A study by researchers at Washington University School of Medicine in St. Louis suggests that international travelers are bringing home new and potentially deadly strains of antimicrobial resistant superbugs in their gut microbiomes. The scientists, collaborating with researchers at Maastricht University, analyzed bacterial communities in the gut microbiomes of 190 Dutch adults before and after travel to Southeastern Asia, South Asia, North Africa and Eastern Africa, which are all regions where the prevalence of resistance genes is high. The results confirmed that international travelers commonly return home with an unexpected payload of new bacterial strains among the thousands that normally reside within the gut microbiome.

“Even before the COVID-19 pandemic, we knew that international travel was contributing to the rapid global increase and spread of antimicrobial resistance,” said Alaric D’Souza, an MD/PhD student at Washington University and a co-first author of the team’s published research in Genome Medicine. “But what’s new here is that we’ve found numerous completely novel genes associated with antimicrobial resistance that suggest a worrisome problem on the horizon.” D’Souza and colleagues describe their findings in a paper titled, “Destination shapes antibiotic resistance gene acquisitions, abundance increases, and diversity changes in Dutch travelers.”

Antimicrobial resistance (AMR) is a major global public health threat, with resistant bacteria now rendering antibiotics ineffective and limiting treatment options, the authors wrote. International agencies including The World Health Organization, and U.S. Centers for Disease Control and Prevention, have described the rapid spread of antimicrobial resistance as one of the most serious public health threats now facing the world. “Global AMR spread threatens decades of success in treating bacterial infections with antibiotics,” the authors noted.

While AMR is rising worldwide, there are major geographical differences in the prevalence and type of resistant bacteria and their AMR genes, the team continued. It’s a looming medical catastrophe that could outweigh the chaos created by the COVID-19 pandemic. Low- and middle-income countries generally have a higher burden of endemic AMR than high-income countries. Poverty, poor sanitation, changing agricultural practices and overuse of antibiotics in people and livestock have turned many developing regions into hot spots for diseases spread by bacteria, including infections that are increasingly resistant to a range of antibiotic drug treatments.

Moreover, “International travel can facilitate the transfer of resistant bacteria and AMR genes from their endemic regions to other locations around the globe,” the scientists noted. Population overcrowding in endemic regions make it easy for these AMR bacteria to spread among community residents and travelers, through exposure to contaminated drinking water and food, or poorly sanitized restrooms, restaurants, hotel rooms and public transportation, the investigators pointed out. And when people return home from their travels, they then run the risk of transferring these novel bacteria to family, friends and other community residents. However, the scientists noted, “Returning travelers are rarely tested for resistant bacteria or AMR genes unless they manifest clinical symptoms, so the magnitude of AMR gene acquisition risk from international travel remains underdetermined.”

Traditional genomic techniques look for distinctive genetic signatures of individual pathogens, but may only find known pathogens. In contrast, metagenomic sequencing makes it possible to identify all organisms present in a given sample, providing new insights into the human microbiome’s role as an AMR reservoir, and how this role might be affected by international travel. “We can sequence all extracted DNA using shotgun metagenomic sequencing, and we can directly identify AMR genes in these shotgun metagenomes by mapping reads to curated AMR gene database,” the scientists wrote.

For their new study, the team harnessed techniques including whole metagenomic shotgun sequencing, and functional metagenomics, to investigate the abundance, diversity, function, resistome architecture, and context of AMR genes in the fecal microbiomes of 190 Dutch individuals, before and after travel to different international locations. Fecal samples analyzed as part of the study were randomly selected from a larger, multicenter investigation of about 2,000 Dutch travelers, the majority of whom were tourists, known as the Carriage Of Multi-resistant Bacteria After Travel (COMBAT) study.

The study was designed by co-senior authors John Penders, PhD, a medical microbiologist at Maastricht University, and Gautam Dantas, PhD, a professor of pathology & immunology at Washington University. Manish Boolchandani, PhD, a member of the Dantas Lab during the research and a 2020 graduate of the university’s doctoral program in Computational and Systems Biology, is also a first author on the paper.

Their analyzes detected 121 antimicrobial resistance genes across the gut microbiomes of the 190 Dutch travelers. More than 40% of these resistance genes (51 of them) were only discovered using the more sensitive metagenomics technique, suggesting that potentially dangerous genes are being missed by the more conventional approaches. “While previous studies have scanned travelers’ stool samples for well-known antimicrobial resistant bacteria, we used a combination of whole metagenome shotgun sequencing and functional metagenomics to identify both known and novel genes that code for antimicrobial resistance,” Dantas said.

D’Souza added, “We found significant travel-related increases in the acquisition of resistance genes, abundance and diversity encoded by bacteria that are endemic to the region visited. These findings provide strong support for international travel as a vector for the global spread of clinically important antimicrobial resistance genes and highlight the need for broader surveillance of antimicrobial resistant bacteria in the gut microbiomes of returning travelers.” Interestingly, the team further commented, “… the travel-induced shaping of the gut resistome correlated with geographical destination, so individuals returning to The Netherlands from the same destination country were more likely to have similar resistome features.”

Of particular concern, the study’s results confirmed that 56 unique antimicrobial resistance genes had become part of the travelers’ gut microbiomes during their trips abroad, including several mobile, high-risk resistance genes, such as extended-spectrum β-lactamases (ESBL) and the plasmid-borne colistin resistance gene, mcr-1. Resistance to beta-lactam antibiotics is emerging worldwide and confers broad resistance to treatment by penicillins and other important antibiotics.

The mcr-1 genes protect bacteria from another antimicrobial drug called colistin, which is the last-resort treatment for infections by multidrug-resistant gram-negative bacteria. If colistin resistance spreads to bacteria that are resistant to other antibiotics, those bacteria could cause truly untreatable infections, the CDC has warned.

Because metagenomic analysis allows researchers to study all the bacteria and genes in a collection of gut microbiome samples as one, large mixed community of organisms, it also provides opportunity to explore complex ecological interactions between these organisms.

While bacteria may slowly evolve resistance from repeated exposures to antibiotics over time, diverse bacterial communities also share antimicrobial resistance genes through a more rapid process known as horizontal transfer, usually via the exchange of mobile genetic elements that allow snippets of DNA to jump from one bacterium to another. “Since genes that code for resistance to different classes of antibiotics are often located on the same mobile elements, a single horizontal exchange has the potential to convert bacteria previously susceptible to antibiotics into a multi-drug resistant organism,” said Dantas.

Researchers also used metagenomic techniques to piece together important contextual information about resistance gene location and function. “There was significant association of resistance genes with mobile genetic elements, a primary way that resistance genes spread among bacteria,” D’Souza said. “Though our study was unable to demonstrate resistance genes are carried by pathogenic bacteria, it’s clear that this is possible. Additionally, international travelers have the potential to introduce resistance genes into their own communities when they return home, and future studies directly addressing this possibility are a priority.”

The authors concluded, “Our results demonstrate that international travel is a significant perturbation to the gut resistome and reveal destination-specific changes to travelers’ resistomes including AMR gene acquisitions against last resort antibiotics and AMR gene colocalization with mobile genetic elements … Interventions to reduce AMR burden in low- and middle-income countries with current high endemic AMR burdens may reduce traveler AMR gene acquisitions.”

Added Dantas: “Identifying new antimicrobial resistant bacteria and genes could play an important role in slowing the global spread of resistance and guide potential treatments for related diseases. Our study lays the groundwork for those efforts by offering new insight into the genetic mechanisms that underlie the rapid acquisition and sharing of antimicrobial resistance genes across people’s gut microbiomes during international travel.”