Consensus Multilocus Sequence Typing Scheme for Pneumocystis jirovecii

Pneumocystis jirovecii is an opportunistic human pathogenic fungus causing severe pneumonia mainly in immunocompromised hosts. Multilocus sequence typing (MLST) remains the gold standard for genotyping of this unculturable fungus. However, the lack of a consensus scheme impedes a global comparison, large scale population studies and the development of a global MLST database. To overcome this problem this study compared all genetic regions (19 loci) currently used in 31 different published Pneumocystis MLST schemes. The most diverse/commonly used eight loci, β-TUB, CYB, DHPS, ITS1, ITS1/2, mt26S and SOD, were further assess for their ability to be successfully amplified and sequenced, and for their discriminatory power. The most successful loci were tested to identify genetically related and unrelated cases. A new consensus MLST scheme consisting of four genetically independent loci: β-TUB, CYB, mt26S and SOD, is herein proposed for standardised P. jirovecii typing, successfully amplifying low and high fungal burden specimens, showing adequate discriminatory power, and correctly identifying suspected related and unrelated isolates. The new consensus MLST scheme, if accepted, will for the first time provide a powerful tool to investigate outbreak settings and undertake global epidemiological studies shedding light on the spread of this important human fungal pathogen.

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A review of HLA and COVID-19 association studies

Molecular and experimental biology in medicine ◽

10.33602/mebm.3.2.3 ◽

2020 ◽

Vol 3 (2) ◽

pp. 25-30

Author(s):

Renata Zunec

Keyword(s):

Large Scale ◽

Association Studies ◽

Human Leukocyte ◽

Genetic System ◽

Epidemiological Studies ◽

Population Based ◽

Case Control ◽

Case Control Studies ◽

First Case ◽

Scale Population

Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is reported to vary across different populations in the prevalence of infection, in the death rate of patients, in the severity of symptoms and in the drug response of patients. Among host genetic factors that can influence all these attributes human leukocyte antigen (HLA) genetic system stands out as one of the leading candidates. Case-control studies, large-scale population-based studies, as well as experimental bioinformatics studies are of utmost importance to confirm HLA susceptibility spectrum of COVID-19. This review presents the results of the first case-control and epidemiological studies performed in several populations, early after the pandemic breakout. The results are pointing to several susceptible and protective HLA alleles and haplotypes associations with COVID-19, some of which might be of interest for the future studies in Croatia, due to its common presence in the population. However, further multiple investigations from around the world, as numerous as possible, are needed to confirm or deteriorate these preliminary results.

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Optimization of Analytical Parameters for Inferring Relationships among Escherichia coli Isolates from Repetitive-Element PCR by Maximizing Correspondence with Multilocus Sequence Typing Data

Applied and Environmental Microbiology ◽

10.1128/aem.00355-06 ◽

2006 ◽

Vol 72 (9) ◽

pp. 6049-6052 ◽

Cited By ~ 22

Author(s):

Tony L. Goldberg ◽

Thomas R. Gillespie ◽

Randall S. Singer

Keyword(s):

Escherichia Coli ◽

Multilocus Sequence Typing ◽

Large Scale ◽

Repetitive Element ◽

Phylogenetic Analyses ◽

Epidemiological Studies ◽

Genetic Distances ◽

Accurate Information ◽

Data Types ◽

Wide Range

ABSTRACT Repetitive-element PCR (rep-PCR) is a method for genotyping bacteria based on the selective amplification of repetitive genetic elements dispersed throughout bacterial chromosomes. The method has great potential for large-scale epidemiological studies because of its speed and simplicity; however, objective guidelines for inferring relationships among bacterial isolates from rep-PCR data are lacking. We used multilocus sequence typing (MLST) as a “gold standard” to optimize the analytical parameters for inferring relationships among Escherichia coli isolates from rep-PCR data. We chose 12 isolates from a large database to represent a wide range of pairwise genetic distances, based on the initial evaluation of their rep-PCR fingerprints. We conducted MLST with these same isolates and systematically varied the analytical parameters to maximize the correspondence between the relationships inferred from rep-PCR and those inferred from MLST. Methods that compared the shapes of densitometric profiles (“curve-based” methods) yielded consistently higher correspondence values between data types than did methods that calculated indices of similarity based on shared and different bands (maximum correspondences of 84.5% and 80.3%, respectively). Curve-based methods were also markedly more robust in accommodating variations in user-specified analytical parameter values than were “band-sharing coefficient” methods, and they enhanced the reproducibility of rep-PCR. Phylogenetic analyses of rep-PCR data yielded trees with high topological correspondence to trees based on MLST and high statistical support for major clades. These results indicate that rep-PCR yields accurate information for inferring relationships among E. coli isolates and that accuracy can be enhanced with the use of analytical methods that consider the shapes of densitometric profiles.

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The Epidemiology of Acute Stress Disorder and Other Early Responses to Trauma in Adults

The Oxford Handbook of Traumatic Stress Disorders ◽

10.1093/oxfordhb/9780195399066.013.0006 ◽

2012 ◽

pp. 68-83

Author(s):

Quinn M. Biggs ◽

Jennifer M. Guimond ◽

Carol S. Fullerton ◽

Robert J. Ursano ◽

Christine Gray ◽

...

Keyword(s):

Large Scale ◽

Stress Disorder ◽

Acute Stress ◽

Traumatic Event ◽

Female Gender ◽

Epidemiological Studies ◽

Acute Stress Disorder ◽

Population Based ◽

Scale Population ◽

Assault Victims

Acute stress disorder (ASD) is an anxiety disorder characterized by exposure to a traumatic event followed by symptoms of re-experiencing, avoidance, hyper-arousal, peritraumatic dissociation, and impairment in functioning. ASD's time-limited duration (two days to one month) makes it distinct from but related to posttraumatic stress disorder (PTSD), which is diagnosed after one month. ASD's brief duration has contributed to a dearth of large-scale, population-based studies. Smaller studies have sought to determine rates of ASD after specific events in select populations; others have focused on ASD's role in predicting PTSD. Much can be learned from existing epidemiological studies. ASD's prevalence varies from 3% in a population of accident victims to 59% in female sexual assault victims. Female gender is a key risk factor; marital status, ethnicity, and socioeconomic status have also been associated with ASD in some studies. Comorbidities include depressive and anxiety disorders and substance use disorders.

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Large-scale, Population-based Epidemiological Studies with Record Linkage can be done in Germany

European Journal of Epidemiology ◽

10.1007/s10654-004-1752-2 ◽

2004 ◽

Vol 19 (12) ◽

pp. 1073-1074 ◽

Cited By ~ 15

Author(s):

Ulrich Ronellenfitsch ◽

Catherine Kyobutungi ◽

Heiko Becher ◽

Oliver Razum

Keyword(s):

Record Linkage ◽

Large Scale ◽

Epidemiological Studies ◽

Population Based ◽

Scale Population

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Multilocus Sequence Typing of Leuconostoc gelidum subsp. gasicomitatum, a Psychrotrophic Lactic Acid Bacterium Causing Spoilage of Packaged Perishable Foods

Applied and Environmental Microbiology ◽

10.1128/aem.04013-14 ◽

2015 ◽

Vol 81 (7) ◽

pp. 2474-2480 ◽

Cited By ~ 9

Author(s):

Riitta Rahkila ◽

Per Johansson ◽

Elina Säde ◽

Lars Paulin ◽

Petri Auvinen ◽

...

Keyword(s):

Population Structure ◽

Lactic Acid ◽

Lactic Acid Bacterium ◽

Multilocus Sequence Typing ◽

Genetic Material ◽

Housekeeping Genes ◽

Content Type ◽

Mlst Scheme ◽

Global Comparison ◽

Leuconostoc Gelidum

ABSTRACTLeuconostoc gelidumsubsp.gasicomitatumis a psychrotrophic lactic acid bacterium (LAB) that causes spoilage of a variety of modified-atmosphere-packaged (MAP) cold-stored food products. During the past 10 years, this spoilage organism has been increasingly reported in MAP meat and vegetable products in northern Europe. In the present study, the population structure within 252L. gelidumsubsp.gasicomitatumstrains was determined based on a novel multilocus sequence-typing (MLST) scheme employing seven housekeeping genes. These strains had been isolated from meat and vegetable sources over a time span of 15 years, and all 68 previously detected pulsed-field gel electrophoresis (PFGE) genotypes were represented. A total of 46 sequence types (STs) were identified, with a majority of the strains (>60%) belonging to three major STs, which were grouped into three clonal complexes (CCs) and 17 singletons by Global Optimal eBURST (goeBURST). The results by Bayesian analysis of population structure (BAPS) mostly correlated with the grouping by goeBURST. Admixture analysis by BAPS indicated a very low level of exchange of genetic material between the subpopulations. Niche specificity was observed within the subpopulations: CC1 and BAPS cluster 1 consisted mostly of strains from a variety of MAP meats, whereas vegetable strains grouped together with strains from MAP poultry within CC2 and BAPS cluster 2. The MLST scheme presented in this study provides a shareable and continuously growing sequence database enabling global comparison of strains associated with spoilage cases. This will further advance our understanding of the microbial ecology of this industrially important LAB.

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β-(1,3)-Glucan Exposure Assessment by Passive Airborne Dust Sampling and New Sensitive Immunoassays

Applied and Environmental Microbiology ◽

10.1128/aem.01486-09 ◽

2009 ◽

Vol 76 (4) ◽

pp. 1158-1167 ◽

Cited By ~ 28

Author(s):

Ilka Noss ◽

Inge M. Wouters ◽

Gillina Bezemer ◽

Nervana Metwali ◽

Ingrid Sander ◽

...

Keyword(s):

Exposure Assessment ◽

House Dust ◽

Large Scale ◽

Epidemiological Studies ◽

Inflammatory Reactions ◽

Airborne Dust ◽

Scale Population ◽

Floor Dust ◽

Low Exposure ◽

Dust Sampling

ABSTRACT Associations between house dust-associated β-(1,3)-glucan exposure and airway inflammatory reactions have been reported, while such exposures in early childhood have been suggested to protect against asthma and wheezing. Most epidemiological studies have used reservoir dust samples and an inhibition enzyme immunoassay (EIA) for β-(1,3)-glucan exposure assessment. The objective of this study was to develop inexpensive but highly sensitive enzyme immunoassays to measure airborne β-(1,3)-glucans in low-exposure environments, like homes. Specificities of available anti-β-(1,3)-glucan antibodies were defined by direct and inhibition experiments. Three suitable antibody combinations were selected for sandwich EIAs. β-(1,3)-Glucans in passive airborne dust collected with an electrostatic dust fall collector (EDC) and floor dust from seven homes were measured with the three EIAs. Floor dust samples were additionally analyzed in the inhibition EIA. The sandwich EIAs were sensitive enough for airborne glucan measurement and showed different specificities for commercial glucans, while the β-(1,3)-glucan levels in house dust samples correlated strongly. The feasibility of measuring glucans in airborne dust with the recently introduced EDC method was further investigated by selecting the most suitable of the three EIAs to measure and compare β-(1,3)-glucan levels in the EDC and in floor and actively collected airborne dust samples of the previously performed EDC validation study. The EDC β-(1,3)-glucan levels correlated moderately with β-(1,3)-glucans in actively collected airborne dust and floor dust samples, while the glucan levels in the airborne dust and floor dust samples did not correlate. The combination of the newly developed β-(1,3)-glucan sandwich EIA with EDC sampling now allows assessment in large-scale population studies of exposure to airborne β-(1,3)-glucans in homes or other low-exposure environments.

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Lack of an association between gallstone disease and bilirubin levels with risk of colorectal cancer: a Mendelian randomisation analysis

British Journal of Cancer ◽

10.1038/s41416-020-01211-x ◽

2021 ◽

Author(s):

Richard Culliford ◽

Alex J. Cornish ◽

Philip J. Law ◽

Susan M. Farrington ◽

Kimmo Palin ◽

...

Keyword(s):

Colorectal Cancer ◽

Large Scale ◽

Causal Effect ◽

Gallstone Disease ◽

Epidemiological Studies ◽

Mendelian Randomisation ◽

Linear Relationships ◽

Potential Risk Factors ◽

The Relationship ◽

Circulating Levels

Abstract Background Epidemiological studies of the relationship between gallstone disease and circulating levels of bilirubin with risk of developing colorectal cancer (CRC) have been inconsistent. To address possible confounding and reverse causation, we examine the relationship between these potential risk factors and CRC using Mendelian randomisation (MR). Methods We used two-sample MR to examine the relationship between genetic liability to gallstone disease and circulating levels of bilirubin with CRC in 26,397 patients and 41,481 controls. We calculated the odds ratio per genetically predicted SD unit increase in log bilirubin levels (ORSD) for CRC and tested for a non-zero causal effect of gallstones on CRC. Sensitivity analysis was applied to identify violations of estimator assumptions. Results No association between either gallstone disease (P value = 0.60) or circulating levels of bilirubin (ORSD = 1.00, 95% confidence interval (CI) = 0.96–1.03, P value = 0.90) with CRC was shown. Conclusions Despite the large scale of this study, we found no evidence for a causal relationship between either circulating levels of bilirubin or gallstone disease with risk of developing CRC. While the magnitude of effect suggested by some observational studies can confidently be excluded, we cannot exclude the possibility of smaller effect sizes and non-linear relationships.

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Multimorbidity clusters in patients with chronic obstructive airway diseases in the EpiChron Cohort

Scientific Reports ◽

10.1038/s41598-021-83964-w ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Jonás Carmona-Pírez ◽

Beatriz Poblador-Plou ◽

Ignatios Ioakeim-Skoufa ◽

Francisca González-Rubio ◽

Luis Andrés Gimeno-Feliú ◽

...

Keyword(s):

Substance Use ◽

Chronic Conditions ◽

Large Scale ◽

Mental Health Problems ◽

Epidemiological Studies ◽

Chronic Obstructive ◽

High Morbidity ◽

Airway Diseases ◽

Obstructive Sleep ◽

Obstructive Airway Diseases

AbstractChronic obstructive airway diseases such as chronic obstructive pulmonary disease (COPD), asthma, rhinitis, and obstructive sleep apnea (OSA) are amongst the most common treatable and preventable chronic conditions with high morbidity burden and mortality risk. We aimed to explore the existence of multimorbidity clusters in patients with such diseases and to estimate their prevalence and impact on mortality. We conducted an observational retrospective study in the EpiChron Cohort (Aragon, Spain), selecting all patients with a diagnosis of allergic rhinitis, asthma, COPD, and/or OSA. The study population was stratified by age (i.e., 15–44, 45–64, and ≥ 65 years) and gender. We performed cluster analysis, including all chronic conditions recorded in primary care electronic health records and hospital discharge reports. More than 75% of the patients had multimorbidity (co-existence of two or more chronic conditions). We identified associations of dermatologic diseases with musculoskeletal disorders and anxiety, cardiometabolic diseases with mental health problems, and substance use disorders with neurologic diseases and neoplasms, amongst others. The number and complexity of the multimorbidity clusters increased with age in both genders. The cluster with the highest likelihood of mortality was identified in men aged 45 to 64 years and included associations between substance use disorder, neurologic conditions, and cancer. Large-scale epidemiological studies like ours could be useful when planning healthcare interventions targeting patients with chronic obstructive airway diseases and multimorbidity.

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