Shigella PCR-positive Gastroenteritis in Children: Insights From a Comparison Between Culture-positive and Culture-negative Cases

Pediatr Infect Dis J. 2026 Jan 1;45(1):61-67. doi: 10.1097/INF.0000000000004965. Epub 2025 Sep 15.

Abstract

Background: Detection of Shigella in stool by polymerase chain reaction (PCR) is rapid and highly sensitive but presents challenges in distinguishing between disease-associated and asymptomatic Shigella carriage. This study compared children with gastroenteritis who had Shigella identified in their stool by PCR-testing and a positive stool culture to those with Shigella identified by PCR-testing but a negative culture.

Methods: All stool samples of outpatients and inpatients (<18 years) tested by multiplex-PCR at the Soroka University Medical Center laboratory between January 2020 and July 2024 were analyzed. Shigella PCR-positive samples underwent culture for species identification and antimicrobial susceptibility testing. The Vesikari scale was used to determine disease severity. Logistic regression assessed associations between culture-positivity and clinical findings, while receiver operating characteristic analysis evaluated the relationship between cycle threshold (Ct) values, culture-positivity and disease severity.

Results: Among 39,777 stools tested by multiplex PCR, 2041 (5.1%) were Shigella -positive, of which 897 (43.9%) were also culture-positive. Among culture-positive cases, 77% grew S. sonnei and 18% S. flexneri . Antibiotic susceptibility testing showed 36% sensitivity to ceftriaxone and 77% to azithromycin. Culture-positive cases had lower Ct values than culture-negative cases [23 (95% confidence interval [CI]: 20-26) vs. 30 (95% CI: 25-36), P < 0.001]. Among 395 hospitalized children with Shigella PCR-positive samples, 167 (42%) had positive stool cultures. Severe disease was more common in culture-positive cases (71% vs. 54%, P < 0.001). A Ct value of 28 predicted culture-positivity (adjusted odds ratios = 6.97, 95% CI: 5.62-8.68; P < 0.001) and 27 predicted severe disease (adjusted odds ratios = 1.93, 95% CI: 1.20-3.12; P = 0.007).

Conclusions: Among children with Shigella -positive PCR results, those with culture-positive samples exhibited greater disease severity and lower Ct values.

Keywords: PCR-positive; Shigella; children; gastroenteritis; stool culture.

Publication types

  • Comparative Study

MeSH terms

  • Adolescent
  • Anti-Bacterial Agents / pharmacology
  • Anti-Bacterial Agents / therapeutic use
  • Child
  • Child, Preschool
  • Dysentery, Bacillary* / diagnosis
  • Dysentery, Bacillary* / microbiology
  • Feces / microbiology
  • Female
  • Gastroenteritis* / diagnosis
  • Gastroenteritis* / microbiology
  • Humans
  • Infant
  • Male
  • Microbial Sensitivity Tests
  • Multiplex Polymerase Chain Reaction
  • Polymerase Chain Reaction
  • Shigella* / drug effects
  • Shigella* / genetics
  • Shigella* / isolation & purification

Substances

  • Anti-Bacterial Agents