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

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.