023; Suppl. Table S4). All genomic data from our isolates are submitted in GenBank under JBDKAF000000000 to JBDKEA000000000 [https://www.ncbi.nlm.nih.gov/nuccore/JBDKAF000000000. to https://www.ncbi.nlm.nih.gov/nuccore/JBDKEA000000000.] within BioProject PRJNA1110724 [https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1110724]. All isolates were submitted to the culture collection Weihenstephan Strain Collection (WS; Freising, Germany; CCInfo #1163 [https://ccinfo.wdcm.org/details?regnum=1163]). Strain numbers are WS 5642 to WS 5738 (Suppl. Table S6). Funding: M.H.S. is supported by Higher Education Commission, Pakistan (HEC), and German Academic Exchange Service (DAAD) scholarship (K.N. as supervisor). L.J.H. is supported by a Wellcome Investigator Award [No. 220876/Z/20/Z}, and a BBSRC Institute Strategic Programme Food, Microbiome and Health BB/X011054/1 and its constituent project BBS/E/QU/230001B. M.C.C. would like to acknowledge the support from H2020-ERC Starting Grant (MAMI, ref. 639226), Spanish Ministry of Science and Innovation (MCIN) research grant [MAMI plus, ref. PID2022-139475OB-I00] and from Generalitat Valenciana PROMETEO grant [NEOHEALTH ref. 2020/012, MICROGLOCAL ref. CIPROM/2023/3]). M.B. is grateful to have received a post-doctoral “Juan de la Cierva” grant [ref. JDC2022- 050269-I] MCIU/AEI and European Union “Next Generation EU”/PRTR grant. M.C.C. and M.B. would also like to acknowledge the award of the Spanish Government MCIN/AEI to the IATA-CSIC as Centre of Excellence Severo Ochoa [CEX2021-001189-S MCIN/AEI/10.13039/501100011033]. |
Uncontrolled Keywords: | amr,enterococcus,genomics,healthy infants,phylogenomics,resistome,microbiology,microbiology (medical),gastroenterology,infectious diseases,sdg 3 - good health and well-being ,/dk/atira/pure/subjectarea/asjc/2400/2404 |
Faculty \ School: | Faculty of Medicine and Health Sciences > Norwich Medical School |
UEA Research Groups: | Faculty of Medicine and Health Sciences > Research Centres > Metabolic Health |
Related URLs: | |
Depositing User: | LivePure Connector |
Date Deposited: | 20 Aug 2025 14:30 |
Last Modified: | 27 Aug 2025 08:28 |
URI: | https://ueaeprints.uea.ac.uk/id/eprint/100179 |
DOI: | 10.1080/19490976.2025.2516699 |
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