Study suggests link between diet and antibiotic resistance in gut bacteria

A study published yesterday in mBio suggests a diverse, high-fiber diet is associated with fewer antibiotic-resistance genes (ARGs) in gut bacteria.

In the study, researchers from the US Department of Agriculture-Agriculture Research Service (USDA-ARS) used shotgun metagenomic sequencing to analyze stool samples from 290 healthy adults participating in the USDA Nutritional Phenotyping Study. The analysis revealed a large diversity, both in abundance and composition, of ARGs, with people having a high ARG abundance generally having a higher diversity of resistance mechanisms.

Aminoglycoside resistance was the most common mechanism of resistance within the cohort, followed by resistance to macrolide-lincosamide-streptogramin and tetracyclines.

Examining the participants' diet using a food frequency survey and 24-hour dietary recalls, the researchers found that participants who consumed more fiber, fewer animal proteins, and more diverse foods had lower total abundances of ARGs, while participants with less diverse diets had the highest levels of ARGs. Machine learning analysis showed a strong association between more diverse diets with higher amounts of soluble fiber and low ARG levels. Those with the lowest levels of ARGs in their gut microbiome also had a greater abundance of strict anaerobic microbes, especially from the family Clostridiaceae.

"Surprisingly, the most important predictor of low levels of ARG, even more than fiber, was the diversity of the diet," senior study author Danielle Lemay, PhD, of the USDA-ARS Western Human Nutrition Research Center, said in an agency press release. "This suggests that we may want to eat from diverse sources of foods that tend to be higher in soluble fiber for maximum benefit."

Lemay added that while further research is needed, the findings suggest dietary interventions could play a role in reducing antibiotic resistance.
May 10 mBio study
May 10 USDA-ARS press release

Global number of unexplained hepatitis cases in kids climbs to 450

In an epidemiologic update today, the European Centre for Disease Prevention and Control (ECDC) said the number of unexplained hepatitis cases in young children has risen to about 450, including 11 deaths. The agency also said it's not clear if the cases identified following an alert from the United Kingdom are part of a true increase compared to baseline rates of idiopathic hepatitis in children.

The ECDC said a possible link to adenovirus is still possible, but other hypotheses and cofactors are under investigation. It said most cases are sporadic, without links to each other.

Of the 450 or so global cases, 163 are from the United Kingdom, from 102 to 106 are from European Union countries, and 181 are from other parts of the world. Eleven deaths have been reported in Indonesia, Palestine, and the United States.

In a related development today, the US Centers for Disease Control and Prevention (CDC), in a Health Alert Network (HAN) notice, updated its recommendations for adenovirus testing and case reporting. It said a cluster of unexplained pediatric hepatitis cases was reported to the CDC in November 2021. So far, 109 cases in 25 states have been reported, including 5 deaths.

US scientists are examining a potential adenovirus link but are considering other causes, as well. The CDC urged clinicians to consider adenovirus testing for patients with unknown hepatitis and submit the following sample types, if possible: blood, respiratory, stool, and liver tissue.

Yesterday, a WHO official said countries are in the process of confirming 70 more cases. Though adenovirus is the leading hypothesis, investigators are also looking at COVID-19 infection as a cofactor, adding that serology studies are needed to assess previous exposure to SARS-CoV-2.
May 11 ECDC epidemiologic update
May 11 CDC HAN update
May 10 CIDRAP News story

Avian flu strikes more poultry in 5 states

Five states reported more highly pathogenic avian flu outbreaks, including Michigan and Pennsylvania, which both reported the virus on commercial farms, according to the latest notifications from the USDA Animal and Plant Health Inspection Service (APHIS).

In Michigan, an outbreak struck a turkey farm housing 35,100 birds in Muskegon County, located in the western part of the state near Grand Rapids. And in Pennsylvania, the virus hit two commercial duck farms in Berks County, which had a total of 61,100 birds, and a layer farm in neighboring Lancaster County housing 72,300 chickens. The two counties are in the southeastern corner of the state.

Meanwhile, three states reported more outbreaks in backyard birds, including Washington, which reported two in Pierce County near Tacoma. Also, Idaho reported an outbreak at a facility in Ada County near Boise, and Minnesota reported two more outbreaks, in Crow Wing and Todd counties in the central part of the state.

The outbreaks involve the Eurasian H5N1 strain, which is also sickening waterfowl, raptors, and other birds in several states. The virus has fueled poultry outbreak in 34 states, leading to the loss of 37.55 million birds, according to the USDA.
USDA APHIS poultry outbreak update page