Timothy Ryan Julian

• Ph.D.
• Swiss Federal Institute of Aquatic Science and Technology

Successful wastewater-based infectious disease surveillance programs depend on regular, reliable molecular detection of nucleic acids in municipal wastewater systems. This process is challenged by the gradual degradation of the viral content of the wastewater over time. Testing protocols are complex and often cannot be performed on site, resulting...

Measles outbreaks remain a significant public health challenge, despite high vaccination coverage in many regions. Wastewater-based surveillance (WBS) offers a noninvasive and community-level approach to monitoring the circulation of pathogens, including the measles virus. Here, we retrospectively applied a duplex digital PCR assay to distinguish b...

Wastewater as a medium contains information on both circulating pathogens and drug consumption at the population level. This study combines tracking of respiratory viruses and quantification of pharmaceuticals as untargeted indicators of symptoms related to acute respiratory infections and influenza-like illnesses such as coughing, fever and pain....

Noroviruses and enteroviruses are major causes of endemic gastrointestinal disease associated with substantial disease burden. However, viral gastroenteritis is often diagnosed based on symptoms, with etiology infrequently tested or reported, so little information exists on community-level transmission dynamics. In this study, we demonstrate that n...

Monkeypox virus (MPXV) is a zoonotic pathogen that has recently caused outbreaks in non-endemic areas. Wastewater-based surveillance (WBS) offers substantial potential for monitoring MPVX clades, and it can inform population-level disease dynamics. Here, we report a four-plex digital PCR assay to detect and quantify different clades and subclades o...

Influenza A virus poses significant public health challenges, causing seasonal outbreaks and pandemics. Its rapid evolution motivates continuous monitoring of circulating influenza genomes to inform vaccine and antiviral development. Wastewater-based surveillance offers an unbiased, cost-effective approach for genomic surveillance. We developed a n...

As more data on virus concentrations in influent water from wastewater treatment plants (WWTPs) becomes available, establishing best practices for virus measurements, monitoring, and statistical modelling can improve the understanding of virus concentration distributions in wastewater. To support this, we assessed the temporal variability of norovi...

Measles outbreaks remain a significant public health challenge despite high vaccination coverage in many regions. Wastewater-based surveillance (WBS) offers a non-invasive and community-level approach to monitoring the circulation of pathogens, including the measles virus. Here, we retrospectively applied a duplex digital PCR assay to distinguish b...

Respiratory Syncytial Virus (RSV) infections pose a substantial health burden, especially for vulnerable populations such as infants and the elderly. While novel immunoprophylaxis offer promising protection, many countries lack robust surveillance systems to monitor circulating RSV lineages and detect mutations that might compromise the effectivene...

Monkeypox virus (MPXV) is a zoonotic pathogen that has recently caused outbreaks in non-endemic areas. Wastewater-based surveillance (WBS) offers substantial potential for monitoring MPVX clades, and it can inform population-level disease dynamics. Here, we report a four-plex digital PCR assay to detect and quantify different clades and subclades o...

Inhalation of aerosols produced during showering exposes people to chemical and microbial contaminants present in the water. To improve quantitative estimates of exposure and to inform the efficacy of potential interventions to reduce exposures, we conducted empirical measurements of aerosol concentration and size distribution during showering even...

Quantitative PCR (qPCR) and digital PCR (dPCR) are applied for quantifying molecular targets in disease diagnostics, pathogen detection and ecological monitoring. Uptake of dPCR is increasing due to its higher quantification accuracy relative to qPCR which stems from its independence from standard curves and its increased resistance to PCR inhibito...

Wastewater-based surveillance systems can track trends in multiple pathogens simultaneously by leveraging efficient, streamlined laboratory processing. In Switzerland, wastewater surveillance is conducted for fourteen locations representing 2.3 million people, or 26% of the national population, with simultaneous surveillance of four respiratory pat...

The growing field of wastewater-based infectious disease surveillance relies on the quantification of pathogen concentrations in wastewater using polymerase chain reaction (PCR) techniques. However, existing models for monitoring pathogen spread using wastewater have often been adapted from methods for case count data and neglect the statistical fe...

Wastewater-based surveillance is widely used for the detection and tracking of priority respiratory pathogens. In this study, pharmaceuticals are tracked in wastewater as an untargeted indicator of symptoms related to acute respiratory infections and influenza-like illnesses, such as coughing, fever, and pain, coincident to respiratory viral loads....

Wastewater-based epidemiology offers a complementary approach to clinical case-based surveillance of emergent diseases and can help identify regions with infected people to prioritize clinical surveillance strategies. However, tracking emergent diseases in wastewater requires reliance on novel testing assays with uncertain sensitivity and specifici...

Wastewater-based epidemiology has proven to be an important public health asset during the COVID-19 pandemic. It can provide less biassed and more cost-effective population-level monitoring of the disease burden as compared to clinical testing. An essential component of SARS-CoV-2 wastewater monitoring is next-generation sequencing, providing genom...

The coronavirus disease 2019 pandemic highlighted the need for more rapid and routine application of modeling approaches such as quantitative microbial risk assessment (QMRA) for protecting public health. QMRA is a transdisciplinary science dedicated to understanding, predicting, and mitigating infectious disease risks. To better equip QMRA researc...

Background: Respiratory tract infections are major contributors to the global disease burden. Quantitative microbial risk assessment (QMRA) holds potential as a rapidly deployable framework to understand respiratory pathogen transmission and inform policy on infection control. Objectives: The goal of this paper was to evaluate, motivate, and inf...

Quantitative polymerase chain reaction (qPCR) offers a rapid, automated, and potentially on-site method for quantifying L. pneumophila in building potable water systems, complementing and potentially replacing traditional culture-based techniques. However, the application of qPCR in assessing human health risks is complicated by its tendency to ove...

Greywater reuse is a strategy to address water scarcity, necessitating the selection of treatment processes that balance cost-efficiency and human health risks. A key aspect in evaluating these risks is understanding pathogen contamination levels in greywater, a complex task due to intermittent pathogen occurrences. To address this, faecal indicato...

AIM OF THE STUDY: The COVID-19 pandemic has drawn attention to the benefit of wastewater-based epidemiology, particularly when case numbers are underreported. Underreporting may be an issue with mpox, where biological reasons and stigma may prevent patients from getting tested. Therefore, we aimed to assess the validity of wastewater surveillance f...

INTRODUCTION: Influenza infections are challenging to monitor at the population level due to many mild and asymptomatic cases and similar symptoms to other common circulating respiratory diseases, including COVID-19. Methods for tracking cases outside of typical reporting infrastructure could improve monitoring of influenza transmission dynamics. I...

The COVID-19 pandemic has accelerated the development and adoption of wastewater-based epidemiology. Wastewater samples can provide genomic information for detecting and assessing the spread of SARS-CoV-2 variants in communities and for estimating important epidemiological parameters such as the growth advantage of the variant. However, despite dem...

Basic local-alignment search tool (BLAST) is a versatile and commonly used sequence analysis tool in bioinformatics. BLAST permits fast and flexible sequence similarity searches across nucleotide and amino acid sequences, leading to diverse applications such as protein domain identification, orthology searches, and phylogenetic annotation. Most BLA...

Background: Antimicrobial resistance (AMR) poses a global health threat, causing millions of deaths annually, with expectations of increased impact in the future. Wastewater surveillance offers a cost-effective, non-invasive tool to understand AMR carriage trends within a population. Aim: We monitored extended-spectrum β-lactamase producing Escheri...

The COVID-19 pandemic has accelerated the development and adoption of wastewater-based epidemiology. Wastewater samples can provide genomic information for detecting and assessing the spread of SARS-CoV-2 variants in communities and for estimating important epidemiological parameters such as the growth advantage of the variant. However, despite dem...

[This corrects the article DOI: 10.1371/journal.ppat.1010952.].

Preventing failures of water treatment barriers can play an important role in meeting the increasing demand for microbiologically safe water. The development and integration of failure prevention strategies into quantitative microbial risk assessment (QMRA) offer opportunities to support the design and operation of treatment trains. This study pres...

Influenza infections are challenging to monitor at the population level due to a high proportion of mild and asymptomatic cases and confounding of symptoms with other common circulating respiratory diseases, including COVID-19. Alternate methods capable of tracking cases outside of clinical reporting infrastructure could improve monitoring of influ...

United Nations Sustainable Development Goal 6.3 aims to half the proportion of untreated wastewater and increase recycling and safe water reuse. Therefore, developing robust technologies to achieve these goals, specifically...

Antibiotic resistance is a leading cause of hospitalization and death worldwide. Heavy metals such as arsenic have been shown to drive co-selection of antibiotic resistance, suggesting arsenic-contaminated drinking water is a risk factor for antibiotic resistance carriage. This study aimed to determine the prevalence and abundance of antibiotic-res...

Widespread implementation of on-site water reuse systems is hindered by the limited ability to ensure the level of treatment and protection of human health during operation. In this study, we tested the ability of five commercially available online sensors (free chlorine (FC), oxidation-reduction potential (ORP), pH, turbidity, UV absorbance at 254...

Waterborne enteric viruses in lakes, especially at recreational water sites, may have a negative impact on human health. However, their fate and transport in lakes are poorly understood. In this study, we propose a coupled water quality and quantitative microbial risk assessment (QMRA) model to study the transport, fate and infection risk of four c...

The continuing emergence of SARS-CoV-2 variants of concern and variants of interest emphasizes the need for early detection and epidemiological surveillance of novel variants. We used genomic sequencing of 122 wastewater samples from three locations in Switzerland to monitor the local spread of B.1.1.7 (Alpha), B.1.351 (Beta) and P.1 (Gamma) varian...

Wastewater-based epidemiology (WBE) has emerged as an effective tool for monitoring SARS-CoV-2 dynamics during the COVID-19 pandemic. Here, we add a spatial component to WBE and use it to investigate SARS-CoV-2 spread in the canton of Ticino during the onset of the pandemic in Switzerland (end of February 2020 to beginning of March 2020). Ticino is...

Background Designing oligonucleotide primers and probes is one of the key steps of various laboratory experiments such as multiplexed PCR or digital multiplexed ligation assays. When designing multiplexed primers and probes to complex, heterogeneous DNA data sets, an optimization problem can arise where the smallest number of oligonucleotides cover...

Healthy development of the gut microbiome provides long-term health benefits. Children raised in countries with high infectious disease burdens are frequently exposed to diarrhoeal pathogens and antibiotics, which perturb gut microbiome assembly. A recent cluster-randomized trial leveraging >4,000 child observations in Dhaka, Bangladesh, found that...

Background: The effective reproductive number, Re, is a critical indicator to monitor disease dynamics, inform regional and national policies, and estimate the effectiveness of interventions. It describes the average number of new infections caused by a single infectious person through time. To date, Re estimates are based on clinical data such as...

Background Water, sanitation, and hygiene (WASH) services have the potential to interrupt transmission of antimicrobial-resistant bacteria and reduce the need for antibiotics, thereby reducing selection for resistance. However, evidence of WASH impacts on antimicrobial resistance (AMR) is lacking. Methods We evaluated extended-spectrum beta-lactam...

During the first wave of the COVID-19 pandemic, widespread clinical testing was unavailable in Switzerland. Researchers developed a robust, reproducible, and reliable method of accurately tracking SARS-CoV-2 RNA genome fragments in wastewater.

Background Throughout the COVID-19 pandemic, SARS-CoV-2 genetic variants of concern (VOCs) have repeatedly and independently arisen. VOCs are characterised by increased transmissibility, increased virulence or reduced neutralisation by antibodies obtained from prior infection or vaccination. Tracking the introduction and transmission of VOCs relies...

The prevalence of fecal colonization with extended-spectrum β-lactamase-producing Escherichia coli (ESBL-Ec) among children in low- and middle-income countries is alarmingly high. This study aimed to identify the sources of ESBL-Ec colonization in children < 1 year old through comparative analysis of E. coli isolates from child stool, child’s mothe...

The objective of the Reducing Enteropathy, Undernutrition, and Contamination in the Environment (REDUCE) program is to identify exposure pathways to fecal pathogens that are significant contributors to morbidity among young children in the Democratic Republic of the Congo (DRC), and on developing and evaluating scalable interventions to reduce feca...

Background The effective reproductive number, Re, is a critical indicator to monitor disease dynamics, inform regional and national policies, and estimate the effectiveness of interventions. It describes the average number of new infections caused by a single infectious person through time. To date, Re estimates are based on clinical data such as o...

Opportunistic pathogens can linger on surfaces in hospital and building plumbing environments, leading to infections in at-risk populations. Further, biofilm-associated bacteria are protected from removal and inactivation protocols, such as disinfection. Bacteriophages show promise as tools to treat antibiotic resistant infections. As such, phages...

Throughout the global COVID-19 pandemic, SARS-CoV-2 genetic variants of concern (VOCs) have repeatedly and independently arisen. VOCs are characterized by increased transmissibility, increased virulence, or reduced neutralization by antibodies obtained from prior infection or vaccination. Tracking the introduction and transmission of VOCs relies on...

Wastewater-based epidemiology (WBE) has been shown to coincide with, or anticipate, confirmed COVID-19 case numbers. During periods with high test positivity rates, however, case numbers may be underreported, whereas wastewater does not suffer from this limitation. Here we investigated how the dynamics of new COVID-19 infections estimated based on...

Wastewater-based epidemiology (WBE) has been shown to coincide with, or anticipate, confirmed COVID-19 case numbers. During periods with high test positivity rates, however, case numbers may be underreported, whereas wastewater does not suffer from this limitation. Here we investigated how the dynamics of new COVID-19 infections estimated based on...

The SARS-CoV-2 lineages B.1.1.7 and 501.V2, which were first detected in the United Kingdom and South Africa, respectively, are spreading rapidly in the human population. Thus, there is an increased need for genomic and epidemiological surveillance in order to detect the strains and estimate their abundances. Here, we report a genomic analysis of S...

SARS-CoV-2, the virus responsible for the COVID-19 pandemic, is perceived to be primarily transmitted via person-to-person contact through droplets produced while talking, coughing, and sneezing. Transmission may also occur through other routes, including contaminated surfaces; nevertheless, the role that surfaces have on the spread of the disease...

Objective The Reducing Enteropathy, Undernutrition, and Contamination in the Environment (REDUCE) program focuses on identifying exposure pathways to faecal pathogens for young children in the Democratic Republic of the Congo (DRC) and on developing scalable interventions to reduce faecal contamination from these pathways. Methods A prospective co...

Environmental surveillance of surface contamination is an unexplored tool for understanding transmission of SARS-CoV-2 in community settings. We conducted longitudinal swab sampling of high-touch non-porous surfaces in a Massachusetts town during a COVID-19 outbreak from April to June 2020. Twenty-nine of 348 (8.3%) surface samples were positive fo...

SARS-CoV-2, the virus responsible for the COVID-19 pandemic, is perceived to be primarily transmitted via person-to-person contact, through droplets produced while talking, coughing, and sneezing. Transmission may also occur through other routes, including contaminated surfaces; nevertheless, the role that surfaces have on the spread of the disease...

Environmental surveillance of surface contamination is an unexplored tool for understanding transmission of SARS-CoV-2 in community settings. We conducted longitudinal swab sampling of high-touch non-porous surfaces in a Massachusetts town during a COVID-19 outbreak from April to June 2020. Twenty-nine of 348 (8.3 %) surface samples were positive f...

The frequent contact people have with liquids containing pathogenic microorganisms provides opportunities for disease transmission. In this work, we quantified the transfer of bacteria—using E. coli as a model- from liquid to skin, estimated liquid retention on the skin after different contact activities (hand immersion, wet-cloth and wet-surface c...

Background The increase in antimicrobial resistance is of worldwide concern. Surrogate tracers attempt to simulate microbial transmission by avoiding the infectious risks associated with live organisms. We evaluated silica nanoparticles with encapsulated DNA (SPED) as a new promising surrogate tracer in healthcare. Methods SPED and Escherichia col...

Sunlight, temperature, and microbial grazing are among the environmental factors promoting the inactivation of viral pathogens in surface waters. Globally, these factors vary across time and space. The persistence of viral pathogens, and ultimately their ecology and dispersion, hinges on their ability to withstand the environmental conditions encou...

Current microbial exposure models assume that microbial exchange follows a concentration gradient during hand-to-surface contacts. Our objectives were to evaluate this assumption using transfer efficiency experiments and to evaluate a model's ability to explain concentration changes using approximate Bayesian computation (ABC) on these experimental...

Antimicrobial resistance (AMR) is a growing public health challenge that is expected to disproportionately burden lower- and middle-income countries (LMICs) in the coming decades. Although the contributions of human and veterinary antibiotic misuse to this crisis are well-recognized, environmental transmission (via water, soil or food contaminated...

A leading challenge in drinking water treatment is to remove small-sized viruses from the water in a simple and efficient manner. Multi-walled carbon nanotubes (MWCNT) are new generation adsorbents with previously demonstrated potential as filter media to improve virus removal. This study therefore aimed to evaluate the field applicability of MWCNT...

Increasing incidence of antibiotic resistance in clinical and environmental settings calls for increased scalability in their surveillance. Current screening technologies are limited by the number of samples and genes that can easily be screened. We demonstrate here digital multiplex ligation assay (dMLA) as a low-cost targeted genomic detection wo...

Background Infectious diseases can be transmitted via fomites (contaminated surfaces/objects); disinfection can interrupt this transmission route. However, disinfection guidelines for low-resource outbreak settings are inconsistent and not evidence-based. Methods A systematic review of surface disinfection efficacy studies was conducted to inform...

Both multi-walled carbon nanotubes (MWCNTs) and metal or metal oxides have demonstrated virus removal efficacy in drinking water applications. In this study, MWCNTs were coated with copper(I) oxide (Cu2O) using three distinct synthesis procedures (copper ion attachment, copper hydroxide precipitation, and [Cu(NH3)4]²⁺ complex attachment) and virus...

Background The increase in antimicrobial resistance is of worldwide concern. Surrogate tracers attempt to simulate microbial transmission by avoiding the infectious risks associated with live organisms. We evaluated silica nanoparticles with encapsulated DNA (SPED) as a new promising surrogate tracer in healthcare.MethodsSPED and Escherichia coli w...

Background: The increase in antimicrobial resistance is of worldwide concern. Surrogate tracers attempt to simulate microbial transmission by avoiding the infectious risks associated with live organisms. We evaluated silica nanoparticles with encapsulated DNA (SPED) as a new promising surrogate tracer in healthcare. Methods: SPED and Escherichia co...

Enteric viruses, such as enterovirus, norovirus, and rotavirus are among the leading causes of disease outbreaks due to contaminated drinking and recreational water. Viruses are difficult to remove from water through filtration based on physical size exclusion – for example by gravity driven filters - due to their nanoscale size. To understand viru...

Escherichia coli is reported in high levels in household soil in low-income settings. When E. coli reaches a soil environment, different mechanisms, including survival, clonal expansion, and genetic exchange, have the potential to either maintain or generate E. coli variants with capabilities of causing harm to people. In this study, we used whole-...

Leptospirosis is a widespread and potentially life-threatening zoonotic disease caused by spirochaetes of the genus Leptospira . Humans become infected primarily via contact with environmental reservoirs contaminated by the urine of shedding mammalian hosts. Populations in high transmission settings, such as urban slums and subsistence farming comm...

Container-based sanitation (CBS) within a comprehensive service system value chain offers a low-cost sanitation option with potential for revenue generation, but may increase microbial health risks to sanitation service workers. This study assessed occupational exposure to rotavirus and Shigella spp. during CBS urine collection and subsequent struv...

Third generation cephalosporins (3GC) are one of the main choices for treatment of infections caused by multidrug-resistant (MDR) Gram-negative bacteria. Due to their overuse, an increasing trend of resistance to 3GC has been observed in developing countries. Here, we describe fecal colonization of 3GC-resistant (3GCr) Escherichia coli in healthy i...

Sustainable Development Goal (SDG) Indicator 6.2.1 requires household handwashing facilities to have soap and water, but there are no guidelines for handwashing water quality. In contrast, drinking water quality guidelines are defined: water must be “free from contamination” to be defined as “safely-managed” (SDG Indicator 6.1.1). . We modeled the...

The assessment of a novel enzyme-based assay showed it to be reliable to detect and quantify E. coli in water.

Soils in household environments in low- and middle-income countries may play an important role in the persistence, proliferation, and transmission of Escherichia coli. Our goal was to investigate the risk factors for detection, survival, and growth of E. coli in soils collected from household plots. E. coli was enumerated in soil and fecal samples...

Enteric viruses (viruses that infect the gastrointestinal tract) are responsible for most water-transmitted diseases. They are shed in high concentrations in the feces of infected individuals, persist for an extended period of time in water, and are highly infective. Exposure to contaminated water directly (through ingestion) or indirectly (for exa...

Advancements in DNA sequencing technologies rapidly change the landscape of modern biology. The novel next-generation sequencing (NGS) applications often have special requirements regarding experimental data processing. Software tools developed and used for novel applications are generally designed for specific use cases and as such may be difficul...

Viral evolutionary pathways are determined by the fitness landscape, which maps viral genotype to fitness. However, a quantitative description of the landscape and the evolutionary forces on it remain elusive. Here, we apply a biophysical fitness model based on capsid folding stability and antibody binding affinity to predict the evolutionary pathw...

Quantitative data on human-environment interactions are needed to fully understand infectious disease transmission processes and conduct accurate risk assessments. Interaction events occur during an individual's movement through, and contact with, the environment, and can be quantified using diverse methodologies. Methods that utilize videography,...

Infectious disease transmission is frequently mediated by the environment, where people's movements through and interactions with the environment dictate risks of infection and/or illness. Capturing these interactions, and quantifying their importance, offers important insights into effective interventions. In this study, we capture high time-resol...

As more countries engage in water reuse, either intended or de facto, there is an urgent need to more comprehensively evaluate resulting environmental and public health concerns. While antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs) are increasingly coming under the spotlight, as emerging contaminants, existing water reus...