Metagenomics analysis of bacteriophages and antimicrobial resistance from global urban sewage

Abstract

Bacteriophages, or phages, are ubiquitous bacterial and archaeal viruses with an estimated total global population of 10³¹. It is well-known that wherever there are bacteria, their phage counterparts will be found, aiding in shaping the bacterial population. The present study used metagenomic data from global influent sewage in 79 cities in 60 countries to identify phages associated with bacteria and to explore their potential role in antimicrobial resistance gene (ARG) dissemination. The reads were mapped to known databases for bacteriophages and their abundances determined and correlated to geographic origin and the countries socio-economic status, as well as the abundances of bacterial species and ARG. We found that some phages were not equally distributed on a global scale, but their distribution was rather dictated by region and the socioeconomic status of the specific countries. This study provides a preliminary insight into the global and regional distribution of phages and their potential impact on the transmission of ARGs between bacteria. Moreover, the findings may indicate that phages in sewage could have adopted a lytic lifestyle, meaning that most may not be associated with bacteria and instead may be widely distributed as free-living phages, which are known to persist longer in the environment than their hosts. In addition, a significant correlation between phages and ARGs was obtained, indicating that phages may play a role in ARG dissemination. However, further analyses are needed to establish the true relationship between phages and ARGs due to a low abundance of the phages identified.

Figure 1

Fragment count (A) and relative abundance (B) summary of phages and viruses. AF Africa, AS Asia, EU Europe, NA North America, ME Middle East, OC Oceania, SA South America.

Figure 2

Regional distributions of phages (left) and other viruses (right) from all databases. AF Africa, AS Asia, EU Europe, NA North America, ME Middle East, OC Oceania, SA South America.

Figure 3

Distribution of NCBI phages (A), IMG/VR genomes (B) and huge phages (C) stratified by income class. Densities indicated by blue curves.

Figure 4

Pooled relative abundance of phages in their respective phage families (NCBI, top) and clades (huge phages, bottom). Intensities based on 10%- and 3.3%-quantiles, respectively. AF Africa, AS Asia, EU Europe, NA North America, ME Middle East, OC Oceania, SA South America.

Figure 5

SNP trees of uncultured crAssphage (NC_024711, left) and Salmonella phage SJ46 (NC_031129, right). AF Africa, AS Asia, EU Europe, NA North America, ME Middle East, OC Oceania, SA South America.