scholarly journals Genomic Epidemiology of Clostridioides difficile Sequence Types 1 and 2 Across Three US Medical Centers

2020 ◽  
Vol 41 (S1) ◽  
pp. s238-s238
Author(s):  
Arianna Miles-Jay ◽  
Vincent Young ◽  
Eric Pamer ◽  
Tor Savidge ◽  
Mini Kamboj ◽  
...  

Background:Clostridioides difficile is a toxin-producing bacterium that is the foremost cause of healthcare-associated diarrhea in the United States. Recent epidemiologic and genomic evidence indicates that divergent C. difficile strains have varying propensities for transmission within healthcare settings. We investigated whether and how these differences are reflected in the genomic epidemiology of 2 common C. difficile strains—sequence type (ST) 1 (analogous to Ribotype 027) and ST2 (associated with Ribotypes 014/020)—across 3 geographically distinct US medical centers. Methods: Between 2011 and 2017, a convenience sample of ST1 and ST2 C. difficile clinical isolates were collected from 3 US sites: The University of Michigan Medical Center, Texas Medical Center Hospitals, and Memorial Sloan Kettering Cancer Center. Isolates underwent whole-genome sequencing and in silico multilocus sequence typing to verify strain types. Sequences were mapped to ST1 and ST2 reference genomes and single nucleotide variants (SNVs) were identified, filtered, and used to construct pairwise SNV distance matrices. A range of pairwise SNV distance thresholds were applied to assess genetic linkages consistent with recent transmission within ST1 compared to within ST2. Proportions of genetically linked isolates were compared using 2 tests. Results: We identified 200 ST1 and 188 ST2 isolates across the 3 collection sites. Overall, ST2 was more genetically diverse than ST1 (pairwise SNV distance range, 0–156 SNVs and 0–78 SNVs, respectively). ST2 isolates displayed significantly less evidence of recent transmission: 10 ST2 isolates (5.3%) were within 2 SNVs of another isolate compared to 88 (44%) ST1 isolates (P .001) (Fig. 1). As the SNV threshold increased to 5 and 10 SNVs, this trend was maintained (all P < .001). ST2 isolates were also more likely to be genetically linked to an isolate from a different collection site than ST1 isolates. Among isolates with genetic links to at least 1 other isolate at the 5 SNV and 10 SNV thresholds, 21 of 37 and 74 of 89 ST2 isolates (57%, 83%) were linked to an isolate from a different collection site, compared to 2 of 88 and 48 of 157 ST1 isolates (2% and 31%, respectively; both P < .001). Conclusions: Compared to C. difficile ST1 isolates, ST2 isolates displayed less evidence of recent healthcare transmission and were more likely to be genetically linked to isolates from divergent collection sites. Interpreting genetic linkages among C. difficile isolates requires an understanding of regional and strain-specific genetic diversity to avoid misattribution of genetic linkages to recent transmission.Funding: NoneDisclosures: None

Author(s):  
Kevin Hauck ◽  
Katherine Hochman ◽  
Mark Pochapin ◽  
Sondra Zabar ◽  
Jeffrey A Wilhite ◽  
...  

Abstract Objective New York City was the epicenter of the outbreak of the 2020 COVID-19 pandemic in the United States. As a large, quaternary care medical center, NYU Langone Medical Center was one of many New York medical centers that experienced an unprecedented influx of patients during this time. Clinical leadership effectively identified, oriented, and rapidly deployed a “COVID Army”, consisting of non-hospitalist physicians, to meet the needs of this patient influx. We share feedback from our providers on our processes and offer specific recommendations for systems experiencing a similar influx in the current and future pandemics. Methods In order to assess the experiences and perceived readiness of these physicians (n=183), we distributed a 32-item survey between March and June of 2020. Thematic analyses and response rates were examined in order to develop results. Results Responses highlighted varying experiences and attitudes of our front-line physicians during an emerging pandemic. Thematic analyses revealed a series of lessons learned, including the need to: (1) provide orientations, (2) clarify roles/ workflow, (3) balance team workload, (4) keep teams updated on evolving policies, (5) make team members feel valued, and (6) ensure they have necessary tools available. Conclusions Lessons from our deployment and assessment are scalable at other institutions.


2018 ◽  
Vol 9 (9) ◽  
pp. 523-533 ◽  
Author(s):  
Alec W. Petersen ◽  
Avantika S. Shah ◽  
Sandra F. Simmons ◽  
Matthew S. Shotwell ◽  
J. Mary Lou Jacobsen ◽  
...  

Background: Polypharmacy is common in hospitalized older adults. Deprescribing interventions are not well described in the acute-care setting. The objective of this study was to describe a hospital-based, patient-centered deprescribing protocol (Shed-MEDS) and report pilot results. Methods: This was a pilot study set in one academic medical center in the United States. Participants consisted of a convenience sample of 40 Medicare-eligible, hospitalized patients with at least five prescribed medications. A deprescribing protocol (Shed-MEDS) was implemented among 20 intervention and 20 usual care control patients during their hospital stay. The primary outcome was the total number of medications deprescribed from hospital enrollment. Deprescribed was defined as medication termination or dose reduction. Enrollment medications reflected all prehospital medications and active in-hospital medications. Baseline characteristics and outcomes were compared between the intervention and usual care groups using simple logistic or linear regression for categorical and continuous measures, respectively. Results: There was no significant difference between groups in mean age, sex or Charlson comorbidity index. The intervention and control groups had a comparable number of medications at enrollment, 25.2 (±6.3) and 23.4 (±3.8), respectively. The number of prehospital medications in each group was 13.3 (±4.6) and 15.3 (±4.6), respectively. The Shed-MEDS protocol compared with usual care significantly increased the mean number of deprescribed medications at hospital discharge and reduced the total medication burden by 11.6 versus 9.1 ( p = 0.032) medications. The deprescribing intervention was associated with a difference of 4.6 [95% confidence interval (CI) 2.5–6.7, p < 0.001] in deprescribed medications and a 0.5 point reduction (95% CI −0.01 to 1.1) in the drug burden index. Conclusions: A hospital-based, patient-centered deprescribing intervention is feasible and may reduce the medication burden in older adults.


Author(s):  
Kevin M. Ryan ◽  
Sina Mostaghimi ◽  
Julianne Dugas ◽  
Eric Goralnick

ABSTRACT Objectives: The aim of this study was to determine the involvement of emergency medicine physicians at academic medical centers across the United States as well as their background training, roles in the hospital, and compensation if applicable for time dedicated to preparedness. Methods: A structured survey was delivered by means of email to 109 Chairs of Emergency Medicine across the United States at academic medical centers. Unique email links were provided to track response rate and entered into REDCap database. Descriptive statistics were obtained, including roles in emergency preparedness, training, and compensation. Results: Forty-four of the 109 participants responded, resulting in a response rate of 40.4%. The majority held an administrative role in emergency preparedness. Formal training for the position (participants could select more than 1) included various avenues of education such as emergency medical services fellowship or in-person or online courses. Of the participants, most (93.18%) strongly agreed that it was important to have a physician with expertise in disaster medicine assisting with preparedness. Conclusions: The majority of responding academic medical center participants have taken an active role in hospital emergency preparedness. Education for the roles varied though, often consisted of courses from emergency management agencies. Volunteering their time for compensation was noted by 27.5%.


2019 ◽  
Vol 6 (10) ◽  
Author(s):  
Jonathan C Cho ◽  
Matthew P Crotty ◽  
Wesley D Kufel ◽  
Elias B Chahine ◽  
Amelia K Sofjan ◽  
...  

Abstract Background Pharmacists with residency training in infectious diseases (ID) optimize antimicrobial therapy outcomes in patients and support antimicrobial stewardship (AS) programs. Although most ID residencies are accredited and assessed by certain standards, the degree to which these programs are similar is not known. Methods A 19-item, cross-sectional, multicentered, electronic survey was distributed via e-mail to pharmacy residency program directors (RPDs) of all 101 second-year postgraduate (PGY-2) ID residency programs in the United States. Results Survey responses were collected from 71 RPDs (70.3%); 64.8% were associated with an academic medical center and 97.2% focused primarily in adult ID. Rotations in the microbiology laboratory, adult AS, and adult ID consult were required in 98.6% of residency programs. Only 28.2% of responding programs required pediatric AS and pediatric ID consult rotations. Programs at academic medical centers were more likely to offer immunocompromised host ID consult (P = .003), pediatric ID consult (P = .006), and hospital epidemiology (P = .047) rotations but less frequently offered outpatient AS (P = .003), viral hepatitis clinics (P = .001), and travel medicine clinics (P = .007) rotations compared to programs at nonacademic medical centers. Residents were frequently involved in AS committees (97.2%), pharmacokinetic dosing of antimicrobials (83.1%), precepting pharmacy trainees (80.3%), and performing research projects (91.5%). Conclusions The PGY-2 ID pharmacy residency programs demonstrated consistency in required adult ID consult, antimicrobial management activities, committee service, and teaching and research opportunities. Pediatric experiences were less common. The PGY-2 ID residency programs prepare pharmacists to become antimicrobial stewards for adult patients.


Author(s):  
Tatum D Mortimer ◽  
Preeti Pathela ◽  
Addie Crawley ◽  
Jennifer L Rakeman ◽  
Ying Lin ◽  
...  

Abstract Background Genomic epidemiology studies of gonorrhea in the United States have primarily focused on national surveillance for antibiotic resistance, and patterns of local transmission between demographic groups of resistant and susceptible strains are unknown. Methods We analyzed a convenience sample of genome sequences, antibiotic susceptibility, and patient data from 897 gonococcal isolates cultured at the NYC Public Health Laboratory from NYC Department of Health and Mental Hygiene (DOHMH) Sexual Health Clinic (SHC) patients, primarily in 2012-13. We reconstructed the gonococcal phylogeny, defined transmission clusters using a 10 non-recombinant single nucleotide polymorphism threshold, tested for clustering of demographic groups, and placed NYC isolates in a global phylogenetic context. Results The NYC gonococcal phylogeny reflected global diversity with isolates from 22/23 of the prevalent global lineages (96%). Isolates clustered on the phylogeny by patient sexual behavior (p&0.001) and race/ethnicity (p&0.001). Minimum inhibitory concentrations were higher across antibiotics in isolates from men who have sex with men compared to heterosexuals (p&0.001) and white heterosexuals compared to black heterosexuals (p&0.01). In our dataset, all large transmission clusters (≥10 samples) of N. gonorrhoeae were susceptible to ciprofloxacin, ceftriaxone, and azithromycin and comprised isolates from patients across demographic groups. Conclusions All large transmission clusters were susceptible to gonorrhea therapies, suggesting that resistance to empiric therapy was not a main driver of spread, even as risk for resistance varied across demographic groups. Further study of local transmission networks is needed to identify drivers of transmission.


2019 ◽  
Vol 6 (Supplement_2) ◽  
pp. S830-S830 ◽  
Author(s):  
Ashley Paulick ◽  
Michelle Adamczyk ◽  
Lauren C Korhonen ◽  
Alice Guh ◽  
Amy Gargis ◽  
...  

Abstract Background In 2009, the Centers for Disease Control and Prevention (CDC) implemented Clostridioides difficile infection (CDI) surveillance through the Emerging Infections Program (EIP) to monitor the incidence and evolving epidemiology of CDI in the United States. Since 2012, ribotypes (RTs) 027, 106, 002, 014, and 020 have constituted the top five strain types among both US community- and healthcare-associated isolates. Here we describe the changes in molecular epidemiology of C. difficile isolates collected in the United States in 2017. Methods In 2017, CDI surveillance was conducted at 10 EIP sites (CA, CO, CT, GA, MD, MN, NM, NY, OR, and TN). A convenience sample of clinical laboratories across EIP sites submitted C. difficile-positive stool specimens to the MN Department of Health Public Health Laboratory and Hines VA Hospital (IL) for culture. Isolates were forwarded to CDC and characterized by capillary-based PCR-ribotyping and PCR detection of tcdA, tcdB, cdtA, cdtB, and deletions in tcdC. Results In 2017, 1,051 C. difficile isolates were submitted; the total number of isolates received from each site ranged from 11 to 286 with a median of 85.5. In total, 143 RTs were observed, with the majority of isolates harboring toxin genes tcdA and tcdB (95%) and a wild-type tcdC sequence (71%). Among 556 healthcare-associated isolates, RT 027 was the most prevalent and the top RT at 5 sites (CA, GA, MD, NM, TN). Ribotype 106 was the most prevalent among 495 community-associated CA isolates and the top RT at 6 sites (CO, CT, GA, MD, MN, TN). Ribotype 027 significantly decreased from 2012 to 2017 among both healthcare-associated (21% vs 15%; p = 0.02) and community-associated isolates (17% vs 6%; P < 0.0001). Among healthcare-associated isolates, RT 076, which was observed in 8 EIP sites, increased from 2% in 2016 to 5% in 2017 (p = 0.05) and replaced RT 020 as one of the top 5 healthcare-associated RTs in 2017. Conclusion Despite an overall decline since 2012, RT 027 remained the most prevalent RT among healthcare-associated isolates submitted in 2017. The increased frequency of RT 076 among healthcare-associated isolates submitted in 2017 highlights the evolving molecular epidemiology of C. difficile and the need for continued surveillance to monitor potential emerging strains. Disclosures All authors: No reported disclosures.


Author(s):  
Tatum D. Mortimer ◽  
Preeti Pathela ◽  
Addie Crawley ◽  
Jennifer L. Rakeman ◽  
Ying Lin ◽  
...  

AbstractBackgroundGenomic epidemiology studies of gonorrhea in the United States have primarily focused on national surveillance for antibiotic resistance, and patterns of local transmission between demographic groups of resistant and susceptible strains are unknown.MethodsWe analyzed a convenience sample of genome sequences, antibiotic susceptibility, and patient data from 897 gonococcal isolates cultured at the NYC Public Health Laboratory from NYC Department of Health and Mental Hygiene (DOHMH) Sexual Health Clinic (SHC) patients, primarily in 2012-13. We reconstructed the gonococcal phylogeny, defined transmission clusters using a 10 non-recombinant single nucleotide polymorphism threshold, tested for clustering of demographic groups, and placed NYC isolates in a global phylogenetic context.ResultsThe NYC gonococcal phylogeny reflected global diversity with isolates from 22/23 of the prevalent global lineages (96%). Isolates clustered on the phylogeny by patient sexual behavior (p<0.001) and race/ethnicity (p<0.001).Minimum inhibitory concentrations were higher across antibiotics in isolates from men who have sex with men compared to heterosexuals (p<0.001) and white heterosexuals compared to black heterosexuals (p<0.01). In our dataset, all large transmission clusters (≥10 samples) of N. gonorrhoeae were susceptible to ciprofloxacin, ceftriaxone, and azithromycin and comprised isolates from patients across demographic groups.ConclusionsAll large transmission clusters were susceptible to gonorrhea therapies, suggesting that resistance to empiric therapy was not a main driver of spread, even as risk for resistance varied across demographic groups. Further study of local transmission networks is needed to identify drivers of transmission.


2021 ◽  
Vol 1 (S1) ◽  
pp. s39-s39
Author(s):  
Ashlyn Norris ◽  
Kalynn Northam ◽  
Lindsay Daniels ◽  
Mildred Kwan ◽  
Gary Burke ◽  
...  

Penicillin (PCN) allergy is one of the most frequently reported medication allergies, with ~10% of the US population reporting a PCN allergy. However, studies have shown that only 1% of the US population have a true IgE-mediated reaction to PCN. Delabeling and appropriately updating patient allergy profiles could decrease the use of alternative broad-spectrum antibiotics, rates of infectious complications [C. difficile, methicillin-resistant Staphylococcus aureus (MRSA), vancomycin-resistant Enterococcus (VRE)], antibiotic resistance, and overall healthcare cost. The emergency department (ED) is an important setting in which to assess PCN allergies and to delabel patients when appropriate because there are >130 million ED visits in the United States each year. We sought to determine the percentage of PCN allergy–labeled patients who could be delabeled through a PCN allergy assessment interview in an ED. Key secondary outcomes included the percentage of interviewed patients who could not be delabeled based on history alone but would be eligible for an amoxicillin oral challenge or a PCN skin test (PST). A prospective PCN allergy assessment pilot was performed for patients aged >18 years presenting to the UNC Medical Center ED between December 1 and December 17, 2020, with a documented PCN allergy. A pharmacist conducted penicillin allergy assessments on a convenience sample of patients presenting to the ED between 8 a.m. and 3 p.m. on weekdays. Based on patients’ reported and documented histories, charts were updated with the most accurate information and allergies were delabeled if appropriate. In total, 95 patients were assessed; 62 (65.3%) were interviewed and 15 (24.2%) were delabeled. In addition, 26 patients (41.9%) were deemed eligible for an oral amoxicillin challenge, 19 (30.6%) qualified for a PST, and 2 (3.2%) patients did not qualify for further assessment due to having a an IgE-mediated reaction in the past 5 years. Of the 15 patients who were delabeled, 6 (40.0%) received antibiotics during their admission: 4 (73.3%) of those patients received a penicillin and 2 (36.7%) received a cephalosporin, all without adverse reactions. Patient assessments took ~20 minutes to complete, including chart review, patient interview, and postinterview chart updating. The results from this pilot study demonstrate the impact of performing PCN allergy assessments in ED. Interdisciplinary opportunities should be explored to develop processes that will improve the efficiency and sustainability of PCN allergy assessments within the ED to allow this important stewardship intervention to continue.Funding: NoDisclosures: None


Author(s):  
Allyssa K. Memmini ◽  
Kathryn L. Van Pelt ◽  
Alissa H. Wicklund ◽  
Katherine M. Breedlove ◽  
Steven P. Broglio

Context: Nearly 44 million youth participate in organized youth sports programs in the United States (US). However, approximately 25% of parents have considered removing their children from sports due to fear of concussion. Objective: To determine which adult decision-making modifiers (e.g., gender, educational attainment, career type, etc.) influence support for youth contact sports participation. Design: Survey research. Setting: Midwestern university and medical center. Patients or Other Participants: Convenience sample of staff and faculty (N=5761; 73.9% female) from 2017–2018. Main Outcome Measures: Support of youth contact sports participation using multivariate binary logistic regression to calculate odds ratios and 95% confidence intervals. Results: The sample was split between adults with children (AWC; n=3465, age=45.39±13.27 years, 76.72% female) and adults without children (AWOC; n=2296, age=30.84±9.01 years, 70.26% female). Among AWC, those who obtained a Bachelor's degree or higher were more likely to support contact sports participation. Females were more inclined to allow all contact sports, specifically football (2.22; CI=1.64,3.01) and ice hockey (1.98; CI=1.42,2.78). Overall, previous adult sport participation, increasing number of children, and child gender were significant modifying variables in greater support of youth contact sports participation amongst AWC (p's&lt;.001). In AWOC, previous sports participation in football (3.27; CI=2.14,4.87), ice hockey (4.26; CI=2.23,8.17), and soccer (2.29; CI=1.48,3.54) increased the likelihood of an adult supporting contact sports participation. Lastly, all adults were less inclined to support a daughter to participate in any contact sport compared to a son. Conclusions: These results unveil adult and child-specific variables which may influence youth contact sports participation. These decisions may be developed through the lens of certain gender role beliefs and may lead adults to perceive certain sports to be appropriate for sons compared to daughters.


2020 ◽  
Vol 7 (Supplement_1) ◽  
pp. S415-S416
Author(s):  
Gayathri Krishnan ◽  
Richa Parikh ◽  
Anna N Witt ◽  
Kulsum Bano ◽  
Sudeepa Bhattacharyya ◽  
...  

Abstract Background Clostridioides difficile (C difficile) infection (CDI) is a major health problem in the United States and despite updated guidelines, the laboratory diagnosis remains vexed. A multistep algorithm is recommended to diagnose CDI that includes antigen, toxin and toxin gene Nucleic Acid Amplification (NAAT) assays. This study was done to assess severity of CDI based on toxin B and NAAT statuses. The other objective was to analyze if antibiotics and PPI/H2B (Proton Pump Inhibitors and H2 blockers) affected severity of CDI. Methods Retrospective analysis of all adult patients admitted to a tertiary medical center with diarrhea and a positive C difficile antigen test from 01/2017- 12/2017. From more than 2000 stool samples submitted to the lab, C diff antigen was positive in 265 patients. 191 were diagnosed with CDI based on the 2-step algorithm. Clinical data was available for 168 patients. Severity of CDI was determined based on published guidelines. Fischer’s exact test was used for statistical analysis. Results The mean age at diagnosis was 55.96. Toxin B was detected in 34% (57/168) patients and Toxin NAAT positive in 66% (111/168) patients. 57% of CDI was health care onset compared to 43% with community onset. 42% (72/168) were classified as severe out of which 40.2% (29) were toxin B positive, and 59.8% (43) were NAAT positive. There were no significant differences in severity of CDI based on toxin B and NAAT status (50.9% vs 38.4%, p=0.14). 46% of cases from community vs 39.6% from hospitals were classified as severe CDI (p=0.415). 72% of cases had antibiotic use in the last 30 days. Use of antibiotics was significantly associated with severe CDI (82% vs 64%, p=0.015). 62.5% (105) patients had history of PPI/H2B use and severity was not significantly associated with its use (p=0.872). Conclusion Our study shows that the presence of toxin did not significantly impact the clinical severity of CDI. The use of antibiotics did not affect the presence of toxin although the total number of CDI cases with previous antibiotic exposure was high. Patients who had recent antibiotic exposure were more likely to have severe clinical presentation. More toxin positive cases were health care onset but the effect was not pronounced. Severity of CDI did not significantly depend on health care onset or on exposure to PPI/H2B. Disclosures Atul Kothari, MD, Ansun Biopharma (Consultant)


Sign in / Sign up

Export Citation Format

Share Document