Protist metagenomics in New York City
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ABSTRACT:
PROVIDER: PRJEB26690 | ENA |
REPOSITORIES: ENA
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Project description:18S rRNA gene V4 region amplicon sequencing of protists in NYC environmental samples
| PRJEB23950 | ENA
Project description:Shotgun metagenomic sequencing of NYC raw sewage samples
| PRJEB28033 | ENA
Project description:Protists are ubiquitous components of terrestrial and aquatic environments, as well as animal and human microbiomes. Despite this, little is known about protists in urban environments. The ~7400-mile sewer system of New York City (NYC) collects human waste from ~8 million human inhabitants as well as from animals, street runoff, and groundwater, providing an ideal system to study these microbes. We used 18S rRNA amplicon sequencing and shotgun metagenomic sequencing to profile raw sewage microbial communities. Raw sewage samples were collected over a 12-month period from 14 treatment plants of the five NYC boroughs, and compared with samples from other environments including soil, stormwater, and sediment. Sewage contained a diverse protist community dominated by free-living clades, and communities were highly differentiated across environments. Seasonal differences in protist composition were observed; however, network analysis and functional profiling demonstrated that sewage communities were robust and functionally consistent. Protists typically associated with human and animal guts or feces were frequently detected. Abundance of these parasites varied significantly both spatially and temporally, suggesting that spikes could reflect trends in the source population. This underscores sewage as a valuable model system for monitoring patterns in urban microbes and provides a baseline protist metagenome of NYC.
| S-EPMC6794324 | biostudies-literature
Project description:Protists targeted sequencing of 18S rRNA HV 9
| PRJNA305513 | ENA
Project description:Cryptosporidiosis is a parasitic diarrheal infection that is transmitted by the fecal-oral route. We assessed trends in incidence and demographic characteristics for the 3,984 cases diagnosed during 1995-2018 in New York City, New York, USA, and reported to the New York City Department of Health and Mental Hygiene. Reported cryptosporidiosis incidence decreased with HIV/AIDS treatment rollout in the mid-1990s, but the introduction of syndromic multiplex diagnostic panels in 2015 led to a major increase in incidence and to a shift in the demographic profile of reported patients. Incidence was highest among men 20-59 years of age, who consistently represented most (54%) reported patients. In addition, 30% of interviewed patients reported recent international travel. The burden of cryptosporidiosis in New York City is probably highest among men who have sex with men. Prevention messaging is warranted for men who have sex with men and their healthcare providers, as well as for international travelers.
| S-EPMC7045836 | biostudies-literature
Project description:Sediment eDNA targeting 18S rDNA V8-V9 region
| PRJDB17880 | ENA
Project description:The incidence of Legionnaires' disease in the United States has been increasing since 2000. Outbreaks and clusters are associated with decorative, recreational, domestic, and industrial water systems, with the largest outbreaks being caused by cooling towers. Since 2006, 6 community-associated Legionnaires' disease outbreaks have occurred in New York City, resulting in 213 cases and 18 deaths. Three outbreaks occurred in 2015, including the largest on record (138 cases). Three outbreaks were linked to cooling towers by molecular comparison of human and environmental Legionella isolates, and the sources for the other 3 outbreaks were undetermined. The evolution of investigation methods and lessons learned from these outbreaks prompted enactment of a new comprehensive law governing the operation and maintenance of New York City cooling towers. Ongoing surveillance and program evaluation will determine if enforcement of the new cooling tower law reduces Legionnaires' disease incidence in New York City.
| S-EPMC5652439 | biostudies-literature
Project description:ImportanceMore evidence on associations between mandated paid sick leave and health service utilization among low-income adults is needed to guide health policy and legislation nationwide.ObjectiveTo evaluate the association between New York City's 2014 paid sick leave mandate and health care utilization among Medicaid-enrolled adults.Design setting and participantsThis retrospective cohort study used New York State Medicaid administrative data for adults 18 to 64 years old continuously enrolled in Medicaid from August 1, 2011, through July 31, 2017. A difference-in-differences approach with entropy balancing weights was used to compare New York City with the rest of New York State to assess the association of the paid sick leave mandate with health care utilization, and for those 40 to 64 years old, with preventive care utilization. The data analysis was performed from June through August 2020.ExposuresTemporal and spatial variation in exposure to the mandate.Main outcomes and measuresAnnual health care utilization (emergency care, specialist visits, and primary care clinician visits) per Medicaid-enrolled adult. Secondary outcomes include categories of emergency utilization and utilization of 5 preventive services.ResultsOf 552 857 individuals (mean [SD] age, 43 [12] years; 351 130 [64%] women) who met inclusion criteria, 99 181 (18%) were White, 162 492 (29%) Black, and 138 061 (25%) Hispanic. Paid sick leave was significantly associated with a reduction in the probability of emergency care (-0.6 percentage points [pp]; 95% CI, -0.7 to -0.5 pp; P < .001), including a 0.3 pp reduction (95% CI, -0.4 to -0.2; P < .001) in care for conditions treatable in a primary care setting and an increase in annual outpatient visits (0.124 pp; 95% CI, 0.040 to 0.208 pp; P < .001). Among those 40 to 64 years old, the mandate was significantly associated with increased probabilities of glycated hemoglobin A1c level testing (2.9 pp; 95% CI, 2.5-3.3 pp; P < .001), blood cholesterol testing (2.7 pp; 95% CI, 2.5-2.9 pp; P < .001), and colon cancer screening (0.4 pp; 95% CI, 0.2-0.6 pp; P < .001).Conclusions and relevanceThis retrospective cohort study of nonelderly adults enrolled in Medicaid New York State showed that mandated paid sick leave in New York City was significantly associated with differences in several dimensions of health care services use.
| S-EPMC8796973 | biostudies-literature
Project description:Neighborhood physical disorder, or the deterioration of urban environments, is associated with negative mental and physical health outcomes. Eleven trained raters used CANVAS, a web-based system for conducting reliable virtual street audits, to collect data on nine indicators of physical disorder using Google Street View imagery of 532 block faces in New York City, New York, USA. We combined the block face indicator data into a disorder scale using item response theory; indicators ranged in severity from presence of litter, a weak indicator of disorder, to abandoned cars, a strong indicator. Using this scale, we estimated disorder at the center point of each sampled block. We then used ordinary kriging to interpolate estimates of disorder levels throughout the city. The resulting map condenses a complex estimation process into an interpretable visualization of the spatial distribution of physical disorder in New York City.
| S-EPMC4963033 | biostudies-literature