Antimicrobial resistance: sewage samples reveal bad sanitation as a key driver
Sequencing genes from DNA found in sewage has led to the conclusion that AMR prevalence is related to sanitation and general health outcomes, rather than use of antibiotics. How can this discovery and the creation of a global surveillance system support the fight against the spread of AMR and disease-causing microorganisms? Allie Nawrat investigates.
Researchers led by the National Food Institute, Technical University of Denmark have mapped the levels and types of antimicrobial resistant (AMR) bacteria across the globe for the first time.
They relied upon metagenomics data from sewage collected from 74 cities in 60 countries; they sequenced the genes in the DNA found in the sewage using the Illumina HiSeq system and processed the data using MGmapper.
In terms of levels of AMR, the team found that North America, Western Europe, Australia and New Zealand generally had lower levels of AMR; with the Netherlands, New Zealand and Sweden having the lowest. Asia, Africa and South America had higher levels; the highest were recorded in Tanzania, Vietnam and Nigeria.
National Food Institute professor and head of the study Professor Frank Aarestrup noted cities in Africa stood out with particularly high levels of AMR.
Brazil, India and Vietnam the greatest diversity in resistant genes in the sewage; Australia and New Zealand have the lowest.
Sanitation explains global variation in AMR levels
Based on their findings, which were correlated with World Bank data on health status in a country and its stage of development, the researchers concluded the prevalence of AMR in a country was more closely related to the sanitary conditions and the population’s general health than to the misuse of antimicrobial products.
Aarestrup describes this as the most interesting finding of the team’s research, stating: “We believe that with bad sanitation the risk of spreading AMR between people increases. Thus, if antimicrobial use is selecting for AMR in a given person then this is rapidly transmitted to other people and thereby increases prevalence in the [local] population.”
With bad sanitation the risk of spreading AMR between people increases.
The research team believes understanding this AMR-sanitation correlation can improve global efforts against AMR spread. Aarestrup said: "In the fight against antimicrobial resistance, our findings suggest that it would be a very effective strategy if concerted efforts were made to improve sanitary conditions in countries with high levels of antimicrobial resistance." This would reduce the transmission of AMR between people in the locality.
Outliers to the sanitation-AMR correlation
Although in general, Asia, Africa and South America had the highest levels of AMR, Aarestrup identified some countries that bucked this trend.
One example noted by Aarestrup is China. He explains that Chinese AMR levels were “lower than expected because we in general have this perception that a lot of novel resistance problems are coming from China.” He also mentions Sri Lanka as having lower AMR levels than expected.
However, Aarestrup states “we might be wrong”, and more research needs to be done to “verify our findings through new sampling [and] look more in detail regarding variation within countries.”
Global surveillance to coordinate the AMR campaign
Future data will be added to the current data in a global surveillance system, which aims to continually monitor the occurrence and spread of AMR.
This data will help support and coordinate the international and national fights against AMR. However, Aarestrup and his international team believe the data can also be useful in the management of diseases that threaten to spread across national borders and develop into pandemics, such as Ebola, measles and polio.
The Global Polio Eradication Initiative has stated that there are only three countries that still see polio cases: Nigeria, Afghanistan and Pakistan. The main reason why polio remains impervious to eradication in the latter two is due to cross-border migration and the administrative challenges this creates.
The National Food Institute wants this global surveillance to become the international standard of detection, surveillance and studies of disease-causing microorganisms and AMR bacteria.
Analysing sewage can quickly and relatively cheaply show exactly which bacteria abound in an area.
Its researchers believe that their sewage-based metagenomics data approach can revolutionise how we combat the spread of AMR and infectious diseases and are supporting a widespread adoption of this approach through the European Union’s COMPARE programme.
Aarestrup said: "Analysing sewage can quickly and relatively cheaply show exactly which bacteria abound in an area—and collecting and analysing sewage doesn’t require ethical approval, as the material cannot be traced back to individuals.
“Both parameters help to make a surveillance system via sewage a viable option—[especially] in developing countries.”
The completed project was supported by a range of non-profit entities, including Danish pharmaceutical company Novo Nordisk’s foundation, which has also given Aarestrup a grant for the next four years “to continue exploring the value of using sewage for global surveillance”.
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