A gut bug that spreads during sex is running out of antibiotic options

A bacterial infection best known for ruining holidays and spreading through daycare centres is quietly acquiring a new identity — and a new danger. Shigella, which causes an intestinal illness called shigellosis, can spread through sexual contact, and the strains circulating in sexual networks are becoming resistant to the antibiotics doctors rely on to treat severe cases. A CDC analysis published in 2026 found that the share of U.S. Shigella samples classified as extensively drug-resistant rose from zero percent between 2011 and 2015 to 8.5 percent in 2023. A study published in The Lancet Infectious Diseases found that in the United Kingdom, strains linked to sexual transmission were spreading farther and forming denser chains of infection than other domestically acquired strains.

Neither finding means a nationwide surge in total infections is underway. Through September 26, 2026, the CDC's provisional surveillance figures put reported U.S. cases at 13,921, down from 14,277 over the same stretch in 2025. According to CDC estimates, about 450,000 infections take place across the U.S. every year. The problem is not the number of cases — it is what happens when the cases that do occur can no longer be treated with standard drugs.

The number of cases does not seem to have increased over the last few years, although the proportion of the bacteria that are extensively drug-resistant has increased.— Dr. Sarath Nath, infectious disease expert, Stony Brook Medicine

Shigella spreads through the fecal-oral route — bacteria from an infected person's stool reach another person's mouth. The CDC notes that swallowing as few as 10 organisms is enough to cause infection, making it exceptionally contagious. Routes of transmission include contaminated food and water, unwashed hands, contact with infected surfaces, and sexual activity involving exposure to microscopic amounts of fecal matter — among them oral-anal contact, anal sex, and contact with contaminated hands or sex toys. Because the symptoms closely resemble food poisoning, many people never connect an infection to a sexual encounter.

Symptoms typically begin one to two days after exposure: diarrhea (which may be bloody), fever, abdominal cramps, and a persistent urge to use the toilet even when the bowels are empty. Most cases last five to seven days and resolve with rest and hydration alone. Severe infections — particularly in people with weakened immune systems — may require antibiotics and hospital care.

The drug-resistance picture is what is concentrating expert attention. Examining nearly 17,000 bacterial samples collected between 2011 and October 2023, CDC researchers turned up 510 extensively drug-resistant isolates — each resistant to ampicillin, azithromycin, ceftriaxone, ciprofloxacin, and trimethoprim-sulfamethoxazole. The CDC has warned that no FDA-approved oral antibiotics can treat infections resistant to all five. Of the 258 extensively drug-resistant patients with known hospitalization status, about four in ten had been admitted to hospital. No deaths were reported in that dataset.

Concerned but not alarmed. The latest data demonstrates that extensively drug-resistant Shigella went from 0 percent of isolates in 2011-2015 to 8.5 percent in 2023, with about a third of XDR patients requiring hospitalization. For most people who enjoy general good health, the individual risk is low. The looming public-health problem is that standard antibiotics are failing for a growing share of cases.— Matthew J. Bertini, physician and founder and CEO of Austere Medicine Consultants

The 86.2 percent of extensively drug-resistant U.S. patients with available demographic data who were men points toward sexual transmission as a significant driver, though the CDC researchers could not directly establish the proportion of infections acquired that way because exposure information was incomplete. Speaking to CIDRAP News, UCLA molecular biologist Shangxin Yang said hospital workers there are now encountering roughly one case of extensively drug-resistant Shigella each month, a sharp rise from a single case recorded across all of 2022. According to Science Alert, Yang described the situation as "almost like an explosion of this pathogen in the community."

In a Lancet Infectious Diseases study, University of Cambridge geneticist Kate Baker led an analysis of more than 3,500 Shigella sonnei samples gathered in the U.K. between 2004 and 2020. Cases in men between the ages of 16 and 60 who had not recently travelled to higher-risk regions were classified by the researchers as likely sexually transmitted. Compared with other domestically acquired infections, that group's cases were travelling greater distances and passing between individuals more intensely.

This is multiple overlapping variants emerging that are all quickly becoming resistant to the drugs we use to treat them. It's highly likely that if you contracted your Shigella through sex you require different treatment to someone who contracted it through travel.— Kate Baker, senior author, University of Cambridge

Baker's study also identified a mechanism that may help explain why sexually transmitted Shigella is developing resistance faster: 'bystander resistance.' When someone carries both Shigella and another sexually transmitted infection such as gonorrhea, an antibiotic prescribed for the second infection can kill off Shigella bacteria that are susceptible to that drug while leaving resistant strains to survive and spread. The study found that after U.K. treatment guidelines dropped azithromycin as a recommended therapy for gonorrhea, the rate at which azithromycin-resistant Shigella emerged slowed — a link that researchers caution does not establish causation but does suggest that treating other STIs may be a risk factor for drug-resistant Shigella.

The pattern is not confined to the U.S. or U.K. The ECDC, Europe's disease agency, has raised alarms about the growing spread of multidrug-resistant and extensively drug-resistant Shigella across the continent, with gay, bisexual, and other men who have sex with men particularly affected. Across Europe and the United States, more than 2,300 infections tied to seven genetically distinct resistant clusters of Shigella sonnei and Shigella flexneri have been reported since 2023. The ECDC flagged the upcoming travel season, Pride events, and festivals as factors that may increase cross-border transmission.

In England, data from the U.K. Health Security Agency showed that in 2025, resistance to at least some antibiotics was present in 86 percent of Shigella sonnei samples and 94 percent of Shigella flexneri samples — the two strains most commonly spread through sexual contact among men who have sex with men. The UKHSA warned in March that while most cases resolve without treatment, 'the options available are becoming limited' for those who do need it.

Many men who have sex with men are unaware of the serious and increasing risk posed by sexually transmitted Shigella. This disease has gone from being relatively treatable with off-the-shelf drugs to being close to untreatable over the course of the last decade or so.— Kate Baker, University of Cambridge

According to the CDC, gay, bisexual, and other men who have sex with men carry a heightened risk, although shigellosis is not exclusively a sexually transmitted infection. Other groups at higher risk include young children, international travellers, people experiencing homelessness, and those with compromised immune systems. Looking at 1,208 reported U.S. outbreaks between 2009 and 2022, a separate 2026 study determined that person-to-person transmission was the dominant route, with childcare settings responsible for a substantial share of outbreaks.

Clinicians are being urged to ask patients presenting with dysentery about sexual history and to order antimicrobial susceptibility testing before prescribing antibiotics. The ECDC is urging countries to bolster microbiological surveillance and expand genomic sequencing so that outbreaks can be detected and resistant strains tracked. The U.K. Health Security Agency recommends that anyone diagnosed with Shigella also be checked for other sexually transmitted infections.

For individuals, the practical guidance is straightforward: if you or a partner is experiencing diarrhoea or gastrointestinal symptoms, refrain from sexual activity; use barrier protection during oral and anal sex; scrub hands thoroughly with soap and water after using the bathroom and before eating; and hold off on sexual activity for at least two weeks after diarrhoea clears, given that Shigella can remain present in stool for up to two weeks after symptoms disappear. Anyone with severe or prolonged symptoms should seek medical care and tell their doctor about recent sexual contact.

Clinicians should be asking patients with dysentery about sexual transmission and giving advice accordingly. They need to know that sexually transmitted Shigella has more antimicrobial resistance than other forms of the disease, and that patients may need checking for other sexually transmissible illnesses.— Daniel Richardson, consultant in sexual health, University Hospitals Sussex

Why it matters — Drug-resistant Shigella strains are spreading through sexual networks globally, and the most resistant cases already have no FDA-approved oral treatment — making early diagnosis, proper antibiotic stewardship, and awareness of sexual transmission routes increasingly urgent for clinicians and patients alike.

Reported by newsweek.com, sciencealert.com, thelancet.com, ecdc.europa.eu, discovermagazine.com