# Assessing sequencing-based pathogen surveillance of a recreational swimming area in Oslo, Norway

## TL;DR

This study evaluates the use of DNA sequencing to detect harmful microbes in a popular Oslo swimming area, finding it effective for identifying certain pathogens and signs of sewage contamination.

## Contribution

The study introduces the combined use of long- and short-read sequencing for environmental pathogen surveillance in recreational waters.

## Key findings

- Metagenomic and full-length 16S sequencing effectively detected seasonal Vibrio pathogens.
- Rhodoferax abundance was identified as a potential indicator of sewage contamination.
- Metagenomic sequencing detected β-lactamases not captured by culturing methods.

## Abstract

Sequencing-based surveillance can enable rapid and sensitive detection of environmental pathogens. The Oslofjord inlet is relatively narrow and is exposed to substantial human activity, including occasional wastewater contamination. Restricted water exchange also allows for occasional summer heat spells with elevated water temperatures. Thus, infections stemming from wastewater contamination and seasonal opportunistic pathogens are potential health threats to recreational users of the fjord. In this pilot study, we assess the suitability of sequencing-based surveillance for the detection of pathogens at a popular urban location for recreational water activities, employing both long- and short-read sequencing platforms, paired with selective culturing. We find both metagenomic and full-length 16S sequencing to be promising tools for surveillance of seasonal opportunistic Vibrio pathogens. Furthermore, we identified Rhodoferax abundance to be a potentially attractive indicator of sewage contamination using low to medium-depth full-length 16S sequencing. Selective plating revealed minimal abundance of culturable extended-spectrum β-lactam-resistant bacteria, of which none were detected by metagenomic sequencing. Metagenomic analyses did, however, pick up several other β-lactamases in various bacterial taxa, including some that were closely related to those identified by selective plating and sequencing.