Leveraging genomes and metagenome-assembled genomes unveils novel diversity and transmission between public transport and clinical settings in Acinetobacter
This study demonstrates that integrating metagenome-assembled genomes (MAGs) from public transport systems with clinical isolates reveals extensive unrecognized diversity and evidence of transmission for multiple *Acinetobacter* species, highlighting the critical role of MAGs in genomic surveillance of man-made environments and their public health implications.
Original paper licensed under CC BY 4.0 (https://creativecommons.org/licenses/by/4.0/). This is an AI-generated explanation of a preprint that has not been peer-reviewed. It is not medical advice. Do not make health decisions based on this content. Read full disclaimer
Bacteria are everywhere, living in soil, water, and on our skin, but scientists have traditionally studied them by growing them in petri dishes in a laboratory. This method works well for some types of bacteria but fails for many others that are difficult or impossible to grow outside their natural environment. As a result, our understanding of the microbial world has been skewed toward the few species that thrive in a dish, leaving vast gaps in our knowledge of the rest. To fill these gaps, researchers now use a technique called metagenomics, which involves reading the genetic material directly from environmental samples without needing to culture the organisms first. By piecing together these genetic fragments, they can reconstruct the full genomes of bacteria that have never been seen before. This approach is particularly important for tracking how bacteria move between different environments, such as from the outside world into hospitals, and for understanding how they acquire the ability to resist antibiotics, a growing threat to public health.
A team of researchers set out to explore a specific, overlooked corner of this microbial world: the public transport systems of cities around the globe. While hospitals are well-known reservoirs for dangerous bacteria, it was unclear whether the same organisms were also hiding in subways, buses, and trains, and if so, whether they were moving between these public spaces and clinical settings. The scientists analyzed genetic data from 15 different projects covering 128 cities across 19 countries, including major hubs like New York, London, and Tokyo. From these samples, they reconstructed 839 partial genomes, known as metagenome-assembled genomes, which represent the genetic blueprints of bacteria living in these transit systems. They focused their detailed analysis on 269 of these high-quality genomes, which belonged to more than 20 different species of a bacterial genus called Acinetobacter. While one species, Acinetobacter baumannii, is famous for causing hospital infections, the researchers found that the public transport systems were dominated by five other, less-studied species: A. nosocomialis, A. ursingii, A. radioresistens, A. schindleri, and A. variabilis.
The study revealed that these bacteria in public transport are not just random visitors; they represent a rich, previously hidden diversity. When the researchers compared the genetic makeup of the bacteria found in subways with those found in hospitals, they discovered that the subway bacteria added a significant amount of new genetic variety. For some species, including A. variabilis, the inclusion of these transport-based genomes increased the known genetic diversity by more than 90 percent. Furthermore, these bacteria carried thousands of genes that had never been seen in the laboratory-grown versions of the same species. This suggests that by relying only on bacteria that can be grown in a dish, scientists have been missing a large portion of the genetic toolkit these organisms possess. The analysis showed that for four of the five species studied, the bacteria found in public transport were genetically almost identical to those found in hospitals, with no clear genetic separation between the two environments. This indicates that these bacteria are moving freely between the city's transit systems and medical facilities, likely carried by passengers and staff.
Beyond just tracking where the bacteria come from, the researchers investigated what kinds of antibiotic resistance genes these organisms carry. They found that the bacteria in public transport harbor genes that can make them resistant to powerful drugs, including genes that protect against sulfa drugs and aminoglycosides. However, the study also highlighted a limitation in how scientists usually search for these resistance genes. When the researchers looked only at the reconstructed genomes, they found far fewer resistance genes than when they used a different method that scanned the entire environmental sample and then matched the results against known bacterial genomes. This alternative approach revealed up to seven times more resistance genes in some cases. The findings suggest that while the reconstructed genomes are excellent for understanding the evolutionary history and diversity of the bacteria, they may underestimate the full extent of the antibiotic resistance threat. In some species, the resistance profiles of the transport bacteria were indistinguishable from those in hospitals, while in others, there were clear differences. Ultimately, the work demonstrates that public transport systems are active hubs for bacterial diversity and transmission, and that combining new genetic reconstruction methods with traditional analysis is essential for getting a complete picture of the risks these invisible passengers pose to human health.
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