Universal microbial indicators provide surveillance of sewage contamination in harbours worldwide

Human population pressures and activities pose unprecedented challenges to water resources in urban environments. However, standard methods of assessing microbial water quality have relied on the same cultured organisms for decades. We show that there is a conserved microbial assemblage in untreated sewage that can be exploited to improve global sewage surveillance. Among harbour and coastal water samples from 18 cities across 5 continents (n = 442), nearly half had evidence of sewage contamination using two human faecal bacteria as molecular indicators. In contrast, conventional measures using cultured Escherichia coli or enterococci only exceeded water quality limits in ~18% of samples, with less than half of these demonstrating sewage indicators. Contaminated locations also displayed a signature characteristic of microorganisms mainly derived from sewer infrastructure. Given the human health risk, loss of ecosystem services and economic costs associated with contaminated coastal waters, molecular approaches could provide more reliable information on sewage contamination of urban waterways.