SEA-PHAGES and SEA-GENES: Advancing Virology and Science Education.

Research opportunities for undergraduate students are strongly advantageous, but implementation at a large scale presents numerous challenges. The enormous diversity of the bacteriophage population and a supportive programmatic structure provide opportunities to engage early-career undergraduates in phage discovery, genomics, and genetics. The Science Education Alliance (SEA) is an inclusive Research-Education Community (iREC) providing centralized programmatic support for students and faculty without prior experience in virology at institutions from community colleges to research-active universities to participate in two course-based projects, SEA-PHAGES (SEA Phage Hunters Advancing Genomic and Evolutionary Science) and SEA-GENES (SEA Gene-function Exploration by a Network of Emerging Scientists). Since 2008, the SEA has supported more than 50,000 undergraduate researchers who have isolated more than 23,000 bacteriophages of which more than 4,500 are fully sequenced and annotated. Students have functionally characterized hundreds of phage genes, and the phage collection has fueled the therapeutic use of phages for treatment of Mycobacterium infections. Participation in the SEA promotes student persistence in science education, and its inclusivity promotes a more equitable scientific community.

A genome-wide cytotoxicity screen of cluster F1 mycobacteriophage Girr reveals novel inhibitors of Mycobacterium smegmatis growth.

Over the past decade, thousands of bacteriophage genomes have been sequenced and annotated. A striking observation from this work is that known structural features and functions cannot be assigned for >65% of the encoded proteins. One approach to begin experimentally elucidating the function of these uncharacterized gene products is genome-wide screening to identify phage genes that confer phenotypes of interest like inhibition of host growth. This study describes the results of a screen evaluating the effects of overexpressing each gene encoded by the temperate Cluster F1 mycobacteriophage Girr on the growth of the host bacterium Mycobacterium smegmatis. Overexpression of 29 of the 102 Girr genes (~28% of the genome) resulted in mild to severe cytotoxicity. Of the 29 toxic genes described, 12 have no known function and are predominately small proteins of <125 amino acids. Overexpression of the majority of these 12 cytotoxic no known functions proteins resulted in moderate to severe growth reduction and represent novel antimicrobial products. The remaining 17 toxic genes have predicted functions, encoding products involved in phage structure, DNA replication/modification, DNA binding/gene regulation, or other enzymatic activity. Comparison of this dataset with prior genome-wide cytotoxicity screens of mycobacteriophages Waterfoul and Hammy reveals some common functional themes, though several of the predicted Girr functions associated with cytotoxicity in our report, including genes involved in lysogeny, have not been described previously. This study, completed as part of the HHMI-supported SEA-GENES project, highlights the power of parallel, genome-wide overexpression screens to identify novel interactions between phages and their hosts.

Quality of Life After Axillary Lymph Node Dissection Among Racial and Ethnic Minority Women.

Importance: Higher lymphedema rates after axillary lymph node dissection (ALND) have been found in Black and Hispanic women; however, there is poor correlation between subjective symptoms, quality of life (QOL), and measured lymphedema. Additionally, racial and ethnic differences in QOL have been understudied. Objective: To evaluate the association of race and ethnicity with long-term QOL in patients with breast cancer treated with ALND. Design, Setting, and Participants: This cohort study enrolled women aged 18 years and older with breast cancer who underwent unilateral ALND at a tertiary cancer center between November 2016 and March 2020. Preoperatively and at 6-month intervals, arm volume was measured by perometer and QOL was assessed using the Upper Limb Lymphedema-27 (ULL-27) questionnaire, a validated tool for assessing lymphedema that evaluates how arm symptoms affect physical, psychological, and social functioning. Data were analyzed from November 2016 to October 2023. Exposures: Breast surgery and unilateral ALND in the primary setting or after sentinel lymph node biopsy. Main Outcomes and Measures: Scores in each domain of the ULL-27 were compared by race and ethnicity. Factors impacting QOL were identified using multivariable regression analyses. Results: The study included 281 women (median [IQR] age, 48 [41-58] years) with breast cancer who underwent unilateral ALND and had at least 6 months of follow-up. Of these, 30 patients (11%) self-identified as Asian individuals, 57 (20%) as Black individuals, 23 (8%) as Hispanic individuals, and 162 (58%) as White individuals; 9 individuals (3%) who did not identify as part of a particular group or who were missing race and ethnicity data were categorized as having unknown race and ethnicity. Median (IQR) follow-up was 2.97 (1.96-3.67) years. The overall 2-year lymphedema rate was 20% and was higher among Black (31%) and Hispanic (27%) women compared with Asian (15%) and White (17%) women (P = .04). Subjective arm swelling was more common among Asian (57%), Black (70%), and Hispanic (87%) women than White (44%) women (P < .001), and lower physical QOL scores were reported by racial and ethnic minority women at nearly every follow-up. For example, at 24 months, median QOL scores were 87, 79, and 80 for Asian, Black, and Hispanic women compared with 92 for White women (P = .003). On multivariable analysis, Asian race (ß = -5.7; 95% CI, -9.5 to -1.8), Hispanic ethnicity (ß = -10.0; 95% CI, -15.0 to -5.2), and having Medicaid (ß = -5.4; 95% CI, -9.2 to -1.7) or Medicare insurance (ß = -6.9; 95% CI, -10.0 to -3.4) were independently associated with worse physical QOL (all P < .001). Conclusions and Relevance: Findings of this cohort study suggest that Asian, Black, and Hispanic women experience more subjective arm swelling after unilateral ALND for breast cancer compared with White women. Black and Hispanic women had higher rates of objective lymphedema than their White counterparts. Both minority status and public medical insurance were associated with worse physical QOL. Understanding disparities in QOL after ALND is an unmet need and may enable targeted interventions to improve QOL for these patients.

A genome-wide overexpression screen reveals Mycobacterium smegmatis growth inhibitors encoded by mycobacteriophage Hammy.

During infection, bacteriophages produce diverse gene products to overcome bacterial antiphage defenses, to outcompete other phages, and to take over cellular processes. Even in the best-studied model phages, the roles of most phage-encoded gene products are unknown, and the phage population represents a largely untapped reservoir of novel gene functions. Considering the sheer size of this population, experimental screening methods are needed to sort through the enormous collection of available sequences and identify gene products that can modulate bacterial behavior for downstream functional characterization. Here, we describe the construction of a plasmid-based overexpression library of 94 genes encoded by Hammy, a Cluster K mycobacteriophage closely related to those infecting clinically important mycobacteria. The arrayed library was systematically screened in a plate-based cytotoxicity assay, identifying a diverse set of 24 gene products (representing ∼25% of the Hammy genome) capable of inhibiting growth of the host bacterium Mycobacterium smegmatis. Half of these are related to growth inhibitors previously identified in related phage Waterfoul, supporting their functional conservation; the other genes represent novel additions to the list of known antimycobacterial growth inhibitors. This work, conducted as part of the HHMI-supported Science Education Alliance Gene-function Exploration by a Network of Emerging Scientists (SEA-GENES) project, highlights the value of parallel, comprehensive overexpression screens in exploring genome-wide patterns of phage gene function and novel interactions between phages and their hosts.

Sexual Harassment in Surgery-Is Operating Room Culture the Culprit?

BACKGROUND: Sexual harassment is a known problem in surgical training and a focus of growing attention in recent years. However, the environments where sexual harassment in surgical training most commonly takes place are not yet described. METHODS: An anonymous, voluntary, electronic survey was distributed to surgical trainees, and all programs nationally were invited to participate. RESULTS: Sixteen general surgery training programs elected to participate, and the survey achieved a response rate of 30%. 48.9% of respondents reported experiencing sexual harassment. The most common location for harassment was in the operating room (OR) (74% of harassed respondents). The second most common location for harassment was the wards (67.4% of harassed respondents). In the OR, attendings and nurses were the most common harassers. The most common harassment in the OR was being called a sexist slur or intimate nickname. DISCUSSION: Surgical trainees report that the OR was the most common location for trainee harassment. Given that harassment is most commonly perpetrated by both attendings and nurses, harassment in surgical training may not entirely be due to hierarchies but may also be attributed to a flawed and permissive OR culture. Surgical training programs should vigilantly eliminate the circumstances that permit sexual harassment in the OR.

Ancillary Treatment Referrals and Visits After Breast Cancer Surgery in a Sociodemographically Diverse Population.

BACKGROUND: Ancillary therapies with rehabilitative, palliative, and survivorship specialists mitigate adverse effects of breast cancer surgery. Existing data suggest that patients from disadvantaged backgrounds may be less likely to receive these services. This study aimed to assess variations in ancillary provider referrals and patient visits at a high-volume urban cancer center. METHODS: Electronic health records of breast cancer surgical patients at the Yale-New Haven Health System between 2010 and 2017 were reviewed. The primary end points were postoperative referral to ancillary service providers and patient use of ancillary services (defined as attending ≥ 1 consultation). Associations between end points and demographic/disease variables were identified in uni- and multivariable logistic regression analyses. RESULTS: The study identified 5496 patients: 2288 patients (41.6%) referred to ancillary services and 1572 patients (28.6%) who attended one or more consultations. Referrals were highest among the patients with Hispanic (57.5%) or black (54.9%) ancestry, no health insurance (57.6%), lowest percentage of high school degrees for the zip code area (50.5%), and poorest median income bracket (50.7%). Associations remained significant in the multivariable analysis (p < 0.05). Minority race remained associated with referrals in analyses of each ancillary service individually. Visits to ancillary specialists were greatest among the patients with private insurance (70.7%), highest percentage of high school degrees (72.8%), highest median household income (72.2%), and Hispanic ethnicity (73.5%). Highest median household income (odds ratio [OR] 1.45; p = 0.02) and Hispanic ethnicity (OR, 1.50; p = 0.05) remained associated in the multivariable analysis. CONCLUSIONS: In a well-resourced health system serving a demographically diverse population, traditional markers of poor health care access were associated with referral for ancillary treatment after breast cancer surgery but not with utilization of ancillary treatment. Health care access remains a critical barrier to adjunctive therapies that target postoperative morbidity and elevate quality of life.

Systematic overexpression of genes encoded by mycobacteriophage Waterfoul reveals novel inhibitors of mycobacterial growth.

Bacteriophages represent an enormous reservoir of novel genes, many of which are unrelated to existing entries in public databases and cannot be assigned a predicted function. Characterization of these genes can provide important insights into the intricacies of phage-host interactions and may offer new strategies to manipulate bacterial growth and behavior. Overexpression is a useful tool in the study of gene-mediated effects, and we describe here the construction of a plasmid-based overexpression library of a complete set of genes for Waterfoul, a mycobacteriophage closely related to those infecting clinically important strains of Mycobacterium tuberculosis and/or Mycobacterium abscessus. The arrayed Waterfoul gene library was systematically screened in a plate-based cytotoxicity assay, identifying a diverse set of 32 Waterfoul gene products capable of inhibiting the growth of the host Mycobacterium smegmatis and providing a first look at the frequency and distribution of cytotoxic products encoded within a single mycobacteriophage genome. Several of these Waterfoul gene products were observed to confer potent anti-mycobacterial effects, making them interesting candidates for follow-up mechanistic studies.

Genomic Sequence and Characteristics of EmiRose, a Bacteriophage Isolated on Corynebacterium flavescens.

Bacteriophage EmiRose is a siphovirus infecting Corynebacterium flavescens. The EmiRose genome is 37,431 bp long and composed of 47 protein-coding genes. Based on gene content similarity, EmiRose is not closely related to any previously sequenced bacteriophages in the actinobacteriophage database to date, including other corynebacteriophages. EmiRose is classified as a singleton.

Genome Sequence and Characteristics of Cluster C1 Mycobacterium smegmatis Phage EasyJones.

Bacteriophage EasyJones is a myovirus infecting Mycobacterium smegmatis mc2155, with a genome length and gene content similar to those of phages grouped in subcluster C1. Interestingly, EasyJones contains a gene found in a subset of C1 genomes that is similar to the well-characterized immunity repressor of subcluster A1 mycobacteriophage Bxb1.

Comparing complications in irradiated and non-irradiated free-flaps in patients with bilateral immediate breast reconstruction and unilateral post-mastectomy radiotherapy.

BACKGROUND: Numerous studies have evaluated the effect of post-mastectomy radiotherapy (PMRT) on autologous breast reconstruction, but the variability of PMRT regimens and inadequate controls have made results difficult to interpret. Therefore, in this study, irradiated free-flaps are compared to non-irradiated internal controls in patients who underwent immediate bilateral reconstruction followed by unilateral PMRT to better delineate the effect of PMRT. The role of regional nodal irradiation (RNI) is also specifically assessed. METHODS: Appropriate patients were identified through retrospective review. Complications such as fat necrosis, fibrosis, infection, delayed healing, and flap loss, as well as revision surgeries, among the irradiated free-flaps were compared to those on the contralateral non-irradiated side. Additional analyses were performed to evaluate the effect of patient demographics and treatment characteristics, such as RNI, on complications involving the irradiated free-flaps. RESULTS: Seventy-three women were included. There was no significant difference between complication rates for the irradiated and non-irradiated free-flaps (39.7% vs. 38.4%, p = .78), although irradiated free-flaps were more likely to have fibrosis (17.0% vs. 0.0%; p < .0001) and multiple complications (9.6% vs. 0.0%; p = .02). Both groups underwent a similar number of revision surgeries (42.5% vs. 41.1%; p = .29). Looking at the irradiated free-flaps, internal mammary node (IMN) irradiation was the only factor predictive of complications (IRR 3.80, CI 1.32-10.97; p = .01). CONCLUSIONS: PMRT may contribute to free-flap fibrosis, but does not appear to affect the overall risk of complications or revision surgeries. However, additional counseling is warranted if IMN irradiation is likely, as it is potentially associated with increased complications.

Characteristics and Long-Term Risk of Breast Angiosarcoma.

BACKGROUND: Angiosarcoma of the breast is rare and aggressive. It can occur as a de novo tumor or secondary to breast cancer treatment. The purpose of this study is to analyze differences between patients with primary and secondary angiosarcoma of the breast and investigate potential risk factors for its development. PATIENTS AND METHODS: The Surveillance, Epidemiology, and End Results program of the National Cancer Institute database was queried to identify patients with angiosarcoma of the breast, trunk, shoulder, and upper arm. The population-based incidence was analyzed. Primary and secondary angiosarcoma cases were identified and compared. Breast cancer characteristics of secondary angiosarcoma patients were compared with all breast cancer patients in the database who did not develop angiosarcoma. RESULTS: Overall, 904 patients were included, and 65.4% were secondary angiosarcomas. These patients had worse survival, were older, more likely to be White, more likely to have regionally advanced disease, and had angiosarcoma tumors of higher pathologic grade. Independent factors associated with development of secondary angiosarcoma among breast cancer patients included White race, older age, invasive tumor, lymph node removal, lumpectomy, radiation treatment, and left-sided tumor. Although the mean time to develop angiosarcoma after breast cancer diagnosis was 8.2 years, the risk continues to increase up to 30 years after breast cancer treatment. CONCLUSION: Angiosarcoma is rare but increasing in incidence. Secondary angiosarcomas are more common and exhibit more aggressive behavior. Several factors for angiosarcoma after breast cancer treatment could be identified, which may help us counsel and identify patients at risk.

What's it Worth?: The Costs and Benefits of an Initiative to Decrease Post-Call Fatigued Driving Among Surgery Residents.

BACKGROUND: In 2017 the ACGME enacted new regulations requiring sponsoring institutions to ensure "safe transportation options for residents who may be too fatigued to safely return home." We investigate here the impact of a pilot "Safe Ride" program designed to mitigate the risks of fatigued driving. METHODS: During a 2-month pilot period at a single university-affiliated general surgery residency with four urban clinical sites, all residents (n = 72) were encouraged to hire a rideshare (e.g., Uber, Lyft) to and from 24-h clinical shifts if they felt too fatigued to drive safely. The cost of the rideshare was fully reimbursed to the resident. The impact of this intervention was evaluated using utilization data and a post-intervention resident survey. RESULTS: A total of 16.6% of trainees utilized a rideshare at least one time. Sixty-three post-call rides were taken, predominantly by junior residents (92.4%) and for commutes greater than 15 miles (91%). The cost for the 60-day pilot was $3030. Comparing pre-intervention to post-intervention data, there was a significant improvement in the reported frequency of falling asleep or nearly asleep while driving (P < 0.001). Trainees nearly unanimously (98%) supported efforts to make the program permanent. DISCUSSION: Driving while fatigued is common among surgical residents, with increased risk among junior residents, during longer commutes and following longer shifts. A reimbursed rideshare program effectively targets these risk factors and was associated with a significant decrease in rates of self-reported fatigued driving. Future efforts should focus on strategies to promote use of reimbursed rideshare programs while remaining cost efficient.

Driving Safety Among Surgical Residents in the Era of Duty Hour Restrictions.

OBJECTIVE: Fatigued driving is a known contributor to adverse motor vehicle events (AMVEs), defined as crashes and near misses. Surgical trainees work long and irregular hours; the safety of work-related driving since the introduction of work hour regulations has not yet been studied in this population. We aimed to assess the impact of fatigue on driving safety and explore perceptions of a funded rideshare program. DESIGN: An electronic survey was delivered and inquired in retrospective fashion about fatigue and sleepiness while driving, occurrences of AMVEs, and projected use of a funded rideshare program as a potential solution to unsafe driving. Chi-square testing determined categorical differences between response choices. SETTING: Yale University School of Medicine, Department of Surgery, New Haven, CT-a general surgery program with 4 urban clinical sites positioned along a roughly twenty mile stretch of interstate highway in Southeastern Connecticut. PARTICIPANTS: General Surgery residents at the Yale University School of Medicine. RESULTS: Of 58 respondents (81% response rate), 97% reported that fatigue compromised their safety while driving to or from work. Eighty-three percent reported falling nearly or completely asleep, and 22% reported AMVEs during work-related driving. Junior residents were more likely than Seniors to drive fatigued on a daily-to-weekly basis (69% vs 47%, p = 0.02) and twice as likely to fall asleep on a weekly-to-monthly basis (67% vs 33%, p = 0.02). Despite this, only 7% of residents had ever hired a ride service when fatigued, though 88%, would use a free rideshare service if provided. CONCLUSIONS: Work-related fatigue impairs the driving safety of nearly all residents, contributing to frequent AMVEs. Currently, few residents hire rideshare services. Eliminating the cost barrier by funding a rideshare and encouraging its routine use may protect surgical trainees and other drivers.

Surgical Outcomes of Mastectomy with Immediate Autologous Reconstruction Followed by Radiation.

INTRODUCTION: Timing of autologous reconstruction relative to postmastectomy radiation therapy (PMRT) is debated. Benefits of immediate reconstruction must be weighed against a possibly heightened risk of complications from flap irradiation. We reviewed flap outcomes after single operation plus PMRT in a large institutional cohort. METHODS: Medical records were reviewed for women who underwent simultaneous mastectomy-autologous reconstruction with PMRT from 2007 to 2016. Primary endpoints were rates and types of radiation-related flap complications and reoperations, whose predictors were assessed by multivariable analysis. A p value < 0.10 was deemed significant to avoid type II error. Non-parametric logistic regression generated a model of PMRT timing associated with probabilities of complications and reoperations. RESULTS: One-hundred and thirty women underwent 208 mastectomy reconstruction operations, with a median follow up of 35.1 months (interquartile range 23.6-56.5). Forty-seven (36.2%) women experienced radiation-related complications, commonly fat necrosis (44.1%) and chest wall asymmetry (28.8%). Complications were higher among women who received PMRT < 3 months after surgery (46.8% for < 3 months vs. 29.3% for ≥ 3 months; p = 0.06), most of whom received neoadjuvant chemotherapy, and among women treated with internal mammary nodal (IMN) radiation (65.2% vs. 26.4%; p < 0.01); IMN radiation remained strongly associated in multivariable analysis (odds ratio [OR] 5.24; p < 0.01). Thirty-two (24.6%) women underwent 70 reoperations, commonly fat grafting (51.9%) and fat necrosis excision (17.1%). Reoperations were higher among women who received PMRT < 3 months after surgery (48.9 for < 3 months vs. 36.6 for ≥ 3 months; p = 0.19), which was significantly associated in multivariable analysis (OR 0.42; p = 0.08 for ≥ 3 months). The probabilities of complications and reoperations were lowest when PMRT was administered ≥ 3 months after surgery. CONCLUSIONS: Among a large institutional cohort, immediate autologous reconstruction was associated with similar rates of adverse flap outcomes as historically reported alternatively sequenced protocols. IMN radiation increased risk, while PMRT ≥ 3 months after surgery decreased risk. Additional studies are needed to elaborate the impact of IMN radiation and early PMRT in immediate versus delayed autologous reconstruction.

Association of Medicaid Expansion Under the Affordable Care Act With Breast Cancer Stage at Diagnosis.

Importance: The expansion of Medicaid sought to fill gaps in insurance coverage among low-income Americans. Although coverage has improved, little is known about the relationship between Medicaid expansion and breast cancer stage at diagnosis. Objective: To review the association of Medicaid expansion with breast cancer stage at diagnosis and the disparities associated with insurance status, age, and race/ethnicity. Design, Setting, and Participants: This cohort study used data from the National Cancer Database to characterize the relationship between breast cancer stage and race/ethnicity, age, and insurance status. Data from 2007 to 2016 were obtained, and breast cancer stage trends were assessed. Additionally, preexpansion years (2012-2013) were compared with postexpansion years (2015-2016) to assess Medicaid expansion in 2014. Data were analyzed from August 12, 2019, to January 19, 2020. The cohort included a total of 1 796 902 patients with primary breast cancer who had private insurance, Medicare, or Medicaid or were uninsured across 45 states. Main Outcomes and Measures: Percent change of uninsured patients with breast cancer and stage at diagnosis, stratified by insurance status, race/ethnicity, age, and state. Results: This study included a total of 1 796 902 women. Between 2012 and 2016, 71 235 (4.0%) were uninsured or had Medicaid. Among all races/ethnicities, in expansion states, there was a reduction in uninsured patients from 22.6% (4771 of 21 127) to 13.5% (2999 of 22 150) (P < .001), and in nonexpansion states, there was a reduction from 36.5% (5431 of 14 870) to 35.6% (4663 of 13 088) (P = .12). Across all races, there was a reduction in advanced-stage disease from 21.8% (4603 of 21 127) to 19.3% (4280 of 22 150) (P < .001) in expansion states compared with 24.2% (3604 of 14 870) to 23.5% (3072 of 13 088) (P = .14) in nonexpansion states. In African American patients, incidence of advanced disease decreased from 24.6% (1017 of 4136) to 21.6% (920 of 4259) (P < .001) in expansion states and remained at approximately 27% (27.4% [1220 of 4453] to 27.5% [1078 of 3924]; P = .94) in nonexpansion states. Further analysis suggested that the improvement was associated with a reduction in stage 3 diagnoses. Conclusions and Relevance: In this cohort study, expansion of Medicaid was associated with a reduced number of uninsured patients and a reduced incidence of advanced-stage breast cancer. African American patients and patients younger than 50 years experienced particular benefit. These data suggest that increasing access to health care resources may alter the distribution of breast cancer stage at diagnosis.