Obstetrics and gynecology applicant perceptions of residency program culture with virtual interviews: a qualitative analysis of social media posts.

BACKGROUND: In the United States, Obstetrics and Gynecology residency interviews are instrumental in assessing the compatibility between medical student applicants and residency programs during the match process. Applicant perceptions of Obstetrics and Gynecology residency culture are a key component in determining how they rank residency programs. In 2020, residency interviews transitioned to a virtual format, and little is known about how applicants evaluated program culture during this first round of universal virtual interviews. Medical students in the United States commonly use Reddit, a popular social media platform, to discuss residency programs and share interview experiences. We explored Obstetrics and Gynecology applicants' considerations regarding residency program culture during the first universal virtual interview season in 2020-2021 by analyzing posts on a Google spreadsheet accessed through Reddit. METHODS: In 2022, we imported 731 posts from the "2020-21 OB GYN Residency Applicant Spreadsheet" Google spreadsheet posted to the 2020-2021 Residency Interview Spreadsheet megathread on the r/medicalschool subreddit to NVivo 12(QSR International, Burlington, MA), a qualitative analysis software program. Three investigators used qualitative inductive techniques to code and identify themes. RESULTS: Applicants used visual, verbal and behavioral cues during virtual Obstetrics and Gynecology residency interviews to understand three components of the workplace culture: prioritization of diversity, equity and inclusion, social environment, and resident workload. CONCLUSIONS: Obstetrics and Gynecology residency programs convey information about their culture during virtual interviews through the behavior, appearances and responses of residents and interviewers to applicant questions. To ensure they accurately represent their culture to applicants, programs should consider educating residents and faculty around the implications of interview-day conduct.

An online alternative: a qualitative study of virtual abortion values clarification workshops.

BACKGROUND: Following the U.S. Supreme Court Dobbs decision, access to abortion education is increasingly regionally dependent. Participation in values clarification workshops on abortion can improve abortion knowledge and reduce stigma. Traditionally, values clarification workshops occur in person, yet medical education increasingly utilizes online learning. We sought to understand how a virtual platform impacted medical students and Obstetrics and Gynecology (ObGyn) residents' experience with a values clarification workshop on abortion. METHODS: We conducted values clarification workshops over Zoom with medical students and ObGyn residents at four midwestern teaching hospitals from January 2021-December 2021 during the COVID-19 pandemic. We held semi-structured interviews with participants and facilitators to learn about how the virtual format impacted their experience with the workshop. Four researchers analyzed transcripts using an inductive approach to generate codes then themes. RESULTS: We interviewed 24 medical students, 13 ObGyn residents, and five workshop facilitators. Participants and facilitators found the virtual platform to have both unique advantages and disadvantages. Four central themes were identified: 1) Screen as a barrier: participants noted obstacles to conversation and intimacy. 2) Emotional safety: participants felt comfortable discussing sensitive topics. 3) Ease of access: participants could access virtual workshops regardless of location. 4) Technology-specific features: Zoom features streamlined aspects of the workshop and allowed for anonymous contributions to discussion. CONCLUSIONS: Our findings suggest that a virtual platform can be a convenient and effective way to deliver values clarification workshops on abortion, and this technology could be leveraged to expand access to this training in areas without trained facilitators.

Determinants of Gastrointestinal Group B Streptococcus Carriage in Adults.

Background: Streptococcus agalactiae (Group B Streptococcus, GBS) is a commensal Gram-positive bacterium found in the human gastrointestinal and urogenital tracts. Much of what is known about GBS relates to the diseases it causes in pregnant people and neonates. However, GBS is a common cause of disease in the general population with 90% of GBS mortality occurring in non-pregnant people. There are limited data about the predisposing factors for GBS and the reservoirs in the body. To gain an understanding of the determinants of gastrointestinal GBS carriage, we used stool samples and associated metadata to determine the prevalence and abundance of GBS in the gut microbiome of adults and find risk factors for GBS status. Methods: We used 754 stool samples collected from adults in Wisconsin from 2016-2017 to test for the prevalence and abundance of GBS using a Taqman probe-based qPCR assay targeting two GBS-specific genes: cfp and sip. We compared the microbiome compositions of the stool samples by GBS status using 16S rRNA analysis. We compared associations with GBS status and 557 survey variables collected during sample acquisition (demographics, diet, overall health, and reproductive health) using univariate and multivariate analyses. Results: We found 137/754 (18%) of participants had detectable GBS in their stool samples with a median abundance of 104 copies per nanogram of starting DNA. There was no difference in GBS status or abundance based on gender. Beta-diversity, Bray-Curtis and Unweighted UniFrac, was significantly different based on carrier status of the participant. Prior to p-value correction, 59/557 (10.6%) survey variables were significantly associated with GBS carrier status and 11/547 (2.0%) variables were significantly associated with abundance (p-value<0.05). After p-value correction, 2/547 (0.4%) variables were associated with GBS abundance: an increased abundance of GBS was associated with a decreased frequency since last dental checkup (p<0.001) and last dental cleaning (p<0.001). Increased GBS abundance was significantly associated with increased frequency of iron consumption (p=0.007) after p-value correction in multivariate models. Conclusions: GBS is found in stool samples from adults in Wisconsin at similar frequencies as pregnant individuals screened with rectovaginal swabs. We did not find associations between risk factors historically associated with GBS in pregnant people, suggesting that risk factors for GBS carriage in pregnancy may differ from those in the general population. We found that frequency of iron consumption and dental hygiene are risk factors for GBS carriage in Wisconsin adults. Given that these variables were not assayed in previous GBS surveys, it is possible they also influence carriage in pregnant people. Taken together, this work serves as a foundation for future work in developing approaches to decrease GBS abundance in carriers.

"We had to put ourselves in their shoes": Experiences of Medical Students and ObGyn Residents with a Values Clarification Workshop on Abortion.

Purpose: Values clarification workshops on abortion have been shown to increase support for abortion among healthcare workers. However, few studies have examined the impact of values clarification workshops on abortion among medical trainees. This study aimed to understand medical student and obstetrics and gynecology (ObGyn) residents' experiences with a virtual values clarification workshop on abortion. Methods: Clerkship year medical students and ObGyn residents at four midwestern teaching hospitals were invited to be interviewed about their experiences in a virtual values clarification workshop on abortion from January 2021 through December 2021. A single interviewer conducted interviews via Zoom using a standardized interview guide. Participants were asked to provide feedback and discuss their experiences in the workshop. Four qualitatively trained evaluators coded the interview transcripts in NVivo, using an inductive approach to establish consensus codes then themes. Results: This study interviewed 37 trainees, including 24 medical students and 13 ObGyn residents, as well as five facilitators, between November 2021 and February 2022. Three themes emerged in both trainee groups. First, participants found the workshops helped trainees clarify and understand their own views on abortion through thought exploration, peer validation, and reflection on their views' potential societal impacts. Second, through the workshop, participants reflected on others' opinions on abortion and better understood the spectrum of beliefs their peers held. Finally, participants found the workshops helped them explore and develop their professional identity as physicians-in-training, through practicing communication skills and building trust and mutual respect among peers. Conclusions: Medical trainees found values clarification workshops on abortion to be valuable, helping them establish their own beliefs about abortion, contextualize these beliefs among their peers', and practice professionalism. These findings indicate that values clarification workshops can play a key role in helping medical trainees discuss abortion and prepare for their professional future.

Formation of secondary allo-bile acids by novel enzymes from gut Firmicutes.

The gut microbiome of vertebrates is capable of numerous biotransformations of bile acids, which are responsible for intestinal lipid digestion and function as key nutrient-signaling molecules. The human liver produces bile acids from cholesterol predominantly in the A/B-cis orientation in which the sterol rings are "kinked", as well as small quantities of A/B-trans oriented "flat" stereoisomers known as "primary allo-bile acids". While the complex multi-step bile acid 7α-dehydroxylation pathway has been well-studied for conversion of "kinked" primary bile acids such as cholic acid (CA) and chenodeoxycholic acid (CDCA) to deoxycholic acid (DCA) and lithocholic acid (LCA), respectively, the enzymatic basis for the formation of "flat" stereoisomers allo-deoxycholic acid (allo-DCA) and allo-lithocholic acid (allo-LCA) by Firmicutes has remained unsolved for three decades. Here, we present a novel mechanism by which Firmicutes generate the "flat" bile acids allo-DCA and allo-LCA. The BaiA1 was shown to catalyze the final reduction from 3-oxo-allo-DCA to allo-DCA and 3-oxo-allo-LCA to allo-LCA. Phylogenetic and metagenomic analyses of human stool samples indicate that BaiP and BaiJ are encoded only in Firmicutes and differ from membrane-associated bile acid 5α-reductases recently reported in Bacteroidetes that indirectly generate allo-LCA from 3-oxo-Δ4-LCA. We further map the distribution of baiP and baiJ among Firmicutes in human metagenomes, demonstrating an increased abundance of the two genes in colorectal cancer (CRC) patients relative to healthy individuals.

Diversity and distribution of sulfur metabolic genes in the human gut microbiome and their association with colorectal cancer.

BACKGROUND: Recent evidence implicates microbial sulfidogenesis as a potential trigger of colorectal cancer (CRC), highlighting the need for comprehensive knowledge of sulfur metabolism within the human gut. Microbial sulfidogenesis produces genotoxic hydrogen sulfide (H2S) in the human colon using inorganic (sulfate) and organic (taurine/cysteine/methionine) substrates; however, the majority of studies have focused on sulfate reduction using dissimilatory sulfite reductases (Dsr). RESULTS: Here, we show that genes for microbial sulfur metabolism are more abundant and diverse than previously observed and are statistically associated with CRC. Using ~ 17,000 bacterial genomes from publicly available stool metagenomes, we studied the diversity of sulfur metabolic genes in 667 participants across different health statuses: healthy, adenoma, and carcinoma. Sulfidogenic genes were harbored by 142 bacterial genera and both organic and inorganic sulfidogenic genes were associated with carcinoma. Significantly, the anaerobic sulfite reductase (asr) genes were twice as abundant as dsr, demonstrating that Asr is likely a more important contributor to sulfate reduction in the human gut than Dsr. We identified twelve potential pathways for reductive taurine metabolism and discovered novel genera harboring these pathways. Finally, the prevalence of metabolic genes for organic sulfur indicates that these understudied substrates may be the most abundant source of microbially derived H2S. CONCLUSIONS: Our findings significantly expand knowledge of microbial sulfur metabolism in the human gut. We show that genes for microbial sulfur metabolism in the human gut are more prevalent than previously known, irrespective of health status (i.e., in both healthy and diseased states). Our results significantly increase the diversity of pathways and bacteria that are associated with microbial sulfur metabolism in the human gut. Overall, our results have implications for understanding the role of the human gut microbiome and its potential contributions to the pathogenesis of CRC. Video abstract.

METABOLIC: high-throughput profiling of microbial genomes for functional traits, metabolism, biogeochemistry, and community-scale functional networks.

BACKGROUND: Advances in microbiome science are being driven in large part due to our ability to study and infer microbial ecology from genomes reconstructed from mixed microbial communities using metagenomics and single-cell genomics. Such omics-based techniques allow us to read genomic blueprints of microorganisms, decipher their functional capacities and activities, and reconstruct their roles in biogeochemical processes. Currently available tools for analyses of genomic data can annotate and depict metabolic functions to some extent; however, no standardized approaches are currently available for the comprehensive characterization of metabolic predictions, metabolite exchanges, microbial interactions, and microbial contributions to biogeochemical cycling. RESULTS: We present METABOLIC (METabolic And BiogeOchemistry anaLyses In miCrobes), a scalable software to advance microbial ecology and biogeochemistry studies using genomes at the resolution of individual organisms and/or microbial communities. The genome-scale workflow includes annotation of microbial genomes, motif validation of biochemically validated conserved protein residues, metabolic pathway analyses, and calculation of contributions to individual biogeochemical transformations and cycles. The community-scale workflow supplements genome-scale analyses with determination of genome abundance in the microbiome, potential microbial metabolic handoffs and metabolite exchange, reconstruction of functional networks, and determination of microbial contributions to biogeochemical cycles. METABOLIC can take input genomes from isolates, metagenome-assembled genomes, or single-cell genomes. Results are presented in the form of tables for metabolism and a variety of visualizations including biogeochemical cycling potential, representation of sequential metabolic transformations, community-scale microbial functional networks using a newly defined metric "MW-score" (metabolic weight score), and metabolic Sankey diagrams. METABOLIC takes ~ 3 h with 40 CPU threads to process ~ 100 genomes and corresponding metagenomic reads within which the most compute-demanding part of hmmsearch takes ~ 45 min, while it takes ~ 5 h to complete hmmsearch for ~ 3600 genomes. Tests of accuracy, robustness, and consistency suggest METABOLIC provides better performance compared to other software and online servers. To highlight the utility and versatility of METABOLIC, we demonstrate its capabilities on diverse metagenomic datasets from the marine subsurface, terrestrial subsurface, meadow soil, deep sea, freshwater lakes, wastewater, and the human gut. CONCLUSION: METABOLIC enables the consistent and reproducible study of microbial community ecology and biogeochemistry using a foundation of genome-informed microbial metabolism, and will advance the integration of uncultivated organisms into metabolic and biogeochemical models. METABOLIC is written in Perl and R and is freely available under GPLv3 at https://github.com/AnantharamanLab/METABOLIC . Video abstract.

Microbial community dynamics and coexistence in a sulfide-driven phototrophic bloom.

BACKGROUND: Lagoons are common along coastlines worldwide and are important for biogeochemical element cycling, coastal biodiversity, coastal erosion protection and blue carbon sequestration. These ecosystems are frequently disturbed by weather, tides, and human activities. Here, we investigated a shallow lagoon in New England. The brackish ecosystem releases hydrogen sulfide particularly upon physical disturbance, causing blooms of anoxygenic sulfur-oxidizing phototrophs. To study the habitat, microbial community structure, assembly and function we carried out in situ experiments investigating the bloom dynamics over time. RESULTS: Phototrophic microbial mats and permanently or seasonally stratified water columns commonly contain multiple phototrophic lineages that coexist based on their light, oxygen and nutrient preferences. We describe similar coexistence patterns and ecological niches in estuarine planktonic blooms of phototrophs. The water column showed steep gradients of oxygen, pH, sulfate, sulfide, and salinity. The upper part of the bloom was dominated by aerobic phototrophic Cyanobacteria, the middle and lower parts by anoxygenic purple sulfur bacteria (Chromatiales) and green sulfur bacteria (Chlorobiales), respectively. We show stable coexistence of phototrophic lineages from five bacterial phyla and present metagenome-assembled genomes (MAGs) of two uncultured Chlorobaculum and Prosthecochloris species. In addition to genes involved in sulfur oxidation and photopigment biosynthesis the MAGs contained complete operons encoding for terminal oxidases. The metagenomes also contained numerous contigs affiliating with Microviridae viruses, potentially affecting Chlorobi. Our data suggest a short sulfur cycle within the bloom in which elemental sulfur produced by sulfide-oxidizing phototrophs is most likely reduced back to sulfide by Desulfuromonas sp. CONCLUSIONS: The release of sulfide creates a habitat selecting for anoxygenic sulfur-oxidizing phototrophs, which in turn create a niche for sulfur reducers. Strong syntrophism between these guilds apparently drives a short sulfur cycle that may explain the rapid development of the bloom. The fast growth and high biomass yield of Chlorobi-affiliated organisms implies that the studied lineages of green sulfur bacteria can thrive in hypoxic habitats. This oxygen tolerance is corroborated by oxidases found in MAGs of uncultured Chlorobi. The findings improve our understanding of the ecology and ecophysiology of anoxygenic phototrophs and their impact on the coupled biogeochemical cycles of sulfur and carbon.

An in-room observation study of hand hygiene and contact precaution compliance for Clostridioides difficile patients.

Using an innovative, covert, in-room observer method to evaluate infection control practices for patients with Clostridioides difficile infection, we found no difference between physician and nursing hand hygiene compliance and contact precaution usage. There was also no diurnal variation in hand hygiene practices, but decreased contact precaution usage at night. Conversely, hospital-wide data from overt observations collected over the same time period showed significantly higher hand hygiene compliance among nurses than physicians.

Trace incorporation of heavy water reveals slow and heterogeneous pathogen growth rates in cystic fibrosis sputum.

Effective treatment for chronic infections is undermined by a significant gap in understanding of the physiological state of pathogens at the site of infection. Chronic pulmonary infections are responsible for the morbidity and mortality of millions of immunocompromised individuals worldwide, yet drugs that are successful in laboratory culture are far less effective against pathogen populations persisting in vivo. Laboratory models, upon which preclinical development of new drugs is based, can only replicate host conditions when we understand the metabolic state of the pathogens and the degree of heterogeneity within the population. In this study, we measured the anabolic activity of the pathogen Staphylococcus aureus directly in the sputum of pediatric patients with cystic fibrosis (CF), by combining the high sensitivity of isotope ratio mass spectrometry with a heavy water labeling approach to capture the full range of in situ growth rates. Our results reveal S. aureus generation times with a median of 2.1 d, with extensive growth rate heterogeneity at the single-cell level. These growth rates are far below the detection limit of previous estimates of CF pathogen growth rates, and the rates are slowest in acutely sick patients undergoing pulmonary exacerbations; nevertheless, they are accessible to experimental replication within laboratory models. Treatment regimens that include specific antibiotics (vancomycin, piperacillin/tazobactam, tobramycin) further appear to correlate with slow growth of S. aureus on average, but follow-up longitudinal studies must be performed to determine whether this effect holds for individual patients.

Pediatric Cystic Fibrosis Sputum Can Be Chemically Dynamic, Anoxic, and Extremely Reduced Due to Hydrogen Sulfide Formation.

UNLABELLED: Severe and persistent bacterial lung infections characterize cystic fibrosis (CF). While several studies have documented the microbial diversity within CF lung mucus, we know much less about the inorganic chemistry that constrains microbial metabolic processes and their distribution. We hypothesized that sputum is chemically heterogeneous both within and between patients. To test this, we measured microprofiles of oxygen and sulfide concentrations as well as pH and oxidation-reduction potentials in 48 sputum samples from 22 pediatric patients with CF. Inorganic ions were measured in 20 samples from 12 patients. In all cases, oxygen was depleted within the first few millimeters below the sputum-air interface. Apart from this steep oxycline, anoxia dominated the sputum environment. Different sputum samples exhibited a broad range of redox conditions, with either oxidizing (16 mV to 355 mV) or reducing (-300 to -107 mV) potentials. The majority of reduced samples contained hydrogen sulfide and had a low pH (2.9 to 6.5). Sulfide concentrations increased at a rate of 0.30 µM H2S/min. Nitrous oxide was detected in only one sample that also contained sulfide. Microenvironmental variability was observed both within a single patient over time and between patients. Modeling oxygen dynamics within CF mucus plugs indicates that anoxic zones vary as a function of bacterial load and mucus thickness and can occupy a significant portion of the mucus volume. Thus, aerobic respiration accounts only partially for pathogen survival in CF sputum, motivating research to identify mechanisms of survival under conditions that span fluctuating redox states, including sulfidic environments. IMPORTANCE: Microbial infections are the major cause of morbidity and mortality in people living with CF, and yet microbial growth and survival in CF airways are not well understood. Insufficient information about the chemistry of the in vivo environment contributes to this knowledge gap. Our documentation of variable redox states corresponding to the presence or absence of sulfide begins to fill this void and motivates understanding of how different opportunistic pathogens adapt in these dynamic environments. Given the changing chemical state of CF sputum over time, it is important to consider a spectrum of aerobic and anaerobic lifestyles when studying CF pathogens in the laboratory. This work not only provides relevant constraints that can shape the design of laboratory experiments, it also suggests that sulfide might be a useful proxy for assessing the redox state of sputum in the clinic.

Sputum glucose and glycemic control in cystic fibrosis-related diabetes: a cross-sectional study.

Cystic fibrosis-related diabetes affects up to half of cystic fibrosis patients and is associated with increased mortality and more frequent pulmonary exacerbations. However, it is unclear to what degree good glycemic control might mitigate these risks and clinical outcomes have not previously been studied in relation to glucose from the lower airways, the site of infection and CF disease progression. We initially hypothesized that diabetic cystic fibrosis patients with glycosylated hemoglobin (HbA(1c)) > 6.5% have worse pulmonary function, longer and more frequent exacerbations and also higher sputum glucose levels than patients with HbA(1c) ≤ 6.5% or cystic fibrosis patients without diabetes. To test this, we analyzed spontaneously expectorated sputum samples from 88 cystic fibrosis patients. The median sputum glucose concentration was 0.70 mM (mean, 4.75 mM; range, 0-64.6 mM). Sputum glucose was not correlated with age, sex, body mass index, diabetes diagnosis, glycemic control, exacerbation frequency or length, or pulmonary function. Surprisingly, sputum glucose was highest in subjects with normal glucose tolerance, suggesting the dynamics of glycemic control, sputum glucose and pulmonary infections are more complex than previously thought. Two-year mean HbA(1c) was positively correlated with the length of exacerbation admission (p < 0.01), and negatively correlated with measures of pulmonary function (p < 0.01). While total number of hospitalizations for exacerbations were not significantly different, subjects with an HbA(1c) > 6.5% were hospitalized on average 6 days longer than those with HbA(1c) ≤ 6.5% (p < 0.01). Current clinical care guidelines for cystic fibrosis-related diabetes target HbA(1c) ≤ 7% to limit long-term microvascular damage, but more stringent glycemic control (HbA(1c) ≤ 6.5%) may further reduce the short-term pulmonary complications.

Anaerobic bacteria grow within Candida albicans biofilms and induce biofilm formation in suspension cultures.

The human microbiome contains diverse microorganisms, which share and compete for the same environmental niches. A major microbial growth form in the human body is the biofilm state, where tightly packed bacterial, archaeal, and fungal cells must cooperate and/or compete for resources in order to survive. We examined mixed biofilms composed of the major fungal species of the gut microbiome, Candida albicans, and each of five prevalent bacterial gastrointestinal inhabitants: Bacteroides fragilis, Clostridium perfringens, Escherichia coli, Klebsiella pneumoniae, and Enterococcus faecalis. We observed that biofilms formed by C. albicans provide a hypoxic microenvironment that supports the growth of two anaerobic bacteria, even when cultured in ambient oxic conditions that are normally toxic to the bacteria. We also found that coculture with bacteria in biofilms induces massive gene expression changes in C. albicans, including upregulation of WOR1, which encodes a transcription regulator that controls a phenotypic switch in C. albicans, from the "white" cell type to the "opaque" cell type. Finally, we observed that in suspension cultures, C. perfringens induces aggregation of C. albicans into "mini-biofilms," which allow C. perfringens cells to survive in a normally toxic environment. This work indicates that bacteria and C. albicans interactions modulate the local chemistry of their environment in multiple ways to create niches favorable to their growth and survival.

Apratoxin H and apratoxin A sulfoxide from the Red Sea cyanobacterium Moorea producens.

Cultivation of the marine cyanobacterium Moorea producens, collected from the Nabq Mangroves in the Gulf of Aqaba (Red Sea), led to the isolation of new apratoxin analogues apratoxin H (1) and apratoxin A sulfoxide (2), together with the known apratoxins A-C, lyngbyabellin B, and hectochlorin. The absolute configuration of these new potent cytotoxins was determined by chemical degradation, MS, NMR, and CD spectroscopy. Apratoxin H (1) contains pipecolic acid in place of the proline residue present in apratoxin A, expanding the known suite of naturally occurring analogues that display amino acid substitutions within the final module of the apratoxin biosynthetic pathway. The oxidation site of apratoxin A sulfoxide (2) was deduced from MS fragmentation patterns and IR data, and 2 could not be generated experimentally by oxidation of apratoxin A. The cytotoxicity of 1 and 2 to human NCI-H460 lung cancer cells (IC50 = 3.4 and 89.9 nM, respectively) provides further insight into the structure-activity relationships in the apratoxin series. Phylogenetic analysis of the apratoxin-producing cyanobacterial strains belonging to the genus Moorea, coupled with the recently annotated apratoxin biosynthetic pathway, supports the notion that apratoxin production and structural diversity may be specific to their geographical niche.