The Cano-eMLST Program: An Approach for the Calculation of Canonical Extended Multi-Locus Sequence Typing, Making Comparison of Genetic Differences Among Bunches of Bacterial Strains

Extended multi-locus sequence typing (eMLST) methods have become popular in the field of genomic epidemiology. Before eMLST methods can be applied in epidemiological investigations, the selection of a suitable scheme is critical. The core genome scheme (cgMLST) has become the most popular eMLST approach for strain typing in the epidemiological domain. In addition to strain typing, many public health researchers and clinical microbiologists wish to investigate which genes cause genetic differences between compared strains. Therefore, a tool that can be used to extract canonical genes with an eMLST scheme would be particularly useful. In this study, we present cano-eMLST, a well-designed program that applies a feature-selection methodology to create a canonical locus combination with discriminatory power by traversing a genetic relatedness tree based on a user-selected scheme. The cano-eMLST program is provided mainly to help infectious disease laboratory researchers identify potential factors related to bacterial pathogenesis. The core program (tree-traversing approach) of cano-eMLST is implemented in Perl and Python. All the necessary dependencies and environmental settings are provided in the encapsulated version (VirtualBox or VMware) and self-installation version (all use source code and libraries).

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Pan-genome analysis provides much higher strain typing resolution than multi-locus sequence typing

Microbiology ◽

10.1099/mic.0.035188-0 ◽

2010 ◽

Vol 156 (4) ◽

pp. 1060-1068 ◽

Cited By ~ 34

Author(s):

Barry G. Hall ◽

Garth D. Ehrlich ◽

Fen Z. Hu

Keyword(s):

High Resolution ◽

Low Cost ◽

Bacterial Species ◽

Resolving Power ◽

Multi Locus Sequence Typing ◽

Strain Typing ◽

Bacterial Strains ◽

Clustering Method ◽

Prognostic Information ◽

Microarray Analyses

The most widely used DNA-based method for bacterial strain typing, multi-locus sequence typing (MLST), lacks sufficient resolution to distinguish among many bacterial strains within a species. Here, we show that strain typing based on the presence or absence of distributed genes is able to resolve all completely sequenced genomes of six bacterial species. This was accomplished by the development of a clustering method, neighbour grouping, which is completely consistent with the lower-resolution MLST method, but provides far greater resolving power. Because the presence/absence of distributed genes can be determined by low-cost microarray analyses, it offers a practical, high-resolution alternative to MLST that could provide valuable diagnostic and prognostic information for pathogenic bacterial species.

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Strain Typing of Trichosporon asahii Clinical Isolates by Random Amplification of Polymorphic DNA (RAPD) Analysis

Journal of Laboratory Physicians ◽

10.1055/s-0041-1731111 ◽

2021 ◽

Author(s):

Thayanidhi Premamalini ◽

Vijayaraman Rajyoganandh ◽

Ramaraj Vijayakumar ◽

Hemanth Veena ◽

Anupma Jyoti Kindo ◽

...

Keyword(s):

Genetic Relatedness ◽

Rapd Analysis ◽

Clinical Isolates ◽

Clinical Samples ◽

Strain Typing ◽

Trichosporon Asahii ◽

Pcr Fingerprinting ◽

Specific Pcr ◽

Rapd Primer ◽

Random Amplification

Abstract Objective The aim of this study was to identify and isolate Trichosporon asahii (T. asahii) from clinical samples and to assess the genetic relatedness of the most frequently isolated strains of T. asahii using random amplification of polymorphic DNA (RAPD) primers GAC-1 and M13. Methods All the clinical samples that grew Trichosporon species, identified and confirmed by polymerase chain reaction (PCR) using Trichosporon genus-specific primers, were considered for the study. Confirmation of the species T. asahii was carried out by T. asahii-specific PCR. Fingerprinting of the most frequently isolated T. asahii isolates was carried out by RAPD using random primers GAC-1 and M13. Results Among the 72 clinical isolates of Trichosporon sp. confirmed by Trichosporon-specific PCR, 65 were found to be T. asahii as identified by T. asahii-specific PCR. Fingerprinting of the 65 isolates confirmed as T. asahii using GAC-1 RAPD primer yielded 11 different patterns, whereas that of M13 primer produced only 5 patterns. The pattern I was found to be the most predominant type (29.2%) followed by pattern III (16.9%) by GAC-1 primer. Conclusions This study being the first of its kind in India on strain typing of T. asahii isolates by adopting RAPD analysis throws light on genetic diversity among the T. asahii isolates from clinical samples. Fingerprinting by RAPD primer GAC-1 identified more heterogeneity among the T. asahii isolates than M13.

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Implementation of the Comprehensive Operating Room Ergonomics Program for Surgeons Through an OT Approach: A Feasibility Study

American Journal of Occupational Therapy ◽

10.5014/ajot.2021.75s2-po314 ◽

2021 ◽

Vol 75 (Supplement_2) ◽

pp. 7512515314p1-7512515314p1

Author(s):

Pamela Hess ◽

Penelope Moyers Cleveland

Keyword(s):

Operating Room ◽

Feasibility Study ◽

Mixed Methods Research ◽

Implementation Process ◽

Evidence Based ◽

Health And Wellness ◽

Design And Implementation ◽

The Core ◽

Core Program ◽

Primary Author

Abstract Date Presented 04/22/21 The Comprehensive Operating Room Ergonomics (CORE) program was developed to address the physical and environmental demands among surgeons. This feasibility study examined the design and implementation process of an evidence-based OT ergonomics intervention using a mixed-methods research design. The CORE program supports the American Occupational Therapy Association’s Vision 2025 of promoting population health and wellness, especially among surgeons who are essential to our health care system. Primary Author and Speaker: Pamela Hess Additional Authors and Speakers: Elena Donoso Brown

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The core genome multi-locus sequence typing of Mycoplasma anserisalpingitidis

BMC Genomics ◽

10.1186/s12864-020-06817-2 ◽

2020 ◽

Vol 21 (1) ◽

Author(s):

Áron B. Kovács ◽

Zsuzsa Kreizinger ◽

Barbara Forró ◽

Dénes Grózner ◽

Alexa Mitter ◽

...

Keyword(s):

Core Genome ◽

Multi Locus Sequence Typing ◽

The Core

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The Language Arts Enrich the Core Program

The School Review ◽

10.1086/442208 ◽

1955 ◽

Vol 63 (4) ◽

pp. 220-227

Author(s):

Helen E. Deans

Keyword(s):

Language Arts ◽

The Core ◽

Core Program

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2408. Genotypic Corroboration of Epidemiologically Linked Clusters to Detect Outbreaks of C. difficile at a Tertiary Care Hospital

Open Forum Infectious Diseases ◽

10.1093/ofid/ofz360.2086 ◽

2019 ◽

Vol 6 (Supplement_2) ◽

pp. S831-S831

Author(s):

Nagla Bayoumi ◽

Tracy McMillen ◽

Anoshé Aslam ◽

Mini Kamboj

Keyword(s):

Genetic Relatedness ◽

Tertiary Care ◽

Healthcare Facility ◽

Cancer Center ◽

Strain Typing ◽

Care Hospital ◽

Routine Surveillance ◽

Clinical Surveillance ◽

Strain Type ◽

Hospital Acquired

Abstract Background The Society for Healthcare Epidemiology of America (SHEA) recommends that surveillance for healthcare facility-onset C. difficile infections (HO CDI) be conducted to detect elevated rates or outbreaks of CDI and stratify data by hospital unit when possible to facilitate detection of clusters. At Memorical Sloan Kettering Cancer Center, strain typing of isolates using multi-locus sequence typing (MLST) is performed routinely and in real time to inform control efforts. Genotyping can conclusively establish or debunk transmission events based on routine surveillance. Management of C. difficile outbreaks is time and resource intensive. Methods A retrospective analysis was conducted to identify all nosocomial C. difficile cases between July 2013 and July 2018. Based on Memorial Sloan Kettering’s baseline surveillance data, a cluster of C. difficile was defined as three or more hospital-acquired cases (as defined by NHSN) on the same inpatient unit within a 7-day period. Data were analyzed to quantify the number of clusters observed and determine genetic relatedness among cases to detect an outbreak. Results A total of 1,116 HO CDI cases occurred during the 5-year time period. Annual nosocomial rates of CDI remained stable (P = 0.052). Eighty clusters were identified; 63 clusters had 3 cases within each cluster, 16 were each made up of 4 cases, and 1 cluster consisted of 5 cases. Two clusters had strain typing concordance amongst all 3 cases; strain type 42 and strain type 1. Among all the epidemiologically linked clusters over the 5-year period, only 2.5% were genetically linked suggestive of true outbreaks. Conclusion The majority of HO-CDI clusters detected on clinical surveillance are non-clonal. Genotyping should be routinely used to corroborate clusters identified on microbiological surveillance before costly outbreak control interventions are deployed. Disclosures All authors: No reported disclosures.

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COROT – A Unique Database for Low Amplitude Variability Between 1 Minute and 150 Days

International Astronomical Union Colloquium ◽

10.1017/s0252921100057122 ◽

2000 ◽

Vol 176 ◽

pp. 69-70

Author(s):

E. Michel ◽

A. Baglin ◽

P. Barge ◽

C. Catala ◽

M. Auvergne ◽

...

Keyword(s):

Quality Data ◽

Wide Field ◽

High Quality ◽

High Quality Data ◽

Amplitude Variability ◽

The Core ◽

Core Program ◽

Rich Material ◽

Stellar Seismology ◽

Low Amplitude

AbstractCOROT is a high precision wide field photometry experiment from space, funded in the framework of the CNES “Petites Missions” program (the PI is A. Baglin). It will observe approximately 30000 objects with mV between 4.5 and 15.5 over long observational periods (up to 150 d), with a time sampling between 1 s and 16 min, a precision of the order of 10−4 per measurement. The scientific objectives are stellar seismology and the search for telluric planets. The instrument and the core program have already been presented in several places. We here focus on a description of the characteristics of the data to be obtained with COROT. The large amount of high quality data collected by COROT will constitute rich material for several research programs beyond the core program as already defined (http://www.astrsp-mrs.fr/www/corot.html). A call for proposal of additional programs will be made during Northern Spring 2000.

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