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Drug-resistant bacteria that causes stomach bug symptoms on the rise, CDC warns

Doctors and patients should be on the lookout for symptoms of this worrying infection.
Illustration of Enterobacteriaceae (Shigella) bacteria.
Drug-resistant shigella, which causes gastrointestinal symptoms, is becoming more common in the U.S., public health officials are warning.Alissa Eckert / Getty Images/Science Photo Library
/ Source: TODAY

A drug-resistant strain of bacteria is quickly becoming more common, the Centers for Disease Control and Prevention warned in a call with health care providers on Feb. 28.

The bacteria, shigella, causes an infection called shigellosis that can come with gastrointestinal symptoms, like diarrhea and stomach cramps, as well as a fever. While the infection is mild for most people, it can be serious for some vulnerable groups.

There are established guidelines for using common antibiotics to treat shigellosis, but “the obvious challenge is that emerging extensively drug-resistant shigella strains are resistant to all of these recommended agents,” Dr. Louise Francois Watkins, medical officer with the National Antimicrobial Resistance Monitoring System for Enteric Bacteria Team, said on the CDC call.

Indeed, more and more shigella samples are turning out to be extensively resistant, meaning they have resistance to all five recommended antibiotic treatments, the CDC warned in a health alert on Feb. 24. These are "potentially serious public health concerns," the CDC said.

The alert comes as norovirus, another common cause of stomach flu symptoms, is also spreading in the U.S.

A concerning rise in drug-resistant shigellosis

In 2015, there were no recorded shigella infections caused by extensively antibiotic-resistant strains. But in 2022, these highly antibiotic-resistant strains accounted for 5% of infections, according to new data from NARMS.

Previous CDC data showed that, in 2017, about 24% of shigella bacteria sampled were resistant to the antibiotic azithromycin, which was up from just 10% the year before. And 10% were resistant to ciprofloxacin, which increased from 5% in 2016. The CDC estimated in 2017 that 77,000 infections were caused every year by shigella strains resistant to either azithromycin or ciprofloxacin.

"Anytime any bacteria is evolving higher rates of antibiotic resistance, it's definitely something to keep an eye on and be a bit concerned about," Kaitlyn Kortright, Ph.D., a postdoctoral researcher in the department of ecology and evolutionary biology at Yale University, tells

The issue is not that drug-resistant shigella bacteria cause more severe disease than the nonresistant strains but that "if you can't clear (the infection) on your own, you're going to need antibiotics to treat it," Dr. Mahdee Sobhanie, an infectious disease specialist at The Ohio State University Wexner Medical Center, tells

And an infection that's deemed extensively drug-resistant indicates that it's resistant to all recommended antibiotics, Dr. Roy Gulick, chief of infectious disease at Weill Cornell Medicine, tells "So that's of obvious concern," he says.

In this case, rising antibiotic resistance means that doctors may not have many — or any — recommendations to go on when treating people with serious shigella infections, Sobhanie explains.

That's why, with fewer and fewer medication options available to manage the infections caused by this easily transmissible bacteria, the "CDC asks health care professionals to be vigilant about suspecting and reporting cases of (antibiotic-resistant shigella) to their local or state health department," the new warning urged.

Previously, researchers and public health agencies have warned about drug-resistant gonorrhea and urinary tract infections, Sobhanie says, adding that antibiotic resistance is the kind of thing "that keeps infectious disease physicians up at night."

The dynamics of U.S. shigella infections are changing

The rise in antibiotic-resistant shigellosis seems to be affecting certain populations more than others, Gulick says.

"Traditionally, it's been young children who would pass this to one another in day care settings with hygiene not being good," he explains. "More recently, and with this outbreak of resistance, we're seeing this in the men who have sex with men community." 

Since 2016, the CDC reported 232 cases of extensively drug-resistant shigella, NBC News reported, and 197 of them occurred in adult men. And 130 of those cases occurred in 2022 alone, according to new CDC data. Among the 41 people for whom the CDC has sexual demographic data, 88% were men who reported having recent sexual contact with men.

Other populations who now seem to be at a higher risk for drug-resistant shigellosis include people living in communal settings like shelters, Gulick says, as well as international travelers.

The CDC data also reveal that the most common strain of shigella in the U.S. is changing. Prior to 2020, the S. sonnei strain had always been dominant. But since 2021, another strain, S. flexneri, began to take over.

"This challenges the conventional view that sonnei predominates in high-income countries while flexnei predominates in low- and middle-income countries," Dr. Neemah Logan, a lieutenant commander in the U.S. Public Health Service and medical officer with NARMS, explained on the call.

"The recent increase of flexnei in the U.S. demonstrates the incredibly opportunistic ability of this pathogen to afflict vulnerable populations and perhaps also urges us to reconsider previous views," Logan added.

How does shigella spread?

The bacteria can be spread through stool, direct contact between people and via sexual activity. For example, this can happen if you eat food prepared by someone who has the infection or by touching a contaminated surface and then touching your mouth, the CDC explains.

"One of the things that distinguishes this illness is that it can be transmitted by a very few bacteria, so it's highly contagious," Gulick says.

Outside of the U.S., shigella bacteria can spread in "places that don't have as much access to clean water," Kortright explains.

To prevent a shigella infection, which is called shigellosis, the CDC says it's important to:

  • Wash your hands before eating or preparing food.
  • Wash your hands before sexual activity.
  • Wash your hands after going to the bathroom.
  • Follow recommendations for safe food and water handling when traveling internationally.
  • Don't swallow water from lakes, ponds or swimming pools.
  • Be careful when handling diapers.
  • Hold off on sex when you or your partner has diarrhea.

Symptoms of shigellosis, aka shigella infection

The symptoms of shigella infection are similar to other stomach bugs.

"For the majority of patients that have shigella, it essentially presents as diarrhea," Sobhanie says. And, in general, it's a self-limiting disease that people can treat at home with hydration and rest.

"If you're a healthy individual, it's like a case of food poisoning," Kortright adds.

According to the CDC, the most common symptoms include:

  • Diarrhea, which may be bloody and/or last for more than three days.
  • Stomach pain and abdominal cramping.
  • Fever.
  • Tenesmus, feeling like you need to poop even when your bowels are empty.

For most people, the symptoms start a day or two after becoming infected and last about a week. But some people may find that their bowel habits don’t go back to normal for “several months,” the CDC says.

In rare and severe cases of shigellosis, the bacteria may enter the bloodstream causing bacteremia or even sepsis, Gulick says. Other serious complications of shigellosis can include seizure, reactive arthritis and hemolytic uremic syndrome (which affects the kidneys), CDC experts said on the call.

But the most common complication by far is dehydration, Gulick adds.

Treatment for shigellosis

In most cases, people can recover from a shigella infection without antibiotics, the CDC says. Staying hydrated by drinking plenty of fluids and electrolytes is key.

When cases are more severe or for those at a higher risk for developing severe symptoms, antibiotic treatment may be necessary. People who have an increased risk for shigellosis include young children, travelers to areas with poor sanitation, people who are immunocompromised, men who have sex with men, and people experiencing homelessness, the CDC explains.

But, according to the new CDC warning, health care providers should be cautious to not overprescribe antibiotics because that can encourage antibacterial resistance.

In the infectious disease world, doctors call it an "antibiotic timeout," Sobhanie explains. Even for patients who might be immunocompromised, their provider may want to wait and see how they do before prescribing an antibiotic, he adds.

And doctors should use specialized test results of the patient’s sample to guide them in selecting specific medications.

Providers have become increasingly reliant on gastrointestinal panels, which can detect the presence of 20 possible pathogens, Gulick explains. "We're leaning heavily on those tests these days because you get answers back very quickly," he says.

But, when it comes to shigella, the CDC alert encourages doctors to "make sure that their laboratory is doing the old-fashioned culture," which can assess the strain's susceptibility to particular antibiotics, Gulick explains.

If someone gets severely ill with extensively antibiotic-resistant shigellosis, doctors may be able to draw on U.K. research with a class of antibiotics called carbapenems, the CDC alert says. (The U.K. has seen an elevated rate of drug-resistant shigellosis primarily affecting gay and bisexual men since last January.)

But those antibiotics are generally administered intravenously, Sobhanie says, which means they can't be taken at home.

They're also typically reserved for "the most resistant infections that are out there," Gulick explains. That's why "we really need to double down to try to prevent the development of multidrug resistant organisms and invest more in finding new treatments," he says.

Other antibiotic options, like fosfomycin, may be helpful, but there isn't enough data yet for the CDC to recommend them, experts said on the call.

One emerging option down the line may be what's called phage therapy, says Kortright, whose work focuses on interactions between phages and bacteria. "Phages are basically viruses that only infect bacteria, and they're highly specific towards the bacteria they infect," she explains. Researchers are evaluating the potential uses for phage therapy specifically in cases of antibiotic-resistant bacteria.

For now, anyone who's concerned about their symptoms or knows that they're at a higher risk for severe shigellosis should not hesitate to get in touch with their provider. That's yet another reason "that the doctor-patient relationship is incredibly important in every aspect of your life," Sobhanie says.