Posted on Mar 08, 2019, 2 p.m.
International research has created a global map of antimicrobial resistance by analyzing samples of untreated domestic sewage to identify antimicrobial resistant genes in a metagenomic analysis of sewage samples across 60 countries to characterize abundance and diversity of AMR, as published in Nature Communications.
Systematic differences in the diversity and abundance of AMR gene between North America, Europe, New Zealand, South America, and Australia were highlighted. Based on findings the greatest diversity of AMR was found to be in India, Vietnam, and Brazil, with New Zealand and Australia having the lowest AMR gene diversity.
Antimicrobial resistance is fast becoming an increasing threat to public health, based on this study it may be an effective strategy if efforts were made to improve sanitary conditions in countries with high levels of AMR. Surveillance methods typically focus on a few pathogens and may not be based on patient specimen data, yielded data may not be comparable and also only encompasses a narrow pathogen spectrum rather than capturing all relevant antimicrobial resistance genes.
Sampling raw sewage from urban areas makes an appealing option from the perspective of antimicrobial resistance surveillance as it effectively samples from large populations. Sewage surveillance for AMR is quick and relatively cheap, and can show exactly which bacteria abound in areas without needing ethical approval as material can’t be traced back to any one individual; these parameters make sewage surveillance systems for AMR a viable option.
For the metagenomic study domestic sewage was analysed from 79 sampling locations in 7 geographic regions of 74 cities across 60 countries; 1546 different bacterial genera were identified. The highest levels of AMR gene abundance were observed in African countries in terms of geographical abundance, but Brazil had the highest abundance of all countries; Australia and New Zealand were on the lowest end of the spectrum. According to the researchers comparable data on global occurrence of AMR genes of predominantly health people doesn’t exist to the best of their knowledge.
1625 different antimicrobial resistant genes from 408 genes groups were identified in total. Genes encoding resistance towards aminoglycosides, macrolides, tetracyclines, sulfonamides, and beta-lactams were the most abundant. Asian and African samples exhibited high proportions of genes conferring resistance to phenicols and sulphonamides, while North America and Europe samples had a high relative proportion of macrolide resistance genes geographically; and 15 AMR genes contributed to 50% of the total abundance, with none of the dominant genes being known to be specific to a particular bacterial genera.
World Bank regional development and population health data was utilized to investigate factors other than antimicrobial drug use that may have had impact on the development of AMR in the different countries; most relevant variables were found to be related to sanitary conditions and the population’s general state of health. Irrespective of the diversity of antimicrobial resistant genes the total AMR abundance was found to be highly correlated with a limited number of World Bank variables which mainly concerned health and sanitation. Global AMR gene abundance and diversity were found to vary by region, and improving health and sanitation could potentially limit the global burden.
Results from two different computational models applied to the data indicates while the abundance of AMR genes belonging to specific antimicrobial class increases with increasing levels of residues from that drug class there was no relationship between total drug residue level and the antimicrobial resistant genes; results did not find any significant effect of total usage of all antimicrobials on the abundance of the different classes, suggesting use of a specific class is an important driver of AMR genes encoding resistance to that class, effects of cross and/or co-resistance appear to have minor contribution to abundances.
Human air travel was found to have had little influence on antimicrobial resistant gene abundance, suggesting the total abundance is mainly influenced by national and/or local parameters; all genes might rapidly disseminate and be found in all corners of the world, local selection is required for them to reach appreciable frequencies.
Levels of antimicrobial resistance was predicted for 259 countries using the World Bank data, a world map of resistance in healthy populations was drafted based on their results. Based on their yielded estimates New Zealand, Sweden, and the Netherlands are suggested to have the lowest levels of resistance, while Nigeria, Tanzania, and Vietnam have the highest levels of resistance.
Metagenomics were utilized to quantify thousands of genes simultaneously to generate data that can be reanalyzed and re-examined in this study; other methods such as PCR or culturing could also have been used to achieve greater sensitivity, as acknowledged by the researchers. Developing a system to better enable researchers to exchange and interpret information in real time using global surveillance data in order to help manage diseases which threaten to spread across borders is the main objective, according to the researchers.
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