The Underworlds Project and the “Collective Microbiome”: Mining Biovalue from Sewage

Reis‐Castro, Luísa

doi:10.1007/978-3-319-55651-2_5

Cited by 2 publications

(2 citation statements)

References 27 publications

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“…Monitoring of microorganisms in municipal wastewater is presently a less common approach to community health surveillance, although it has a long history of use for enteric disease detection (49)(50)(51), has been employed to better understand source species involved in Cryptosporidium outbreaks (52), and even supported a successful public health response in the case of wild-type poliovirus detection in wastewater in Israel (53). Large-scale initiatives to monitor community microbiomes have recently been initiated with the rise of affordable genomic analyses, for example, the Underworlds project at the Massachusetts Institute of Technology (54). In the past, public health investigators have used sewage swabs during field studies (followed by subsequent culturing) to localize the homes of presumptive typhoid carriers (33,50) and the sources of foodborne outbreaks (51).…”

Section: Resultsmentioning

confidence: 99%

Clinically Unreported Salmonellosis Outbreak Detected via Comparative Genomic Analysis of Municipal Wastewater Salmonella Isolates

Diemert

Yan

2019

Appl Environ Microbiol

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Municipal wastewater includes human waste that contains both commensal and pathogenic enteric microorganisms, and this collective community microbiome can be monitored for community diseases. In a previous study, we assessed the salmonellosis disease burden using municipal wastewater from Honolulu, Hawaii, which was monitored over a 54-week period. During that time, a strain of Salmonella enterica serovar Paratyphi B variant L(ϩ) tartrate(ϩ) (also known as Salmonella enterica serovar Paratyphi B variant Java) was identified; this strain was detected simultaneously with a clinically reported outbreak, and pulsed-field gel electrophoresis patterns were identical for clinical and municipal wastewater isolates. Months after the outbreak subsided, the same pulsotype was detected as the dominant pulsotype in municipal wastewater samples, with no corresponding clinical cases reported. Using genomic characterization (including core single-nucleotide polymorphism alignment, core genome multilocus sequence typing, and screening for virulence and antibiotic resistance genes), all S. Java municipal wastewater isolates were determined to be clonal, indicating a resurgence of the original outbreak strain. This demonstrates the feasibility and utility of municipal wastewater surveillance for determining enteric disease outbreaks that may be missed by traditional clinical surveillance methods. IMPORTANCE Underdetection of microbial infectious disease outbreaks in human communities carries enormous health costs and is an ongoing problem in public health monitoring (which relies almost exclusively on data from health clinics). Surveillance of municipal wastewater for community-level monitoring of infectious disease burdens has the potential to fill this information gap, due to its easy access to the mixed community microbiome. In the present study, the genomes of 21 S. Java isolates (collected from municipal wastewater in Honolulu) were analyzed; results showed that the same Salmonella strain that caused a known salmonellosis clinical outbreak in spring 2010 remerged as the most dominant strain in municipal wastewater in spring 2011, indicating a new outbreak that was not detected by health clinics. Our results show that wastewater monitoring holds great promise to inform the field of public health regarding outbreak status within communities.

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Section: Resultsmentioning

confidence: 99%

Clinically Unreported Salmonellosis Outbreak Detected via Comparative Genomic Analysis of Municipal Wastewater Salmonella Isolates

Diemert

Yan

2019

Appl Environ Microbiol

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“…Beyond the articles cited at the beginning of this paper (those published since 2012), the prospects of monitoring sewage for endogenous biomarkers for gauging the status of community-wide health has begun to attract additional interest with respect to smart and sustainable cities (e.g., Poletti and Treville, 2016 )—one example being the “Underworlds” project at MIT’s Senseable City Lab ( Fitzgerald, 2015 ; Graber, 2017 ; Reis-Castro, 2017 ). It has also become a focus of transdisciplinary research under the European COoperation in Scientific and Technology (COST) program ( COST, 2013 ).…”

Section: The Futurementioning

confidence: 99%

Monitoring wastewater for assessing community health: Sewage Chemical-Information Mining (SCIM)

Daughton

2018

Science of The Total Environment

150

117

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Timely assessment of the aggregate health of small-area human populations is essential for guiding the optimal investment of resources needed for preventing, avoiding, controlling, or mitigating human exposure risks, as well as for maintaining or promoting health. Seeking those interventions yielding the greatest benefit with respect to the allocation of resources is critical for making progress toward community sustainability, reducing health disparities, promoting social justice, and maintaining or improving collective health and well-being. More informative, faster, and less-costly approaches are needed for guiding investigation of cause-effect linkages involving communities and stressors originating from both the built and natural environments. One such emerging approach involves the continuous monitoring of sewage for chemicals that serve as indicators of the collective status of human health (or stress/disease) or any other facet relevant to gauging time-trends in community-wide health. This nascent approach can be referred to as Sewage Chemical-Information Mining (SCIM) and involves the monitoring of sewage for the information that resides in the form of natural and anthropogenic chemicals that enter sewers as a result of the everyday actions, activities, and behaviors of humans. Of particular interest is a specific embodiment of SCIM that would entail the targeted monitoring of a broad suite of endogenous biomarkers of key physiologic processes (as opposed to xenobiotics or their metabolites). This application is termed BioSCIM—an approach roughly analogous to a hypothetical community-wide collective clinical urinalysis, or to a hypothetical en masse human biomonitoring program. BioSCIM would be used for gauging the status or time-trends in community-wide health on a continuous basis. This paper presents an update on the progress made with the development of the BioSCIM concept in the period of time since its original publication in 2012, as well as the next steps required for its continued development.

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The Underworlds Project and the “Collective Microbiome”: Mining Biovalue from Sewage

Cited by 2 publications

References 27 publications

Clinically Unreported Salmonellosis Outbreak Detected via Comparative Genomic Analysis of Municipal Wastewater Salmonella Isolates

Clinically Unreported Salmonellosis Outbreak Detected via Comparative Genomic Analysis of Municipal Wastewater Salmonella Isolates

Monitoring wastewater for assessing community health: Sewage Chemical-Information Mining (SCIM)

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