Surabhi Singh1
Amina Ismail Ahmed1Sumayya Almansoori1Shaikha Alameri1Ashraf Adlan1Giovanni Odivilas1Marie Anne Chattaway2Samara Bin Salem3Grzegorz Brudecki1
Wael Elamin1*- 1Microbiology Lab, Reference and Surveillance Intelligence Department, Abu Dhabi, United Arab Emirates
- 2United Kingdom Health Security Agency, Gastrointestinal Bacteria Reference Laboratory, London, United Kingdom
- 3Central Testing Laboratory, Abu Dhabi Quality and Conformity Council, Abu Dhabi, United Arab Emirates
Introduction: The emergence and resurgence of pathogens have led to significant global health challenges. Wastewater surveillance has historically been used to track water-borne or fecal-orally transmitted pathogens, providing a sensitive means of monitoring pathogens within a community. This technique offers a comprehensive, real-time, and cost-effective approach to disease surveillance, especially for diseases that are difficult to monitor through individual clinical screenings.
Methods: This narrative review examines the current state of knowledge on wastewater surveillance, emphasizing important findings and techniques used to detect potential pathogens from wastewater. It includes a review of literature on the detection methods, the pathogens of concern, and the challenges faced in the surveillance process.
Results: Wastewater surveillance has proven to be a powerful tool for early warning and timely intervention of infectious diseases. It can detect pathogens shed by asymptomatic and pre-symptomatic individuals, providing an accurate population-level view of disease transmission. The review highlights the applications of wastewater surveillance in tracking key pathogens of concern, such as gastrointestinal pathogens, respiratory pathogens, and viruses like SARS-CoV-2.
Discussion: The review discusses the benefits of wastewater surveillance in public health, particularly its role in enhancing existing systems for infectious disease surveillance. It also addresses the challenges faced, such as the need for improved detection methods and the management of antimicrobial resistance. The potential for wastewater surveillance to inform public health mitigation strategies and outbreak response protocols is emphasized.
Conclusion: Wastewater surveillance is a valuable tool in the fight against infectious diseases. It offers a unique perspective on the spread and evolution of pathogens, aiding in the prevention and control of disease epidemics. This review underscores the importance of continued research and development in this field to overcome current challenges and maximize the potential of wastewater surveillance in public health.
1 Introduction
Recent decades have seen a rise in both the emergence and reemergence of pathogens, which has led to significant and deadly outbreaks (1, 2, 3). Authorities such as the global scientific community, the National Institutes of Health (NIH), USAID, and the World Health Organization (WHO) are aware of the substantial worldwide impact these outbreaks have and the importance of developing predictive and preventive systems. Since 1970, there has been the identification of over 1,500 new pathogens, with about 40 being deemed emerging infectious diseases (4). Regular mass screening in clinical settings poses difficulties, and those who are asymptomatic or exhibit mild symptoms frequently go undetected. The increase in the global population is likely to escalate these challenges and the risk of infectious diseases, highlighting the need for a surveillance method that is comprehensive, provides real-time results, can monitor multiple diseases—including rare ones—and is both scalable and cost-effective. Wastewater surveillance historically serves to monitor water-borne or fecal-orally transmitted pathogens by collecting samples from sewage systems, offering a sensitive way to observe changes and varieties of pathogens within communities (5). Over the past three decades, studies have consistently shown the accuracy of wastewater testing in representing disease at the population level (6). Chemical and biological markers in wastewater could even act as an early alert system for disease breakouts, potentially improving current surveillance systems for infections (7). The origins of wastewater surveillance can be traced to John Snow’s seminal work on London’s cholera outbreak in 1854, where he identified contaminated water as a primary source (8–10). In the 1940s in the United States, wastewater was pivotal for tracking and managing polio outbreaks, with poliovirus detection still considered highly sensitive today, becoming common practice in many parts of the world (11, 12).
The advantage of sampling wastewater lies in its high pathogen content compared to other environmental samples (13, 14). It also allows for the inclusion of pathogens from individuals who are either asymptomatic or pre-symptomatic, unlike clinical tests, thus presenting a potent early indicator and prompt intervention tool for infectious diseases. Moreover, recent interest has emerged in using wastewater examination for AMR (antimicrobial resistance) surveillance, with studies revealing seasonal distributions of AMR, worldwide gene abundance, and correlations between AMR found in wastewater and clinical contexts (15, 16, 17).
Despite various reviews discussing wastewater surveillance’s significance, there’s a gap in literature providing a thorough review that collectively highlights concerning pathogens, wastewater surveillance applications, available technologies, and pathogen detection challenges in wastewater. Thus, this narrative review focuses on wastewater surveillance for infectious diseases, aiming to consolidate these issues. In preparing this narrative review, a methodical approach was used, using a selection of prominent medical search engines to ensure a comprehensive exploration of the literature. The databases harnessed for this review included PubMed, Scopus, ScienceDirect, The Cochrane Library, and Google Scholar. Only published studies were included for this review. Non–peer-reviewed articles such as short communications and research letters were excluded.
The methodology entailed a systematic and structured search using a set of predetermined search terms that were central to the theme of wastewater surveillance and its role in public health. These terms included “wastewater surveillance,” “pathogens,” “detection methods,” “public health,” and “epidemiology,” among others. The search was refined to capture articles that shed light on the methodologies for pathogen detection in wastewater, the challenges encountered in the surveillance process, and the implications for public health policy and disease prevention.
2 Wastewater surveillance: monitoring key pathogens of concern
Human pathogens, causing infections and even death, remain a leading threat to global public health. Currently, there are approximately 538 species of pathogenic bacteria, 208 viruses, 57 species of parasitic protozoa and some fungi and helminths infecting humans (24, 25). Numerous pathogen species found in wastewater pose a serious threat to human health. Different type of pathogens and concerned diseases have been listed in Table 1. Also, the pathway for and effective wastewater surveillance has been explained in Figure 1.
Table 1. Major pathogens of concern in water system and relatable diseases.
Figure 1. Wastewater surveillance pathway.
Most pathogens in wastewater are shed by humans, although some might originate from other sources such as animals. Some of these pathogens have been discussed in detail below.
2.1 Gastrointestinal pathogens
Campylobacter spp. is major cause of diarrhea, and human gastroenteritis worldwide (48). It is comprised of 17 species and 6 subspecies, out of which Campylobacter jejuni and Campylobacter coli account for 80–85% and 10–15% of total infections, respectively (Leblanc et al., 2011) and are also the main species widely detected and isolated from wastewater (49, 50). C. jejuni was first isolated from the feces of patients with gastrointestinal disease in the 1970s (51). Subsequently, many studies have demonstrated C. jejuni to be a major cause of human infections (52) transmitted by the fecal-oral route through contaminated food and water (53).
Salmonella is another important enteropathogenic bacteria, causing approximately 94 million infections and 155,000 deaths annually worldwide (54, 55). Salmonella enterica serovar Typhi and Salmonella enterica serovar Paratyphi are the main causes of typhoid fever and paratyphoid fever, respectively (56, 57). Both are gram-negative, human-restricted, and species-specific bacterial diseases. The transmission can occur from person to person by eating contaminated food or water or by contact with an acute or chronic infected person (58, 59). To evaluate the water quality and the likelihood of contracting waterborne infections, a study was carried out in Nigeria that examined several sources of drinking water (19). Areas with a high number of reported waterborne cases and those with a low number of cases had their water samples taken. Most tests contained Vibrio cholerae, Salmonella typhi, and Shigella dysenteriae, and it was hypothesized that discharge of polluted water during the intense rainy season had contaminated drinking water sources (19).
Enterohaemorrhagic and enteroinvasive Escherichia coli are pathogenic and causes illness in mammals including humans. Shiga toxin producing E. coli (STEC) O157:H7 causes diarrhea, haemorrhagic colitis, haemolytic uremic syndrome, that leads to serious long-term complication, and it is often employed as a model for pathogenic bacteria study in wastewater (20). Through PCR, high amount of E. coli O157:H7 gene were detected in the sewage sludge (1,819,700 copies of gene/100 mL). The common feature of STEC E. coli O157:H7 is that even a low inoculum as little as 10 cells may trigger disease (60). In 2000, an outbreak in Walkerton, Ontario was linked to E. coli O157:H7 in the Great Lakes area, resulting in 2300 illness cases (61). In 2011 in Germany, a STEC E. coli (strain O104:H4) was the causative agent of severe cases of acute diarrhea and bloody diarrhea due to the consumption of uncooked sprouts that were irrigated with contaminated water (62).
The protozoan parasites, Cryptosporidium and Giardia, are also important enteric pathogens of public health concern and major waterborne pathogens (63, 64). Cryptosporidium is the second most important cause of moderate to severe diarrhea and mortality in children under 5 years of age in developing countries (65). The largest cryptosporidiosis outbreak due to Cryptosporidium protozoa occurred in 1993 in United States, which affected over 400,000 individuals, was due to drinking water becoming contaminated with wastewater (66). Giardiasis is the most common enteric protozoan parasitic infection worldwide, with an estimated 280 million people infected annually (67). Both parasites are prevalent in wastewater with concentrations in as high as 60,000 Cryptosporidium oocysts and 100,000 Giardia cysts (68).
Among viruses, Adenoviruses are a leading pathogen of clinical diseases, such as gastroenteritis, conjunctivitis, respiratory illnesses, haemorrhagic cystitis, and systemic infections. Adenoviral infections accounts for 2 to 10% cases of diarrhea. They are commonly detected in raw wastewater and have been cited as among the most significantly abundant human viruses in wastewater. Adenoviruses have also been detected in human excrement of infected persons, including both feces and urine (69).
In both low to middle-income and high-income countries, Norovirus is considered the second main cause of viral acute gastroenteritis after rotavirus. Globally, norovirus is responsible for nearly 20% of all acute gastroenteritis cases, with 677 million cases per year and over 213,000 deaths. Studies have linked the level of enteric viruses such as Norovirus, Hepatitis E and Hepatitis A virus in wastewater with incidence of clinical cases. Hence, wastewater surveillance can provide an early warning of outbreaks involving enteric viruses (70, 71).
2.2 Respiratory pathogen
The emergence in 2020 of the severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2), which causes viral pneumonia, has heightened the focus on Wastewater as a surveillance tool to provide early detection of disease in the community. There are more than 2,000 locales in 55 nations where wastewater surveillance for SARS-CoV-2 is ongoing, and there are many cases across the literature reporting on the detection of SARS-CoV-2 from sewage (72). Although SARS-CoV-2 typically causes respiratory symptoms, and is shed in nasal, buccal, esophageal, and respiratory discharges into wastewater, it can also result in gastrointestinal symptoms and/or viral shedding in feces (73, 74). In a meta-analysis of COVID-19 studies, finding revealed that 17.6% of COVID-19 patients had gastrointestinal symptoms and 48.1% of COVID-19 patients had SARS-CoV-2 RNA detected in their feces. Thus, monitoring the presence of SARS-CoV-2 RNA in wastewater is becoming widely used to track changes in COVID-19 case numbers in communities.
Among other respiratory pathogens, 13 respiratory viruses were detected from different wastewater treatment plants in Queensland, Australia. Out of these 13 viruses, Bocavirus (BoV), Parechovirus (PeV), Rhinovirus A (RhV A) and Rhinovirus B (RhV B) were detected in all wastewater samples (21). Different studies reported here shows that the application of wastewater surveillance to monitor respiratory viruses can be a potential tool in community disease surveillance.
3 Application of wastewater surveillance
3.1 Understanding outbreaks and public health through wastewater studies
The detection of the Polio virus nationwide in late 1930s United States sewers (75), the presence of non-polio enteroviruses in the Philippines’ children (76), and recent traces in New York (77, 78) and London (79, 80) highlighted the need for swift governmental action against potential outbreaks.
Detection of SARS-CoV-2, Mpox virus and PMMoV in community wastewater of United States was evaluated by Keegan et al. (81). A study done in Hong Kong Zheng reported that wastewater surveillance can even provide spatiotemporal SARS-CoV-2 infection dynamics (82). Wolken et al. (83), in Houston demonstrated role of wastewater surveillance in detection of SARS CoV-2 and Influenza outbreaks. Similarly, Evidence of SARS-CoV-2 in Australian wastewater was presented by Ahmed et al. (84), shedding light on community prevalence and aiding public health measures (85, 86). Hasan et al. (87), and Vo et al. (88) completed further wastewater studies in the UAE, discovering early indications of SARS-CoV-2 variants prior to clinical case identification. Kirby et al. (89) detected omicron mutation markers in the United States sewage, underscoring the predictive capability of wastewater-based epidemiology.
In South Africa, a study done by Yousif et al. (90), demonstrated the utility of wastewater genomics to monitor evolution and spread of endemic viruses. Investigation in Sweden by Hellmér et al. (91), using qPCR found substantial amounts of Norovirus GII and Hepatitis A indicating upcoming outbreaks. This technique allows estimation of affected individuals based on viral load in sewage. Countries like Spain and United States with documented clinical cases and community spread detected the Mpox virus in wastewater samples (92, 93). In Nepal, Salmonella typhi bacteriophages were detected from surface waters which was reported as a scalable approach to environmental surveillance (94).
Rechenburg and Kistemann (95) found Campylobacter contamination in German rivers increased infection risks, while Liu et al. (58), reported typhoid-causing bacteria in India and Bangladesh’s wastewater. Diemart and Yan’s study (96) exposed undiscovered S. enterica outbreaks linked to wastewater strains via genetic analysis. Barrett et al. (97), isolated Vibrio cholerae O1 from Louisiana sewage, and Zohra et al. (98), identified toxigenic strains in Pakistan’s water presenting continual infection threats unrelated to season patterns.
Razzolini et al. (99), disclosed a high frequency of Cryptosporidium and Giardia in Brazilian chlorine-treated wastewater, leading to gastrointestinal disease transmission through poor hygiene. Additionally, Amoah et al. (100), observed multiple parasites in South African wastewater, with particular concern for worm-infested community water sources as evidenced by a Monte Carlo study (101).
These comprehensive wastewater surveillance studies aid in formulating public health policies and establishing outbreak response, demonstrating their value in epidemiological research.
3.2 Antimicrobial resistance detection in wastewater
One of the major factors affecting the re-emergence of infectious diseases is antimicrobial resistance (102). According to the United Nations, around 700,000 people die yearly of infections associated with antimicrobial resistant microorganisms. Wastewater is one of the primary routes for resistant pathogens and antimicrobe to enter the environment.
Mao et al. (103) studied prevalence of antibiotic resistance genes reported in wastewater treatment plants. Similarly (104), studied diverse range of multiple antibiotic resistance genes in 10 large-scale membrane bioreactors for municipal wastewater treatment. The effects of seasonality upon antibiotic resistance genes in wastewater is another underexplored area, though (105) reported that strong seasonal presence of ARGs (Antibiotic Resistance Genes) within wastewater, with higher levels observed in autumn and winter which coincided with increased antibiotic prescribing in those months (105). Higher levels of resistance have been found in wastewater with higher antibiotic concentrations (e.g., hospitals discharge vs. municipality) (106). Understanding the relationship between antibiotic concentrations and resistance further could inform where to target mitigation measures more effectively.
3.3 Markers of pharmacological intervention
The proportion of regular pharmaceutical in wastewater has been assessed in numerous studies as a metric of disease prevalence. Analyses of metformin (a medication frequently used to treat type 2 diabetes), found in wastewater have been used to assess the prevalence of type 2 diabetes (107, 108). Measurement of pharmaceutical concentrations in wastewater has been used alongside non-wastewater indicators, such as survey data, socio-economic or demographic data, or environmental data to identify correlations (109).
Elevated levels of isoprostanes detected from wastewater, were suggested to be an indicator of increased levels of community anxiety during the COVID-19 (110). The use of these pharmaceutical biomarkers needs to be validated more, and extensive research is required to determine how the data may be used to improve public health measures.
4 Sample collection methods
4.1 Moore swab
The Moore swab was first proposed by Brendan Moore (111) to trace S. paratyphi B from sewage contaminated water in a small town in England (112, 113). In this method, a cotton gauze swab tied with string is submerged in water. The method traps pathogens as water passes through swab. After leaving it in water for 2–4 days, the swabs are sent to the laboratory inside sterile jars and processed further (111, 114). This method has been utilized throughout the world to detect several pathogens such as human norovirus, poliovirus, E. coli, V. cholerae and now SARS-CoV-2 as well.
Liu et al. (115), conducted a study in which Moore swab method was used for wastewater surveillance of COVID-19 at institutional level. Among the 219 swab samples tested, 28 (12.8%) swabs collected were found positive for SARS-CoV-2. Sbodio et al. (116), detected E. coli O157:H7 and S. enterica using Moore swab methodology in large volume field samples of irrigation water. Similarly, McEgan et al. (117), detected Salmonella spp. from larger volume of water by Moore swab method. In Farnham, United Kingdom, Hobbs (118) reported a case of typhoid in a 7-year-old child who had exposure to a sewage-contaminated river and the use of Moore swabs to trace the carrier. Greenberg et al. (119), and Shearer et al. (120), described detection of a single carrier in the isolated town of Portola, CA via use of Moore swabs in sewers; that carrier had been responsible for cases of typhoid occurring intermittently over 5 years (Figure 2).
4.2 Grab method
In this method, raw sewage is collected from sampling point either at 1 point in time or at specified points in time to form a composite sample. Many wastewater treatment plants use automated equipment to take samples at regular intervals during a 24-h period or during peak periods of domestic wastewater flow (122). The larger the volume of wastewater analyzed, higher the theoretical sensitivity to detect pathogen circulation in the source population (23). However, volumes greater than 1 L can be difficult to handle in the laboratory and can be replaced by multiple parallel regular samples.
Sampling is preferred to trapping because it is a more quantitative method that allows an estimation of the detection sensitivity of the system (123). In addition, long-term experience indicates that programs using concentrated sampling detect Polioviruses and non-polio enteroviruses more frequently than those using trap sampling (124) (Figure 3).
5 Methods available for detection of pathogens in wastewater
5.1 Culture based method
The utilization of culture-based approaches to capture antibiotic-resistant bacteria (ARB) is beneficial for various reasons such as verifying viability, testing for virulence (26), profiling phenotypic and genotypic multi-drug resistance (MDR) (125), and producing data that may be utilized for risk assessment related to human health. However, much of the media used to isolate opportunistic infections were not effective on environmental samples because they were created for clinical use.
Certain bacteria found in wastewater originate from the feces and can survive in surface water, while other populations of these bacteria are autochthonous and found in aquatic habitats. Acinetobacter spp., Aeromonas spp., and Pseudomonas spp., have been found to be important opportunistic pathogens that can grow in wastewater and natural aquatic environments. These pathogens can also acquire genes that confer multiple antibiotic resistance, making them potentially useful targets for culture-based monitoring (27).
The drawback of the culture-based approach is that, while some organisms may be inactivated (dead) or unable to grow on the chosen media (bacteria) or cell culture (used for viruses), molecular approaches can detect quantities from 1 to 10,000 greater than those of culture methods (126) (Table 2).
Table 2. Methods available for detection of pathogens in wastewater.
5.2 Polymerase chain reaction
The identification of pathogens in wastewater can be accomplished by culture-based approaches, however the process can take many days or weeks. Without the requirement for cultivation, alternative molecular techniques like the PCR have proven successful in identifying bacterial, viral, and protozoan pathogens in sewage (127). PCR is the most common molecular-based technique to detect lesser amounts of a specific nucleic acid and is widely used for detection of pathogens (28). It enables the detection of a single pathogenic strain by targeting specific DNA sequences (28). This benefit makes it possible to identify and detect even lower amount of the target DNA sequence. It is thus widely used in the diagnosis of human pathogens (128). Fan et al. (129), reported PCR assay to achieve the simultaneous detection of various human pathogens in a single tube, with the detection sensitivities between 10 to 102 CFU/100 mL in seawater. Omar et al. (29), identified commensal and pathogenic E. coli from medical and environmental water sources by using multiplex PCR technique. PCR technique, due to its high specificity, was also adopted to detection of enteroviruses and Hepatitis A virus (HAV) in environment.
Quantitative real-time PCR (qPCR), another PCR variant, allows for the measurement of DNA targets by tracking amplified products throughout cycle as evidenced by rising fluorescence (130). This approach decreases the potential of cross-contamination, offers excellent sensitivity and specificity, a faster rate of detection, and eliminates the requirement for post-PCR analysis (131). Shannon et al. (132), detected E. coli, Klebsiella pneumoniae, Clostridium perfringens and Enterococcus faecalis through wastewater by application of qPCR. With a lower quantification limit of 2.5 oocysts/sample, qPCR techniques have also been devised for the detection and identification of Cryptosporidium spp. in river water (133). qPCR had a sensitivity of 0.45 cysts per reaction for the detection of G. lamblia and Giardia ardeae in wastewater samples (134). For detection of RNA viruses, quantitative reverse-transcriptase (qRT)-PCR was developed to provide quantitative estimation of the pathogen concentration in water (135).
Limitations of PCR includes the inability to discriminate between viable from non-viable cells that both contain DNA, the low concentration of several pathogens in water such as Cryptosporidium, Giardia and viruses, and the lack of data to indicate the real infectious risk to a population (128, 131).
5.3 DNA microarray
One of the most innovative molecular biology-based techniques, DNA microarray technology enables researchers to run several environmental samples simultaneously in large-scale, data-intensive investigations (136). It is widely utilized to monitor gene expression under different cell growth conditions, detecting specific mutations in DNA sequences and characterizing microorganisms in environmental samples. It is a unique glass or silicon chip that has a DNA microarray that covers a surface area of several square centimeters with many nucleic acid probes. After being coupled with the probes, DNA, complementary DNA (cDNA), and RNA in the sample are identified by fluorescence or electric signal (137). DNA microarrays allow the hybridization-based detection of numerous targets in a single experiment. As a result, it is a quick and accurate diagnostic approach for analyzing several clinical or environmental samples (30). Wilson et al. (138), identified 18 pathogenic bacteria, eukaryotes, and viruses by using species-specific primer sets to amplify multiple regions unique toward individual pathogen in the microarray. Inoue and et al. (139) studied the occurrence of 941 pathogenic bacterial species in groundwater and were able to differentiate between human and animal sources. Leski et al. (140), developed a high-density re-sequencing microarray that has the capability of detecting 84 different types of pathogens ranging from bacteria, protozoa, and viruses, including Bacillus anthracis, Ebola virus and Francisella tularensis with detection limit of 104 to 106 copies per test for most of the pathogens exhibiting high specificity.
This technology is helpful as most known bacteria found in samples can be detected without the need for culturing, and the sensitivity of this approach allows for the detection of species with lower abundances (detection limit of 0.01% of microbial communities) (141). However, accuracy of the microarray data, complex probe design work, and clinical relevance of the early results have been criticized (127).
A single microarray experiment can be very expensive, there are many probe designs based on low-specificity sequences, and most widely used microarray platforms only use one set of manufacturer-designed probes, which leaves little control over the pool of transcripts that are analyzed. These are the main drawbacks of microarray technology. Along with their high sensitivity to changes in the hybridization temperature (142), the purity and rate of genetic material degradation (31), and the amplification process (143), microarrays also have other limitations. These factors, when combined, have the potential to affect gene expression estimates.
5.4 Fluorescent in situ hybridization
A cytogenetic method called FISH is used to locate the nucleic acids in cells or sample matrices. In molecular ecology, fluorescently labeled nucleic acid probes can be used to identify genes on chromosomes or to label ribosomal RNA in various taxonomic bacteria or archaea by hybridizing only with highly similar nucleic acids. It is possible to use FISH to count specific microbial populations (144).
Santiago et al. (32), detected Salmonella spp. from wastewater reused for irrigation by using FISH as a molecular method tool. Amann and Fuchs (144) isolated members of the family Enterobacteriaceae and E. coli in drinking water systems, freshwater and river water by this tool. In addition, emerging human pathogens in water, wastewater, sludge, and cellular survival and infection mechanisms have all been investigated with FISH (32, 33). Because it is less sensitive to inhibitory substances than PCR, FISH is better suited for complex matrices. However, the fact that only a limited number of phylogenetically distinct targets can be detected simultaneously is a major drawback of FISH.
5.5 Loop-mediated isothermal amplification
LAMP is a method for isothermal nucleic acid amplification. Currently, LAMP has been used to identify and quantify pathogenic bacteria with benefits in terms of sensitivity, specificity, and speed (145, 146). With a detection limit of 10 copies or less in the template for one reaction, the LAMP approach was also proven to be 10–100 times more sensitive than PCR detection (34). Lu et al. (35), utilized LAMP-based method for a rapid identification of Legionella spp. from the environmental water source. Koizumi et al. (147), used loop-mediated isothermal amplification method for rapid, simple, and sensitive detection of Leptospira spp. in urine sample.
This method can directly detect pathogenic microorganisms in wastewater avoiding the tedious step of culture and nucleic acid extraction (36). However, the major drawback of LAMP is it is more difficult to design specific primers for LAMP than for PCR (because LAMP requires 4–6 primers and PCR only two).
5.6 Pyrosequencing
Pyrosequencing is a DNA sequencing technique that facilitates microbial genome sequencing to identify bacterial species, discriminate pathogenic strains, and detect genetic mutations that confer resistance to anti-microbial agents (148). Hong et al. (149), analyzed bacterial biofilm communities in water meters of a drinking water distribution system by Pyrosequencing technique. Study conducted by Ibekwe et al. (150), identified most of the potential pathogenic bacterial sequences from three major phyla, namely, Proteobacteria, Bacteroidetes, and Firmicutes in a mixed urban watershed as revealed by pyrosequencing. The advantages of pyrosequencing for microbiology applications include rapid and reliable high-throughput screening and accurate identification of microbes and microbial genome mutations. The pyrosequencing instrument can also analyze the complete genetic diversity of anti-microbial drug resistance, including SNP typing, point mutations, insertions, and deletions, as well as quantification of multiple gene copies that may occur in some anti-microbial resistance patterns (151).
However, the DNA present in wastewater samples could limit the sensitivity of this tool as it requires DNA templates at picomole level, but a much lower amount of DNA can hamper the output (37, 38). This technology is also limited by the cost, the complexity of analysis, the need for increasing availability of massive computing power and the efficiency of data generation (152).
5.7 Digital PCR
To identify enteric virus contamination in water and wastewater, PCR and its variants such as quantitative PCR (qPCR), real-time RT-PCR, RT-qPCR, nested PCR, and digital PCR (dPCR) have been implemented (153). In contrast, qPCR can detect multiplex viral targets (154). Digital PCR (dPCR) has proven to be efficient for wastewater surveillance, owing to its increased robustness against PCR inhibitors commonly encountered in more difficult sample types (39, 155).
Heijnen et al. (40), evaluated that digital PCR may be utilized to detect and quantify mutations in SARS-CoV-2 in raw sewage samples from the cities of Amsterdam and Utrecht in The Netherlands. With its sensitivity and precision in quantification, digital PCR (dPCR) was quickly identified as a suitable choice for monitoring SARS-CoV-2 in wastewater monitoring (156). In terms of quantifying human-associated fecal markers in water, it was discovered that dPCR displayed superior precision and reproducibility than qPCR (41). With dPCR, the sample analysis cost and processing time are higher than qPCR. For the quantification of pathogens, dPCR can be a viable alternative if enhanced analytical performance (i.e., accuracy and sensitivity) is essential (42).
5.8 Whole genome sequencing
Profiling bacterial diversity and potential pathogens in wastewater has been a widely used application of sequencing, a robust analytical tool. For surveillance and outbreak investigations, the state of the art is shifting toward WGS (Whole Genome Sequencing) as a replacement for conventional molecular techniques (43, 157). WGS study of the complete pathogen genome has the potential to transform outbreak analysis by providing understanding of distinguishing even closely related bacterial lineages (158).
As demonstrated by Christoph et al. (44), numerous SARS-CoV-2 genotypes were found through sequencing of viral concentrations and RNA recovered directly from wastewater. Fumian et al. (45), identified Norovirus GII genotypes through genome sequencing from a wastewater treatment plant in Rio de Janeiro, Brazil. Mahfouz et al. (159), analyzed whole genome sequences for the indicator species E. coli of the inflow and outflow of a sewage treatment plant which revealed that nearly all isolates are multi-drug resistant, and many are potentially pathogenic. Recently, Mbanga et al. (160), reported genomics of antibiotic resistant Klebsiella grimontii novel sequence type ST350 isolated from a wastewater source in South Africa.
Whole genome sequencing reveals insights into recent improvements in sequencing technologies and analysis tools have rapidly increased the output and analysis speed as well as reduced the overall costs of WGS (158). Nevertheless, Genomic surveillance is still challenging due to low target concentration, complex microbial and chemical background, and lack of robust nucleic acid recovery experimental procedures (161).
5.9 MALDI-TOF
Matrix-assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF MS) is a rapid and accurate method of identification of bacterial and fungal isolates in the laboratory (162). The identification of microorganisms is based on the protein fingerprint unique to the microorganism (163, 164).
V. cholerae non-O1 isolates from wastewater were identified by MALDI TOF MS by Eddabra et al. (165). V. alginolyticus isolated from Perna perna mussles was efficiently identified by MALDI TOF MS by Bronzato et al. (166).
There are numerous studies that have proven the use of MALDI TOF MS on bacterial and fungal isolates. Croxatto et al. (167), have reported that numerous studies have been attempted to perform direct testing of urine using MALDI TOF MS. The method could be used with up to 94% accuracy but only if bacterial count is 105/ml. Nachtigall et al. (168), found that MALDI TOF was 80% concordant with RT-PCR in identifying SARS-CoV-2 from nasal mucus secretions. Rybicka et al. (169), found that MALDI TOF was better than RT-PCR in detecting SARS-Cov-2. Gerbersdorf et al. (170), have shown that dextran, gellan and xanthan from anaerobic microbial aggregates can be differentially demonstrated by MALDI TOF MS in different wastewater. The exopolysaccharides in biofilms are found to be important in microbial adhesion and aggregation (171). Picó et al. (172), found that MALDI TOF can be adapted for rapid detection and characterization of proteins in wastewater. However, MALDI-TOF MS has relatively low resolution power if compared to other high-resolution mass spectrometers and the accuracy of identification depends on the quality of the reference database (46, 47).
6 Challenges of wastewater-based epidemiology
6.1 Complexity of wastewater matrix
Although Wastewater-Based Epidemiology (WBE) offers appealing advantages for the monitoring of public health, it comes along with several challenges. One major challenge being the level of biomarkers (chemical and/or biological compounds) as it is far more diluted in wastewater which makes it difficult to trace (173). The complex matrix is also challenging for pathogen detection (174). Nucleic acid-based Polymerase chain reaction (PCR) is the primary technique for analyzing pathogens; however, wastewater contains a variety of PCR inhibitors, including fat, protein, and other compounds, that might affect PCR analysis (18).
6.2 Estimation of population size
The dynamic population size estimation is another challenge (175, 176). For example, it may be difficult to determine whether the presence of a pathogen in wastewater was caused by visitors passing through or by residents of the community in the concerned area (177). However, the presence of pathogens in wastewater, whether from the local population, undoubtedly provides valuable information, which may indicate an outbreak of disease in the community, thereby providing real time data for proper preparedness and response (178). This also ensures that WBE is used to provide timely warning of infectious disease outbreaks.
6.3 Detection methods
The physical distinctions between the major pathogen groups, the presence of inhibitors in the sample, established standard techniques for sample collection, culture-independent detection methods, and identification of pathogen host origin are the problems of detection methods (179). Specificity, sensitivity, repeatability of results, rapidity, automation, and cheap cost are the most significant prerequisites for reliable analysis (180). Furthermore, because human pathogens that reside in a viable but non-culturable (VBNC) form, such as E. coli, Helicobacter pylori, and V. cholerae, have a wide environmental dispersion, culture-dependent approaches may provide false negative results (28, 181).
7 Economics of wastewater surveillance
Performing clinical testing for mass surveillance puts a huge financial burden on low-and middle-income countries (LMICs), because WHO recommended testing protocols are costly to implement. In addition, the recent recommendation of the real-time surveillance of pathogens of concern that need prohibitively expensive next generation sequencing technology is less affordable by LMICs (182). While clinical surveillance will always be vital for the response to infectious diseases, wastewater-based surveillance allow for quick and economical surveillance–even in areas that are currently unexplored. Wastewater monitoring enables community prevalence quantification and rapid detection of pathogen. At sites where wastewater from the population collects and mixes, so do a diverse array of microbes shed from individuals (183). Pathogen concentrations accurately estimate prevalence (the number of current infections in the population) and given that wastewater trends often precede corresponding clinical detections, they may allow for early detection (184, 185).
To summarize, because wastewater surveillance covers a wide-scale population, the additional cost per resident would be very small, even when focusing on an institutionalized population. Primary screening with wastewater surveillance is highly likely to be economically more justifiable, scalable, providing results in real time than a primary screening with clinical tests. However, progressing toward more equitable and sustainable surveillance will require continued development of local, self-sustaining scientific ecosystems through laboratory and computational methods development and training, capacity building efforts, and financial support of domestic scientific enterprise.
8 Conclusion
Wastewater surveillance had shown great potential in providing complete health status information in a comprehensive and near-real-time manner at the community level. It offers a unique perspective on the spread and evolution of pathogens, aiding in the prevention and control of disease epidemics. This review underscores the importance of continued research and development in this field to overcome current challenges and maximize the potential of wastewater surveillance in public health. It also offers a framework and evidence foundation to guide laboratories in selecting the most suitable tools for implementing wastewater surveillance.
Since, there are so many emerging new pathogens that are causing illnesses and waterborne outbreaks, pathogen indicators need to be continually strengthened. Optimizing presently available technologies could increase our understanding of infectious pathogens, our ability to predict pathogen contamination, and our potential to safeguard public health. These technologies would be able to identify causal agents more precisely and quickly, detect viable microorganisms and characterize them according to microbial communities, and enable the creation of accessible data.
If wastewater monitoring is conducted consistently, it may be utilized to locate possible pathogen carriers, provide comprehensive data, determine the origin of the infections, and deliver reliable early warning. However, there is still a lot of work to be done for adoption on a broader scale.
Author contributions
SS: Supervision, Visualization, Writing – original draft, Writing – review & editing. AmA: Writing – original draft. SuA: Writing – original draft. ShA: Writing – original draft. AsA: Writing – original draft. GO: Writing – original draft. MC: Writing – review & editing. SBS: Writing – original draft. GB: Writing – review & editing. WE: Writing – original draft, Writing – review & editing.
Funding
The author(s) declare that no financial support was received for the research, authorship, and/or publication of this article.
Acknowledgments
MC is affiliated to the National Institute for Health Research Health Protection Research Unit (NIHR HPRU) in Genomics and Enabling Data at University of Warwick in partnership with the United Kingdom Health Security Agency (UKHSA), in collaboration with University of Cambridge and Oxford. MC is based at UKHSA.
Conflict of interest
The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.
Publisher’s note
All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article, or claim that may be made by its manufacturer, is not guaranteed or endorsed by the publisher.
Author disclaimer
The views expressed are those of the author(s) and not necessarily those of the NIHR, the Department of Health and Social Care or the United Kingdom Health Security Agency.
References
1. Sabin, NS, Calliope, AS, Simpson, SV, Arima, H, Ito, H, Nishimura, T, et al. Implications of human activities for (re)emerging infectious diseases, including COVID-19. J Physiol Anthropol. (2020) 39:29. doi: 10.1186/s40101-020-00239-5
2. Baker, RE, Mahmud, AS, Miller, IF, Rajeev, M, Rasambainarivo, F, Rice, BL, et al. Infectious disease in an era of global change. Nat Rev Microbiol. (2022) 20:193–205. doi: 10.1038/s41579-021-00639-z
3. Van Doorn, HR. The epidemiology of emerging infectious diseases and pandemics. Medicine (Abingdon). (2021) 49:659–62. doi: 10.1016/j.mpmed.2021.07.011
4. World Health Organization. Managing epidemics key facts about major deadly diseases. Geneva: World Health Organisation (2018).
5. Xagoraraki, I, and O’Brien, E. Wastewater-based epidemiology for early detection of viral outbreaks. Women in water quality: Investigations by prominent female engineers, 75–97. (2020).
7. Been, F, Bastiaensen, M, Lai, FY, Libousi, K, Thomaidis, NS, Benaglia, L, et al. Mining the chemical information on urban wastewater: monitoring human exposure to phosphorus flame retardants and plasticizers. Environ Sci Technol. (2018) 52:6996–7005. doi: 10.1021/acs.est.8b01279
8. Snow, J. Snow on cholera. On the mode of communication of cholera. London, John Churchil (1st edition, 1849, 2nd Editon, 1855) (1855).
9. Cameron, D, and Jones, IG. John Snow, the broad street pump and modern epidemiology. Int J Epidemiol. (1983) 12:393–6. doi: 10.1093/ije/12.4.393
10. Johnson, S. The ghost map: The story of London’s Most terrifying epidemic--and how it changed science, cities, and the modern world. London, UK: Penguin (2006).
11. Nakamura, T, Hamasaki, M, Yoshitomi, H, Ishibashi, T, Yoshiyama, C, Maeda, E, et al. Environmental surveillance of poliovirus in sewage water around the introduction period for inactivated polio vaccine in Japan. Appl Environ Microbiol. (2015) 81:1859–64. doi: 10.1128/AEM.03575-14
12. Shaffer, PT, Metcalf, TG, and Sproul, OJ. Chlorine resistance of poliovirus isolates recovered from drinking water. Appl Environ Microbiol. (1980) 40:1115–21. doi: 10.1128/aem.40.6.1115-1121.1980
13. Diamond, MB, Keshaviah, A, Bento, AI, Conroy-Ben, O, Driver, EM, Ensor, KB, et al. Wastewater surveillance of pathogens can inform public health responses. Nat Med. (2022) 28:1992–5. doi: 10.1038/s41591-022-01940-x
14. Singer, AC, Thompson, JR, Filho, CRM, Street, R, Li, X, Castiglioni, S, et al. A world of wastewater-based epidemiology. Nat Water. (2023) 1:408–15. doi: 10.1038/s44221-023-00083-8
15. Aarestrup, FM, and Woolhouse, MEJ. Using sewage for surveillance of antimicrobial resistance. Science Feb 7. (2020) 367:630–2. doi: 10.1126/science.aba3432
16. Nguyen, AQ, Vu, HP, Nguyen, LN, Wang, Q, Djordjevic, SP, Donner, E, et al. Monitoring antibiotic resistance genes in wastewater treatment: current strategies and future challenges. Sci Total Environ. (2021) 783:146964. doi: 10.1016/j.scitotenv.2021.146964
17. Chau, KK, Barker, L, Budgell, EP, Vihta, KD, Sims, N, Kasprzyk-Hordern, B, et al. Systematic review of wastewater surveillance of antimicrobial resistance in human populations. Environ Int. (2022) 162:107171. doi: 10.1016/j.envint.2022.107171
18. Zhang, S, Li, X, Wu, J, Coin, L, O’Brien, J, Hai, F, et al. Molecular methods for pathogenic Bacteria detection and recent advances in wastewater analysis. Water. (2021) 13:3551. doi: 10.3390/w13243551
19. Ramirez-Castillo, FY, Loera-Muro, A, Jacques, M, Garneau, P, Avelar-Gonzalez, FJ, Harel, J, et al. Waterborne pathogens: detection methods and challenges. Pathogens. (2015) 4:307–34. doi: 10.3390/pathogens4020307
20. Fijalkowski, KL, Kacprzak, MJ, and Rorat, A. Occurrence changes of Escherichia coli (including O157:H7 serotype) in wastewater and sewage sludge by quantitation method of (EMA) real time—PCR. Desalination Water Treat. (2014) 52:3965–72. doi: 10.1080/19443994.2014.887499
21. Ahmed, W, Bivins, A, Stephens, M, Metcalfe, S, Smith, WJM, Sirikanchana, K, et al. Occurrence of multiple respiratory viruses in wastewater in Queensland, Australia: potential for community disease surveillance. Sci Total Environ. (2023) 864:161023. doi: 10.1016/j.scitotenv.2022.161023
22. U.S. Environmental Protection Agency. Control of pathogens and vector attraction in sewage sludge. (2003).
23. World Health Organization. (2015). Available at: http://www.polioeradication.org/dataandmonitoring.aspx. (Accessed March 26 2020).
24. Bitton, G. Microbiology of drinking water production and distribution. 1st ed. Hoboken, NJ: John Wiley and Sons, Inc. (2014). 312 p.
25. Woolhouse, MEJ. Where do emerging pathogens come from? Microbe. (2006) 1:511–5. doi: 10.1128/microbe.1.511.1
26. Lagier, J-C, Dubourg, G, Amrane, S, and Raoult, D. Koch postulate: why should we grow Bacteria? Arch Med Res. (2017) 48:774–9. doi: 10.1016/j.arcmed.2018.02.003
27. Joly-Guillou, ML. Clinical impact and pathogenicity of Acinetobacter. Clin Microbiol Infect. (2005) 11:868–73. doi: 10.1111/j.1469-0691.2005.01227.x
28. Law, JW-F, Ab Mutalib, N-S, Chan, K-G, and Lee, L-H. Rapid methods for the detection of foodborne bacterial pathogens: principles, applications, advantages and limitations. Front Microbiol. (2015) 5:770. doi: 10.3389/fmicb.2014.00770
29. Omar, K, and Barnard, T. Detection of diarrhoeagenic Escherichia coli in clinical and environmental water sources in South Africa using single-step 11-gene m-PCR. World J Microbiol Biotechnol. (2014) 30:2663–71. doi: 10.1007/s11274-014-1690-4
30. Severgnini, M, Cremonesi, P, Consolandi, C, De Bellis, G, and Castiglioni, B. Advances in DNA microarray technology for the detection of foodborne pathogens. Food Bioprocess Tech. (2011) 4:936–53. doi: 10.1007/s11947-010-0430-5
31. Opitz, L, Salinas-Riester, G, Grade, M, Jung, K, Jo, P, Emons, G, et al. Impact of RNA degradation on gene expression profiling. BMC Med Genet. (2010) 3:36. doi: 10.1186/1755-8794-3-36
32. Santiago, P, Jiménez-Belenguer, A, García-Hernández, J, Estellés, RM, Hernández Pérez, M, Castillo López, MA, et al. High prevalence of Salmonella spp. in wastewater reused for irrigation assessed by molecular methods. Int J Hyg Environ Health. (2018) 221:95–101. doi: 10.1016/j.ijheh.2017.10.007
33. Lukumbuzya, M, Schmid, M, Pjevac, P, and Daims, H. A multicolor fluorescence in situ hybridization approach using an extended set of fluorophores to visualize microorganisms. Front Microbiol. (2019) 10:1383. doi: 10.3389/fmicb.2019.01383
34. Niu, JH, Jian, H, Guo, QX, Chen, CL, Wang, XY, Liu, Q, et al. Evaluation of loop-mediated isothermal amplification (LAMP) assays based on 5S rDNA-IGS2 regions for detecting Meloidogyne enterolobii. Plant Pathol. (2012) 61:809–19. doi: 10.1111/j.1365-3059.2011.02562.x
35. Lu, X, Mo, ZY, Zhao, HB, Yan, H, and Shi, L. LAMP-based method for a rapid identification of Legionella spp. and Legionella pneumophila. Appl Microbiol Biotechnol. (2011) 92:179–87. doi: 10.1007/s00253-011-3496-8
36. Nzelu, CO, Cáceres, AG, Guerrero-Quincho, S, Tineo-Villafuerte, E, Rodriquez-Delfin, L, Mimori, T, et al. A rapid molecular diagnosis of cutaneous leishmaniasis by colorimetric malachite green-loop mediated isothermal amplification (LAMP) combined with an FTA card as a direct sampling tool. Acta Trop. (2016) 153:116–9. doi: 10.1016/j.actatropica.2015.10.013
37. Wu, F, Lee, WL, Chen, H, Gu, X, Chandra, F, Armas, F, et al. Making waves: wastewater surveillance of SARS-CoV-2 in an endemic future. Water Res. (2022) 219:118535. doi: 10.1016/j.watres.2022.118535
38. Peccia, J, Zulli, A, Brackney, DE, Grubaugh, ND, Kaplan, EH, Casanovas-Massana, A, et al. Measurement of SARS-CoV-2 RNA in wastewater tracks community infection dynamics. Nat Biotechnol. (2022) 38:1164–7. doi: 10.1038/s41587-020-0684-z
39. Sedji, MI, Varbanov, M, Meo, M, Colin, M, Mathieu, L, and Bertrand, I. Quantification of human adenovirus and norovirus in river water in the north-east of France. Environ Sci Pollut Res. (2018) 25:30497–507. doi: 10.1007/s11356-018-3045-4
40. Heijnen, L, Elsinga, G, de Graaf, M, Molenkamp, R, Koopmans, MPG, and Medema, G. Droplet digital RT-PCR to detect SARS-CoV-2 signature mutations of variants of concern in wastewater. Sci Total Environ. (2021) 799:149456. doi: 10.1016/j.scitotenv.2021.149456
41. Cao, Y, Yu, M, Dong, G, Chen, B, and Zhang, B. Digital PCR as an emerging tool for monitoring of microbial biodegradation. Molecules. (2020) 25:706. doi: 10.3390/molecules25030706
42. Tiwari, A, Ahmed, W, Oikarinen, S, Sherchan, SP, Heikinheimo, A, Jiang, G, et al. Application of digital PCR for public health-related water quality monitoring. Sci Total Environ. (2022) 837:155663. doi: 10.1016/j.scitotenv.2022.155663
43. Behjati, S, and Tarpey, PS. What is next generation sequencing? Arch Dis Child Educ Pract. (2013) 98:236–8. doi: 10.1136/archdischild-2013-304340
44. Crits-Christoph, A, Kantor, RS, Olm, MR, Whitney, ON, Al-Shayeb, B, Lou, YC, et al. Genome sequencing of sewage detects regionally prevalent SARS-CoV-2 variants. MBio. (2021) 12:e02703–20. doi: 10.1128/mBio.02703-20
45. Fumian, TM, Fioretti, JM, Lun, JH, dos Santos, IAL, White, PA, and Miagostovich, MP. Detection of norovirus epidemic genotypes in raw sewage using next generation sequencing. Environ Int. (2019) 123:282–91. doi: 10.1016/j.envint.2018.11.054
46. Camacho, JB, Nilsson, J, Larsson, DGJ, and Flach, C-F. Evaluation of culture conditions for sewage-based surveillance of antibiotic resistance in Klebsiella pneumoniae. J Glob Antimicrob Resist. (2024) 37:122–8. doi: 10.1016/j.jgar.2024.03.005
47. Rychert, J. Benefits and limitations of MALDI-TOF mass spectrometry for the identification of microorganisms. J Infect. (2019) 2:1–5. doi: 10.29245/2689-9981/2019/4.1142
48. Abbasi, E, Van Belkum, A, and Ghaznavi-Rad, E. Quinolone and macrolide-resistant Campylobacter jejuni in pediatric gastroenteritis patients from Central Iran. Microb Drug Resist. (2019) 25:1080–6. doi: 10.1089/mdr.2018.0455
49. Rinsoz, T, Hilfiker, S, and Oppliger, A. Quantification of Thermotolerant Campylobacter in Swiss water treatment plants, by real-time quantitative polymerase chain reaction. Water Environ Res. (2009) 81:929–33. doi: 10.2175/106143009X407429
50. Moreno, Y, Botella, S, Alonso, JL, Ferrús, MA, Hernández, M, and Hernández, J. Specific detection of Arcobacter and Campylobacter strains in water and sewage by PCR and fluorescent in situ hybridization. Appl Environ Microbiol. (2003) 69:1181–6. doi: 10.1128/AEM.69.2.1181-1186.2003
51. Dekeyser, PMJ, Gossuin-Detrain, M, Butzler, JP, and Sternon, J. Acute enteritis due to related vibrio: first positive stool cultures. J Infect Dis. (1972) 125:390–2. doi: 10.1093/infdis/125.4.390
52. Banihashemi, A, Van Dyke, MI, and Huck, PM. Long-amplicon propidium monoazide-PCR enumeration assay to detect viable Campylobacter and Salmonella. J Appl Microbiol. (2012) 113:863–73. doi: 10.1111/j.1365-2672.2012.05382.x
53. Clark, CG, Price, L, Ahmed, R, Woodward, DL, Melito, PL, Rodgers, FG, et al. Characterization of waterborne outbreak–associated Campylobacter jejuni, Walkerton. Ontario Emerging infectious diseases. (2003) 9:1232–41. doi: 10.3201/eid0910.020584
54. Majowicz, SE, Musto, J, Scallan, E, Angulo, FJ, Kirk, M, O’Brien, SJ, et al. The global burden of non-typhoidal Salmonella gastroenteritis. Clin Infect Dis. (2010) 50:882–9. doi: 10.1086/650733
55. Ferrari, RG, Rosario, DKA, Cunha-Neto, A, Mano, SB, Figueiredo, EES, and Conte-Junior, CA. Worldwide epidemiology of Salmonella serovars in animal-based foods: a meta-analysis. Appl Environ Microbiol. (2019) 85:e00591–19. doi: 10.1128/AEM.00591-19
56. Issenhuth-Jeanjean, S, Roggentin, P, Mikoleit, M, Guibourdenche, M, de Pinna, E, Nair, S, et al. Supplement 2008–2010 (no. 48) to the White–Kauffmann–Le minor scheme. Res Microbiol. (2014) 165:526–30. doi: 10.1016/j.resmic.2014.07.004
57. Furukawa, I, Ishihara, T, Teranishi, H, Saito, S, Yatsuyanagi, J, Wada, E, et al. Prevalence and characteristics of Salmonella and Campylobacter in retail poultry meat in Japan. Jpn J Infect Dis. (2017) 70:239–47. doi: 10.7883/yoken.JJID.2016.164
58. Liu, P, Ibaraki, M, Kapoor, R, Amin, N, Das, A, Miah, R, et al. Development of Moore swab and ultrafiltration concentration and detection methods for Salmonella Typhi and Salmonella Paratyphi a in wastewater and application in Kolkata, India and Dhaka, Bangladesh. Front Microbiol. (2021) 12:684094. doi: 10.3389/fmicb.2021.684094
59. House, D, Bishop, A, Parry, C, Dougan, G, and Wain, J. Typhoid fever: pathogenesis and disease. Curr Opin Infect Dis. (2001) 14:573–8. doi: 10.1097/00001432-200110000-00011
60. Ameer, MA, Wasey, A, and Salen, P. Escherichia coli (e coli 0157 H7). Treasure Island, FL: StatPearls Publishing (2023).
61. Hrudey, SE, Payment, P, Huck, PM, Gillham, RW, and Hrudey, EJ. A fatal waterborne disease epidemic in Walkerton, Ontario: comparison with other waterborne outbreaks in the developed world. Water Sci Technol. (2003) 47:7–14. doi: 10.2166/wst.2003.0146
62. Muniesa, M, Hammerl, JA, Hertwig, S, Appel, B, and Brussow, H. Shiga toxin-producing Escherichia coli O104:H4: a new challenge for microbiology. Appl Environ Microbiol. (2012) 78:4065–73. doi: 10.1128/AEM.00217-12
63. Zahedi, A, Monis, P, Deere, D, and Ryan, U. Wastewater-based epidemiology–surveillance and early detection of waterborne pathogens with a focus on SARS-CoV-2, Cryptosporidium and Giardia. Parasitol Res. (2021) 120:4167–88. doi: 10.1007/s00436-020-07023-5
64. Tram, NT, Phuc, PD, Phi, NH, Trang, LT, Nga, TT, Ha, HTT, et al. Cryptosporidium and Giardia in biogas wastewater: Management of Manure Livestock and Hygiene Aspects Using Influent, effluent, Sewage Canal samples, vegetable, and soil samples. Pathogens. (2022) 11:174. doi: 10.3390/pathogens11020174
65. Dong, S, Yang, Y, Wang, Y, Yang, D, Yang, Y, Shi, Y, et al. Prevalence of Cryptosporidium infection in the global population: a systematic review and meta-analysis. Acta Parasitol. (2020) 65:882–9. doi: 10.2478/s11686-020-00230-1
66. MacKenzie, WR, Hoxie, NJ, Proctor, ME, Gradus, MS, Blair, KA, Peterson, DE, et al. A massive outbreak in Milwaukee of Cryptosporidium infection transmitted through the public water supply. N Engl J Med. (1994) 331:161–7. doi: 10.1056/NEJM199407213310304
67. Leung, AKC, Leung, AAM, Wong, AHC, Sergi, CM, and Kam, JKM. Giardiasis: An Overview. Recent Patents Inflamm Allergy Drug Discov. (2019) 13:134–43. doi: 10.2174/1872213X13666190618124901
68. Hamilton, KA, Waso, M, Reyneke, B, Saeidi, N, Levine, A, Lalancette, C, et al. Cryptosporidium and Giardia in wastewater and surface water environments. J Environ Qual. (2018) 47:1006–23. doi: 10.2134/jeq2018.04.0132
69. Allayeh, AK, Al-Daim, SA, Ahmed, N, El-Gayar, M, and Mostafa, A. Isolation and genotyping of adenoviruses from wastewater and diarrheal samples in Egypt from 2016 to 2020. Viruses. (2022) 14:2192. doi: 10.3390/v14102192
70. Bosh, B. Human enteric viruses in the water environment: a mini review. Int Microbiol. (1998) 1:191–6.
71. Li, W, Wang, X, Yuan, CQ, Zheng, JL, Jin, M, Song, N, et al. Detection of enteroviruses and hepatitis a virus in water by consensus primer multiplex RT-PCR. Word J Gastroenterol. (2002) 8:699–702. doi: 10.3748/wjg.v8.i4.699
72. COVID-19 WBE Collaborative. COVID19 poops dashboard. Online: COVID-19 wastewater-based epidemiology collaborative. (2021). Available at: https://www.covid19wbec.org/covidpoops19 (Accessed August 9, 2021).
73. Betancourt, WQ, Schmitz, BW, Innes, GK, Prasek, SM, Pogreba, BKM, Stark, ER, et al. COVID-19 containment on a college campus via wastewater-based epidemiology, targeted clinical testing and an intervention. Sci Total Environ. (2021) 779:146408. doi: 10.1016/j.scitotenv.2021.146408
74. Wong, JCC, Tan, J, Lim, YX, Arivalan, S, Hapuarachchi, HC, Mailepessov, D, et al. Non-intrusive wastewater surveillance for monitoring of a residential building for COVID-19 cases. Sci Total Environ. (2021) 786:147419. doi: 10.1016/j.scitotenv.2021.147419
75. Paul, JR, Trask, JD, and Culotta, CS. Poliomyelitic virus in sewage. Science. (1939) 90:258–9. doi: 10.1126/science.90.2333.258
76. Jiao, MMA, Apostol, LN, de Quiroz-Castro, M, Jee, Y, Roque, V, Mapue, M, et al. Non-polio enteroviruses among healthy children in the Philippines. BMC Public Health. (2020) 20:1–7. doi: 10.1186/s12889-020-8284-x
77. Link-Gelles, R, Lutterloh, E, Ruppert, PS, Backenson, PB, St George, K, Rosenberg, ES, et al. Public health response to a case of paralytic poliomyelitis in an unvaccinated person and detection of poliovirus in wastewater—New York, June–august 2022. Am J Transplant. (2022) 22:2470–4. doi: 10.1111/ajt.16677
78. Ryerson, AB. Wastewater testing and detection of poliovirus type 2 genetically linked to virus isolated from a paralytic polio case–New York, March 9–October 11, 2022. MMWR Morb Mortal Wkly Rep. (2022) 71:1418–24. doi: 10.15585/mmwr.mm7144e2
79. Klapsa, D, Wilton, T, Zealand, A, Bujaki, E, Saxentoff, E, Troman, C, et al. Sustained detection of type 2 poliovirus in London sewage between February and July 2022, by enhanced environmental surveillance. Lancet. (2022) 400:1531–8. doi: 10.1016/S0140-6736(22)01804-9
80. Hill, M, and Andrew, J. Pollard. Detection of poliovirus in London highlights the value of sewage surveillance. Lancet. (2022) 400:1491–2. doi: 10.1016/S0140-6736(22)01885-2
81. Brighton, K, Fisch, S, Huiyun, W, Vigil, K, and Aw, TG. Targeted community wastewater surveillance for SARS-CoV-2 and Mpox virus during a festival mass-gathering event. Sci Total Environ. (2024) 906:167443. doi: 10.1016/j.scitotenv.2023.167443
82. Zheng, X, Leung, K, Xu, X, Yu, D, Zhang, Y, Chen, X, et al. Wastewater surveillance provides spatiotemporal SARS-CoV-2 infection dynamics. Engineering. (2024) 1:16. doi: 10.1016/j.eng.2024.01.016
83. Wolken, M, Sun, T, McCall, C, Schneider, R, Caton, K, Hundley, C, et al. Wastewater surveillance of SARS-CoV-2 and influenza in preK-12 schools shows school, community, and citywide infections. Water Res. (2023) 231:119648. doi: 10.1016/j.watres.2023.119648
84. Ahmed, W, Angel, N, Edson, J, Bibby, K, Bivins, A, O'Brien, JW, et al. First confirmed detection of SARS-CoV-2 in untreated wastewater in Australia: a proof of concept for the wastewater surveillance of COVID-19 in the community. Sci Total Environ. (2020) 728:138764. doi: 10.1016/j.scitotenv.2020.138764
85. Xing, Y-H, Ni, W, Wu, Q, Li, W-J, Li, G-J, Wang, W-D, et al. Prolonged viral shedding in feces of pediatric patients with coronavirus disease 2019. J Microbiol Immunol Infect. (2020) 53:473–80. doi: 10.1016/j.jmii.2020.03.021
86. Ali, W, Zhang, H, Wang, Z, Chang, C, Javed, A, Ali, K, et al. Occurrence of various viruses and recent evidence of SARS-CoV-2 in wastewater systems. J Hazard Mater. (2021) 414:125439. doi: 10.1016/j.jhazmat.2021.125439
87. Hasan, SW, Ibrahim, Y, Daou, M, Kannout, H, Jan, N, Lopes, A, et al. Detection and quantification of SARS-CoV-2 RNA in wastewater and treated effluents: surveillance of COVID-19 epidemic in the United Arab Emirates. Sci Total Environ. (2021) 764:142929. doi: 10.1016/j.scitotenv.2020.142929
88. Vo, V, Tillett, RL, Papp, K, Shen, S, Gu, R, Gorzalski, A, et al. Use of wastewater surveillance for early detection of alpha and epsilon SARS-CoV-2 variants of concern and estimation of overall COVID-19 infection burden. Sci Total Enviro. (2022) 835:155410. doi: 10.1016/j.scitotenv.2022.155410
89. Kirby, AE, Welsh, RM, Marsh, ZA, Yu, AT, Vugia, DJ, Boehm, AB, et al. Notes from the field: early evidence of the SARS-CoV-2 B. 1.1. 529 (omicron) variant in community wastewater—United States, November–December 2021. Morb Mortal Wkly Rep. (2022) 71:103–5. doi: 10.15585/mmwr.mm7103a5
90. Yousif, M, Rachida, S, Taukobong, S, Ndlovu, N, Iwu-Jaja, C, Howard, W, et al. SARS-CoV-2 genomic surveillance in wastewater as a model for monitoring evolution of endemic viruses. Nat Commun. (2023) 14:6325. doi: 10.1038/s41467-023-41369-5
91. Hellmér, M, Paxéus, N, Magnius, L, Enache, L, Arnholm, B, Johansson, A, et al. Detection of pathogenic viruses in sewage provided early warnings of hepatitis a virus and norovirus outbreaks. Appl Environ Microbiol. (2014) 80:6771–81. doi: 10.1128/AEM.01981-14
92. Girón-Guzmán, I, Díaz-Reolid, A, Truchado, P, Carcereny, A, García-Pedemonte, D, Hernáez, B, et al. Spanish wastewater reveals the current spread of Monkeypox virus. Water Res. (2023) 231:119621. doi: 10.1016/j.watres.2023.119621
93. Sharkey, ME, Babler, KM, Shukla, BS, Abelson, SM, Alsuliman, B, Amirali, A, et al. Monkeypox viral nucleic acids detected using both DNA and RNA extraction workflows. Sci Total Environ. (2023) 890:164289. doi: 10.1016/j.scitotenv.2023.164289
94. Shrestha, S, Da Silva, KE, Shakya, J, Yu, AT, Katuwal, N, Shrestha, R, et al. Detection of Salmonella Typhi bacteriophages in surface waters as a scalable approach to environmental surveillance. PLoS Negl Trop Dis. (2024) 18:e0011912. doi: 10.1371/journal.pntd.0011912
95. Rechenburg, A, and Kistemann, T. Sewage effluent as a source of Campylobacter sp. in a surface water catchment. Int J Environ Health Res. (2009) 19:239–49. doi: 10.1080/09603120802460376
96. Diemart, S, and Yan, T. Clinically unreported salmonellosis outbreak detected via comparative genomic analysis of municipal wastewater Salmonella isolates. Appl Environ Microbiol. (2019) 85:e00139–19. doi: 10.1128/AEM.00139-19
97. Barrett, TJ, Blake, PA, Morris, GK, Puhr, ND, Bradford, HB, and Wells, JG. Use of Moore swabs for isolating Vibrio cholerae from sewage. J Clin Microbiol. (1980) 11:385–8. doi: 10.1128/jcm.11.4.385-388.1980
98. Zohra, T, Ikram, A, Salman, M, Amir, A, Saeed, A, Ashraf, Z, et al. Wastewater based environmental surveillance of toxigenic Vibrio cholerae in Pakistan. PLoS One. (2021) 16:e0257414. doi: 10.1371/journal.pone.0257414
99. Razzolini, MTP, da Silva Santos, TF, and Bastos, VK. Detection of Giardia and Cryptosporidium cysts/oocysts in watersheds and drinking water sources in Brazil urban areas. J Water Health. (2010) 8:399–404. doi: 10.2166/wh.2009.172
100. Amoah, ID, Reddy, P, Seidu, R, and Stenström, TA. Removal of helminth eggs by centralized and decentralized wastewater treatment plants in South Africa and Lesotho: health implications for direct and indirect exposure to the effluents. Environ Sci Pollut Res. (2018) 25:12883–95. doi: 10.1007/s11356-018-1503-7
101. Mara, DD, and Sleigh, A. Understanding and updating the 2006 WHO guidelines for the safe use of wastewater in agriculture. (2009).
102. Church, DL. Major factors affecting the emergence and re-emergence of infectious diseases. Clin Lab Med. (2004) 24:559–86. doi: 10.1016/j.cll.2004.05.008
103. Mao, D, Yu, S, Rysz, M, Luo, Y, Yang, F, Li, F, et al. Prevalence and proliferation of antibiotic resistance genes in two municipal wastewater treatment plants. Water Res. (2015) 85:458–66. doi: 10.1016/j.watres.2015.09.010
104. Sun, Y, Shen, Y, Liang, P, Zhou, J, Yang, Y, and Huang, X. Multiple antibiotic resistance genes distribution in ten large-scale membrane bioreactors for municipal wastewater treatment. Bioresour Technol. (2016) 222:100–6. doi: 10.1016/j.Biortech.2016.09.117
105. Caucci, S, Karkman, A, Cacace, D, Rybicki, M, Timpel, P, Voolaid, V, et al. Seasonality of antibiotic prescriptions for outpatients and resistance genes in sewers and wastewater treatment plant outflow. FEMS Microbiol Ecol. (2016) 92:60. doi: 10.1093/femsec/fiw060
106. Hutinel, M, Huijbers, PMC, Fick, J, Åhrén, C, Larsson, DGJ, and Flach, C-F. Population-level surveillance of antibiotic resistance in Escherichia coli through sewage analysis. Euro Surveill. (2019) 24:37. doi: 10.2807/1560-7917.ES.2019.24.37.1800497
107. Xiao, Y, Shao, X-T, Tan, D-Q, Yan, J-H, Pei, W, Wang, Z, et al. Assessing the trend of diabetes mellitus by analysing metformin as a biomarker in wastewater. Sci Total Environ. (2019) 688:281–7. doi: 10.1016/j.scitotenv.2019.06.117
108. Yan, JH, Xiao, Y, Tan, DQ, Shao, XT, Wang, Z, and Wang, DG. Wastewater analysis reveals spatial pattern in consumption of anti-diabetes drug metformin in China. Chemosphere. (2019) 222:688–95. doi: 10.1016/j.chemosphere.2019.01.151
109. Boogaerts, T, Jurgelaitiene, L, Dumitrascu, C, Kasprzyk-Hordern, B, Kannan, A, Been, F, et al. Application of wastewater-based epidemiology to investigate stimulant drug, alcohol and tobacco use in Lithuanian communities. Sci Total Environ. (2021) 777:145914. doi: 10.1016/j.scitotenv.2021.145914
110. Bowers, I, and Subedi, B. Isoprostanes in wastewater as biomarkers of oxidative stress during COVID-19 pandemic. Chemosphere. (2021) 271:129489. doi: 10.1016/j.chemosphere.2020.129489
111. Moore, B. The detection of paratyphoid carriers in towns by means of sewage examination. Mon Bull Minist Health Public Health Lab Serv. (1948) 7:241.
112. Moore, B. Typhoid: epidemiological investigation and control measures. Public Health. (1971) 85:152–8. doi: 10.1016/s0033-3506(71)80054-9
113. Sikorski, MJ, and Levine, MM. Reviving the Moore swab: a classic environmental surveillance tool involving filtration of flowing surface water and sewage water to recover typhoidal Salmonella bacteria. Appl Environ Microbiol. (2020) 86:e00060–20. doi: 10.1128/AEM.00060-20
114. Moore, B. The detection of enteric cancers in towns by means of sewage examination. J R Sanit Inst. (1951) 71:57–60. doi: 10.1177/146642405107100109
115. Liu, P, Ibaraki, M, VanTassell, J, Geith, K, Cavallo, M, Kann, R, et al. A novel COVID-19 early warning tool: Moore swab method for wastewater surveillance at an institutional level. MedRxiv. (2020) 2020:151047. doi: 10.1016/j.scitotenv.2021.151047
116. Sbodio, A, Maeda, S, Lopez-Velasco, G, and Suslow, TV. Modified Moore swab optimization and validation in capturing E. coli O157: H7 and Salmonella enterica in large volume field samples of irrigation water. Food Res Int. (2013) 51:654–62. doi: 10.1016/j.foodres.2013.01.011
117. McEgan, R, Rodrigues, CAP, Sbodio, A, Suslow, TV, Goodridge, LD, and Danyluk, MD. Detection of Salmonella spp. from large volumes of water by modified Moore swabs and tangential flow filtration. Lett Appl Microbiol. (2013) 56:88–94. doi: 10.1111/lam.12016
118. Hobbs, FB. Tracing a typhoid carrier by means of sewer swabs. Lancet. (1956) 267:855–6. doi: 10.1016/s0140-6736(56)91319-8
119. Greenberg, AE, Wickenden, RW, and Lee, TW. Tracing typhoid carriers by means of sewage. Sewage Ind Waste. (1956) 29:1237–42.
120. Shearer, LA, Browne, AS, Gordon, RB, and Hollister, AC. Discovery of typhoid carrier by sewage sampling. JAMA. (1959) 169:1051–5. doi: 10.1001/jama.1959.03000270033008
121. Rafiee, M, Isazadeh, S, Mohseni-Bandpei, A, Mohebbi, SR, Jahangiri-rad, M, Eslami, A, et al. Moore swab performs equal to composite and outperforms grab sampling for SARS-CoV-2 monitoring in wastewater. Sci Total Environ. (2021) 790:148205. doi: 10.1016/j.scitotenv.2021.148205
122. Amereh, F, Negahban-Azar, M, Isazadeh, S, Dabiri, H, Masihi, N, Jahangiri-rad, M, et al. Sewage systems surveillance for SARS-CoV-2: identification of knowledge gaps, emerging threats, and future research needs. Pathogens. (2021) 10:946. doi: 10.3390/pathogens10080946
123. Augusto, MR, Claro, ICM, Siqueira, AK, Sousa, GS, Caldereiro, CR, Duran, AFA, et al. Sampling strategies for wastewater surveillance: evaluating the variability of SARS-COV-2 RNA concentration in composite and grab samples. J Environ Chem Eng. (2022) 10:107478. doi: 10.1016/j.jece.2022.107478
124. Cristóvão, MB, Bento-Silva, A, Bronze, MR, Crespo, JG, and Pereira, VJ. Detection of anticancer drugs in wastewater effluents: grab versus passive sampling. Sci Total Environ. (2021) 786:147477. doi: 10.1016/j.scitotenv.2021.147477
125. Lagier, JC, Dubourg, G, Million, M, Cadoret, F, Bilen, M, Fenollar, F, et al. Culturing the human microbiota and culturomics. Nat Rev Microbiol. (2018) 16:540–50. doi: 10.1038/s41579-018-0041-0
126. Ward, RL, Knowlton, DR, and Pierce, MJ. Efficiency of human rotavirus propagation in cell-culture. J Clin Microbiol. (1984) 19:748–53. doi: 10.1128/jcm.19.6.748-753.1984
127. Gilbride, KA, Lee, DY, and Beaudette, LA. Molecular techniques in wastewater: understanding microbial communities, detecting pathogens, and real-time process control. J Microbiol Methods. (2006) 66:1–20. doi: 10.1016/j.mimet.2006.02.016
128. Girones, R, Ferrus, MA, Alonso, JL, Rodriguez-Manzano, J, Calgua, B, Correa Ade, A, et al. Molecular detection of pathogens in water – the pros and cons of molecular techniques. Water Res. (2010) 44:4325–39. doi: 10.1016/j.watres.2010.06.030
129. Fan, H, Wu, Q, and Kou, X. Co-detection of five species of water-borne bacteria by multiplex PCR. Life Sci J. (2008) 5:47–54.
130. Valasek, MA, and Repa, JJ. The power of real-time PCR. Adv Physiol Educ. (2005) 29:151–9. doi: 10.1152/advan.00019.2005
131. Omiccioli, E, Amagliani, G, Brandi, G, and Magnani, M. A new platform for real-time PCR detection of Salmonella spp., listeria monocytogenes and Escherichia coli O157 in milk. Food Microbiol. (2009) 26:615–22. doi: 10.1016/j.fm.2009.04.008
132. Shannon, KE, Lee, DY, Trevors, JT, and Beaudette, LA. Application of real-time quantitative PCR for the detection of selected bacterial pathogens during municipal wastewater treatment. Sci Total Environ. (2007) 382:121–9. doi: 10.1016/j.scitotenv.2007.02.039
133. Masago, Y, Oguma, K, Katayama, H, and Ohgaki, S. Quantification and genotyping of Cryptosporidium spp. in river water by quenching probe PCR and denaturing gradient gel electrophoresis. Water Sci Technol. (2006) 54:119–26. doi: 10.2166/wst.2006.457
134. Bertrand, I, Gantzer, C, Chesnot, T, and Schwartzbrod, J. Improved specificity for Giardia lamblia cyst quantification in wastewater by development of a real-time PCR method. J Microbiol Methods. (2004) 57:41–53. doi: 10.1016/j.mimet.2003.11.016
135. Donaldson, KA, Griffin, DW, and Paul, JH. Detection, quantitation and identification of enteroviruses from surface waters and sponge tissue from the florida keys using real-time RT-PCR. Water Res. (2002) 36:2505–14. doi: 10.1016/S0043-1354(01)00479-1
136. Zhou, J. Microarrays for bacterial detection and microbial community analysis. Curr Opin Microbiol. (2003) 6:288–94. doi: 10.1016/S1369-5274(03)00052-3
137. Trevino, V, Falciani, F, and Barrera-Saldana, HA. DNA microarrays: a powerful genomic tool for biomedical and clinical research. Mol Med. (2007) 13:527–41. doi: 10.2119/2006-00107.Trevino
138. Wilson, WJ, Strout, CL, DeSantis, TZ, Stilwell, JL, Carrano, AV, and Andersen, GL. Sequence-specific identification of 18 pathogenic microorganisms using microarray technology. Mol Cell Probes. (2002) 16:119–27. doi: 10.1006/mcpr.2001.0397
139. Inoue, D, Hinoura, T, Suzuki, N, Pang, J, Malla, R, Shrestha, S, et al. High-throughput DNA microarray detection of pathogenic bacteria in shallow well groundwater in the Kathmandu Valley. Nepal Curr Microbiol. (2015) 70:43–50. doi: 10.1007/s00284-014-0681-x
140. Leski, TA, Lin, B, Malanoski, AP, Wang, Z, Long, NC, Meador, CE, et al. Testing and validation of high density resequencing microarray for broad range biothreat agents detection. PLoS One. (2009) 4:e6569. doi: 10.1371/journal.pone.0006569
141. DeSantis, TZ, Brodie, EL, Moberg, JP, Zubieta, IX, Piceno, YM, and Andersen, GL. High-density universal 16S rRNA microarray analysis reveals broader diversity than typical clone library when sampling the environment. Microb Ecol. (2007) 53:371–83. doi: 10.1007/s00248-006-9134-9
142. Blair, S, Williams, L, Bishop, J, and Chagovetz, A. Microarray temperature optimization using hybridization kinetics. Methods Mol Biol. (2009) 529:171–96. doi: 10.1007/978-1-59745-538-1_12
143. Croner, RS, Lausen, B, Schellerer, V, Zeittraeger, I, Wein, A, Schildberg, C, et al. Comparability of microarray data between amplified and non amplified RNA in colorectal carcinoma. J Biomed Biotechnol. (2009) 2009:7170. doi: 10.1155/2009/837170
144. Amann, R, and Fuchs, BM. Single-cell identification in microbial communities by improved fluorescence in situ hybridization techniques. Nat Rev Microbiol. (2008) 6:339–48. doi: 10.1038/nrmicro1888
145. Lee, J-E, Mun, H, Kim, S-R, Kim, M-G, Chang, J-Y, and Shim, W-B. A colorimetric loop-mediated isothermal amplification (LAMP) assay based on HRP-mimicking molecular beacon for the rapid detection of Vibrio parahaemolyticus. Biosens Bioelectron. (2020) 151:111968. doi: 10.1016/j.bios.2019.111968
146. Sheet, O, Grabowski, N, Klein, G, and Abdulmawjood, A. Development and validation of a loop mediated isothermal amplification (LAMP) assay for the detection of Staphylococcus aureus in bovine mastitis milk samples. Mol Cell Probes. (2016) 30:320–5. doi: 10.1016/j.mcp.2016.08.001
147. Koizumi, N, Nakajima, C, Harunari, T, Tanikawa, T, Tokiwa, T, Uchimura, E, et al. A new loop-mediated isothermal amplification method for rapid, simple, and sensitive detection of Leptospira spp. in urine. J Clin Microbiol. (2012) 50:2072–4. doi: 10.1128/JCM.00481-12
148. Aw, TG, and Rose, JB. Detection of pathogens in water: from phylochips to qPCR to pyrosequencing. Curr Opin Biotechnol. (2012) 23:422–30. doi: 10.1016/j.copbio.2011.11.016
149. Hong, PY, Hwang, C, Ling, F, Andersen, GL, LeChevallier, MW, and Liu, WT. Pyrosequencing analysis of bacterial biofilm communities in water meters of a drinking water distribution system. Appl Environ Microbiol. (2010) 76:5631–5. doi: 10.1128/AEM.00281-10
150. Ibekwe, AM, Leddy, M, and Murinda, SE. Potential human pathogenic bacteria in a mixed urban watershed as revealed by pyrosequencing. PLoS One. (2013) 8:e79490. doi: 10.1371/journal.pone.0079490
151. Allegra, S, Berger, F, Berthelot, P, Grattard, F, Pozzetto, B, and Riffard, S. Use of flow cytometry to monitor Legionella viability. Appl Environ Microbiol. (2008) 74:7813–6. doi: 10.1128/AEM.01364-08
152. Wade, M, Lo Jacomo, A, Armenise, E, Brown, MR, Bunce, JT, Cameron, GJ, et al. Understanding and managing uncertainty and variability for wastewater monitoring beyond the pandemic: lessons learned from the United Kingdom national COVID-19 surveillance programmes. J Hazard Mater. (2022) 424:127456. doi: 10.1016/j.jhazmat.2021.127456
153. Bonadonna, L, Briancesco, R, and La Rosa, G. Innovative analytical methods for monitoring microbiological and virological water quality. Micro Chem J. (2019) 150:104160. doi: 10.1016/j.microc.2019.104160
154. Lee, DY, Leung, KT, Lee, H, and Habash, MB. Simultaneous detection of selected enteric viruses in water samples by multiplex quantitative PCR. Water Air Soil Pollut. (2016) 227:107. doi: 10.1007/s11270-016-2811-5
155. Monteiro, S, and Santos, R. Enzymatic and viability RT-qPCR assays for evaluation of enterovirus, hepatitis a virus and norovirus inactivation: implications for public health risk assessment. J Appl Microbiol. (2018) 124:965–76. doi: 10.1111/jam.13568
156. Hart, OE, and Halden, RU. Computational analysis of SARS-CoV-2/COVID-19 surveillance by wastewater-based epidemiology locally and globally: feasibility, economy, opportunities and challenges. Sci Total Environ. (2020) 730:138875. doi: 10.1016/j.scitotenv.2020.138875
157. Treangen, TJ, and Salzberg, SL. Repetitive DNA and next-generation sequencing: computational challenges and solutions. Nat Rev Genet. (2012) 13:36–46. doi: 10.1038/nrg3117
158. Quainoo, S, Coolen, JPM, van Hijum, SAFT, Huynen, MA, Melchers, WJG, van Schaik, W, et al. Whole-genome sequencing of bacterial pathogens: the future of nosocomial outbreak analysis. Clin Microbiol Rev. (2017) 30:1015–63. doi: 10.1128/CMR.00016-17
159. Mahfouz, N, Caucci, S, Achatz, E, Semmler, T, Guenther, S, Berendonk, TU, et al. High genomic diversity of multi-drug resistant wastewater Escherichia coli. Sci Rep. (2018) 8:1–12. doi: 10.1038/s41598-018-27292-6
160. Mbanga, J, Amoako, DG, Abi, AL, Fatoba, D, and Essack, S. Whole genome sequencing reveals insights into antibiotic resistant Klebsiella grimontii novel sequence type ST350 isolated from a wastewater source in South Africa. J Biotech Res. (2022) 13:40–5.
161. Feng, S, Owens, SM, Shrestha, A, Poretsky, R, Hartmann, EM, and Wells, G. Intensity of sample processing methods impacts wastewater SARS-CoV-2 whole genome amplicon sequencing outcomes. Sci Total Environ. (2023) 876:162572. doi: 10.1016/j.scitotenv.2023.162572
162. McElvania TeKippe, E, and Burnham, C-AD. Evaluation of the Bruker Biotyper and VITEK MS MALDI-TOF MS systems for the identification of unusual and/or difficult-to-identify microorganisms isolated from clinical specimens. Eur J Clin Microbiol Infect Dis. (2014) 33:2163–71. doi: 10.1007/s10096-014-2183-y
163. Patel, R. MALDI-TOF MS for the diagnosis of infectious diseases. Clin Chem. (2015) 61:100–11. doi: 10.1373/clinchem.2014.221770
164. J, L, and Jackson, O. MALDI-TOF mass spectrometry of bacteria. Mass Spectrom Rev. (2001) 20:172–94. doi: 10.1002/mas.10003
165. Eddabra, R, Moussaoui, W, Prévost, G, Delalande, F, van Dorsselaer, A, Meunier, O, et al. Occurrence of Vibrio cholerae non-O1 in three wastewater treatment plants in Agadir (Morocco). World J Microbiol Biotechnol. (2011) 27:1099–108. doi: 10.1007/s11274-010-0556-7
166. Bronzato, GF, Oliva, MS, Alvin, MG, Pribul, BR, Rodrigues, DP, Coelho, SMO, et al. MALDI-TOF MS as a tool for the identification of Vibrio alginolyticus from Perna perna mussels (Linnaeus, 1758). Pesqui. Vet. Bras. (2018) 38:1511–7. doi: 10.1590/1678-5150-pvb-5233
167. Croxatto, A, Prod'hom, G, and Greub, G. Applications of MALDI-TOF mass spectrometry in clinical diagnostic microbiology. FEMS Microbiol Rev. (2012) 36:380–407. doi: 10.1111/j.1574-6976.2011.00298.x
168. Nachtigall, FM, Pereira, A, Trofymchuk, OS, and Santos, LS. Detection of SARS-CoV-2 in nasal swabs using MALDI-MS. Nat Biotechnol. (2020) 38:1168–73. doi: 10.1038/s41587-020-0644-7
169. Rybicka, M, Miłosz, E, and Bielawski, KP. Superiority of MALDI-TOF mass spectrometry over real-time PCR for SARS-CoV-2 RNA detection. Viruses. (2021) 13:730. doi: 10.3390/v13050730
170. Gerbersdorf, SU, and Wieprecht, S. Biostabilization of cohesive sediments: revisiting the role of abiotic conditions, physiology and diversity of microbes, polymeric secretion, and biofilm architecture. Geobiology. (2015) 13:68–97. doi: 10.1111/gbi.12115
171. Sutherland, IW. Biofilm exopolysaccharides: a strong and sticky framework. Microbiology. (2001) 147:3–9. doi: 10.1099/00221287-147-1-3
172. Picó, Yolanda, and Campo, Julian. (2022). An overview of the state-of-the-art: mass spectrometry in food and environment. Berlin: Springer, pp. 1–23.
173. Daughton, CG. Using biomarkers in sewage to monitor community-wide human health: isoprostanes as conceptual prototype. Sci Total Environ. (2012) 424:16–38. doi: 10.1016/j.scitotenv.2012.02.038
174. Benedict, KM, Reses, H, Vigar, M, Roth, DM, Roberts, VA, Mattioli, M, et al. Surveillance for waterborne disease outbreaks associated with drinking water—United States, 2013–2014. MMWR Morb Mortal Wkly Rep. (2017) 66:1216–21. doi: 10.15585/mmwr.mm6644a3
175. Ort, C, Banta-Green, CJ, Bijlsma, L, Castiglioni, S, Emke, E, Gartner, C, et al. Sewage-based epidemiology requires a truly transdisciplinary approach. GAIA Ecol Perspect Sci Soc. (2014) 23:266–8. doi: 10.14512/gaia.23.3.12
176. Castiglioni, S, Bijlsma, L, Covaci, A, Emke, E, Hernández, F, Reid, M, et al. Evaluation of uncertainties associated with the determination of community drug use through the measurement of sewage drug biomarkers. Environ Sci Technol. (2013) 47:1452–60. doi: 10.1021/es302722f
177. Been, F, Rossi, L, Ort, C, Rudaz, S, Delémont, O, and Esseiva, P. Population normalization with ammonium in wastewater-based epidemiology: application to illicit drug monitoring. Environ Sci Technol. (2014) 48:8162–9. doi: 10.1021/es5008388
178. Van Nuijs, ALN, Mougel, JF, Tarcomnicu, I, Bervoets, L, Blust, R, Jorens, PG, et al. Sewage epidemiology — a real-time approach to estimate the consumption of illicit drugs in Brussels. Belgium Environ Int. (2011) 37:612–21. doi: 10.1016/j.envint.2010.12.006
179. Zhao, X, Lin, CW, Wang, J, and Oh, DH. Advances in rapid detection methods for foodborne pathogens. J Microbiol Biotechnol. (2014) 24:297–312. doi: 10.4014/jmb.1310.10013
180. Straub, TM, and Chandler, DP. Towards a unified system for detecting waterborne pathogens. J Microbiol Methods. (2003) 53:185–97. doi: 10.1016/S0167-7012(03)00023-X
181. Kostic, T, Stessl, B, Wagner, M, and Sessitsch, A. Microarray analysis reveals the actual specificity of enrichment media used for food safety assessment. J Food Prot. (2011) 74:1030–4. doi: 10.4315/0362-028X.JFP-10-388
182. Shrestha, S, Yoshinaga, E, Chapagain, SK, Mohan, G, Gasparatos, A, and Fukushi, K. Wastewater-based epidemiology for cost-effective mass surveillance of COVID-19 in Low-and middle-income countries: challenges and opportunities. Water. (2021) 13:2897. doi: 10.3390/w13202897
183. Sims, N, and Kasprzyk-Hordern, B. Future perspectives of wastewater-based epidemiology: monitoring infectious disease spread and resistance to the community level. Environ Int. (2020) 139:105689. doi: 10.1016/j.envint.2020.105689
184. Sano, D, Watanabe, T, Matsuo, T, and Omura, T. Detection of infectious pathogenic viruses in water and wastewater samples from urbanised areas. Water Sci Technol. (2004) 50:247–51. doi: 10.2166/wst.2004.0062
Keywords: wastewater surveillance, infectious disease, pathogens, detection methods, challenges, public health, epidemiology
Citation: Singh S, Ahmed AI, Almansoori S, Alameri S, Adlan A, Odivilas G, Chattaway MA, Salem SB, Brudecki G and Elamin W (2024) A narrative review of wastewater surveillance: pathogens of concern, applications, detection methods, and challenges. Front. Public Health. 12:1445961. doi: 10.3389/fpubh.2024.1445961
Edited by:
Jessica L. Jones, United States Food and Drug Administration, United StatesReviewed by:
Bhupinder Kaur, Akal Degree College Mastuana, IndiaIoannis Adamopoulos, Hellenic Republic Region of Attica, Greece
Copyright © 2024 Singh, Ahmed, Almansoori, Alameri, Adlan, Odivilas, Chattaway, Salem, Brudecki and Elamin. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
*Correspondence: Wael Elamin, welamin@m42.ae