Spatial heterogeneity of prostate cancer-specific mortality in Pennsylvania remains unclear. We utilized advanced geospatial survival regressions to examine spatial variation of prostate cancer-specific mortality in PA and evaluate potential effects of individual- and county-level risk factors.

Fosfomycin resistance in Escherichia coli is rare in the United States. An extended-spectrum β-lactamase-producing E. coli clinical strain identified in Pennsylvania, USA, showed high-level fosfomycin resistance caused by the fosA3 gene. The IncFII plasmid carrying this gene had a structure similar to those found in China, where fosfomycin resistance is commonly described.

Unconventional oil and gas (UOG) extraction, also known as hydraulic fracturing, is becoming more prevalent with the increasing use and demand for natural gas; however, the full extent of its environmental impacts is still unknown. Here we measured physicochemical properties and bacterial community composition of sediment samples taken from twenty-eight streams within the Marcellus shale formation in northeastern Pennsylvania differentially impacted by hydraulic fracturing activities. Fourteen of the streams were classified as UOG+, and thirteen were classified as UOG- based on the presence of UOG extraction in their respective watersheds. One stream was located in a watershed that previously had UOG extraction activities but was recently abandoned. We utilized high-throughput sequencing of the 16S rRNA gene to infer differences in sediment aquatic bacterial community structure between UOG+ and UOG- streams, as well as correlate bacterial community structure to physicochemical water parameters. Although overall alpha and beta diversity differences were not observed, there were a plethora of significantly enriched operational taxonomic units (OTUs) within UOG+ and UOG- samples. Our biomarker analysis revealed many of the bacterial taxa enriched in UOG+ streams can live in saline conditions, such as Rubrobacteraceae. In addition, several bacterial taxa capable of hydrocarbon degradation were also enriched in UOG+ samples, including Oceanospirillaceae. Methanotrophic taxa, such as Methylococcales, were significantly enriched as well. Several taxa that were identified as enriched in these samples were enriched in samples taken from different streams in 2014; moreover, partial least squares discriminant analysis (PLS-DA) revealed clustering between streams from the different studies based on the presence of hydraulic fracturing along the second axis. This study revealed significant differences between bacterial assemblages within stream sediments of UOG+ and UOG- streams and identified several potential biomarkers for evaluating and monitoring the response of autochthonous bacterial communities to potential hydraulic fracturing impacts.

The Penn State Cancer Initiative implemented LionVu 1.0 (Penn State University, United States) in 2017 as a web-based mapping tool to educate and inform public health professionals about the cancer burden in Pennsylvania and 28 counties in central Pennsylvania, locally known as the catchment area. The purpose of its improvement, LionVu 2.0, was to assist investigators answer person-place-time questions related to cancer and its risk factors by examining several data variables simultaneously. The primary objective of this study was to conduct a usability assessment of a prototype of LionVu 2.0 which included area- and point-based data. The assessment was conducted through an online survey; 10 individuals, most of whom had a masters or doctorate degree, completed the survey. Although most participants had a favorable view of LionVu 2.0, many had little to no experience with web mapping. Therefore, it was not surprising to learn that participants wanted short 10-15-minute training videos to be available with future releases, and a simplified user-interface that removes advanced functionality. One unexpected finding was the suggestion of using LionVu 2.0 for teaching and grant proposals. The usability study of the prototype of LionVu 2.0 provided important feedback for its future development.

Testing of 1701 water wells in northeastern Pennsylvania shows that methane is ubiquitous in groundwater, with higher concentrations observed in valleys vs. upland areas and in association with calcium-sodium-bicarbonate, sodium-bicarbonate, and sodium-chloride rich waters--indicating that, on a regional scale, methane concentrations are best correlated to topographic and hydrogeologic features, rather than shale-gas extraction. In addition, our assessment of isotopic and molecular analyses of hydrocarbon gases in the Dimock Township suggest that gases present in local water wells are most consistent with Middle and Upper Devonian gases sampled in the annular spaces of local gas wells, as opposed to Marcellus Production gas. Combined, these findings suggest that the methane concentrations in Susquehanna County water wells can be explained without the migration of Marcellus shale gas through fractures, an observation that has important implications for understanding the nature of risks associated with shale-gas extraction.

The development of hydraulic fracturing ("fracking") is considered the biggest change to the global energy production system in the last half-century. However, several communities have banned fracking because of unresolved concerns about the impact of this process on human health. To evaluate the potential health impacts of fracking, we analyzed records of more than 1.1 million births in Pennsylvania from 2004 to 2013, comparing infants born to mothers living at different distances from active fracking sites and those born both before and after fracking was initiated at each site. We adjusted for fixed maternal determinants of infant health by comparing siblings who were and were not exposed to fracking sites in utero. We found evidence for negative health effects of in utero exposure to fracking sites within 3 km of a mother's residence, with the largest health impacts seen for in utero exposure within 1 km of fracking sites. Negative health impacts include a greater incidence of low-birth weight babies as well as significant declines in average birth weight and in several other measures of infant health. There is little evidence for health effects at distances beyond 3 km, suggesting that health impacts of fracking are highly local. Informal estimates suggest that about 29,000 of the nearly 4 million annual U.S. births occur within 1 km of an active fracking site and that these births therefore may be at higher risk of poor birth outcomes.

Native microbiota represent a potential resource for biocontrol of arthropod vectors. Ixodes scapularis is mostly inhabited by the endosymbiotic Rickettsia buchneri, but the composition of bacterial communities varies with life stage, fed status, and/or geographic location. We compared bacterial community diversity among I. scapularis populations sampled within a small geographic range in Central Pennsylvania. We collected and extracted DNA from ticks and sequenced amplicons of the eubacterial 16S rRNA gene from individuals and pooled samples. We then used taxon-specific PCR and/or qPCR to confirm the abundance or infection frequency of select pathogenic and symbiotic bacteria. Bacterial communities were more diverse in pools of males than females and the most abundant taxon was Rickettsia buchneri followed by Coxiellaceae (confirmed by sequencing as an unknown Rickettsiella species). High Rickettsiella titers in pools were likely due to a few heavily infected males. We determined that the infection frequency of Borrelia burgdorferi ranged from 20 to 75%. Titers of Anaplasma phagocytophilum were significantly different between sexes. Amplicon-based bacterial 16S sequencing is a powerful tool for establishing the baseline community diversity and focusing hypotheses for targeted experiments, but care should be taken not to overinterpret data based on too few individuals. We identified intracellular bacterial candidates that may be useful as targets for manipulation.

Living in communities with more vegetation during pregnancy has been associated with higher birth weights, but fewer studies have evaluated other birth outcomes, and only one has been conducted in the Eastern United States, in regions with a broad range, including high levels, of greenness. We evaluated associations between prenatal residential greenness and birth outcomes (term birth weight, small for gestational age, preterm birth, and low 5 min Apgar score) across a range of community types using electronic health record data from 2006-2013 from the Geisinger Health System in Pennsylvania. We assigned greenness based on mother's geocoded address using the normalized difference vegetation index from satellite imagery. We used propensity scores to restrict the study population to comparable groups among those living in green vs. less-green areas. Analyses were adjusted for demographic, clinical, and environmental covariates, and stratified by community type (city, borough, and township). In cities, higher greenness (tertiles 2-3 vs. 1) was protective for both preterm (OR = 0.78, 95% CI: 0.61-0.99) and small for gestational age birth (OR = 0.73, 95% CI: 0.58-0.97), but not birth weight or Apgar score. We did not observe associations between greenness and birth outcomes in adjusted models in boroughs or townships. These results add to the evidence that greener cities might be healthier cities.

The state of emergency department (ED) crowding in Pennsylvania has not previously been reported.

An outbreak of cyclosporiasis occurred in attendees of a wedding reception held in Philadelphia, Pennsylvania, on June 10, 2000. In a retrospective cohort study, 54 (68.4%) of the 79 interviewed guests and members of the wedding party met the case definition. The wedding cake, which had a cream filling that included raspberries, was the food item most strongly associated with illness (multivariate relative risk, 5.9; 95% confidence interval, 3.6 to 10.5). Leftover cake was positive for Cyclospora DNA by polymerase chain reaction analyses. Sequencing of the amplified fragments confirmed that the organism was Cyclospora cayetanensis. The year 2000 was the fifth year since 1995 that outbreaks of cyclosporiasis definitely or probably associated with Guatemalan raspberries have occurred in the spring in North America. Additionally, this is the second documented U.S. outbreak, and the first associated with raspberries, for which Cyclospora has been detected in the epidemiologically implicated food item.

The Borrelia genus contains two major clades, the Lyme borreliosis group, which includes the causative agents of Lyme disease/borreliosis (B. burgdorferi sensu stricto and other related B. burgdorferi sensu lato genospecies), and the relapsing fever borreliosis group (B. hermsii, B. turicatae, and B. parkeri). Other unclassified reptile- and echidna-associated Borrelia spp. (i.e., B. turcica and 'Candidatus Borrelia tachyglossi', respectively) do not belong in either of these two groups. In North America, Borrelia spp. from both of the major clades are important pathogens of veterinary and public health concern. Lyme disease is of particular interest because the incidence in the northeastern United States continues to increase in both dogs and humans. Birds have a potentially important role in the ecology of Borrelia species because they are hosts for numerous tick vectors and competent hosts for various Borrelia spp. Our goal was to investigate the prevalence of Borrelia spp. in four free-living species of upland game birds in Pennsylvania, USA including wild turkey (Meleagris gallopavo), ruffed grouse (Bonasa umbellus), ring-necked pheasants (Phasianus colchicus), and American woodcock (Scolopax minor). We tested 205 tissue samples (bone marrow and/or spleen samples) from 169 individuals for Borrelia using a flagellin gene (flab) nested PCR, which amplifies all Borrelia species. We detected Borrelia DNA in 12% (24/205) of samples, the highest prevalence was in wild turkeys (16%; 5/31), followed by ruffed grouse (13%; 16/126) and American woodcock (3%; 1/35). All pheasants (n = 13) were negative. We sequenced amplicons from all positive game birds and all were B. burgdorferi sensu stricto. Our results support previous work indicating that certain species of upland game birds are commonly infected with Borrelia species, but unlike previous studies, we did not find any relapsing fever borreliae.

The evolution of Marek's disease virus (MDV, Gallid herpesvirus 2) has threatened the sustainability of poultry farming in the past and its continued evolution remains a concern. Genetic diversity is key to understanding evolution, yet little is known about the diversity of MDV in the poultry industry. Here, we investigate the diversity of MDV on 19 Pennsylvanian poultry farms over a 3-year period. Using eight polymorphic markers, we found that at least twelve MDV haplotypes were co-circulating within a radius of 40 km. MDV diversity showed no obvious spatial clustering nor any apparent clustering by bird line: all of the virus haplotypes identified on the commercial farms could be found within a single, commonly reared bird line. On some farms, a single virus haplotype dominated for an extended period of time, while on other farms the observed haplotypes changed over time. In some instances, multiple haplotypes were found simultaneously on a farm, and even within a single dust sample. On one farm, co-occurring haplotypes clustered into phylogenetically distinct clades, putatively assigned as high and low virulence pathotypes. Although the vast majority of our samples came from commercial poultry farms, we found the most haplotype diversity on a noncommercial backyard farm experiencing an outbreak of clinical Marek's disease. Future work to explore the evolutionary potential of MDV might therefore direct efforts toward farms that harbor multiple virus haplotypes, including both backyard farms and farms experiencing clinical Marek's disease.

The nicotine metabolite ratio (NMR) as measured by the ratio of 3'hydroxycotinine to cotinine has been examined in relation to tobacco use patterns including cigarettes per day and quit success to determine its role in nicotine dependence. We examined the NMR in relation to smoking topography and tested the hypothesis that normal metabolizers have a greater total daily puff volume than slow metabolizers.

Tobacco advertising is widespread in urban areas with racial/ethnic minority and low-income households that participate in nutrition assistance programs. Tobacco sales and advertising are linked to smoking behavior, which may complicate matters for low-income families struggling with disparate health risks relating to nutrition and chronic disease. We investigated the relationship between the amount and type of tobacco advertisements on tobacco outlets and the outlet type and location.

Patients with alopecia areata (AA) may experience episodic disease flares characterized by increasing hair loss that follow a seasonal pattern. However, no studies have examined whether specific climate factors contribute to the seasonal pattern of AA flares. Using Spearman rank correlation analyses, we assessed the association between climate variables and AA flare frequency per month in 336 children with AA in Philadelphia, Pennsylvania. Region-specific monthly values for average ambient temperature, air pressure, cloudiness, hours of sunlight, relative humidity, number of days with sun, number of days with rain, volume of precipitation, wind gust, wind speed, and UV index from January 2015 to December 2017 were obtained from World Weather Online. We found significant (P < 0.05) correlations between AA flare frequency and UV index (R = - 0.66), precipitation (R = - 0.66), number of days with rain (R = - 0.70), number of days with sun (R = 0.62), and air pressure (R = 0.80). Stratified analyses showed even stronger associations with UV index and precipitation in patients with an atopic comorbidity. New significant correlations appeared with temperature, wind speed, and UV index of the prior month. However, in patients who did not have atopic comorbidities, we generally observed weaker and non-significant correlations between climate and AA flare frequency. This study suggests that certain climate factors may mediate the seasonal pattern of AA flares and may contribute to AA pathogenesis. Atopic AA patients may be more susceptible to the influence of climate compared to those with no history of atopy.

European studies suggest that living near high-density livestock production increases the risk of sequence type (ST) 398 methicillin-resistant Staphylococcus aureus (MRSA) colonization. To our knowledge, no studies have evaluated associations between livestock production and human infection by other strain types.

Little is known about acute hemodialysis in the US. Here we describe predictors of receipt of acute hemodialysis in one state and estimate the marginal impact of acute hemodialysis on survival after accounting for confounding due to illness severity.

Rapid whole genome sequencing of SARS-CoV-2 has presented the ability to detect new emerging variants of concern in near real time. Here we report the genome of a virus isolated in Pennsylvania in March 2021 that was identified as lineage B.1.1.7 (VOC-202012/01) that also harbors the E484K spike mutation, which has been shown to promote "escape" from neutralizing antibodies in vitro . We compare this sequence to the only 5 other B.1.1.7+E484K genomes from Pennsylvania, all of which were isolated in mid March. Beginning in February 2021, only a small number (n=60) of isolates with this profile have been detected in the US, and only a total of 253 have been reported globally (first in the UK in December 2020). Comparative genomics of all currently available high coverage B.1.1.7+E484K genomes (n=235) available on GISAID suggested the existence of 7 distinct groups or clonal complexes (CC; as defined by GNUVID) bearing the E484K mutation raising the possibility of 7 independent acquisitions of the E484K spike mutation in each background. Phylogenetic analysis suggested the presence of at least 3 distinct clades of B.1.1.7+E484K circulating in the US, with the Pennsylvanian isolates belonging to two distinct clades. Increased genomic surveillance will be crucial for detection of emerging variants of concern that can escape natural and vaccine induced immunity.

We sought to characterize clinical presentation and healthcare utilization for pediatric COVID-19 in Western Pennsylvania (PA).

Attention to environmental sources of Mycobacterium avium complex (MAC) infection is a vital component of disease prevention and control. We investigated MAC colonization of household plumbing in suburban Philadelphia, Pennsylvania, USA. We used variable-number tandem-repeat genotyping and whole-genome sequencing with core genome single-nucleotide variant analysis to compare M. avium from household plumbing biofilms with M. avium isolates from patient respiratory specimens. M. avium was recovered from 30 (81.1%) of 37 households, including 19 (90.5%) of 21 M. avium patient households. For 11 (52.4%) of 21 patients with M. avium disease, isolates recovered from their respiratory and household samples were of the same genotype. Within the same community, 18 (85.7%) of 21 M. avium respiratory isolates genotypically matched household plumbing isolates. Six predominant genotypes were recovered across multiple households and respiratory specimens. M. avium colonizing municipal water and household plumbing may be a substantial source of MAC pulmonary infection.