Via Microbiome, a report with some disquieting implications: The structure and diversity of human, animal and environmental resistomes. "ARGs" stands for "antibiotic resistance genes." Excerpt from the results section:
Antibiotic-polluted environments have the highest abundances of ARGs
Environments affected by pollution from pharmaceutical manufacturing were not only rich in ARGs but also carried the highest relative abundance of ARGs of all investigated environments (Fig. 1a). In particular, we identified exceptionally high relative abundances of the sulfonamide resistance gene sul2 and aminoglycoside resistance genes aph(6)-Id and aph(3”)-Ib together with a set of resistance genes to quinolones (qnr) and beta-lactams. The exact quantitative estimates of resistance genes should, however, be interpreted with caution since DNA from 7 out of 11 metagenomes from pharmaceutically polluted environments were amplified before sequencing, which can potentially introduce bias.
The relative abundances of ARGs in wastewater/sludge were also higher (0.17 copies per 16S rRNA on average) compared to most other environmental habitats (sediment, water, soil and mine; 0.002–0.02 copies per 16S rRNA on average) all of which are likely less impacted by human faecal residues.
Air from Beijing smog (see below), pharmaceutically polluted (38.9 different ARG types) and wastewater/sludge (19.4 different ARG types) environments carried more diverse sets of ARGs than did metagenomes from other external environments (1.6–3.3 different types of ARGs), animals (11.8 different ARG types) and humans (1.0–16.6 different ARG types). Note that these estimates only refer to genes identical or highly similar to known ARGs.
Urban air has high abundance and diversity of ARGs
Microbial communities from Beijing smog harboured the highest richness of known ARGs (64.4 different ARG types), as well as the highest bacterial richness of all environments. The relative abundance was however on the same level as the human gut and wastewater/sludge (0.3 copies of ARGs per 16S rRNA).
To investigate if the high ARG richness was a general feature of air microbiomes, we compared the resistome profile of Beijing smog samples to indoor and outdoor air samples (generated on the 454 sequencing platform) from houses, office buildings and hospitals located in New York and San Diego. After normalizing for the very large differences in sequencing depth between the two datasets (using down-sampling), the air microbiomes from the US cities showed comparable relative abundances of ARGs.
However, the richness of ARGs was higher in Beijing smog than in the air samples from US cities with the exception of office indoor air samples. Notably, the Beijing smog metagenomes contained several resistance genes to carbapenems, a class of last resort antibiotics, including IND, GES, IMP, OXA-50, OXA-51 and OXA-58 beta-lactamase gene types.
See this report in today's South China Morning Post for details on these findings. And as if that weren't bad enough, Beijing's air quality index stations are today reporting counts mostly in 300s (hazardous).
