Metagenomic analysis of an urban resistome before and after wastewater treatment

Abstract

Determining the effect of wastewater treatment in water resistome is a topic of interest for water quality, mainly under re-use and one-Health perspectives. the resistome, the plasmidome, and the bacterial community composition of samples from influents and treated effluents from a wastewater treatment plant located in northern portugal were studied using metagenomic techniques. Wastewater treatment contributed to reduce the abundance of resistance genes and of plasmid replicons, coinciding with a decline in the number of intrinsic resistance genes from Enterobacteriaceae, as well as with a reduction in the relative abundance of Firmicutes and Proteobacteria after treatment. these taxons comprise bacterial pathogens, including those belonging to the eSKApe group, which encompasses bacteria with the highest risk of acquiring antibiotic resistance, being the most relevant hosts of resistance genes acquired through horizontal gene transfer. our results support that wastewater treatment efficiently removes the hosts of antibiotic resistance genes and, consequently, the harboured antibiotic resistance genes. principal component analysis indicates that the resistome and the bacterial composition clustered together in influent samples, while did not cluster in final effluent samples. our results suggest that wastewater treatment mitigates the environmental dissemination of urban resistome, through the removal of the hosts harbouring mobile resistance genes. Most studies on antibiotic resistance have concentrated their efforts on human pathogens and in human-linked environments (hospitals, human hosts,…). However, the full understanding of the origin, evolution, spread, and maintenance of antibiotic resistance (AR) requires an integrative approach in which all ecosystems that may contribute to such evolution are studied; a One Health approach 1,2. One Heath is a concept derived from the idea proposed by Rudolph Virchow in the 19th Century, stating that "between animal and human medicine there are no dividing lines-nor should there be". The idea behind is that, at least in the case of infectious diseases, different ecosystems, not just the human host, may contribute to the spread of the infective agents. This is particularly relevant in the case of AR, since it is generally accepted that antibiotic resistance genes (ARGs), currently present in human pathogens, are originated in environmental organisms and, therefore, natural ecosystems can be reservoirs and participate in the spread of AR 3-9. Consequently, it has been proposed that AR is the quintessential One Health issue 2 , and that studies, integrating all habitats potentially involved in the evolution and spread of AR are needed 1,10,11. Indeed, seminal work showed that animal farms could be a reservoir of AR 12. As a consequence, the use of antibiotics in farming, for non-therapeutic or prophylactic procedures (as animal fattening), has been banned in different countries 13,14. More recently, non-clinical environments (natural and man-made ecosystems) have been pro...

Structure of Bacterial Community with Resistance to Antibiotics in Aquatic Environments. A Systematic Review

“…Of these, there were 128 duplicates, and 16,013 were excluded on the basis of title and abstract screening. A total of 68 studies [ 11 , 12 , 13 , 14 , 15 , 16 , 17 , 18 , 19 , 20 , 21 , 22 , 23 , 24 , 25 , 26 , 27 , 28 , 29 , 30 , 31 , 32 , 33 , 34 , 35 , 36 , 37 , 38 , 39 , 40 , 41 , 42 , 43 , 44 , 45 , 46 , 47 , 48 , 49 , 50 , 51 , 52 , 53 , 54 , 55 , 56 , 57 , 58 , 59 , 60 , 61 , 62 , 63 , 64 , 65 , ...…”

“…These bacteria are abundant in WWTPs in cities in Portugal, Spain, Germany, Sweden, South Korea, and Brazil [ 11 , 41 , 42 , 47 , 48 , 49 , 59 ]. However, they were also determined in treated waters and in natural water systems of marine environments, rivers and lagoons, mainly in Latin American countries [ 34 , 45 , 49 , 50 , 56 , 60 ].…”

“…In Europe, North America and Latin America, the most prevalent ARGs are the bla genes, with approximate prevalence values of 40%, 34% and 89%, respectively [ 11 , 15 , 38 , 40 , 44 , 47 , 59 , 60 , 72 , 76 ]. In Africa, the sul genes (67%) [ 41 ], and in Asia the tet genes, are the most reported (30%) [ 32 , 35 , 48 , 65 , 70 , 71 ] ( Figure 6 ). Most of these genes are reported in WWTPs, which indicates that the processes carried out there must be optimized to reduce the load of ARGs that reaches these plants, especially from products generated from clinical and domestic activities.…”

“…The increasing anthropogenic and industrial activity near or directly in water systems has contributed to the growth and strengthening of the bacterial resistome [ 7 , 9 , 41 , 61 ]. There is no doubt that aquatic environments act as reservoirs for the acquisition and spread of bacteria with resistance to antibiotics, so human exposure to bacteria resistant to antibiotics and ARGs from these environments may represent an additional risk to health.…”

Fecal Microbiome and Resistome Profiling of Healthy and Diseased Pakistani Individuals Using Next-Generation Sequencing

“…Policies regulating antibiotic usage in humans and animals have been reported to influence the prevalence of ARGs in the resistomes of various individuals from different countries [19,20]. Metagenomics studies contributed significantly to understanding the bacterial communities associated ARGs in diverse samples such as human stools samples, animal fecal samples, ready-to-eat food [21], and urban resistome [22]. Large-scale metagenomic studies [19,20] explored the gut resistome of healthy people from different countries and studied the abundance pattern of ARGs.…”