The research team, led by scientists at Shahid Beheshti University of Medical Sciences in collaboration with Hakim Children’s Hospital, collected 79 Shigella isolates from the stool of pediatric patients suffering from diarrhea between September 2023 and April 2025. The children had all been referred to the hospital, one of Tehran’s major pediatric centers, making the sample a representative snapshot of clinically significant infections in the city’s young population. The study was approved by the ethics committee of Shahid Beheshti University of Medical Sciences and funded through a university grant.

Species identification revealed a familiar but shifting landscape. Shigella flexneri remained the predominant species, accounting for 59.5 percent of isolates, while Shigella sonnei made up the remaining 40.5 percent. This distribution matters because the two species differ not only in their epidemiology but also, as the study demonstrated, in their genetic armamentaria and their susceptibility to antibiotics. Globally, S. flexneri has traditionally dominated in low- and middle-income countries while S. sonnei has been more common in industrialized settings, so the near-even split observed in Tehran provides a useful epidemiological marker for a region in epidemiological transition.

The antimicrobial susceptibility testing, performed using the Kirby-Bauer disk diffusion method according to Clinical and Laboratory Standards Institute guidelines, tested isolates against twelve antibiotics. The results were grim. Resistance to ampicillin, a long-standing first-line option, stood at 92.4 percent. Trimethoprim-sulfamethoxazole, another mainstay of treatment in many settings, fared little better, with 91.1 percent of isolates resistant. Tetracycline resistance reached 86.1 percent. These three drugs, which in earlier decades formed the backbone of shigellosis therapy, are now effectively useless against the vast majority of circulating strains.

Not all news was bleak. The majority of isolates remained susceptible to meropenem, a broad-spectrum carbapenem, at 84.8 percent, and to tigecycline, a glycylcycline often held in reserve, at 82.3 percent. These agents thus retain considerable activity against Shigella in this setting, although clinicians must weigh the appropriateness of deploying such broad-spectrum drugs in children, particularly given concerns about preserving these last-line options. More troubling was the species-specific pattern that emerged for other drug classes: S. sonnei isolates demonstrated significantly greater resistance to azithromycin and to the fluoroquinolones than S. flexneri, a difference the authors flagged as statistically significant. Azithromycin and fluoroquinolones such as ciprofloxacin are among the most important oral options for treating shigellosis, so their erosion in S. sonnei narrows the therapeutic window considerably.

Beyond resistance phenotypes, the heart of the study lay in its molecular analysis. The researchers used polymerase chain reaction to screen every isolate for a panel of eleven virulence-related genes, including ipaH, ipaA through ipaD, ipgD, sen, virA, virB, virF, ial, sigA, icsA, and icsB. Many of these genes encode components or effectors of the type III secretion system, a syringe-like molecular apparatus that Shigella uses to inject effector proteins directly into human intestinal epithelial cells. This injection machinery allows the bacterium to invade host cells, escape immune detection, manipulate cell signaling, and spread from cell to cell, producing the colitis and bloody diarrhea characteristic of shigellosis.

The PCR results revealed a strikingly conserved virulence core. Every single one of the 79 isolates carried ipaH, a multicopy gene that is frequently used as a diagnostic target precisely because of its ubiquity and its presence in multiple copies on both the large virulence plasmid and the chromosome. More than 90 percent of isolates also harbored ipaB, ipaC, and ipaD, the genes encoding the invasion plasmid antigens that form the translocation pore and the effector proteins that trigger host cell uptake. The near-universal presence of this core set underscores that the invasive capacity of Shigella remains intact even as the bacterium accumulates resistance determinants; there is no apparent trade-off in which the bacteria sacrifice virulence for resistance.

Not every gene, however, was evenly distributed. The presence of ipgD, which encodes another type III secretion system effector involved in invasion, and sigA, which encodes an enterotoxin contributing to fluid secretion and tissue inflammation, differed significantly between the two species. These species-specific differences in virulence gene carriage suggest that S. flexneri and S. sonnei circulating in Tehran may cause disease through subtly different molecular mechanisms, and they complicate any one-size-fits-all approach to vaccine design or virulence-based diagnostics. A vaccine or therapeutic strategy targeting a single effector might protect against one species but leave the other untouched.

Perhaps the most conceptually significant finding involved the statistical associations between specific virulence genes and resistance phenotypes. The researchers found that resistance to levofloxacin, a fluoroquinolone, was linked to the presence of ipaB, while resistance to ampicillin was associated with ipaD. Even more broadly, sigA was associated with resistance across multiple drug classes. The authors interpret such correlations as evidence that virulence gene profiles could serve as indirect markers of resistance behavior, and they hint at underlying biological or epidemiological mechanisms. Plasmids carrying virulence genes can also carry resistance determinants, and particular genetic lineages that have succeeded in circulating may have acquired both traits together. Co-selection, in which the presence of one trait facilitates the maintenance of another on the same mobile element, is a well-established driver of resistance spread in enteric bacteria, and these associations are consistent with that framework.

The practical implications of the study extend in several directions. For clinicians in Tehran and comparable settings, the near-total loss of ampicillin, trimethoprim-sulfamethoxazole, and tetracycline as treatment options means that empirical therapy must lean increasingly on carbapenems, tigecycline, or whichever oral agents retain activity, decisions that should ideally be informed by species identification and susceptibility testing. For public health authorities, the distinct resistance and virulence profiles of S. flexneri and S. sonnei argue for species-specific surveillance programs that track the two organisms separately rather than lumping them together as generic Shigella. And for researchers, the demonstrated links between virulence genes and resistance phenotypes open a line of inquiry into whether molecular screening for genes such as sigA, ipaB, or ipaD could help predict resistance patterns before culture-based results become available. As the authors conclude, the findings underscore a need for vigilance: in this Tehran pediatric population, shigellosis has become not only a disease of poverty and sanitation but a showcase for how bacterial virulence and antibiotic resistance evolve together in a clinical setting.

Subject of Research: Virulence gene distribution and antimicrobial resistance in pediatric Shigella isolates from Tehran, Iran

Article Title: Distribution of virulence-related genes in Shigella isolates recovered from pediatric patients in Tehran, Iran: association with antimicrobial resistance

Article References: Kazemzadeh Anari, R., Sadredinamin, M., Hashemi, A., Houri, H., Taheri, M., Yousefi Nojookambari, N., Nikmanesh, A., & Ghalavand, Z. (2026). Distribution of virulence-related genes in Shigella isolates recovered from pediatric patients in Tehran, Iran: association with antimicrobial resistance. Gut Pathogens. https://doi.org/10.1186/s13099-026-00875-9

Image Credits: AI Generated

DOI: 10.1186/s13099-026-00875-9

Keywords: Shigella, antimicrobial resistance, multidrug resistance, Shigella flexneri, Shigella sonnei, virulence genes, children, diarrhea, Tehran, type III secretion system, pediatric infectious disease, public health