Characterization of Salmonella Isolates from Wastewater Treatment Plant Influents to Estimate Unreported Cases and Infection Sources of Salmonellosis

6-plex Crystal Digital PCR® for comprehensive surveillance of respiratory and foodborne bacterial pathogens in wastewater

Bacterial wastewater surveillance (WS) is less explored area compared to viral WS despite high burden of bacterial respiratory and gastrointestinal infections worldwide. This study established a 6-plex Crystal Digital PCR® (cdPCR) system, to comprehensively monitor an acute respiratory pathogen - Group A Streptococcus (GAS) pyogenes, foodborne disease (FBD) pathogens - Clostridium perfringens, Salmonella spp., Campylobacter jejuni, and Campylobacter coli, and an indicator bacterium, Escherichia coli in wastewater. Fifty-two grab influent samples collected weekly from a wastewater treatment plant in Yamanashi Prefecture, Japan, between June 2023 and May 2024 were centrifuged, followed by DNA extraction and cdPCR. cdPCR was performed using the naica® system (Stilla Technologies). The 6-plex cdPCR assays showed strong performance. Among the 52 samples, 100 % of samples were positive for C. perfringens, 98 % for Salmonella spp., 56 % for C. jejuni, 25 % for C. coli, and 63 % for S. pyogenes, with concentrations ranging between 4.2 ± 0.3 to 7.5 ± 0.2 log10 copies/L. The concentration of C. perfringens was significantly higher than that of other pathogens (p < 0.05), indicating its dominance. Salmonella spp. had high detection rate, implying increased Salmonella infection in the population. Seasonal variation was not observed in any of FBD pathogens, except for the detection rate of C. coli. S. pyogenes concentrations were significantly higher in spring than in other seasons, agreeing with the trend of GAS pharyngitis cases in the catchment. In conclusion, the 6-plex cdPCR system is a valuable tool for comprehensive WS, offering significant implications for public health monitoring.

Occurrence of Salmonella enterica in faecal sludge from Nigeria and genetic relatedness with strains associated with human infections in Africa

AIMS

This study investigated occurrence of Salmonella in faecal sludge from public toilets in Nigeria and genetic relatedness of strains that have been reported to cause human infection across Africa.

METHODS AND RESULTS

The study collected 150 human sludge from public toilets and identified Salmonella through culture and PCR. Isolates were tested for antimicrobial susceptibility and sequenced using Illumina MiSeq. Draft sequences were compared with sequence data from Enterobase and GenBank. Twenty-four (16.0%) of sewage samples were positive for Salmonella [CI95 (10.2-21.8)]. Salmonella serotype Give [sequence type (ST) 516], Salmonella serotype Seftenberg (ST-14), and Salmonella serotype Chester (ST-411) were the most prevalent serovars found in 45.8%, 16.7%, and 16.7% of samples, respectively. Most of the isolates were sensitive to the antimicrobials tested, only one isolate of Salmonella serotype Derby showed resistance to ampicillin and cefazolin. Notably, 91.7% of the strains had the aac (6)-Iaa gene and point mutations in parC, gyrA, and acrB. Salmonella serotype Chester showed genetic relatedness with strains from Benin Republic and South Africa.

CONCLUSIONS

There is genetic relatedness of present strains and those associated with human infections in Africa.

Diversity and antimicrobial susceptibility patterns of clinical and environmental Salmonella enterica serovars in Western Saudi Arabia

The diverse environmental distribution of Salmonella makes it a global source of human gastrointestinal infections. This study aimed to detect Salmonella spp. and explore their diversity and antimicrobial susceptibility patterns in clinical and environmental samples. Pre-enrichment, selective enrichment, and selective plating techniques were adopted for the Salmonella detection whereas the API 20E test and Vitek Compact 2 system were used to confirm the identity of isolates. Salmonella serovars were subjected to molecular confirmation by 16S rDNA gene sequencing. Disc diffusion method and Vitek 2 Compact system determined the antibiotic susceptibility of Salmonella serovars. Multiple antibiotic resistance index (MARI) was calculated to explore whether Salmonella serovars originate from areas with heavy antibiotic usage. Results depicted low Salmonella prevalence in clinical and environmental samples (3.5%). The main detected serovars included Salmonella Typhimurium, S. enteritidis, S. Infantis, S. Newlands, S. Heidelberg, S. Indian, S. Reading, and S. paratyphi C. All the detected Salmonella serovars (27) exhibited multidrug resistance to three or more antimicrobial classes. The study concludes that the overall Salmonella serovars prevalence was found to be low in environmental and clinical samples of Western Saudi Arabia (Makkah and Jeddah). However, antimicrobial susceptibility patterns of human and environmental Salmonella serovars revealed that all isolates exhibited multidrug-resistance (MDR) patterns to frequently used antibiotics, which might reflect antibiotic overuse in clinical and veterinary medicine. It would be suitable to apply and enforce rules and regulations from the One Health approach, which aim to prevent antibiotic resistance infections, enhance food safety, and improve human and animal health, given that all Salmonella spp. detected in this investigation were exhibiting MDR patterns.

Monitoring and preventing foodborne outbreaks: are we missing wastewater as a key data source?

In 2022, the number of foodborne outbreaks in Europe increased by 43.9%, highlighting the need to improve surveillance systems and design outbreak predictive tools. This review aims to assess the scientific literature describing wastewater surveillance to monitor foodborne pathogens in association with clinical data. In the selected studies, the relationship between peaks of pathogen concentration in wastewater and reported clinical cases is described. Moreover, details on analytical methods to detect and quantify pathogens as well as wastewater sampling procedures are discussed. Few papers show a statistically significant correlation between high concentrations of foodborne pathogens in wastewater and the occurrence of clinical cases. However, monitoring pathogen concentration in wastewater looks like a promising and cost-effective strategy to improve foodborne outbreak surveillance. Such a strategy can be articulated in three steps, where the first one is testing wastewater with an untargeted method, like shotgun metagenomic, to detect microorganisms belonging to different domains. The second consists of testing wastewater with a targeted method, such as quantitative polymerase chain reaction, to quantify those specific pathogens that in the metagenomic dataset display an increasing trend or exceed baseline concentration thresholds. The third involves the integrated wastewater and clinical data analysis and modeling to find meaningful epidemiological correlations and make predictions.

Simultaneous biomass concentration and subsequent quantitation of multiple infectious disease agents and antimicrobial resistance genes from community wastewater

Wastewater-based surveillance (WBS) of infectious disease agents is increasingly seen as a reliable source of population health data. To date, wastewater-based surveillance efforts have largely focused on individual pathogens. However, given that wastewater contains a broad range of pathogens circulating in the population, a more comprehensive approach could enhance its usability. We focused on the simultaneous detection of SARS-CoV-2, sapovirus, Campylobacter jejuni, Campylobacter coli, Salmonella spp., pathogenic Escherichia coli, Cryptosporidium spp., Giardia spp. and antimicrobial resistance genes (ARGs) of clinical relevance. To achieve this goal, biomass concentration and nucleic acid extraction methods were optimized, and samples were analyzed by using a set of (RT)-qPCR and (HT)-qPCR methods. We determined the prevalence and the spatial and temporal trends of the targeted pathogens and collected novel information on ARGs in Finnish wastewater. In addition, the use of different wastewater concentrates, namely the ultrafiltered concentrate of the supernatant and the centrifuged pellet, and the effect of freezing and thawing wastewater prior to sample processing were investigated with the indicator microbe crAssphage. Freeze-thawing of wastewater decreased the gene copy count of crAssphage in comparison to analyzing fresh samples (p < 0.001). Campylobacters were most abundant in two of the four studied summer months (30 % detection rate) and in wastewaters from regions with intensive animal farming. Salmonella, however, was detected in 40 % of the samples without any clear seasonal trends, and the highest gene copy numbers were recorded from the largest wastewater treatment plants. Beta-lactamase resistance genes that have commonly been detected in bacteria isolated from humans in Finland, namely blaCTX-M, blaOXA48, blaNDM, and blaKPC, were also frequently detected in wastewaters (100, 98, 98, and 70 % detection rates, respectively). These results confirm the reliability of using wastewater in public health surveillance and demonstrate the possibility to simultaneously perform WBS of multiple pathogens.

High-throughput microfluidic quantitative PCR system for the simultaneous detection of antibiotic resistance genes and bacterial and viral pathogens in wastewater

Comprehensive data on bacterial and viral pathogens of diarrhea and studies applying culture-independent methods for examining antibiotic resistance in wastewater are lacking. This study aimed to simultaneously quantify antibiotic resistance genes (ARGs), class 1 integron-integrase (int1), bacterial and viral pathogens of diarrhea, 16S rRNA, and other indicators using a high-throughput quantitative PCR (HT-qPCR) system. Thirty-six grab wastewater samples from a wastewater treatment plant in Japan, collected three times a month between August 2022 and July 2023, were centrifuged, followed by nucleic acid extraction, reverse transcription, and HT-qPCR. Fourteen targets were included, and HT-qPCR was performed on the Biomark X9™ System (Standard BioTools). For all qPCR assays, R2 was ≥0.978 and the efficiencies ranged from 90.5% to 117.7%, exhibiting high performance. Of the 36 samples, 20 (56%) were positive for Norovirus genogroup II (NoV-GII), whereas Salmonella spp. and Campylobacter jejuni were detected in 24 (67%) and Campylobacter coli in 13 (36%) samples, with mean concentrations ranging from 3.2 ± 0.8 to 4.7 ± 0.3 log10 copies/L. NoV-GII detection ratios and concentrations were higher in winter and spring. None of the pathogens of diarrhea correlated with acute gastroenteritis cases, except for NoV-GII, suggesting the need for data on specific bacterial infections to validate bacterial wastewater-based epidemiology (WBE). All samples tested positive for sul1, int1, and blaCTX-M, irrespective of season. The less explored blaNDM-1 showed a wide prevalence (>83%) and consistent abundance ranging from 4.3 ± 1.0 to 4.9 ± 0.2 log10 copies/L in all seasons. sul1 was the predominant ARG, whereas absolute abundances of 16S rRNA, int1, and blaCTX-M varied seasonally. int1 was significantly correlated with blaCTX-M in autumn and spring, whereas it showed no correlation with blaNDM-1, questioning the applicability of int1 as a sole indicator of overall resistance determinants. This study exhibited that the HT-qPCR system is pivotal for WBE.

Advancing Public Health Surveillance: Integrating Modeling and GIS in the Wastewater-Based Epidemiology of Viruses, a Narrative Review

This review article will present a comprehensive examination of the use of modeling, spatial analysis, and geographic information systems (GIS) in the surveillance of viruses in wastewater. With the advent of global health challenges like the COVID-19 pandemic, wastewater surveillance has emerged as a crucial tool for the early detection and management of viral outbreaks. This review will explore the application of various modeling techniques that enable the prediction and understanding of virus concentrations and spread patterns in wastewater systems. It highlights the role of spatial analysis in mapping the geographic distribution of viral loads, providing insights into the dynamics of virus transmission within communities. The integration of GIS in wastewater surveillance will be explored, emphasizing the utility of such systems in visualizing data, enhancing sampling site selection, and ensuring equitable monitoring across diverse populations. The review will also discuss the innovative combination of GIS with remote sensing data and predictive modeling, offering a multi-faceted approach to understand virus spread. Challenges such as data quality, privacy concerns, and the necessity for interdisciplinary collaboration will be addressed. This review concludes by underscoring the transformative potential of these analytical tools in public health, advocating for continued research and innovation to strengthen preparedness and response strategies for future viral threats. This article aims to provide a foundational understanding for researchers and public health officials, fostering advancements in the field of wastewater-based epidemiology.

Review of Antimicrobial Resistance in Wastewater in Japan: Current Challenges and Future Perspectives

Antimicrobial resistance (AMR) circulates through humans, animals, and the environments, requiring a One Health approach. Recently, urban sewage has increasingly been suggested as a hotspot for AMR even in high-income countries (HICs), where the water sanitation and hygiene infrastructure are well-developed. To understand the current status of AMR in wastewater in a HIC, we reviewed the epidemiological studies on AMR in the sewage environment in Japan from the published literature. Our review showed that a wide variety of clinically important antibiotic-resistant bacteria (ARB), antibiotic resistance genes (ARGs), and antimicrobial residues are present in human wastewater in Japan. Their concentrations are lower than in low- and middle-income countries (LMICs) and are further reduced by sewage treatment plants (STPs) before discharge. Nevertheless, the remaining ARB and ARGs could be an important source of AMR contamination in river water. Furthermore, hospital effluence may be an important reservoir of clinically important ARB. The high concentration of antimicrobial agents commonly prescribed in Japan may contribute to the selection and dissemination of AMR within wastewater. Our review shows the importance of both monitoring for AMR and antimicrobials in human wastewater and efforts to reduce their contamination load in wastewater.

Molecular Methods for Pathogenic Bacteria Detection and Recent Advances in Wastewater Analysis

With increasing concerns about public health and the development of molecular techniques, new detection tools and the combination of existing approaches have increased the abilities of pathogenic bacteria monitoring by exploring new biomarkers, increasing the sensitivity and accuracy of detection, quantification, and analyzing various genes such as functional genes and antimicrobial resistance genes (ARG). Molecular methods are gradually emerging as the most popular detection approach for pathogens, in addition to the conventional culture-based plate enumeration methods. The analysis of pathogens in wastewater and the back-estimation of infections in the community, also known as wastewater-based epidemiology (WBE), is an emerging methodology and has a great potential to supplement current surveillance systems for the monitoring of infectious diseases and the early warning of outbreaks. However, as a complex matrix, wastewater largely challenges the analytical performance of molecular methods. This review synthesized the literature of typical pathogenic bacteria in wastewater, types of biomarkers, molecular methods for bacterial analysis, and their recent advances in wastewater analysis. The advantages and limitation of these molecular methods were evaluated, and their prospects in WBE were discussed to provide insight for future development.

Preparing for COVID-2x: Urban Planning Needs to Regard Urological Wastewater as an Invaluable Communal Public Health Asset and Not as a Burden

Prior to the COVID-19 pandemic, the analysis of urological wastewater had been a matter of academic curiosity and community-wide big-picture studies looking at drug use or the presence of select viruses such as Hepatitis. The COVID-19 pandemic saw systematic testing of urological wastewater emerge as a significant early detection tool for the presence of SARS-CoV-2 in a community. Even though the pandemic still rages in all continents, it is time to consider the post-pandemic world. This paper posits that urban planners should treat urological wastewater as a communal public health asset and that future sewer design should allow for stratified multi-order sampling.

A potential risk assessment tool to monitor pathogens circulation in coastal waters

The present study reports data on a 20 months campaign monitoring enteric viruses (hepatitis A, norovirus, rotavirus, astrovirus, sapovirus, and aichivirus) and bacteria (Salmonella spp.) in seawater. The aim of this work was to assess the potential correlation among the presence of viruses/bacteria and different environmental factors like seasonality, water discharge sources (treated and untreated wastewater, mixed waters and raw water) as well as influence of the Italian lockdown measure against COVID-19 pandemic. Results showed different prevalence of the investigated viruses with values equal to 16 % for norovirus GI, 15.1 % for norovirus GII, followed by 13.8 % for astrovirus, and 13.3 % for sapovirus. Rotavirus was detected in the 8.4 % of samples and aichivirus was detected with the lowest prevalence of 3.5 %. Hepatitis A virus was never identified in the monitoring campaign. Salmonella spp. was detected with a prevalence of 36.6 %. Statistical analysis displayed a high correlation for the two noroviruses simultaneous detection (NGI and NGII) while a lower correlation was found for co-presence of noroviruses with astrovirus, sapovirus or Salmonella spp. A significant decrease of enteric pathogens in seawater was observed during the restrictions period. Results on seasonality highlighted a higher viral prevalence correlated to the wet season for all the pathogens but rotavirus and aichivirus, which instead showed an opposite trend and a higher incidence in the dry season. With respect to discharge typology, some viruses displayed a higher prevalence in treated waters (astrovirus, rotavirus, sapovirus and aichivirus) while the other investigated pathogens (noroviruses and Salmonella spp.) showed a higher prevalence in mixed waters. The main observations of this work were used to define a potential monitoring strategy that could be useful for sanitary Authorities to implement surveillance plans aimed at preventing possible sanitary outbreaks and/or environmental quality deterioration.

Isolation of Alpha-Toxin-Deficient Clostridium perfringens Type F from Sewage Influents and Effluents

Clostridium perfringens is classified into types A to G, and all types produce alpha-toxins; however, C. perfringens type F that is negative for phospholipase C (PLC) activity of alpha-toxin has been isolated from the environment and cases of humans afflicted by food poisoning. This study aimed to elucidate the distribution of PLC-negative C. perfringens type F in sewage influents and effluents. Influents and effluents of two wastewater treatment plants were collected monthly between July 2016 and January 2020 and between August 2018 and January 2020, respectively. Isolation rates of PLC-negative C. perfringens type F from sewage influents and effluents were 38% (33/86) and 22% (8/36), and the numbers of isolates were 43 and 13, respectively. The locus of the enterotoxin gene of all isolates was determined to be in a plasmid with an IS1151 sequence, and multilocus sequence typing revealed that all 17 representative isolates were assigned as sequence type 186. Sequencing of the plc gene of these representative isolates showed that nonsense mutation (p.W98*) causing alpha-toxin deficiency should be responsible for a loss of PLC enzymatic activity. These results suggest that alpha toxin-deficient C. perfringens type F is distributed in living and water environments since sewage influents contain community wastewater, and effluents contaminate the environment. Detection of C. perfringens type F, independent of PLC activity, should be carried out on human and environmental samples. IMPORTANCE Understanding the diversity of biochemical characteristics that may affect the identification of bacteria is essential. C. perfringens is a ubiquitous bacterium found in the environment, humans, and animals and is responsible for infectious disease in the intestine. Although the alpha-toxin of C. perfringens may be used for its detection, variants of the alpha-toxin lacking its activity have been isolated from soil and humans experiencing symptoms of diarrhea. It is valuable to disclose the prevalence of the alpha-toxin variant in the sewage of wastewater treatment plants, as it may reflect the hygienic condition of the community, as it would be a pollution source for the environment. This study shows the persistent existence and genetic characteristics of the alpha-toxin variant in sewage and reveals a lacking mechanism of the alpha-toxin activity and proposes the detection method of C. perfringens, independent of the alpha-toxin activity.

Treatment Processes for Microbial Resistance Mitigation: The Technological Contribution to Tackle the Problem of Antibiotic Resistance

Advances generated in medicine, science, and technology have contributed to a better quality of life in recent years; however, antimicrobial resistance has also benefited from these advances, creating various environmental and health problems. Several determinants may explain the problem of antimicrobial resistance, such as wastewater treatment plants that represent a powerful agent for the promotion of antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARG), and are an important factor in mitigating the problem. This article focuses on reviewing current technologies for ARB and ARG removal treatments, which include disinfection, constructed wetlands, advanced oxidation processes (AOP), anaerobic, aerobic, or combined treatments, and nanomaterial-based treatments. Some of these technologies are highly intensive, such as AOP; however, other technologies require long treatment times or high doses of oxidizing agents. From this review, it can be concluded that treatment technologies must be significantly enhanced before the environmental and heath problems associated with antimicrobial resistance can be effectively solved. In either case, it is necessary to achieve total removal of bacteria and genes to avoid the possibility of regrowth given by the favorable environmental conditions at treatment plant facilities.

The Circulation of Type F Clostridium perfringens among Humans, Sewage, and Ruditapes philippinarum (Asari Clams)

Clostridium perfringens is an important pathogen that is responsible for gastroenteritis; the causative agent for the symptoms is C. perfringens enterotoxin (CPE), which is mainly produced by type F C. perfringens. Since shellfishes may gather C. perfringens in the water environment, this study estimated the potential circulation of type F C. perfringens among humans, sewage, and Ruditapes philippinarum (asari clams) as a result of sewage pollution. A comparison of the characteristics among the isolates from 86 sewage influents, 36 effluents, 76 asari clams, and 37 humans was conducted. Serotyping, cpe genotyping, and toxin genotyping showed that C. perfringens with a plasmid IS1151 sequence downstream of cpe was predominant among sewage influents, effluents, humans, and asari clams. Multilocus sequence typing suggested that some isolates from a human, sewage influents, effluents, and asari clams were linked to each other. These results demonstrated that asari clams are the necessary infection sources of C. perfringens responsible for carriers and foodborne diseases, and that these pathogens from humans infected by asari clams can pollute the water environment. It is useful to assess bacteria such as C. perfringens isolates from sewage to estimate the trend of those from the community.