scispace - formally typeset
Open accessJournal ArticleDOI: 10.1371/JOURNAL.PNTD.0009176

Impact of sampling depth on pathogen detection in pit latrines.

02 Mar 2021-PLOS Neglected Tropical Diseases (Public Library of Science)-Vol. 15, Iss: 3
Abstract: Wastewater based epidemiology (WBE) is increasingly used to provide decision makers with actionable data about community health. WBE efforts to date have primarily focused on sewer-transported wastewater in high-income countries, but at least 1.8 billion people in low- and middle-income countries (LMIC) use onsite sanitation systems such as pit latrines and septic tanks. Like wastewater, fecal sludges from such systems offer similar advantages in community pathogen monitoring and other epidemiological applications. To evaluate the distribution of enteric pathogens inside pit latrines–which could inform sampling methods for WBE in LMIC settings unserved by sewers–we collected fecal sludges from the surface, mid-point, and maximum-depth of 33 pit latrines in urban and peri-urban Malawi and analyzed the 99 samples for 20 common enteric pathogens via multiplex quantitative reverse transcription PCR. Using logistic regression adjusted for household population, latrine sharing, the presence of a concrete floor or slab, water source, and anal cleansing materials, we found no significant difference in the odds of detecting the 20 pathogens from the mid-point (adjusted odds ratio, aOR = 1.1; 95% confidence interval = 0.73, 1.6) and surface samples (aOR = 0.80, 95% CI = 0.54, 1.2) compared with those samples taken from the maximum depth. Our results suggest that, for the purposes of routine pathogen monitoring, pit latrine sampling depth does not strongly influence the odds of detecting enteric pathogens by molecular methods. A single sample from the pit latrines’ surface, or a composite of surface samples, may be preferred as the most recent material contributed to the pit and may be easiest to collect.

... read more

Topics: Pit latrine (56%), Latrine (55%), Population (51%)
Citations
  More

5 results found


Open accessJournal ArticleDOI: 10.1021/ACS.EST.1C02168
Drew Capone1, David Berendes2, Oliver Cumming3, David A. Holcomb1  +7 moreInstitutions (6)
Abstract: Environmental fecal contamination is common in many low-income cities, contributing to a high burden of enteric infections and associated negative sequelae. To evaluate the impact of a shared onsite sanitation intervention in Maputo, Mozambique on enteric pathogens in the domestic environment, we collected 179 soil samples at shared latrine entrances from intervention (n = 49) and control (n = 51) compounds during baseline (preintervention) and after 24 months (postintervention) as part of the Maputo Sanitation Trial. We tested soils for the presence of nucleic acids associated with 18 enteric pathogens using a multiplex reverse transcription qPCR platform. We detected at least one pathogen-associated gene target in 91% (163/179) of soils and a median of 3 (IQR = 1, 5) pathogens. Using a difference-in-difference analysis and adjusting for compound population, visibly wet soil, sun exposure, wealth, temperature, animal presence, and visible feces, we estimate the intervention reduced the probability of detecting ≥1 pathogen gene by 15% (adjusted prevalence ratio, aPR = 0.85; 95% CI: 0.70, 1.0) and the total number of pathogens by 35% (aPR = 0.65; 0.44, 0.95) in soil 24 months following the intervention. These results suggest that the intervention reduced the presence of some fecal contamination in the domestic environment, but pathogen detection remained prevalent 24 months following the introduction of new latrines.

... read more

Topics: Population (51%)

4 Citations


Open accessJournal ArticleDOI: 10.1021/ACS.EST.1C05060
Olivia Ginn1, Lucas Rocha-Melogno2, Lucas Rocha-Melogno3, Aaron Bivins1  +10 moreInstitutions (10)
Abstract: Urban sanitation infrastructure is inadequate in many low-income countries, leading to the presence of highly concentrated, uncontained fecal waste streams in densely populated areas. Combined with mechanisms of aerosolization, airborne transport of enteric microbes and their genetic material is possible in such settings but remains poorly characterized. We detected and quantified enteric pathogen-associated gene targets in aerosol samples near open wastewater canals (OWCs) or impacted (receiving sewage or wastewater) surface waters and control sites in La Paz, Bolivia; Kanpur, India; and Atlanta, USA, via multiplex reverse-transcription qPCR (37 targets) and ddPCR (13 targets). We detected a wide range of enteric targets, some not previously reported in extramural urban aerosols, with more frequent detections of all enteric targets at higher densities in La Paz and Kanpur near OWCs. We report density estimates ranging up to 4.7 × 102 gc per mair3 across all targets including heat-stable enterotoxigenic Escherichia coli, Campylobacter jejuni, enteroinvasive E. coli/Shigella spp., Salmonella spp., norovirus, and Cryptosporidium spp. Estimated 25, 76, and 0% of samples containing positive pathogen detects were accompanied by culturable E. coli in La Paz, Kanpur, and Atlanta, respectively, suggesting potential for viability of enteric microbes at the point of sampling. Airborne transmission of enteric pathogens merits further investigation in cities with poor sanitation.

... read more

Topics: Airborne transmission (54%)

1 Citations


Open accessPosted ContentDOI: 10.1101/2021.02.14.21251650
Olivia Ginn1, Lucas Rocha-Melogno2, Aaron Bivins3, Sarah Lowry1  +9 moreInstitutions (9)
19 Feb 2021-medRxiv
Abstract: Urban sanitation infrastructure is inadequate in many low-income countries, leading to the presence of highly concentrated, uncontained fecal waste streams in densely populated areas. Combined with mechanisms of aerosolization, airborne transport of enteric microbes and their genetic material is possible in such settings but remains poorly characterized. We detected and quantified enteric pathogen-associated gene targets in aerosol samples near open wastewater canals (OWCs) or impacted surface waters and control sites in La Paz, Bolivia; Kanpur, India; and Atlanta, USA via multiplex qPCR (37 targets) and ddPCR (13 targets). We detected a wide range enteric pathogen-specific targets, some not previously reported in extramural urban aerosols, with more frequent detections of all enteric targets at higher densities in La Paz and Kanpur near OWCs. We report density estimates ranging from non-detects to 4.7 [x] 102 gc per m3air for targets including ST-ETEC, C. jejuni, EIEC/Shigella spp., Salmonella spp., adenovirus, and Cryptosporidium spp. An estimated 25%, 76%, and 0% of samples containing positive pathogen detects were accompanied by culturable E. coli in La Paz, Kanpur, and Atlanta, respectively, suggesting potential for viability of enteric microbes at the point of sampling. Airborne transmission of enteric pathogens merits further investigation in cities with poor sanitation. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=109 SRC="FIGDIR/small/21251650v1_ufig1.gif" ALT="Figure 1"> View larger version (57K): org.highwire.dtl.DTLVardef@13c817borg.highwire.dtl.DTLVardef@158e108org.highwire.dtl.DTLVardef@1e0626org.highwire.dtl.DTLVardef@125b214_HPS_FORMAT_FIGEXP M_FIG C_FIG SYNOPSISWe detect and quantify molecular targets associated with important enteric pathogens in outdoor aerosols from cities with poor sanitation to assess the potential role of the aeromicrobiological pathway in enteric infection transmission in such settings.

... read more

Topics: Airborne transmission (54%)

1 Citations


Open accessPosted ContentDOI: 10.1101/2021.04.02.438233
Drew Capone1, David Berendes2, Oliver Cumming3, David A. Holcomb1  +7 moreInstitutions (6)
02 Apr 2021-bioRxiv
Abstract: Environmental fecal contamination is common in many low-income cities, contributing to a high burden of enteric infections and associated negative sequelae. To evaluate the impact of a shared onsite sanitation intervention in Maputo, Mozambique on enteric pathogens in the domestic environment, we collected 179 soil samples at shared latrine entrances from intervention (n= 49) and control (n= 51) compounds during baseline (pre-intervention) and after 24 months (post-intervention) as part of the Maputo Sanitation Trial. We tested soils for the presence of nucleic acids associated with 20 enteric pathogens using a multiplex reverse transcription qPCR platform. We detected at least one pathogen-associated target in 91% (163/179) of soils and a median of 3 (IQR=1.5, 5) pathogens. Using a difference-in-difference analysis and adjusting for compound population, visibly wet soil, sun exposure, wealth, temperature, animal presence, and visible feces, we estimate the intervention reduced the probability of ≥1 pathogen detected by 15% (adjusted prevalence ratio, aPR=0.85; 95% CI: 0.70, 1.0) and the total number of pathogens detected by 35% (aPR =0.65; 0.44, 0.95) in soil 24 months following the intervention. These results suggest that the intervention reduced the presence of some fecal contamination in the domestic environment, but pathogen detection remained prevalent 24-months following the introduction of new latrines.

... read more

Topics: Population (51%)

Open accessJournal ArticleDOI: 10.1016/J.SCITOTENV.2021.150680
Willis Gwenzi1Institutions (1)
Abstract: Traditional wastewater-based epidemiology (W-BE) relying on SARS-CoV-2 RNA detection in wastewater is attractive for understanding COVID-19. Yet traditional W-BE based on centralized wastewaters excludes putative SARS-CoV-2 reservoirs such as: (i) wastewaters from shared on-site sanitation facilities, (ii) solid waste including faecal sludge from non-flushing on-site sanitation systems, and COVID-19 personal protective equipment (PPE), (iii) raw/untreated water, and (iv) drinking water supply systems in low-income countries (LICs). A novel hypothesis and decision-support tool based on Wastewater (on-site sanitation, municipal sewer systems), solid Waste, and raw/untreated and drinking Water-based epidemiology (WWW-BE) is proposed for understanding COVID-19 in LICs. The WWW-BE conceptual framework, including components and principles is presented. Evidence on the presence of SARS-CoV-2 and its proxies in wastewaters, solid materials/waste (papers, metals, fabric, plastics), and raw/untreated surface water, groundwater and drinking water is discussed. Taken together, wastewaters from municipal sewer and on-site sanitation systems, solid waste such as faecal sludge and COVID-19 PPE, raw/untreated surface water and groundwater, and drinking water systems in LICs act as potential reservoirs that receive and harbour SARS-CoV-2, and then transmit it to humans. Hence, WWW-BE could serve a dual function in estimating the prevalence and potential transmission of COVID-19. Several applications of WWW-BE as a hypothesis and decision support tool in LICs are discussed. WWW-BE aggregates data from various infected persons in a spatial unit, hence, putatively requires less resources (analytical kits, personnel) than individual diagnostic testing, making it an ideal decision-support tool for LICs. The novelty, and a critique of WWW-BE versus traditional W-BE are presented. Potential challenges of WWW-BE include: (i) biohazards and biosafety risks, (ii) lack of expertise, analytical equipment, and accredited laboratories, and (iii) high uncertainties in estimates of COVID-19 cases. Future perspectives and research directions including key knowledge gaps and the application of novel and emerging technologies in WWW-BE are discussed.

... read more

Topics: Sanitation (56%), Wastewater (53%), Municipal solid waste (52%) ... show more
References
  More

57 results found


Open accessJournal ArticleDOI: 10.18637/JSS.V067.I01
Abstract: Maximum likelihood or restricted maximum likelihood (REML) estimates of the parameters in linear mixed-effects models can be determined using the lmer function in the lme4 package for R. As for most model-fitting functions in R, the model is described in an lmer call by a formula, in this case including both fixed- and random-effects terms. The formula and data together determine a numerical representation of the model from which the profiled deviance or the profiled REML criterion can be evaluated as a function of some of the model parameters. The appropriate criterion is optimized, using one of the constrained optimization functions in R, to provide the parameter estimates. We describe the structure of the model, the steps in evaluating the profiled deviance or REML criterion, and the structure of classes or types that represents such a model. Sufficient detail is included to allow specialization of these structures by users who wish to write functions to fit specialized linear mixed models, such as models incorporating pedigrees or smoothing splines, that are not easily expressible in the formula language used by lmer.

... read more

37,650 Citations



Open accessJournal ArticleDOI: 10.1056/NEJMOA0904797
Shabir A. Madhi1, Nigel A. Cunliffe2, Duncan Steele3, Desiree Witte2  +8 moreInstitutions (8)
Abstract: Background Rotavirus is the most common cause of severe gastroenteritis among young children worldwide. Data are needed to assess the efficacy of the rotavirus vaccine in African children. Methods We conducted a randomized, placebo-controlled, multicenter trial in South Africa (3166 infants; 64.1% of the total) and Malawi (1773 infants; 35.9% of the total) to evaluate the efficacy of a live, oral rotavirus vaccine in preventing severe rotavirus gastroenteritis. Healthy infants were randomly assigned in a 1:1:1 ratio to receive two doses of vaccine (in addition to one dose of placebo) or three doses of vaccine — the pooled vaccine group — or three doses of placebo at 6, 10, and 14 weeks of age. Episodes of gastroenteritis caused by wild-type rotavirus during the first year of life were assessed through active follow-up surveillance and were graded with the use of the Vesikari scale. Results A total of 4939 infants were enrolled and randomly assigned to one of the three groups; 1647 infants received two doses of the vaccine, 1651 infants received three doses of the vaccine, and 1641 received placebo. Of the 4417 infants included in the per-protocol efficacy analysis, severe rotavirus gastroenteritis occurred in 4.9% of the infants in the placebo group and in 1.9% of those in the pooled vaccine group (vaccine efficacy, 61.2%; 95% confidence interval, 44.0 to 73.2). Vaccine efficacy was lower in Malawi than in South Africa (49.4% vs. 76.9%); however, the number of episodes of severe rotavirus gastroenteritis that were prevented was greater in Malawi than in South Africa (6.7 vs. 4.2 cases prevented per 100 infants vaccinated per year). Efficacy against all-cause severe gastroenteritis was 30.2%. At least one serious adverse event was reported in 9.7% of the infants in the pooled vaccine group and in 11.5% of the infants in the placebo group. Conclusions Human rotavirus vaccine significantly reduced the incidence of severe rotavirus gastroenteritis among African infants during the first year of life. (ClinicalTrials.gov number, NCT00241644.)

... read more

Topics: Rotavirus vaccine (68%), Vaccine efficacy (64%), Rotavirus (61%) ... show more

770 Citations


Open accessJournal ArticleDOI: 10.1128/AEM.56.5.1423-1428.1990
D. G. Korich1, J. R. Mead1, M. S. Madore1, Norval A. Sinclair1  +1 moreInstitutions (1)
Abstract: Purified Cryptosporidium parvum oocysts were exposed to ozone, chlorine dioxide, chlorine, and monochloramine. Excystation and mouse infectivity were comparatively evaluated to assess oocyst viability. Ozone and chlorine dioxide more effectively inactivated oocysts than chlorine and monochloramine did. Greater than 90% inactivation as measured by infectivity was achieved by treating oocysts with 1 ppm of ozone (1 mg/liter) for 5 min. Exposure to 1.3 ppm of chlorine dioxide yielded 90% inactivation after 1 h, while 80 ppm of chlorine and 80 ppm of monochloramine required approximately 90 min for 90% inactivation. The data indicate that C. parvum oocysts are 30 times more resistant to ozone and 14 times more resistant to chlorine dioxide than Giardia cysts exposed to these disinfectants under the same conditions. With the possible exception of ozone, the use of disinfectants alone should not be expected to inactivate C. parvum oocysts in drinking water.

... read more

Topics: Chlorine dioxide (61%), Chloramine (56%), Chlorine (55%) ... show more

743 Citations


Open accessJournal ArticleDOI: 10.1016/J.SCITOTENV.2020.138764
Warish Ahmed1, Nicola Angel2, Janette Edson2, Kyle Bibby3  +14 moreInstitutions (4)
Abstract: Infection with SARS-CoV-2, the etiologic agent of the ongoing COVID-19 pandemic, is accompanied by the shedding of the virus in stool. Therefore, the quantification of SARS-CoV-2 in wastewater affords the ability to monitor the prevalence of infections among the population via wastewater-based epidemiology (WBE). In the current work, SARS-CoV-2 RNA was concentrated from wastewater in a catchment in Australia and viral RNA copies were enumerated using reverse transcriptase quantitative polymerase chain reaction (RT-qPCR) resulting in two positive detections within a six day period from the same wastewater treatment plant (WWTP). The estimated viral RNA copy numbers observed in the wastewater were then used to estimate the number of infected individuals in the catchment via Monte Carlo simulation. Given the uncertainty and variation in the input parameters, the model estimated a median range of 171 to 1,090 infected persons in the catchment, which is in reasonable agreement with clinical observations. This work highlights the viability of WBE for monitoring infectious diseases, such as COVID-19, in communities. The work also draws attention to the need for further methodological and molecular assay validation for enveloped viruses in wastewater.

... read more

Topics: Population (52%), Wastewater (51%)

735 Citations


Performance
Metrics
No. of citations received by the Paper in previous years
YearCitations
20221
20214