Dataset Information

Comparing Genomic Characteristics of Streptococcus pyogenes Associated with Invasiveness over a 20-year Period in Korea.

ABSTRACT:

Background

Few studies have investigated the invasiveness of Streptococcus pyogenes based on whole-genome sequencing (WGS). Using WGS, we determined the genomic features associated with invasiveness of S. pyogenes strains in Korea.

Methods

Forty-five S. pyogenes strains from 1997, 2006, and 2017, including common emm types, were selected from the repository at Gyeongsang National University Hospital in Korea. In addition, 48 S. pyogenes strains were randomly selected depending on their invasiveness between 1997 and 2017 to evaluate the genetic evolution and the associations between invasiveness and genetic profiles. Using WGS datasets, we conducted virulence-associated DNA sequence determination, emm genotyping, multi-locus sequence typing (MLST), and superantigen gene profiling.

Results

In total, 87 strains were included in this study. There were no significant differences in the genomic features throughout the study periods. Four genes, csn1, ispE, nisK, and citC, were detected only in invasive strains. There was a significant association between invasiveness and emm cluster type A-C3, including, emm1.0, emm1.18, emm1.3, and emm1.76 (P<0.05). The predominant emm1 lineage belonged to ST28. There were no associations between invasiveness and superantigen gene profiles.

Conclusions

This is the first study using WGS datasets of S. pyogenes strains collected between 1997 and 2017 in Korea. Streptococcal invasiveness is associated with the presence of csn1, ispE, nisK, and citC. The emm1 lineage and ST28 clone are explicitly associated with invasiveness, whereas genomic features remained stable over the 20-year period.

SUBMITTER: Shin H

PROVIDER: S-EPMC8859563 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Similar Datasets

Project description:IntroductionFocal segmental glomerulosclerosis (FSGS) is one of the leading causes of nephrotic syndrome in adults. This epidemiological study describes a renal centre's 20-year experience of primary FSGS.MethodsPatients were identified with a diagnosis of primary FSGS after exclusion of known secondary causes. In this retrospective observational study, data was collected for baseline demographics, immunosuppression and outcomes. A two-step cluster analysis was used to identify natural groupings within the dataset.ResultsThe total cohort was made up of 87 patients. Those who received immunosuppression had lower median serum albumin than those who did not- 23g/L vs 40g/L (p<0.001) and higher median urine protein creatinine ratios (uPCR)- 795mg/mmol vs 318mg/mmol (p <0.001). They were more likely to achieve complete remission (62% vs 40%, p=0.041), but relapsed more 48.6% vs 22% (p=0.027). Overall 5 year mortality was 10.3% and 5 year progression to RRT was seen in 17.2%. Complete remission was observed in 49.4%. The 2-step cluster analysis separated the cohort into 3 clusters: cluster 1 (n=26) with 'nephrotic-range proteinuria'; cluster 2 (n=43) with 'non-nephrotic-range proteinuria'; and cluster 3 (n=18) with nephrotic syndrome. Immunosuppression use was comparable in clusters 1 and 3, but lower in cluster 2 (77.8% and 69.2% vs 11.6%, p<0.001). Rates of complete remission were greatest in clusters 1 and 3 vs cluster 2: 57.7% and 66.7% vs 37.2%.ConclusionPeople who received immunosuppression had lower serum albumin and achieved remission more frequently, but were also prone to relapse. Our cluster analysis highlighted 3 FSGS phenotypes: a nephrotic cluster that clearly require immunosuppression; a cohort with preserved serum albumin and non-nephrotic range proteinuria who will benefit from supportive care; and lastly a cluster with heavy proteinuria but serum albumin > 30g/L. This group may still have immune mediated disease and thus could potentially benefit from immunosuppression.Trial registrationThis study protocol was reviewed and approved by the 'Research and Innovation committee of the Northern Care Alliance NHS Group', study approval number (Ref: ID 22HIP54).

Project description:PurposeTo describe visual impairment (VI) over a 20-year period and its associations with age-related eye diseases and socioeconomic factors in the Beaver Dam Eye Study.DesignPopulation-based cohort study.ParticipantsFour thousand nine hundred twenty-six persons 43 to 86 years of age participated in the baseline examination phase from 1988 through 1990, and 3721, 2962, 2375, and 1913 persons participated in follow-up examinations each spaced 5 years apart from 1993 through 1995, 1998 through 2000, 2003 through 2005, and 2008 through 2010, respectively.MethodsBest-corrected visual acuity after refraction, assessed by the Early Treatment Diabetic Retinopathy Study protocol.Main outcome measuresIncidence of VI, defined as best-corrected visual acuity of poorer than 20/40 in the better eye in persons with one or both eyes 20/40 or better at the beginning of a 5-year interval, and incidence of severe VI, defined as best-corrected visual acuity of 20/200 or worse in the better eye in persons with one or both eyes better than 20/200 at the beginning of a 5-year interval.ResultsOverall incidence of VI between examinations (5-year interval) was 1.4% (varying from 0.1% in persons 50-54 years of age to 14.6% in those 85 years of age and older), whereas for severe VI it was 0.4% (varying from 0.0% in persons 50-54 years of age to 6.9% in those ? 85 years of age). The incidence of VI decreased for each (2003-2005 to 2008-2010; odds ratio fourth interval vs. first interval, 0.53; 95% confidence interval, 0.32-0.87; P = 0.01 period after adjustment for age, from the first 5-year interval between examinations (1988-1990 to 1993-1995) to the fourth and most recent 5-year interval ). This period effect was no longer significant after adjustment for age-related macular degeneration. Age-related macular degeneration remained the leading cause of incident severe VI (54% of eyes with incident severe VI, which was as low as 40% and as high as 57% for specific visits), with no evidence of a trend across visits. The overall frequency of VI correctable with new refraction was 38% of all eyes with VI.ConclusionsThese data provide population-based estimates that show a high (15%) 5-year incidence of VI in persons 85 years of age and older. Age-related macular degeneration remained the leading cause of severe VI in this population over the 20 years of the study.Financial disclosure(s)The author(s) have no proprietary or commercial interest in any materials discussed in this article.

Project description:IntroductionRural placements are an important component of rural medical education programs seeking to develop rural practice pathways for medical students. These placements are usually domestic, but James Cook University in Australia developed an international rural placement program in the first half of the medical course that was funded through bursaries. This study explores how the international rural placement helped to shape the lives (personal development and learning) of the participants, using Transformational Learning Theory as a framework for identifying and describing the transformational elements, process and impact of the program.MethodsSixty-five students received a bursary for an international rural placement between 2001-2019. All were contacted by email and invited to participate in a short survey and a follow-up interview. Fifteen participants agreed and twelve were able to participate in individual semi-structured interviews which were recorded, transcribed and analysed using inductive thematic analysis.ResultsParticipants reported that the bursary provided a "once in a lifetime opportunity" to "experience eye-opening and culturally rich difference". Nonetheless, some elements of the placement experience presented disorientating dilemmas that triggered deep reflections and shifts in perceptions. The bursary recipients realised that "being open-minded" allowed them "enjoy good company". They were also able to assume "outsider view which allowed reassessment of their own country" and the "isolation experiences gingered desire to right health wrongs". The triggers and mental shifts had significant impact on the bursary recipients and fostered the development of "inspirational new horizons" based on an appreciation of the "value of rural practice" and "role-modelling for life-long learning." These findings are consistent with Transformational Learning Theory.ConclusionParticipants in this study reported meaningful and strongly positive impacts from the experiences gained during an international rural clinical placement early in their course. They described transformative experiences which appear to contribute strongly to personal development. This finding supports maintaining opportunities for international experiences during rurally-oriented medical programs as these may impact longer term career choice.

Project description:ImportanceHistorical data reveal that, compared with women, men are more likely to pursue a head and neck surgical oncology fellowship, but little is known about possible gender differences in academic productivity.ObjectiveTo assess demographic trends and academic productivity among American Head & Neck Society (AHNS) fellowship graduates.Design, setting, and participantsThis cross-sectional study used electronically published data from the AHNS on fellowship graduates in the US and Canada from July 1, 1997, to June 30, 2022. Scopus was used to extract h-indices for each graduate.ExposureScholarly activity.Main outcomes and measuresMain outcomes were changes in demographic characteristics and academic productivity among AHNS graduates over time. Data analysis included effect size, η2, and 95% CIs.ResultsA total of 691 AHNS fellowship graduates (525 men [76%] and 166 women [24%]) were included. Over the study period, there was an increase in the number of programs offering a fellowship (η2, 0.84; 95% CI, 0.68-0.89) and an increase in the absolute number of women who completed training (η2, 0.66; 95% CI, 0.38-0.78). Among early-career graduates pursuing an academic career, there was a small difference in the median h-index scores between men and women (median difference, 1.0; 95% CI, -1.1 to 3.1); however, among midcareer and late-career graduates, there was a large difference in the median h-index scores (midcareer graduates: median difference, 4.0; 95% CI, 1.2-6.8; late-career graduates: median difference, 6.0; 95% CI, 1.0-10.9). A higher percentage of women pursued academic positions compared with men (106 of 162 [65.4%] vs 293 of 525 [55.8%]; difference, 9.6%; 95% CI, -5.3% to 12.3%).Conclusions and relevanceThis cross-sectional study suggests that women in head and neck surgery begin their careers with high levels of academic productivity. However, over time, a divergence in academic productivity between men and women begins to develop. These data argue for research to identify possible reasons for this observed divergence in academic productivity and, where possible, develop enhanced early faculty development opportunities for women to promote their academic productivity, promotion, and advancement into leadership positions.

Project description:Infections and graft-versus-host disease (GVHD) have historically resulted in high mortality among children undergoing umbilical cord blood transplantation (UCBT). However, recent advances in clinical practice have likely improved outcomes of these patients. We conducted a retrospective cohort study of children (<18years of age) undergoing UCBT at Duke University between January 1, 1995 and December 31, 2014. We compared 2-year all-cause and cause-specific mortality during 3 time periods based on year of transplantation (1995 to 2001, 2002 to 2007, and 2008 to 2014). We used multivariable Cox regression to identify demographic and UCBT characteristics that were associated with all-cause mortality, transplantation-related mortality, and death from invasive aspergillosis after adjustment for time period. During the 20-year study period 824 children underwent UCBT. Two-year all-cause mortality declined from 48% in 1995 to 2001 to 30% in 2008 to 2014 (P = .0002). White race and nonmalignant UCBT indications were associated with lower mortality. Black children tended to have a higher risk of death for which GVHD (18% versus 11%; P = .06) or graft failure (9% versus 3%; P = .01) were contributory than white children. Comparing 2008 to 2014 with 1995 to 2001, more than half (59%) of the reduced mortality was attributable to a reduction in infectious mortality, with 45% specifically related to reduced mortality from invasive aspergillosis. Antifungal prophylaxis with voriconazole was associated with lower mortality from invasive aspergillosis than low-dose amphotericin B lipid complex (hazard ratio, .09; 95% confidence interval, .01 to .76). With the decline in mortality from invasive aspergillosis, adenovirus and cytomegalovirus have become the most frequentinfectious causes of death in children after UCBT. Advances in clinical practice over the past 20years improved survival of children after UCBT. Reduced mortality from infections, particularly invasive aspergillosis, accounted for the largest improvement in survival and was associated with use of voriconazole for antifungal prophylaxis.