Genomic Survey of E. coli From the Bladders of Women With and Without Lower Urinary Tract Symptoms

Urinary tract infections (UTIs) are one of the most common human bacterial infections. While UTIs are commonly associated with colonization by Escherichia coli, members of this species also have been found within the bladder of individuals with no lower urinary tract symptoms (no LUTS), also known as asymptomatic bacteriuria. Prior studies have found that both uropathogenic E. coli (UPEC) strains and E. coli isolates that are not associated with UTIs encode for virulence factors. Thus, the reason(s) why E. coli sometimes causes UTI-like symptoms remain(s) elusive. In this study, the genomes of 66 E. coli isolates from adult female bladders were sequenced. These isolates were collected from four cohorts, including women: (1) without lower urinary tract symptoms, (2) overactive bladder symptoms, (3) urgency urinary incontinence, and (4) a clinical diagnosis of UTI. Comparative genomic analyses were conducted, including core and accessory genome analyses, virulence and motility gene analyses, and antibiotic resistance prediction and testing. We found that the genomic content of these 66 E. coli isolates does not correspond with the participant’s symptom status. We thus looked beyond the E. coli genomes to the composition of the entire urobiome and found that the presence of E. coli alone was not sufficient to distinguish between the urobiomes of individuals with UTI and those with no LUTS. Because E. coli presence, abundance, and genomic content appear to be weak predictors of UTI status, we hypothesize that UTI symptoms associated with detection of E. coli are more likely the result of urobiome composition

Demographics and mitigation efforts associated with the county-level impact of COVID-19 in Pennsylvania

The COVID-19 pandemic deeply impacted the world in 2020, with the U.S having over 20 million total cases by the end of the year. An important lesson learned through the response effort in the U.S. was that minority groups and those of low socio-economic status were those most affected by the pandemic, both on an individual level and a community level. The main objective of this paper was to determine whether these demographic disparities could explain to an extent the county differences in the impact of COVID-19 in Pennsylvania, and whether the phased re-opening strategy also contributed to this variation between counties. To meet this objective, a linear mixed model was developed to examine associations between demographic variables and the daily incidence rate over time. To assess the impact of phased re-opening on COVID-19 incidence, the number of days spent in phases before complete re-opening was also examined as a factor to the linear mixed model. This analysis found that lower median income, lower median age, and higher a percentage of urban land-use was associated with increases in the daily incidence rate. However, these associations changed depending on the time period, with race being a significant effect especially during March to June. As far as the phased re-opening strategy, the model results suggested that from March to June, phase changes were in response to each county’s incidence rates, but that counties that stayed in the first phases longer had lower incidence rates in the last three months of 2020. This research adds to the growing body of evidence that racial, income, and health disparities impact community-level outcomes of COVID-19, and therefore need to be considered when implementing a public health response

Unanswered clinical questions: a survey of specialists and primary care providers

Objective: With the myriad of cases presented to clinicians every day at the authors’ integrated academic health system, clinical questions are bound to arise. Clinicians need to recognize these knowledge gaps and act on them. However, for many reasons, clinicians might not seek answers to these questions. Our goal was to investigate the rationale and process behind these unanswered clinical questions. Subsequently, we explored the use of biomedical information resources among specialists and primary care providers and identified ways to promote more informed clinical decision making. Methods: We conducted a survey to assess how practitioners identify and respond to information gaps, their background knowledge of search tools and strategies, and their usage of and comfort level with technology. Results: Most of the 292 respondents encountered clinical questions at least a few times per week. While the vast majority often or always pursued answers, time was the biggest barrier for not following through on questions. Most respondents did not have any formal training in searching databases, were unaware of many digital resources, and indicated a need for resources and services that could be provided at the point of care. Conclusions: While the reasons for unanswered clinical questions varied, thoughtful review of the responses suggested that a combination of educational strategies, embedded librarian services, and technology applications could help providers pursue answers to their clinical questions, enhance patient safety, and contribute to patient-based, self-directed learning.  This article has been approved for the Medical Library Association’s Independent Reading Program

Characterization and spontaneous induction of urinary tract Streptococcus anginosus prophages

Streptococcus anginosus is an often overlooked and understudied emerging pathogen inhabiting many areas of the human body. Through our sequencing of S. anginosus strains isolated from the female bladder microbiota, we detected numerous prophage sequences. Bioinformatic analysis of these sequences identified 17 distinct groups of S. anginosus prophages. The majority of these phages exhibit no sequence homology to previously characterized temperate or virulent phage sequences, indicating an unexplored diversity of Streptococcus phages. By culturing these bacterial isolates, we confirmed that the prophages of five of these groups are capable of induction. One of these putative phages was imaged, the first such evidence of an S . anginosus virus-like particle; it exhibits morphological characteristics of siphoviruses.ISSN:0022-1317ISSN:1465-209

Unanswered clinical questions: a survey of specialists and primary care providers

OBJECTIVE: With the myriad of cases presented to clinicians every day at our integrated academic health system, clinical questions are bound to arise. Clinicians need to recognize these knowledge gaps and act on them. However, for many reasons, clinicians might not seek answers to these questions. Our goal was to investigate the rationale and process behind these unanswered clinical questions. Subsequently, we explored the use of biomedical information resources among specialists and primary care providers and identified ways to promote more informed clinical decision making. METHODS: We conducted a survey to assess how practitioners identify and respond to information gaps, their background knowledge of search tools and strategies, and their usage of and comfort level with technology. RESULTS: Most of the 292 respondents encountered clinical questions at least a few times per week. While the vast majority often or always pursued answers, time was the biggest barrier for not following through on questions. Most respondents did not have any formal training in searching databases, were unaware of many digital resources, and indicated a need for resources and services that could be provided at the point of care. CONCLUSIONS: While the reasons for unanswered clinical questions varied, thoughtful review of the responses suggested that a combination of educational strategies, embedded librarian services, and technology applications could help providers pursue answers to their clinical questions, enhance patient safety, and contribute to patient-based, self-directed learning

Complete Genome Sequences of Streptococcus mitis Strains Isolated from the Oral Cavity and Urogenital Tract of a Woman and Her Male Sexual Partner

Streptococcus mitis is a member of the mitis group of the genus Streptococcus, which includes commensal species of the oral cavity and upper respiratory tract. Here, we report 39 complete genome sequences of S. mitis strains isolated from the oral cavity and urogenital tract of a woman and her male sexual partner.ISSN:2576-098