Investigation of giardiasis in captive animals in zoological gardens with strain typing of assemblages in China

Parasitology ◽  
2021 ◽  
pp. 1-19
Author(s):  
Hua Liu ◽  
Bin Wang ◽  
Jianhai Yin ◽  
Zhongying Yuan ◽  
Yanyan Jiang ◽  
...  
Keyword(s):  
Strain Typing

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

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.

Techniques in bacterial strain typing

2021 ◽  
Vol Publish Ahead of Print ◽  
Author(s):  
Shelby R. Simar ◽  
Blake M. Hanson ◽  
Cesar A. Arias
Keyword(s):  
Bacterial Strain ◽  
Strain Typing

Strain Typing of Prion Diseases Using In Vivo Mouse Models

2017 ◽  
pp. 263-283 ◽  
Author(s):  
Aileen Boyle ◽  
Kris Hogan ◽  
Jean C. Manson ◽  
Abigail B. Diack
Keyword(s):  
Mouse Models ◽  
Prion Diseases ◽  
Strain Typing

scholarly journals Homologous Recombination in Clostridioides difficile Mediates Diversification of Cell Surface Features and Transport Systems

mSphere ◽  
2020 ◽  
Vol 5 (6) ◽  
Author(s):  
Hannah D. Steinberg ◽  
Evan S. Snitkin
Keyword(s):  
Cell Wall ◽  
Homologous Recombination ◽  
Sugar Transport ◽  
The United States ◽  
Strain Typing ◽  
Cell Wall Proteins ◽  
Genetic Loci ◽  
Content Type ◽  
Clostridioides Difficile ◽  
Host Pathogen

ABSTRACT Illness caused by the pathogen Clostridioides difficile is widespread and can range in severity from mild diarrhea to sepsis and death. Strains of C. difficile isolated from human infections exhibit great genetic diversity, leading to the hypothesis that the genetic background of the infecting strain at least partially determines a patient’s clinical course. However, although certain strains of C. difficile have been suggested to be associated with increased severity, strain typing alone has proved insufficient to explain infection severity. The limited explanatory power of strain typing has been hypothesized to be due to genetic variation within strain types, as well as genetic elements shared between strain types. Homologous recombination is an evolutionary mechanism that can result in large genetic differences between two otherwise clonal isolates, and also lead to convergent genotypes in distantly related strains. More than 400 C. difficile genomes were analyzed here to assess the effect of homologous recombination within and between C. difficile clades. Almost three-quarters of single nucleotide variants in the C. difficile phylogeny are predicted to be due to homologous recombination events. Furthermore, recombination events were enriched in genes previously reported to be important to virulence and host-pathogen interactions, such as flagella, cell wall proteins, and sugar transport and metabolism. Thus, by exploring the landscape of homologous recombination in C. difficile, we identified genetic loci whose elevated rates of recombination mediated diversification, making them strong candidates for being mediators of host-pathogen interaction in diverse strains of C. difficile. IMPORTANCE Infections with C. difficile result in up to half a million illnesses and tens of thousands of deaths annually in the United States. The severity of C. difficile illness is dependent on both host and bacterial factors. Studying the evolutionary history of C. difficile pathogens is important for understanding the variation in pathogenicity of these bacteria. This study examines the extent and targets of homologous recombination, a mechanism by which distant strains of bacteria can share genetic material, in hundreds of C. difficile strains and identifies hot spots of realized recombination events. The results of this analysis reveal the importance of homologous recombination in the diversification of genetic loci in C. difficile that are significant in its pathogenicity and host interactions, such as flagellar construction, cell wall proteins, and sugar transport and metabolism.

scholarly journals Strain typing with IS200 fingerprints in Salmonella abortusovis.

1996 ◽  
Vol 62 (7) ◽  
pp. 2375-2380 ◽  
Author(s):  
A Schiaffino ◽  
C R Beuzón ◽  
S Uzzau ◽  
G Leori ◽  
P Cappuccinelli ◽  
...  
Keyword(s):  
Strain Typing

Association between CAI microsatellite, multilocus sequence typing, and clinical significance within Candida albicans isolates

2020 ◽  
Author(s):  
Yen-Mu Wu ◽  
Chih-Hua Lee ◽  
Yi-Chuan Cheng ◽  
Jang-Jih Lu ◽  
Shao-Hung Wang
Keyword(s):  
Risk Factors ◽  
Candida Albicans ◽  
Clinical Significance ◽  
Multilocus Sequence Typing ◽  
Molecular Phylogenetics ◽  
Good Alternative ◽  
Epidemiological Studies ◽  
Chang Gung Memorial Hospital ◽  
Strain Typing ◽  
Clinical Scenario

Abstract Candida albicans bloodstream infection (BSI) is epidemiologically important because of its increasing frequency and serious outcome. Strain typing and delineation of the species are essential for understanding the phylogenetic relationship and clinical significance. Microsatellite CAI genotyping and multilocus sequence typing (MLST) were performed on 285 C. albicans bloodstream isolates from patients in Chang Gung Memorial Hospital at Linkou (CGMHL), Taiwan from 2003 to 2011. Data regarding demographics, comorbidities, risk factors, and clinical outcomes were recorded within adult patients with C. albicans BSI. Both CAI genotyping and MLST yielded comparable discriminatory power for C. albicans characterization. Besides, the distribution of CAI repetition showed a satisfactory phylogenetic association, which could be a good alternative method in the molecular phylogenetics of C. albicans and epidemiological studies. As for the clinical scenario, clade 17 isolates with CAI alleles either possessing 29 or more repetitions were related to higher 14-day and 30-day mortality, and shorter median survival days.

scholarly journals Strain-level Determination of the Contribution of Gut Microbiota to the Development of Bacteremia in Patients Undergoing Stem Cell Transplantation

2017 ◽  
Vol 4 (suppl_1) ◽  
pp. S48-S48
Author(s):  
Tessa Andermann ◽  
Fiona B Tamburini ◽  
Ekaterina Tkachenko ◽  
Fiona Senchyna ◽  
Niaz Banaei ◽  
...  
Keyword(s):  
Stem Cell ◽  
Gut Microbiota ◽  
Stem Cell Transplantation ◽  
Cell Transplantation ◽  
Strain Typing ◽  
Metagenomic Sequencing ◽  
Gram Positive ◽  
Specific Level ◽  
Gram Negative ◽  
Enterococcus Spp

Abstract Background Infection is a major preventable cause of transplant-related morbidity and mortality in patients undergoing hematopoietic stem cell transplantation (HCT). Bacteremia is the most common infectious complication in HCT, often occurring during periods of mucositis when the risk for microbial translocation from the intestine is increased. Prior research in HCT patients using 16S rRNA sequencing demonstrated that gut microbiota dominance by either Enterococcus spp. or Proteobacteria was associated with the development of bacteremia with Enterococcus spp. and Gram-negative organisms, respectively. No studies to date, however, have compared bacteremia isolates and gut microbiota samples at a strain-specific level using next-generation shotgun metagenomic sequencing (NGS). Methods In order to assess the degree of genetic similarity between bacteremia isolates and the gut microbiota, we identified patients who had undergone HCT at Stanford and developed a bacteremia between October 2015 and September 2016 for whom we had both saved blood culture isolates and stool samples within 30 days preceding bacteremia. We identified 15 patients from whom we had 17 bacteremia isolates, and performed NGS (Illumina HiSeq 4000) on stool and isolate DNA. We generated draft assemblies of isolate genomes using the SPAdes assembler, and aligned stool metagenomic reads to the draft isolate genomes using Bowtie2, filtering reads for perfect end-to-end alignment. Results Enteric gram-negative bacteremia isolates were identical to those in the gut microbiota, as has been demonstrated in prior studies using older strain-typing Methods. Surprisingly, we also identified gram-positive organisms that were identical in both the blood and stool prior to bacteremia, which challenges existing dogma regarding sources of gram-positive bacteremia-causing organisms. Conclusion Using a highly sensitive and accurate NGS-based strain typing method, we provide evidence of translocation of organisms from the gut microbiota and subsequent bacteremia. The gut was confirmed as a source for both classic enteric gram-negative and classically non-enteric Gram-positive bacteremia in HCT patients. These findings may have implications for the origins of bacteremia in HCT patients previously classified as CLABSIs. Disclosures A. Bhatt, Janssen Human Microbiome Institute / Johnson and Johnson: Consultant, Consulting fee

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