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Metagenomic Analysis Reveals Shifting Skin Microbe Communities on Hong Kong Subway System

Metagenomic Analysis Reveals Shifting Skin Microbe Communities

NEW YORK (GenomeWeb) – Straphanging on the Hong Kong subway system may have a hand in exposing individuals to innocuous and possibly more-pathogenic microbes, along with sets of microbial genes that be swapped between microbes to confer antibiotic resistance, according to a new study in Cell Reports.

"Our study provides an important reference for future public health strategies to mitigate intracity and cross-border pathogen and [antibiotic resistance gene] transmission," senior author Gianni Panagiotou, a systems biologist affiliated with Germany's Hans Knoell Institute and the University of Hong Kong, and his colleagues wrote.

The researchers used metagenomic sequencing to profile microbes and microbial genes present in skin swab samples from half a dozen individuals who volunteered to ride eight Hong Kong subway lines for a least a half an hour during the morning rush hour and again as commuters were heading home in the evening. With these data, they saw some subway line-specific microbes that seemed to reflect distinct environmental exposures.

Even so, the team's results also revealed changes in microbial communities on the hands of subway riders between the morning and evening commutes. In particular, these communities started to converge as the day wore on, coupled with changes in the distribution of both harmless commensal microbes and antibiotic resistance genes (ARG).

"In the morning, each line has unique microbial features reflecting the regions it passes, but with more and more people using the subway during the day, the microbial communities of all the lines become more similar, dominated by human skin commensal bacteria," Panagiotou said in a statement. 

Likewise, he noted, while genes linked to resistance to vancomycin, tetracycline, and other antibiotics only turned up on a few subway lines early on in the day, the ARGs "could be traced in all of them" by the time evening rolled around.

The study was intended to represent a typical day on the subway system in a large city, the team explained, complementing published and ongoing analyses of metagenomic sequences generated for transit samples in New York City and other urban centers.

"[W]e want to better understand how urban planning can impact the types of bacteria we encounter," Panagiotou explained, "so that studies like ours investigating the microbial composition of train compartments may guide future public health strategies and public transit designs."

Instead of directly sampling subway seats, poles, or handrails, though, he and his team focused on palm skin samples from individuals who did or did not ride a Mass Transit Railway system that connects Hong Kong to Shenzhen on the mainland and covers communities in between.

Using the Illumina HiSeq 1500 instrument, collaborators at the University of Hong Kong's Centre for Genomic Sciences did shotgun metagenomic sequencing on palm swab samples from six healthy study participants who held Hong Kong subway handrails for at least 30 minutes at a time, during rides on eight urban lines in the busy periods in the morning or evening.

Based on data for three samples per subway line over three weeks, the team identified prominent microbial species, phyla, and gene sequences within and between sites — microbial sequences it compared with those found in palm swab samples from six control individuals who had gone 30 minutes or more without touching any surfaces.

Along with commensal skin species such as Staphylococcus epidermidis, for example, the researchers detected DNA from a handful of opportunistic pathogen species or strains, albeit at low levels. When it came to resistance genes, meanwhile, a few ARG families decreased in abundance in evening commuters, though nine families of ARGs, including those containing tetracycline and vancomycin resistance genes, increased between the morning and afternoon rush hours.

Somewhat reassuring, though, is that "higher traffic Metro lines do not carry higher health risks, neither in terms of pathogens or in terms of antibiotic resistance genes," Panagiotou noted.

He and his co-authors noted that "more sampling time points could be considered to delineate more exquisite intraday dynamics, especially the time points before and after morning and evening peaks."

"[S]urveillance of the microbial communities responsive to and shaped by the public transit systems could serve as a reference for public policy-making regarding the prevention of ARG spread via intercity and cross-border traffic and protect millions of citizens from potential health hazards in daily life," they added.