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Prevalence and characterization of bacterial rectal colonization patterns in pediatric patients: A cross-sectional

Aynaa Al-Khatib1, Amal Naous2, Elie Salem Sokhn1

  • 1Molecular Testing Laboratory, Medical Laboratory Department, Faculty of Health Sciences, Beirut Arab University, Beirut, Lebanon.

New Microbes and New Infections
|February 2, 2026
PubMed

Insights

Pediatric rectal colonization with multidrug-resistant organisms, particularly ESBL-producing E. coli, is common. Prior antacid use was linked to resistance, suggesting a need for further pediatric surveillance and careful antibiotic evaluation.

Area of Science:

  • Microbiology
  • Public Health
  • Pediatrics

Background:

  • Antimicrobial resistance (AMR) is a significant global health threat.
  • Surveillance of AMR is crucial for understanding its prevalence and contributing factors.
  • Pediatric bacterial isolates require evaluation for resistance patterns and associated clinical data.

Purpose of the Study:

  • To assess the distribution and resistance mechanisms of bacterial isolates from pediatric patients.
  • To identify demographic and clinical factors associated with antimicrobial resistance in children.
  • To investigate the prevalence of specific resistance mechanisms like ESBL, AmpC, CRE, and MRSA.

Main Methods:

  • Rectal swabs were collected from pediatric patients in Beirut.
  • Bacterial identification used standard culture and biochemical techniques.
  • Antimicrobial susceptibility testing and Polymerase Chain Reaction (PCR) were employed to characterize resistance genes and mechanisms.
  • Statistical analysis (chi-square or Fisher's exact test) assessed associations between resistance and sample characteristics.

Main Results:

  • Among 118 rectal isolates, Escherichia coli was predominant (75.4%).
  • 31.36% of isolates exhibited major resistance mechanisms (ESBL, AmpC, CRE, or MRSA).
  • ESBL-producing E. coli (22%) with blaCTX-M was most frequent; prior antacid intake was significantly associated with resistance (p=0.03).

Conclusions:

  • Rectal colonization with multidrug-resistant organisms is frequent in pediatric populations, primarily driven by ESBL-producing E. coli.
  • While AmpC, CRE, and MRSA were less common, they represent critical resistance mechanisms.
  • The link between resistance and antacid use underscores the need for extensive pediatric surveillance and judicious antibiotic and antacid use.
Abstract

Keywords:
Antibiotic resistanceCarbapenem-resistant EnterobacteriaceaeExtended-spectrum beta-lactamaseGram-negative bacteriaGut microbiomePediatricsResistance genes

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