Passenger-surface microbiome interactions in the subway of Mexico City

Abstract

Interaction between hands and the environment permits the interchange of microorganisms. The Mexico City subway is used daily by millions of passengers that get in contact with its surfaces. In this study, we used 16S rRNA gene sequencing to characterize the microbiomes of frequently touched surfaces and compare regular and women-only wagons. We also explored the effect of surface cleaning on microbial resettling. Finally, we studied passenger behavior and characterized microbial changes after traveling. Most passengers (99%), showed some type of surface interaction during a wagon trip, mostly with the hands (92%). We found microbiome differences associated with surfaces, probably reflecting diverse surface materials and usage frequency. The platform floor was the most bacterial diverse surface, while the stair handrail and pole were the least diverse ones. After pole cleaning, the resettling of microbial diversity was fast (5-30 minutes); however, it did not resemble the initial composition. After traveling, passengers significantly increased their hand microbial diversity and converged to a similar microbial composition among passengers. Additionally, passenger hand microbiomes resembled subway surfaces in diversity. However, microbial fingerprints were preserved within passengers after traveling.

Fig 1. Study design.

We swabbed surfaces and used the 16S rRNA gene (red dots) and microbial cultures (blue dots) to describe bacterial diversity. (a) Microbiome comparison of subway surfaces: turnstiles, escalator handrails, stair handrails, platform floors, poles, and train seats. Poles and train seats were sampled in regular and women-only wagons (N = 5 per site). (b) Microbiome succession study after a cleaning event in poles. Microbiome changes were evaluated at pre-cleaning (PC) and 0, 0.5, 2, 8, and 48 h after cleaning. (c) Hand microbial diversity before and after traveling; we evaluated the effect of traveling with and without previous handwashing.

Fig 2. Subway surface microbiome diversity.

Microbial composition differed among subway surface types. (a) Taxa summary showing the most abundant genera. (b) Beta diversity at the genus level, Bray-Curtis based non-metric multidimensional scaling (NMDS) plot of surface types samples.

Fig 3. Unique and shared genera among time groups.

Many genera are unique to each time group, and many resettled genera are not persistent. Upset plot of intersected genera among time points after cleaning; empty intersections are not shown. Taxa shared among all times are shown in green. Resettled taxa are shown with an orange line.

Fig 4. Pole microbiome diversity succession measured by 16S amplicons and colony-forming units (CFUs) after a cleaning event.

(a) Alpha diversity and (b) beta diversity did not resettle within 48 h after cleaning. Nevertheless, the CFU count was regained within minutes (c). (a) Alpha diversity boxplots show the Chao1 richness estimator. (b) Non-metric multidimensional scaling (NMDS) ordination with Bray-Curtis dissimilarity at the genus level. (c) CFUs in seven time-points plus two controls: pre-cleaning (PC) and time control at two h (not cleaning). The last control pretends to evaluate the microbiome’s natural changes in real-time (*p < 0.05 and **p < 0.005, Dunn’s test).

Fig 5. Changes in the passenger hand microbiome before and after traveling without handwashing.

(a) Alpha diversity is increased after traveling (* p < 0.020). (b) Heatmap, using Manhattan distances, showing the relative abundance of all genera shared among subjects (columns, denoted by a number) before or after traveling. The subjects showed a closer microbiome profile after traveling. Letters before taxa indicate the best possible phylogenetic assignment (o: order and f: family). (c) Constrained analysis of principal coordinates (CAP) at the genus level, showing significant segregation for SubjectID and Travel (before and after) variables (p = 0.001, F = 2.4 and p = 0.006, F = 2.0, ANOVA-like permutation test for CAP).

Fig 6. Hand microbiome composition converges after traveling.

Non-multidimensional scaling (NMDS) ordination bi-plot performed with Bray Curtis distance for no handwashing and handwashing and different surface types, at the genus level. Arrows connect the same subjects from before to after traveling. Unpaired dots are samples without matching before or after travel comparison because of low metagenomic DNA yield (washed hands).