Antibiotic resistance genes in the gut microbiota of mothers and linked neonates with or without sepsis from low- and middle-income countries
Open accessAbstract
Early development of the microbiome has been shown to affect general health and physical development of the infant and, although some studies have been undertaken in high-income countries, there are few studies from low- and middle-income countries. As part of the BARNARDS study, we examined the rectal microbiota of 2,931 neonates (term used up to 60 d) with clinical signs of sepsis and of 15,217 mothers screening for bla CTX-M-15 , bla NDM , bla KPC and bla OXA-48 -like genes, which were detected in 56.1%, 18.5%, 0% and 4.1% of neonates’ rectal swabs and 47.1%, 4.6%, 0% and 1.6% of mothers’ rectal swabs, respectively. Carbapenemase-positive bacteria were identified by MALDI-TOF MS and showed a high diversity of bacterial species (57 distinct species/genera) which exhibited resistance to most of the antibiotics tested. Escherichia coli , Klebsiella pneumoniae and Enterobacter cloacae / E. cloacae complex, the most commonly found isolates, were subjected to whole-genome sequencing analysis and revealed close relationships between isolates from different samples, suggesting transmission of bacteria between neonates, and between neonates and mothers. Associations between the carriage of antimicrobial resistance genes (ARGs) and healthcare/environmental factors were identified, and the presence of ARGs was a predictor of neonatal sepsis and adverse birth outcomes.
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Differential exposure to antibiotics between Westernized and non-Westernized cohorts can be considered a selective force that allows the persistence of different strains in populations with low antibiotic exposure.
“Finally, the differential exposure to antibiotics between Westernized and non-Westernized cohorts can also be considered a selective force that allows the persistence of different strains in populations with low antibiotic exposure [102,103] .”
From Genome-scale insights into the metabolic landscape and evolutionary development of Bifidobacterium bifidum (2026) · cites this paper as [102]
The Results section reports antibiotic-resistance profiles in mothers and neonates, but does not compare Westernized and non-Westernized cohorts or link low antibiotic exposure to strain persistence. The Discussion says the study did not collect antibiotic-exposure histories or assess acquisition and loss over time. Searches for the claimed cohort comparison and selective effect found no supporting passage in our copy; page numbers were not available. (LLM, conf=0.76)
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Coming Into Resistance: Clinically Important Antibiotic Resistance Genes in NICU vs. Healthy InfantsPreprint
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- Authors
- Carvalho, M. J., Sands, K., Thomson, K., Portal, E., Mathias, J., Milton, R., Gillespie, D., Dyer, C., Akpulu, C., Boostrom, I., Hogan, P., Saif, H., Ferreira, A., Nieto, M., Hender, T., Hood, K., Andrews, R., Watkins, W. J., Hassan, B., Chan, G., Bekele, D., Solomon, S., Metaferia, G., Basu, S., Naha, S., Sinha, A., Chakravorty, P., Mukherjee, S., Iregbu, K., Modibbo, F., Uwaezuoke, S., Audu, L., Edwin, C. P., Yusuf, A. H., Adeleye, A., Mukkadas, A. S., Zahra, R., Shirazi, H., Muhammad, A., Ullah, S. N., Jan, M. H., Akif, S., Mazarati, J. B., Rucogoza, A., Gaju, L., Mehtar, S., Bulabula, A. N. H., Whitelaw, A., Roberts, L., BARNARDS Group, & Walsh, T. R.
- Affiliations
- University of Aveiro (PT)
- University of Oxford (GB)
- Cardiff University (GB)
- Wellcome Sanger Institute (GB)
- Boston Children's Hospital (US)
- Harvard University (US)
- St. Paul's Hospital Millennium Medical College (ET)
- National Institute of Cholera and Enteric Diseases (IN)
- Institute of Post Graduate Medical Education and Research (IN)
- National Hospital Abuja (NG)
- Medway NHS Foundation Trust (GB)
- Aminu Kano Teaching Hospital (NG)
- Bayero University Kano (NG)
- Quaid-i-Azam University (PK)
- Pakistan Institute of Medical Sciences (PK)
- Rwanda Biomedical Center (RW)
- Stellenbosch University (ZA)
- National Health Laboratory Service (ZA)
- Corresponding author
- Carvalho, M. J.
- ORCID
- Carvalho, M. J.
- Sands, K.
- Thomson, K.
- Portal, E.
- Mathias, J.
- Milton, R.
- Gillespie, D.
- Dyer, C.
- Akpulu, C.
- Boostrom, I.
- Nieto, M.
- Hender, T.
- Hood, K.
- Andrews, R.
- Watkins, W. J.
- Hassan, B.
- Chan, G.
- Bekele, D.
- Solomon, S.
- Basu, S.
- Naha, S.
- Sinha, A.
- Mukherjee, S.
- Iregbu, K.
- Audu, L.
- Yusuf, A. H.
- Zahra, R.
- Muhammad, A.
- Mazarati, J. B.
- Mehtar, S.
- Bulabula, A. N. H.
- Whitelaw, A.
- Walsh, T. R.
- Venue
- Nature Microbiology
- Published
- 2022-08-04
- Volume
- 7
- Issue
- 9
- Pages
- 1337-1347
- ISSN
- 2058-5276 (ISSN-L)
- PMC
- PMC9417982
- OpenAlex
- W4289970924
- Cited by
- 95
- References
- 60
- Citations by year
- 2026: 22 · 2025: 25 · 2024: 28 · 2023: 14 · 2022: 5 · 2012: 1
- FWCI
- 5.89
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Locations
- Nature Microbiology (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- ORCA Online Research @Cardiff (Cardiff University) (acceptedVersion)
- Funders
- Bill and Melinda Gates Foundation (OPP1119772, OP1191522)
- same as above
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Medicine › Antibiotic Resistance in Bacteria
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Health Sciences › Medicine › Public Health, Environmental and Occupational Health › Neonatal and Maternal Infections
- Keywords
- antibiotic resistance genes, neonatal sepsis, gut microbiota, maternal carriage, blaCTX-M-15, carbapenemase genes, rectal microbiota, Escherichia coli, Klebsiella pneumoniae, Enterobacter cloacae, intergenerational transmission, low- and middle-income countries, adverse birth outcomes, neonatal infection
- MeSH terms
- Gastrointestinal Microbiome, Anti-Bacterial Agents, Developing Countries, Drug Resistance, Microbial, Escherichia coli, Female, Humans, Infant, Infant, Newborn, Microbial Sensitivity Tests, Mothers, Sepsis
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