High-risk Escherichia coli clones that cause neonatal meningitis and association with recrudescent infection
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Abstract
Neonatal meningitis is a devastating disease associated with high mortality and neurological sequelae. Escherichia coli is the second most common cause of neonatal meningitis in full-term infants (herein NMEC) and the most common cause of meningitis in preterm neonates. Here, we investigated the genomic relatedness of a collection of 58 NMEC isolates spanning 1974–2020 and isolated from seven different geographic regions. We show NMEC are comprised of diverse sequence types (STs), with ST95 (34.5%) and ST1193 (15.5%) the most common. No single virulence gene profile was conserved in all isolates; however, genes encoding fimbrial adhesins, iron acquisition systems, the K1 capsule, and O antigen types O18, O75, and O2 were most prevalent. Antibiotic resistance genes occurred infrequently in our collection. We also monitored the infection dynamics in three patients that suffered recrudescent invasive infection caused by the original infecting isolate despite appropriate antibiotic treatment based on antibiogram profile and resistance genotype. These patients exhibited severe gut dysbiosis. In one patient, the causative NMEC isolate was also detected in the fecal flora at the time of the second infection episode and after treatment. Thus, although antibiotics are the standard of care for NMEC treatment, our data suggest that failure to eliminate the causative NMEC that resides intestinally can lead to the existence of a refractory reservoir that may seed recrudescent infection.
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Specific sequence types linked to neonatal infections were identified, such as E. coli ST1193, ST73 and ST95, and K. pneumoniae ST432, which are typically drug-resistant and of clinical significance.
“Indeed, we identified specific STs linked to neonatal infections, such as E. coli ST119347, ST73 and ST9547,48, and K. pneumoniae ST43249 strains, which are typically drug-resistant strains and of clinical significance.”
From Impact of early life antibiotic and probiotic treatment on gut microbiome and resistome of very-low-birth-weight preterm infants. (2025) · cites this paper as [47]
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- Authors
- Nhu, N. T. K., Phan, M.-D., Hancock, S. J., Peters, K. M., Alvarez-Fraga, L., Forde, B. M., Andersen, S. B., Miliya, T., Harris, P. N., Beatson, S. A., Schlebusch, S., Bergh, H., Turner, P., Brauner, A., Westerlund-Wikström, B., Irwin, A. D., & Schembri, M. A.
- Affiliations
- The University of Queensland (AU)
- School of Chemistry and Molecular Biosciences, The University of Queensland
- Angkor Hospital for Children (KH)
- Queensland Health (AU)
- University of Queensland Centre for Clinical Research, The University of Queensland
- Karolinska University Hospital (SE)
- Molecular and Integrative Biosciences Research Programme, University of Helsinki
- Corresponding author
- Irwin, Adam D
- Schembri, Mark A
- ORCID
- Venue
- eLife
- Publisher
- eLife Sciences Publications, Ltd
- Published
- 2024-04-16
- Volume
- 12
- ISSN
- 2050-084X (ISSN-L)
- PMC
- PMC11021048
- OpenAlex
- W4389980232
- Cited by
- 41
- References
- 59
- Citations by year
- 2026: 17 · 2025: 16 · 2024: 7 · 2023: 1
- FWCI
- 7.56
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- eLife (publishedVersion, cc-by)
- eLife (acceptedVersion, cc-by)
- medRxiv (acceptedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by-nc-nd)
- PubMed (publishedVersion)
- HAL (submittedVersion, cc-by)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
- Työväentutkimus Vuosikirja (submittedVersion)
- Funders
- National Health and Medical Research Council (APP1181958, GNT1197743, APP2001431)
- Queensland Children's Hospital Foundation (50270)
- Australian Infectious Diseases Research Centre
- Wellcome Trust (10.35802/220211)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Endocrinology › Escherichia coli research studies
- Health Sciences › Medicine › Public Health, Environmental and Occupational Health › Neonatal and Maternal Infections
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Medicine › Antibiotic Resistance in Bacteria
- Keywords
- Escherichia coli, neonatal meningitis, recrudescent infection, sequence types, ST95, ST1193, virulence genes, fimbrial adhesins, iron acquisition systems, K1 capsule, O-antigen, antibiotic resistance genes, gut dysbiosis, fecal carriage, preterm infants, term infants
- MeSH terms
- Clone Cells, Escherichia coli, Escherichia coli Infections, Humans, Infant, Newborn, Meningitis, Virulence
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