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High gastrointestinal carriage rates of extended-spectrum-β-lactamase-producing enterobacterales and associated factors among hospitalized and nonhospitalized children in Kenya
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  • Published: 10 March 2026

High gastrointestinal carriage rates of extended-spectrum-β-lactamase-producing enterobacterales and associated factors among hospitalized and nonhospitalized children in Kenya

  • Susan Githii1,4,
  • Cecilia Ndungu2,4,
  • John M. Maingi3 &
  • …
  • Abednego Musyoki4 

Scientific Reports , Article number:  (2026) Cite this article

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We are providing an unedited version of this manuscript to give early access to its findings. Before final publication, the manuscript will undergo further editing. Please note there may be errors present which affect the content, and all legal disclaimers apply.

Subjects

  • Diseases
  • Gastroenterology
  • Health care
  • Medical research
  • Microbiology

Abstract

Gastrointestinal carriage of extended-spectrum β-lactamase-producing Enterobacterales (ESBL-E) presents a critical public health threat globally. However, in resource-constrained countries with poor sanitation, inadequate drinking water, and limited microbiology laboratories like Kenya, epidemiological data of these strains is limited. This study assessed the gastrointestinal carriage of ESBL-E and the risk factors for colonization among children (≤ 5 years) in the inpatient department (IPD) and outpatient department (OPD). This was a hospital-based cross-sectional study at Thika Level 5 Hospital, Kenya, from February to June 2023. In total, 540 participants (OPD: 270, IPD: 270) were recruited, using systematic random sampling and consecutive sampling in OPD and IPD, respectively. Children admitted for less than 48 h in the paediatrics ward and those with a prior history of hospitalization (≤ 3 months) in OPD were excluded. Demographic data were collected using a well-structured questionnaire. Following the standard microbiology methods, stool or rectal swab samples were cultured, with the identity and antimicrobial susceptibility of isolates elucidated by automated platforms. The overall ESBL-E gastrointestinal carriage rate was 35.4% (191/540), and was highest among outpatients at 40.4% (109/270). Isolates demonstrated co-resistance to aminoglycosides (43–52%), quinolones (52–62%), carbapenems (44–50%), and sulfonamides (92–97%). They were more susceptible to piperacillin/tazobactam (67–95%) and colistin (96–99%). Carbapenemase-producing Enterobacterales (CPE) co-carriage rate was 17.6% (16/91), with similar rates for inpatients (50%, 8/16) and outpatients (50%, 8/16). Escherichia coli was the predominant ESBL-E overall (82.2%, 157/191), among outpatients (83.5%, 91/109), and inpatients (80.5%, 66/82), and was also the main CPE (overall: 81.3%, 13/16; OPD: 75%, 6/8; IPD: 87.5%, 7/8). Independent predictors of colonization included child age (adjusted odds ratio (OR): 1.60, p = 0.045) and a history of antimicrobial use from retail pharmacies without a clinician’s prescription (adjusted OR: 0.18, p = 0.047). This study demonstrates a substantial burden of gastrointestinal carriage of ESBL-E and CPE co-carriage among children (≤ 5 years), with E. coli being the predominant organism. Age less than two years and a history of exposure to non-prescribed antimicrobials were independent factors for colonization. Efforts to limit exposure to contaminated environments and targeted antimicrobial stewardship initiatives are required to mitigate AMR in the current study setting.

Data availability

The datasets utilized in this study can be acquired from the corresponding author upon request.

Abbreviations

WHO:

World Health Organization

AST:

Antimicrobial Susceptibility Testing

CLSI:

Clinical and Laboratory Standards Institute

MALDI-TOF MS:

Matrix assisted laser desorption ionization-time of flight mass spectrometry

MDR:

Multidrug-drug resistant

ESBL:

Extended-spectrum beta-lactamases

ESBL-E:

Extended-spectrum beta-lactamases producing Enterobacterales

OPD:

Outpatient Department

IPD:

Inpatient Department

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Funding

This study did not receive financial support from any funding agencies.

Author information

Authors and Affiliations

  1. National Public Health Laboratory, Kenyatta National Hospital Grounds, Upperhill, Nairobi, 20750-00202, Kenya

    Susan Githii

  2. Department of Medical Laboratory, Murang’a County Referral Hospital, Murang’a, 69-10200, Kenya

    Cecilia Ndungu

  3. Department of Biochemistry, Microbiology and Biotechnology, School of Pure and Applied Sciences, Kenyatta University, Nairobi, 43844-00100, Kenya

    John M. Maingi

  4. Department of Medical Laboratory Science, School of Health Sciences, Kenyatta University, Nairobi, 43844-00100, Kenya

    Susan Githii, Cecilia Ndungu & Abednego Musyoki

Authors
  1. Susan Githii
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  2. Cecilia Ndungu
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  4. Abednego Musyoki
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Contributions

SG, JM and AM conceived and developed the study, interpreted the data, and drafted the manuscript; CN assisted in laboratory work. All authors read and approved the final manuscript.

Corresponding authors

Correspondence to Susan Githii or Abednego Musyoki.

Ethics declarations

Competing interests

The authors declare no competing interests.

Ethics approval and consent to participate

The study was approved by Kenyatta University’s ethical research committee (Protocol Approval No. PKU/2620/E1745) as well as the National Commission of Science, Technology, and Innovation (NACOSTI). Approval for collection of samples was obtained from Ethical Research Committee, Thika Level 5 hospital. An informed consent was obtained from parent or guardian of each child before participating in this study. The research project was conducted in accordance with the Declaration of Helsinki, prioritizing participants’ well-being and ensuring timely communication of critical findings to the doctors responsible for the patients. Each patient was assigned a unique Personal Identification Number (PIN) for anonymity, and all information collected was kept confidential. Participants in the study received no monetary compensation, and there were no penalties for those who chose not to participate.

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Githii, S., Ndungu, C., Maingi, J.M. et al. High gastrointestinal carriage rates of extended-spectrum-β-lactamase-producing enterobacterales and associated factors among hospitalized and nonhospitalized children in Kenya. Sci Rep (2026). https://doi.org/10.1038/s41598-026-43265-6

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  • Received: 21 August 2025

  • Accepted: 03 March 2026

  • Published: 10 March 2026

  • DOI: https://doi.org/10.1038/s41598-026-43265-6

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Keywords

  • Gastrointestinal carriage
  • ESBL-producing enterobacterales
  • Co-resistance
  • Carbapenemase-producing enterobacterales
  • Risk factors
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