Municipal Wastewater Surveillance Revealed a High Community Disease Burden of a Rarely Reported and Possibly Subclinical Salmonella enterica Serovar Derby Strain

Abstract

Clinical surveillance of enteric pathogens like Salmonella is integral to track outbreaks and endemic disease trends. However, clinic-centered disease monitoring biases toward detection of severe cases and underestimates the incidence of self-limiting gastroenteritis and asymptomatic strains. Monitoring pathogen loads and diversity in municipal wastewater (MW) can provide insight into asymptomatic or subclinical infections which are not reflected in clinical cases. Subclinical infection patterns may explain the unusual observation from a year-long sampling campaign in Hawaii: Salmonella Derby was the most abundant pulsotype in MW but was detected infrequently in clinics over the sampling period. Using whole genome sequencing data of Salmonella isolates from MW and public databases, we demonstrate that the Derby serovar has lower virulence potential than other clinical serovars, particularly in genes linked with immune evasion and symptom production, suggesting its potential as a subclinical salmonellosis agent. Furthermore, MW had high abundance of a rare Derby MLST sequence type, ST-72 (rather than the more common Derby ST-40). ST-72 isolates had higher frequencies of fimbrial adherence genes than ST-40 isolates; these are key virulence factors involved in colonization and persistence of infections. However, ST-72 isolates lack the Derby-specific Salmonella Pathogenicity Island SPI-23, which invokes host immune responses. In combination, ST-72's genetic features may lead to appreciable infection rates without obvious symptom production, allowing for subclinical persistence in the community. This study demonstrates wastewater's capability to provide community infectious disease information – such as background infection rates of subclinical enteric illness – which is otherwise inaccessible through clinical approaches. IMPORTANCE Wastewater-based epidemiology (WBE) has been conventionally used to analyze community health via the detection of chemicals, such as legal and illicit drugs; however, municipal wastewater contains microbiological determinants of health and disease as well, including enteric pathogens. Here, we demonstrate that WBE can be used to examine subclinical community salmonellosis patterns. Derby was the most abundant Salmonella serovar detected in Hawaii wastewater over a year-long sampling study, with few corresponding clinical cases. Comparative genomics analyses indicate that the normally rare strain of S. Derby found in wastewater has a unique combination of genes which allow it to persist as a subclinical infection without producing symptoms of severe gastroenteritis. This study shows that WBE can be used to explore trends in community infectious disease patterns which may not be reflected in clinical monitoring, shedding light on overall enteric disease burden and rates of asymptomatic cases.

SARS-CoV-2 RNA in Wastewater Settled Solids Is Associated with COVID-19 Cases in a Large Urban Sewershed

“…Municipal wastewater is a composite biological sample of an entire community with each member of the community inputting biological specimens every day. It is therefore no surprise that wastewater has been tapped as an epidemiological tool to gauge aspects of public health, such as narcotic usage, 1 , 2 the reemergence of poliovirus, 3 , 4 and infection rates of viral 5 , 6 and bacterial 7 , 8 diseases. COVID-19 has accelerated the interest in wastewater-based epidemiology (WBE) due to the fact that SARS-CoV-2 genes are detected in the feces of many infected individuals.…”

Fine-Scale Temporal Dynamics of SARS-CoV-2 RNA Abundance in Wastewater during A COVID-19 Lockdown

“…The use of wastewater to monitor microbial infectious diseases in human communities dates back to the 1950s, and originally focused on enteric bacterial pathogen (in particular Salmonella ) outbreaks ( Shearer et al 1959 , Moore 1951 ). More recently, studies have explored the wastewater surveillance approach for many potential applications, including poliovirus eradication ( Poyry et al 1988 ), enteric disease outbreak detection ( Hellmer et al 2014 , Diemert and Yan 2019 ), and to understand the diversity of microbial pathogens in human communities ( Yang et al 2014 , Diemert and Yan 2020 ). The global pandemic of COVID-19 and the challenges in tracking its community transmission by the traditional clinical approaches have highlighted the unique potential advantages of the wastewater surveillance approach.…”

SARS-CoV-2 in wastewater settled solids is associated with COVID-19 cases in a large urban sewershed

“…Municipal wastewater is a composite biological sample of an entire community with each member of the community inputting biological specimens to the wastewater every day. It is therefore no surprise that wastewater has been tapped as an epidemiological tool to gauge aspects of public health, such as narcotics usage 1,2 , the reemergence of poliovirus 3,4 , and infection rates of viral 5,6 and bacterial 7,8 diseases. COVID-19 has accelerated the interest in wastewater-based epidemiology (WBE) due to the fact that SARS-CoV-2 genes are detected in the feces of many infected individuals [9][10][11] .…”