mSphere

Robust early warning of emerging viruses requires sampling populations that drive spread coupled with assays capable of detecting new viral variants or species. Untargeted viral metagenomic sequencing can, in principle, detect any virus, including completely novel ones. Composite airplane wastewater enables monitoring long-distance travelers from central collection points; however, the performance of untargeted viral metagenomic sequencing in this sample type remains unknown. In municipal wastew...

Digital PCR (dPCR) is increasingly used for SARS-CoV-2 wastewater surveillance due to its precision, absolute quantification, and reduced sensitivity to inhibition compared to quantitative PCR. Although the Bio-Rad ddPCR and QIAGEN QIAcuity dPCR platforms are widely adopted, their performance has not been directly compared for wastewater applications. We conducted a blinded comparison of these platforms using 95 archived wastewater influent samples from North Carolina collected in 2021-2022, spa...

Candida auris is a multidrug-resistant fungal pathogen that presents substantial challenges for healthcare facilities due to its high mortality rates among vulnerable populations. Six C. auris clades have been identified based on their susceptibility to antifungal treatment and environmental stressors. Identifying the circulating C. auris clade(s) is critical for understanding transmission and selecting a disease control strategy. To inform targeted implementation of community wastewater monitor...

Wastewater-based surveillance (WBS) is widely used to monitor respiratory viruses, yet uncertainties remain regarding how viral RNA concentrations in wastewater reflect infection dynamics. Specifically, diurnal variation in shedding and RNA losses during in-sewer transport can impact measured signals. We conducted a field study in a 5-km trunk sewer (travel time of one hour). Wastewater was sampled at the sewer inlet and outlet using autosamplers collecting time-proportional one-hour composite s...

IntroductionWastewater-based epidemiology (WBE) was implemented at the 2024 Republican and Democratic National Conventions (RNC and DNC, respectively)--two prominent large-scale events, each with estimated attendances of >50,000 persons. In preparation for event monitoring, the Wisconsin and Chicago WBE programs (associated with the RNC and DNC public health response, respectively) developed site-specific monitoring strategies and response plans, prioritized additional pathogens for event survei...

BackgroundHeartland virus (HRTV) is an emerging tick-borne virus capable of causing severe illness and death. The burden of disease is likely underestimated due to limited seroprevalence studies, lack of commercially available diagnostic tests, and an overlapping clinical syndrome with more commonly diagnosed bacterial diseases such as spotted fever group rickettsiosis or ehrlichiosis. MethodsActive surveillance for Heartland virus disease was conducted at a large academic center from March to ...

BackgroundClostridium perfringens can cause life-threatening extraintestinal infections in immunocompromised patients, an area in which we have little information regarding strain factors that impact patient risks and outcomes. MethodsWe conducted genomic-epidemiologic analyses on C. perfringens isolates from 70 patients seen at Brigham and Womens Hospital over 2021-2024. Genomic analyses evaluated strain profiles within a broader context of 2,321 C. perfringens genomes from foodborne, veterina...

Antimicrobial resistance (AMR) is a growing problem, with annual deaths set to pass 10 million by 2050 if current trends continue. Wastewater surveillance has been proposed as a strategy to understand population-level resistance, and water reclamation facilities (WRFs) have been identified as a control point for environmental dissemination of resistant bacteria. Understanding dynamics of AMR across WRFs requires advanced molecular tools that elucidate host bacteria, especially for mobile resista...

Measles outbreaks have surged globally in recent years, but current surveillance systems have limited capacity to monitor measles virus (MeV) transmission and evolution at population scale. Although MeV can be detected in wastewater, the public health potential of wastewater genomic surveillance for MeV remains largely unexplored. Here, we deploy sensitive, low-cost MeV wastewater genomic surveillance combining virus concentration, whole-genome amplicon sequencing, and bioinformatic analysis alo...

Inter-alpha Inhibitor Proteins (IAIP) are serine protease inhibitors and a reliable inflammatory biomarker. We have demonstrated that IAIP levels decrease during sepsis in humans and animal models. Currently, enzyme-linked immunosorbent assay (ELISA) is the standard procedure to measure IAIP levels. We developed a lateral flow immunoassay (LFIA) that allows rapid, point of care detection. We compared IAIP levels in infants with sepsis and/or necrotizing enterocolitis (NEC) by ELISA and LFIA in a...

Bacterial infections are a major cause of morbidity and mortality among children under five in low- and middle-income countries (LMICs). Children in LMICs are exposed to and colonized by a range of pathogenic bacteria, yet patterns of bacterial exchange between humans are not well known, in part because culturing and sequencing single bacterial isolates is labor-intensive. Here, we apply a machine learning strain tracking approach to metagenomic data from 511 stool samples from children and moth...

Carbapenem-resistant (CR) bacteria have emerged and been spreading beyond healthcare-associated facilities into the environment. It is recognized that toilet bowl water in patient rooms of healthcare-associated facilities can be one of internal reservoirs of CR bacteria. In accordance with this idea, toilet bowl water samples were collected from patient rooms in a tertiary healthcare-associated facility in North Macedonia, and meropenem (MEM)-resistant bacterial isolates were obtained from the t...

ObjectivesTo quantify how urine sample type and polymicrobial context impact antimicrobial resistance (AMR) in urinary tract infections (UTIs), using routine diagnostics at scale. MethodsIn this retrospective, single-centre study, we analysed 188,687 urine cultures from the Institute of Medical Microbiology, University of Zurich, Switzerland (January 2015 to May 2023). We compared midstream urine (MU), indwelling catheter (IDC), and intermittent catheter (IMC) samples. Samples were classified a...

Wastewater monitoring enables non-invasive, population-scale tracking of community infections independent of healthcare-seeking behavior and clinical diagnosis. Metagenomic sequencing extends this capability by enabling broad, pathogen-agnostic detection, genomic characterization, and identification of novel or unexpected threats. Here, we present data from CASPER (the Coalition for Agnostic Sequencing of Pathogens from Environmental Reservoirs), a U.S.-based wastewater metagenomic sequencing ne...

Antibiotic resistance genes (ARGs) circulating among clinically relevant bacteria pose serious challenges to public health. Given the ancient and environmental bacterial origins of ARGs, a better understanding of the carriers of ARGs beyond the clinically most relevant species is urgently needed for more farsighted resistance monitoring and intervention measures. While the risks of emerging ARGs from environmental sources have been recognized, the identification bottlenecks stem from the limitat...

Clostridioides difficile (C. diff) is a leading cause of hospital-acquired infections with severity ranging from mild diarrhea to fulminant colitis and death. Current antigen tests lack adequate sensitivity and DNA-based nucleic acid amplification tests (DNA-NAATs) exhibit limited specificity for active infection, leading to either underdiagnosis or inappropriate treatment of colonized individuals. Unlike DNA, mRNA is expressed only by metabolically active bacteria and is rapidly hydrolyzed, pro...

BackgroundInfections are the leading cause of non-relapse mortality in pediatric hematopoietic cell transplant (HCT) recipients. Up to 90% of bacteremias in these patients originate from gut microbiome organisms. However, selection for resistance genes, such as Extended-spectrum {beta}-lactamase (ESBL), in these patients gut microbiomes remains poorly understood. MethodsStools were prospectively collected from pediatric HCT recipients at multiple centers (n=133 patients, five centers) on the da...

Household transmission of EV-D68 was identified in 35 of 1040 households (3.4%) in the Pacific Northwest between 2022-2024, with an estimated secondary attack rate of 15%. Sequences from within households clustered closely with 0 to 2 pairwise nucleotide differences (median 1) between cases 6-14 days apart (median 7).

BackgroundThere is a need for synthetic peptide-based serologic assays that exploit avidity to replace whole antigens while enabling low-cost diagnostics in resource-limited settings. ObjectiveTo evaluate the diagnostic accuracy of a polymeric peptide-based ELISA leveraging avidity to enhance signal. MethodA 15-member SARS-CoV-2 peptide library corresponding to multiple epitope clusters and proteins was screened by indirect ELISA using pooled sera from RT-PCR-confirmed COVID-19 patients to ide...

Syphilis remains a major public health concern. However, current serologic assays are limited in their ability to distinguish active from previously treated disease. We applied tandem mass tag-based quantitative proteomics to plasma from 10 adults with active syphilis and 10 age- and gender-matched non-diseased controls. We identified 54 differentially regulated proteins (36 upregulated, 18 downregulated). Those proteins map to immune and inflammatory responses, acute-phase signaling, coagulatio...