Shigella found in one in five young children's diarrhoea, with resistance climbing

Shigella is a leading cause of dysentery and watery diarrhoea in young children in poorer countries, with consequences that reach beyond the gut — including impaired linear growth. A large surveillance study spanning Africa, Asia and Latin America has now measured how common it is, which strains dominate, and how resistant they have become. The resistance findings, published in The Lancet Global Health, are the part that should worry clinicians [s1].

How the surveillance was done

The Enterics for Global Health (EFGH) study was a prospective, facility-based hybrid surveillance study conducted from June 21, 2022, to Aug 25, 2024, across seven countries: Kenya, Malawi, Mali, The Gambia, Bangladesh, Pakistan, and Peru [s1]. It enrolled children aged 6-35 months who presented at selected health facilities with acute diarrhoea — defined as three or more abnormally loose or watery stools in a 24-hour period, lasting less than 14 days [s1].

Shigella was deemed attributable if detected by microbiological culture, or by quantitative PCR using an ipaH quantification-cycle threshold of 29.5 or lower from rectal swabs [s1]. Antimicrobial resistance was measured by disc diffusion, and the team calculated care-seeking-adjusted incidence by combining case counts with local population enumeration and a health-care utilisation survey [s1]. The explicit purpose was to inform vaccine-trial planning and eventual vaccine introduction in high-burden countries [s1].

What it found

Of 9476 enrolled children, 4316 (45.5%) were female and 5160 (54.5%) were male [s1]. Shigella was detected in 881 (9.3%) by culture, and in 1870 (20.0%) by qPCR among the 9354 children with qPCR results available [s1] — a reminder of how much more sensitive molecular testing is than culture.

Shigella flexneri dominated, accounting for 497 (56.2%) of 881 isolates by culture and 756 (39.4%) of 1870 detections by qPCR, with S flexneri 2a and S flexneri 6 the most common serotypes by both methods [s1]. The dominance of S flexneri over S sonnei matters for vaccine design, because candidate vaccines must cover the serotypes actually circulating.

Incidence varied widely by country. Adjusted incidence of Shigella-attributed diarrhoea by culture ranged from 2.7 per 100 child-years (95% CI 1.9-4.3) in Malawi to 11.7 per 100 child-years (8.3-24.2) in Peru; by qPCR it ranged from 3.5 per 100 child-years (2.5-5.4) in Malawi to 26.9 per 100 child-years (19.0-40.9) in The Gambia [s1].

The resistance problem

The sharpest finding concerns the drugs meant to treat the disease. Shigella isolates showed resistance to the antibiotics WHO recommends for dysentery, with wide variation across sites: ciprofloxacin resistance of 37.2% (range 14.0-74.0), azithromycin 22.1% (1.2-34.2), and ceftriaxone 16.2% (0.0-64.4) [s1]. These are the first-line and reserve options for a severe childhood infection; resistance at these levels narrows the shelf quickly, and the 74.0% top of the ciprofloxacin range shows how dire it already is in the worst-affected settings.

The study's own interpretation is that Shigella-attributed diarrhoea is common among young children in these countries, and that its escalating antimicrobial resistance poses a serious threat [s1].

The wide ranges behind the pooled figures are as telling as the averages. Resistance that sits near the bottom of the range in one country and near the top in another means clinicians cannot assume a single empirical treatment will work everywhere, and that national guidelines built on older susceptibility data may already be out of step with what is circulating. For a pathogen spread person-to-person and through contaminated water and food, resistant strains can move between communities faster than treatment guidance can be revised. That combination — a common infection, a shrinking list of reliable drugs, and uneven surveillance — is what turns a treatable childhood illness into a management problem.

Why it matters

Diarrhoeal disease is the third leading cause of death in children aged 1-59 months and, by WHO's count, drives nearly 1.7 billion cases of childhood diarrhoeal disease each year while ranking as a leading cause of malnutrition in the under-fives [s2]. There is no licensed Shigella vaccine, so antibiotics remain the mainstay of treatment for severe cases — which is precisely why rising resistance is so consequential. Surveillance like EFGH exists partly to point vaccine developers at the right serotypes and the right places.

What to watch

Whether Shigella vaccine candidates now in development are designed around the S flexneri 2a and 6 serotypes this study found dominant, and whether they are trialled in the high-incidence settings it identified, such as The Gambia [s1]. And whether resistance surveillance keeps pace — because the value of a future vaccine will be measured against how little the antibiotics it might spare are still working.

This article is informational and does not constitute medical advice.

Sources

• The incidence and antimicrobial resistance of Shigella-attributable diarrhoea in young children in low-income and middle-income countries from the multicountry Enterics for Global Health (EFGH) Shigella Surveillance Study — The Lancet Global Health, 11 March 2026
• Diarrhoeal disease — Fact sheet — World Health Organization