Background: As the relevance of bacteriophages in shaping diversity in microbial ecosystems is becoming increasingly clear, the prediction of phage sequences in metagenomic datasets has become a topic of considerable interest, which has led to the development of many novel bioinformatic tools. A comprehensive comparative analysis of these tools has so far not been performed. Methods: We benchmarked ten state-of-the-art phage identification tools. We used artificial contigs generated from complete RefSeq genomes representing phages, plasmids, and chromosomes, and a previously sequenced mock community containing four phage strains to evaluate the precision, recall and F1-scores of the tools. In addition, a set of previously simulated viromes was used to assess diversity bias in each tool's output. Results: DeepVirFinder performed best across the datasets of artificial contigs and the mock community, with the highest F1-scores (0.98 and 0.61 respectively). Generally, machine learning-based tools performed better on the artificial contigs, while reference and machine learning based tool performed comparably on the mock community. Most tools produced a viral genome set that had similar alpha and beta diversity patterns to the original population with the notable exception of Seeker, whose metrics differed significantly from the diversity of the underlying data. Conclusions: This study provides key metrics used to assess performance of phage detection tools, offers a framework for further comparison of additional viral discovery tools, and discusses optimal strategies for using these tools.

In many low- and middle-income countries antibiotic resistant bacteria spread in the environment due to inadequate treatment of wastewater and the poorly regulated use of antibiotics in agri- and aquaculture. Here we characterised the abundance and diversity of antibiotic-resistant bacteria and antibiotic resistance genes in surface waters and sediments in Bangladesh through quantitative culture of Extended-Spectrum Beta-Lactamase (ESBL)-producing coliforms and shotgun metagenomics. Samples were collected from highly urbanised settings (n = 7), from rural ponds with a history of aquaculture-related antibiotic use (n = 11) and from rural ponds with no history of antibiotic use (n = 6). ESBL-producing coliforms were found to be more prevalent in urban samples than in rural samples. Shotgun sequencing showed that sediment samples were dominated by the phylum Proteobacteria (on average 73.8% of assigned reads), while in the water samples Cyanobacteria (on average 60.9% of assigned reads) were the predominant phylum. Antibiotic resistance genes were detected in all samples, but their abundance varied 1,525-fold between sites, with the highest levels of antibiotic resistance genes being present in urban surface water samples. We identified an IncQ1 sulphonamide resistance plasmid ancestral to the widely studied RSF1010 in one of the urban water samples. The abundance of antibiotic resistance genes was significantly correlated (R2 = 0.73; P = 8.9 x 10-15) with the abundance of bacteria originating from the human gut, which suggests that the release of untreated sewage is a driver for the spread of environmental antibiotic resistance genes in Bangladesh, particularly in highly urbanised settings.

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