Browsing by Author "Ahmed, Warish"
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- Environmental and Adaptive Changes Necessitate a Paradigm Shift for Indicators of Fecal ContaminationPublication . Teixeira, Pedro; Salvador, Daniel; Brandão, João; Ahmed, Warish; Sadowsky, Michael J.; Valério, ElisabeteChanges in the occurrence, distribution, and seasonal variation of waterborne pathogens due to global climate change may increase the risk of human exposure to these microorganisms, thus heightening the need for more reliable surveillance systems. Routine monitoring of drinking water supplies and recreational waters is performed using fecal indicator microorganisms, such as Escherichia coli, Enterococcus spp., and coliphages. However, the presence and numbers of these indicators, especially E. coli and Enterococcus spp., do not correlate well with those of other pathogens, especially enteric viruses, which are a major cause of waterborne outbreaks associated with contaminated water and food, and recreational use of lakes, ponds, rivers, and estuarine waters. For that reason, there is a growing need for a surveillance system that can detect and quantify viral pathogens directly in water sources to reduce transmission of pathogens associated with fecal transmission. In this review, we present an updated overview of relevant waterborne enteric viruses that we believe should be more commonly screened to better evaluate water quality and to determine the safety of water use and reuse and of epidemiological data on viral outbreaks. We also discuss current methodologies that are available to detect and quantify these viruses in water resources. Finally, we highlight challenges associated with virus monitoring. The information presented in this review is intended to aid in the assessment of human health risks due to contact with water sources, especially since current environmental and adaptive changes may be creating the need for a paradigm shift for indicators of fecal contamination.
- Impacts of a changing earth on microbial dynamics and human health risks in the continuum between beach water and sandPublication . Weiskerger, Chelsea J.; Brandão, João; Ahmed, Warish; Aslan, Asli; Avolio, Lindsay; Badgley, Brian D.; Boehm, Alexandria B.; Edge, Thomas A.; Fleisher, Jay M.; Heaney, Christopher D.; Jordao, Luisa; Kinzelman, Julie L.; Klaus, James S.; Kleinheinz, Gregory T.; Meriläinen, Päivi; Nshimyimana, Jean Pierre; Phanikumar, Mantha S.; Piggot, Alan M.; Pitkänen, Tarja; Robinson, Clare; Sadowsky, Michael J.; Staley, Christopher; Staley, Zachery R.; Symonds, Erin M.; Vogel, Laura J.; Yamahara, Kevan M.; Whitman, Richard L.; Solo-Gabriele, Helena M.; Harwood, Valerie J.Although infectious disease risk from recreational exposure to waterborne pathogens has been an active area of research for decades, beach sand is a relatively unexplored habitat for the persistence of pathogens and fecal indicator bacteria (FIB). Beach sand, biofilms, and water all present unique advantages and challenges to pathogen introduction, growth, and persistence. These dynamics are further complicated by continuous exchange between sand and water habitats. Models of FIB and pathogen fate and transport at beaches can help predict the risk of infectious disease from beach use, but knowledge gaps with respect to decay and growth rates of pathogens in beach habitats impede robust modeling. Climatic variability adds further complexity to predictive modeling because extreme weather events, warming water, and sea level change may increase human exposure to waterborne pathogens and alter relationships between FIB and pathogens. In addition, population growth and urbanization will exacerbate contamination events and increase the potential for human exposure. The cumulative effects of anthropogenic changes will alter microbial population dynamics in beach habitats and the assumptions and relationships used in quantitative microbial risk assessment (QMRA) and process-based models. Here, we review our current understanding of microbial populations and transport dynamics across the sand-water continuum at beaches, how these dynamics can be modeled, and how global change factors (e.g., climate and land use) should be integrated into more accurate beachscape-based models.
- Microbial Source Tracking as a Method of Determination of Beach Sand ContaminationPublication . Valério, Elisabete; Santos, Maria Leonor; Teixeira, Pedro; Matias, Ricardo; Mendonça, João; Ahmed, Warish; Brandão, JoãoBeach sand may act as a reservoir for numerous microorganisms, including enteric pathogens. Several of these pathogens originate in human or animal feces, which may pose a public health risk. In August 2019, high levels of fecal indicator bacteria (FIB) were detected in the sand of the Azorean beach Prainha, Terceira Island, Portugal. Remediation measures were promptly implemented, including sand removal and the spraying of chlorine to restore the sand quality. To determine the source of the fecal contamination, during the first campaign, supratidal sand samples were collected from several sites along the beach, followed by microbial source tracking (MST) analyses of Bacteroides marker genes for five animal species, including humans. Some of the sampling sites revealed the presence of marker genes from dogs, seagulls, and ruminants. Making use of the information on biological sources originating partially from dogs, the municipality enforced restrictive measures for dog-walking at the beach. Subsequent sampling campaigns detected low FIB contamination due to the mitigation and remediation measures that were undertaken. This is the first case study where the MST approach was used to determine the contamination sources in the supratidal sand of a coastal beach. Our results show that MST can be an essential tool to determine sources of fecal contamination in the sand. This study shows the importance of holistic management of beaches that should go beyond water quality monitoring for FIB, putting forth evidence for beach sand monitoring.
- Minimizing Errors in RT-PCR Detection and Quantification of SARS-CoV-2 RNA for Wastewater SurveillancePublication . Ahmed, Warish; Simpson, Stuart; Bertsch, Paul; Bibby, Kyle; Bivins, Aaron; Blackall, Linda; Bofill-Mas, Silvia; Bosch, Albert; Brandao, Joao; Choi, Phil; Ciesielski, Mark; Donner, Erica; D'Souza, Nishita; Farnleitner, Andreas; Gerrity, Daniel; Gonzalez, Raul; Griffith, John; Gyawali, Pradip; Haas, Charles; Hamilton, Kerry; Hapuarachchi, Chanditha; Harwood, Valerie; Haque, Rehnuma; Jackson, Greg; Khan, Stuart; Khan, Wesaal; Kitajima, Masaaki; Korajkic, Asja; La Rosa, Giuseppina; Layton, Blythe; Lipp, Erin; McLellan, Sandra; McMinn, Brian; Medema, Gertjan; Metcalfe, Suzanne; Meijer, Wim; Mueller, Jochen; Murphy, Heather; Naughton, Colleen; Noble, Rachel; Payyappat, Sudhi; Petterson, Susan; Pitkanen, Tarja; Rajal, Veronica; Reyneke, Brandon; Roman, Fernando; Rose, Joan; Rusinol, Marta; Sadowsky, Michael; Sala-Comorera, Laura; Setoh, Yin Xiang; Sherchan, Samendra; Sirikanchana, Kwanrawee; Smith, Wendy; Steele, Joshua; Sabburg, Rosalie; Symonds, Erin; Thai, Phong; Thomas, Kevin; Tynan, Josh; Toze, Simon; Thompson, Janelle; Whiteley, Andy; Wong, Judith; Sano, Daisuke; Wuertz, Stefan; Xagoraraki, Irene; Zhang, Qian; Zimmer-Faust, Amity; Shanks, OrinWastewater surveillance for pathogens using the reverse transcription-polymerase chain reaction (RT-PCR) is an effective, resource-efficient tool for gathering additional community-level public health information, including the incidence and/or prevalence and trends of coronavirus disease-19 (COVID-19). Surveillance of SARS-CoV-2 in wastewater may provide an early-warning signal of COVID-19 infections in a community. The capacity of the world’s environmental microbiology and virology laboratories for SARS-CoV-2 RNA characterization in wastewater is rapidly increasing. However, there are no standardized protocols nor harmonized quality assurance and quality control (QA/QC) procedures for SARS-CoV-2 wastewater surveillance. This paper is a technical review of factors that can lead to false-positive and -negative errors in the surveillance of SARS-CoV-2, culminating in recommendations and strategies that can be implemented to identify and mitigate these errors. Recommendations include, stringent QA/QC measures, representative sampling approaches, effective virus concentration and efficient RNA extraction, amplification inhibition assessment, inclusion of sample processing controls, and considerations for RT-PCR assay selection and data interpretation. Clear data interpretation guidelines (e.g., determination of positive and negative samples) are critical, particularly during a low incidence of SARS-CoV-2 in wastewater. Corrective and confirmatory actions must be in place for inconclusive and/or potentially significant results (e.g., initial onset or reemergence of COVID-19 in a community). It will also be prudent to perform inter-laboratory comparisons to ensure results are reliable and interpretable for ongoing and retrospective analyses. The strategies that are recommended in this review aim to improve SARS-CoV-2 characterization for wastewater surveillance applications. A silver lining of the COVID-19 pandemic is that the efficacy of wastewater surveillance was demonstrated during this global crisis. In the future, wastewater will play an important role in the surveillance of a range of other communicable diseases.