Antibiotic-resistant S. Maltophilia Spread Worldwide, Carry Diverse Genes, Study Reports

The antibiotic-resistant bacterium Stenotrophomonas maltophilia, a dangerous bacteria for people with lung diseases such as cystic fibrosis (CF), is widely spread around the world, with most strains carrying virulence and resistance genes, a large genetic study shows.

The study, “The phylogenetic landscape and nosocomial spread of the multidrug-resistant opportunist Stenotrophomonas maltophilia,” was published in the journal Nature Communications.

Stenotrophomonas maltophilia is increasingly recognized as a dangerous pathogen, with the World Health Organization listing it as one of the leading drug-resistant pathogens in hospital settings. This is particularly troublesome for patients with CF and other lung diseases, as well as those with compromised immune systems. The bacterium most frequently causes infections in the airways, in the blood (bacteraemia), or in catheters.

Despite the worrisome clinical scenario associated with S. maltophilia infection, little is known about the bacterium’s infectivity and its transmission worldwide.

To address this question, an international partnership with scientists from eight countries established a standardized method to analyze the genome of the different strains of S. maltophilia.

The team analyzed a global collection of newly sequenced S. maltophilia strains together with publicly available whole-genome data. In total, they collected data of 2,389 strains from 22 countries on four continents.

“Our data provide evidence for the global prevalence of particular circulating lineages with hospital-linked clusters collected within short time intervals suggesting transmission,” the researchers wrote. “The latter emphasises the need to instate or re-enforce hygiene and infection control practices to minimise in-hospital spread of these pathogens.”

Using a bioinformatics method known as Hierarchical Bayesian analysis, which groups genetically similar strains, the researchers found that the global population of S. maltophilia comprises a total of 23 lineages.

Next, they assessed how different S. maltophilia strains and lineages were distributed around the world.

Eight strains — Sm2, Sm3, Sm4a, Sm6, Sm7, Sm9, Sm10, and Sm12 — were found to be present on every continent. In particular, Sm6 was the strain most globally spread, and it was also found in the largest proportion on each sampled continent.

Although some of the 23 lineages — including Sgn1, Sgn2, Sgn3, and Sm11 — were classified as environmental, meaning they came from natural environments, most were anthropogenic, i.e., were adapted to the human host. These, such as Sm4b, were classified as human-invasive when found in blood, urine, drainage fluids, or cerebrospinal fluid (CSF, the fluid surrounding the brain and spinal cord).

To determine the infection potential of S. maltophilia strains, the researchers screened the data for genes related to virulence and resistance. They found that resistance genes were broadly present in S. maltophilia strains — for example, 69% of the strains were able to produce aminoglycoside-modifying enzymes, a common mechanism of antibiotic resistance.

In addition, virulence genes such as SmoR involved in mobility and quorum sensing (a mechanism that bacteria use to feel the presence of large amounts of bacteria from the same strain) was found in 89.3% of the strains.

The researchers highlighted that the Sm6 strain, in particular, was characterized by the presence of crucial virulence and resistance genes that made this strain “potentially best adapted to colonize or infect humans.”

“This suggests that a specific gene configuration may promote the spread of different S. maltophilia subtypes in the hospital setting, i.e. under antimicrobial treatment,” Matthias Gröschel, the study’s first author, from the Research Center Borstel–Leibniz Lung Center, Germany, said in a press release.

Moreover, analysis of strain transmission in hospital outbreaks showed that genetically similar strains were isolated in short intervals of days or weeks in the same hospitals.

“Combined with studies on other pathogens, our results show how systematic genome-based monitoring of S. maltophilia and other pathogens in hospital settings can help detect transmission pathways and improve infection control,” said Thomas Kohl, senior author of the study.