scholarly journals Multilocus Sequence Typing (MLST) and Random Polymorphic DNA (RAPD) Comparisons of Geographic Isolates of Neoparamoeba perurans, the Causative Agent of Amoebic Gill Disease

Pathogens ◽  
2019 ◽  
Vol 8 (4) ◽  
pp. 244
Author(s):  
Johnson-Mackinnon ◽  
Crosbie ◽  
Karlsbakk ◽  
Marcos-Lopez ◽  
Paley ◽  
...  
Keyword(s):  
Multilocus Sequence Typing ◽  
Random Amplified Polymorphic Dna ◽  
Housekeeping Genes ◽  
Island State ◽  
The Usa ◽  
Typing Methods ◽  
Burst Analysis ◽  
Gill Disease ◽  
Farmed Atlantic Salmon ◽  
Geographical Isolates

Neoparamoba perurans, is the aetiological agent of amoebic gill disease (AGD), a disease that affects farmed Atlantic salmon worldwide. Multilocus sequence typing (MLST) and Random Amplified Polymorphic DNA (RAPD) are PCR-based typing methods that allow for the highly reproducible genetic analysis of population structure within microbial species. To the best of our knowledge, this study represents the first use of these typing methods applied to N. perurans with the objective of distinguishing geographical isolates. These analyses were applied to a total of 16 isolates from Australia, Canada, Ireland, Scotland, Norway, and the USA. All the samples from Australia came from farm sites on the island state of Tasmania. Genetic polymorphism among isolates was more evident from the RAPD analysis compared to the MLST that used conserved housekeeping genes. Both techniques consistently identified that isolates of N. perurans from Tasmania, Australia were more similar to each other than to the isolates from other countries. While genetic differences were identified between geographical isolates, a BURST analysis provided no evidence of a founder genotype. This suggests that emerging outbreaks of AGD are not due to rapid translocation of this important salmonid pathogen from the same area.

scholarly journals Molecular Differentiation of Mycoplasma gallisepticum Outbreaks: A Last Decade Study on Italian Farms Using GTS and MLST

Vaccines ◽  
2020 ◽  
Vol 8 (4) ◽  
pp. 665
Author(s):  
Andrea Matucci ◽  
Elisabetta Stefani ◽  
Michele Gastaldelli ◽  
Ilenia Rossi ◽  
Gelinda De Grandi ◽  
...  
Keyword(s):  
Multilocus Sequence Typing ◽  
Evolutionary Dynamics ◽  
Housekeeping Genes ◽  
Mycoplasma Gallisepticum ◽  
Economic Losses ◽  
Strain Identification ◽  
Molecular Differentiation ◽  
Typing Methods ◽  
Infection Monitoring ◽  
Monitoring Activity

Mycoplasma gallisepticum (MG) infects many avian species and leads to significant economic losses in the poultry industry. Transmission of this pathogen occurs both horizontally and vertically, and strategies to avoid the spread of MG rely on vaccination and the application of biosecurity measures to maintain breeder groups as pathogen-free. Two live attenuated MG vaccine strains are licensed in Italy: 6/85 and ts-11. After their introduction, the implementation of adequate genotyping tools became necessary to distinguish between field and vaccine strains and to guarantee proper infection monitoring activity. In this study, 40 Italian MG isolates collected between 2010–2019 from both vaccinated and unvaccinated farms were genotyped using gene-targeted sequencing (GTS) of the cythadesin gene mgc2 and multilocus sequence typing (MLST) based on six housekeeping genes. The discriminatory power of GTS typing ensures 6/85-like strain identification, but the technique does not allow the identification ts-11 strains; conversely, MLST differentiates both vaccine strains, describing more detailed interrelation structures. Our study describes MG genetic scenario within a mixed farming context. In conclusion, the use of adequate typing methods is essential to understand the evolutionary dynamics of MG strains in a particular area and to conduct epidemiological investigations in the avian population.

scholarly journals Development of a Tiered Multilocus Sequence Typing Scheme for Members of the Lactobacillus acidophilus Complex

2013 ◽  
Vol 79 (23) ◽  
pp. 7220-7228 ◽  
Author(s):  
Padmini Ramachandran ◽  
David W. Lacher ◽  
Erika A. Pfeiler ◽  
Christopher A. Elkins
Keyword(s):  
Lactobacillus Acidophilus ◽  
Multilocus Sequence Typing ◽  
Random Amplified Polymorphic Dna ◽  
Rflp Analysis ◽  
Housekeeping Genes ◽  
Nucleotide Substitutions ◽  
Content Type ◽  
Mlst Scheme ◽  
Pcr Rflp ◽  
Pcr Targeting

ABSTRACTMembers of theLactobacillus acidophiluscomplex are associated with functional foods and dietary supplements because of purported health benefits they impart to the consumer. Many characteristics of these microorganisms are reported to be strain specific. Therefore, proper strain typing is essential for safety assessment and product labeling, and also for monitoring strain integrity for industrial production purposes. Fifty-two strains of theL. acidophiluscomplex (L. acidophilus,L. amylovorus,L. crispatus,L. gallinarum,L. gasseri, andL. johnsonii) were genotyped using two established methods and compared to a novel multilocus sequence typing (MLST) scheme. PCR restriction fragment length polymorphism (PCR-RFLP) analysis of thehsp60gene with AluI and TaqI successfully clustered 51 of the 52 strains into the six species examined, but it lacked strain-level discrimination. Random amplified polymorphic DNA PCR (RAPD-PCR) targeting the M13 sequence resulted in highly discriminatory profiles but lacked reproducibility. In this study, an MLST scheme was developed using the conserved housekeeping genesfusA,gpmA,gyrA,gyrB,lepA,pyrG, andrecA, which identified 40 sequence types that successfully clustered all of the strains into the six species. Analysis of the observed alleles suggests that nucleotide substitutions within five of the seven MLST loci have reached saturation, a finding that emphasizes the highly diverse nature of theL. acidophiluscomplex and our unconventional application of a typically intraspecies molecular typing tool. Our MLST results indicate that this method could be useful for characterization and strain discrimination of a multispecies complex, with the potential for taxonomic expansion to a broader collection ofLactobacillusspecies.

scholarly journals Multilocus Sequence Typing of Xylella fastidiosa Causing Pierce's Disease and Oleander Leaf Scorch in the United States

2010 ◽  
Vol 100 (6) ◽  
pp. 601-611 ◽  
Author(s):  
Xiaoli Yuan ◽  
Lisa Morano ◽  
Robin Bromley ◽  
Senanu Spring-Pearson ◽  
Richard Stouthamer ◽  
...  
Keyword(s):  
United States ◽  
Multilocus Sequence Typing ◽  
Xylella Fastidiosa ◽  
Housekeeping Genes ◽  
The United States ◽  
Pierce's Disease ◽  
Whole Genome Analysis ◽  
Leaf Scorch ◽  
Pierce’S Disease ◽  
Typing Methods

Using a modified multilocus sequence typing (MLST) scheme for the bacterial plant pathogen Xylella fastidiosa based on the same seven housekeeping genes employed in a previously published MLST, we studied the genetic diversity of two subspecies, X. fastidiosa subsp. fastidiosa and X. fastidiosa subsp. sandyi, which cause Pierce's disease and oleander leaf scorch, respectively. Typing of 85 U.S. isolates (plus one from northern Mexico) of X. fastidiosa subsp. fastidiosa from 15 different plant hosts and 21 isolates of X. fastidiosa subsp. sandyi from 4 different hosts in California and Texas supported their subspecific status. Analysis using the MLST genes plus one cell-surface gene showed no significant genetic differentiation based on geography or host plant within either subspecies. Two cases of homologous recombination (with X. fastidiosa subsp. multiplex, the third U.S. subspecies) were detected in X. fastidiosa subsp. fastidiosa. Excluding recombination, MLST site polymorphism in X. fastidiosa subsp. fastidiosa (0.048%) and X. fastidiosa subsp. sandyi (0.000%) was substantially lower than in X. fastidiosa subsp. multiplex (0.240%), consistent with the hypothesis that X. fastidiosa subspp. fastidiosa and sandyi were introduced into the United States (probably just prior to 1880 and 1980, respectively). Using whole-genome analysis, we showed that MLST is more effective at genetic discrimination at the specific and subspecific level than other typing methods applied to X. fastidiosa. Moreover, MLST is the only technique effective in detecting recombination.

scholarly journals Trends and developments in oral health literacy: a scientometric research study (1991–2020)

BDJ Open ◽  
2021 ◽  
Vol 7 (1) ◽  
Author(s):  
Yue Sun ◽  
Chunying Li ◽  
Yan Zhao ◽  
Jing Sun
Keyword(s):  
Oral Health ◽  
Health Literacy ◽  
Dental Health ◽  
Oral Health Literacy ◽  
Knowledge Questionnaire ◽  
Bibliographic Records ◽  
Burst Intensity ◽  
The Usa ◽  
Burst Analysis ◽  
Number Of Publications

Abstract Objective This study aimed to establish the current situation, intellectual base, hotspots, development trends, and frontiers of oral health literacy (OHL) from the literature. Methods We analyzed 1505 bibliographic records dated between January 1990 and December 2020 retrieved from the Web of Science Core Collection and the Scopus database. We used CiteSpace for word frequency analysis, co-occurrence analysis, co-citation analysis, clustering analysis, and burst analysis. Results The total number of publications increased year-on-year, with the majority of publications coming from the USA. Most studies focused on the relationship between (oral) health literacy and oral health, and the development of OHL instruments. The top 10 keywords by frequency were “health literacy”, “oral health”, “attitude to health”, “dental caries”, “adult”, “children”, “dental care”, “knowledge”, “questionnaire”, and “adolescent”. The keyword with the highest burst intensity was “dental health education”. Conclusions OHL research is a thriving field. The field is focused on the development of an OHL instrument and health promotion practice. Strategic cooperation among countries, institutions, authors, hospitals, and communities will be important to encourage further OHL research and address oral health problems.

Nonencapsulated or nontypeableHaemophilus influenzaeare more likely than their encapsulated or serotypeable counterparts to have mutations in their fucose operon

2011 ◽  
Vol 57 (12) ◽  
pp. 982-986 ◽  
Author(s):  
Michelle L. Shuel ◽  
Kathleen E. Karlowsky ◽  
Dennis K.S. Law ◽  
Raymond S.W. Tsang
Keyword(s):  
Nucleotide Sequence ◽  
Haemophilus Influenzae ◽  
Dna Sequencing ◽  
Multilocus Sequence Typing ◽  
Population Biology ◽  
Housekeeping Genes ◽  
Sequence Variations ◽  
Sequence Types ◽  
Complete Deletion

Population biology of Haemophilus influenzae can be studied by multilocus sequence typing (MLST), and isolates are assigned sequence types (STs) based on nucleotide sequence variations in seven housekeeping genes, including fucK. However, the ST cannot be assigned if one of the housekeeping genes is absent or cannot be detected by the current protocol. Occasionally, strains of H. influenzae have been reported to lack the fucK gene. In this study, we examined the prevalence of this mutation among our collection of H. influenzae isolates. Of the 704 isolates studied, including 282 encapsulated and 422 nonencapsulated isolates, nine were not typeable by MLST owing to failure to detect the fucK gene. All nine fucK-negative isolates were nonencapsulated and belonged to various biotypes. DNA sequencing of the fucose operon region confirmed complete deletion of genes in the operon in seven of the nine isolates, while in the remaining two isolates, some of the genes were found intact or in parts. The significance of these findings is discussed.

Distribution of virulence genes and the molecular epidemiology of Streptococcus pyogenes clinical isolates by emm and multilocus sequence typing methods

2020 ◽  
Author(s):  
Siti Nur Adila Hamzah ◽  
Mohd Nasir Mohd Desa ◽  
Azmiza Syawani Jasni ◽  
Niazlin Mohd Taib ◽  
Siti Norbaya Masri ◽  
...  
Keyword(s):  
Molecular Epidemiology ◽  
Virulence Factors ◽  
Streptococcus Pyogenes ◽  
Multilocus Sequence Typing ◽  
Virulence Genes ◽  
Clinical Samples ◽  
Pcr Analysis ◽  
Gold Standard Method ◽  
Non Invasive ◽  
Typing Methods

Abstract Background: Streptococcus pyogenes has a variety of virulence factors and the predominant invasive strains differ according to specific emm types and geographical orientation. Although emm typing is commonly used as the gold standard method for the molecular characterization, multilocus sequence typing (MLST) has become an important tool for comparing the genetic profiles globally. This study aimed to screen selected virulence genes from invasive and non-invasive clinical samples and to characterize the molecular epidemiology by emm typing and MLST methods. Methods: A total of 42 S. pyogenes isolates from invasive and non-invasive samples collected from 2014 to 2015 from two different tertiary hospitals were investigated for the distribution of virulence factors and their molecular epidemiology by emm and multilocus sequence typing methods. Detection of five virulence genes (speA , speB , speJ , ssa and sdaB) was performed using multiplex polymerase chain reaction (PCR) using the standard primers and established protocol. Results: Multiplex PCR analysis revealed that sdaB/speF (78.6%) and speB (61.9%) were the predominant virulence genes. Regardless of the type of invasiveness, diverse distribution of emm types/subtypes was noted which comprised of 27 different emm types/subtypes. The predominant emm types/subtypes were emm63 and emm18 with each gene accounted for 11.8% whereas 12% for each gene was noted for emm28, emm97.4 and emm91. The MLST revealed that the main sequence type (ST) in invasive samples was ST402 (17.7%) while ST473 and ST318 (12% for each ST) were the major types in non-invasive samples. Out of 18 virulotypes, Virulotype A (five genes, 55.6%) and Virulotype B (two genes, 27.8%) were the major virulotypes found in this study. Phylogenetic analysis indicated the presence of seven different clusters of S. pyogenes. Interestingly, Cluster VI showed that selected emm/ST types such as emm71/ST318 (n=2), emm70.1/ST318 (n=1), emm44/ST31 (n=1) and emm18/ST442 (n=1) have clustered within a common group (Virulotype A) for both hospitals studied. Conclusion: The present study showed that group A streptococci (GAS) are genetically diverse and possess virulence genes regardless of their invasiveness. Majority of the GAS exhibited no restricted pattern of virulotypes except for a few distinct clusters. Therefore, it can be concluded that virulotyping is partially useful for characterizing a heterogeneous population of GAS in hospitals.

scholarly journals Genetic diversity in Italian Lactobacillus sanfranciscensis strains assessed by multilocus sequence typing and pulsed-field gel electrophoresis analyses

Microbiology ◽  
2010 ◽  
Vol 156 (7) ◽  
pp. 2035-2045 ◽  
Author(s):  
Claudia Picozzi ◽  
Gaia Bonacina ◽  
Ileana Vigentini ◽  
Roberto Foschino
Keyword(s):  
Multilocus Sequence Typing ◽  
Geographical Area ◽  
Housekeeping Genes ◽  
Processing Conditions ◽  
Clonal Population ◽  
Factors Affecting ◽  
Lactobacillus Sanfranciscensis ◽  
Mlst Scheme ◽  
Sequence Types

Lactobacillus sanfranciscensis is a lactic acid bacterium that characterizes the sourdough environment. The genetic differences of 24 strains isolated in different years from sourdoughs, mostly collected in Italy, were examined and compared by PFGE and multilocus sequence typing (MLST). The MLST scheme, based on the analysis of six housekeeping genes (gdh, gyrA, mapA, nox, pgmA and pta) was developed for this study. PFGE with the restriction enzyme ApaI proved to have higher discriminatory power, since it revealed 22 different pulsotypes, while 19 sequence types were recognized through MLST analysis. Notably, restriction profiles generated from three isolates collected from the same firm but in three consecutive years clustered in a single pulsotype and showed the same sequence type, emphasizing the fact that the main factors affecting the dominance of a strain are correlated with processing conditions and the manufacturing environment rather than the geographical area. All results indicated a limited recombination among genes and the presence of a clonal population in L. sanfranciscensis. The MLST scheme proposed in this work can be considered a useful tool for characterization of isolates and for in-depth examination of the strain diversity and evolution of this species.

Comparison of a newly developed binary typing with ribotyping and multilocus sequence typing methods for Clostridium difficile

2018 ◽  
Vol 147 ◽  
pp. 50-55
Author(s):  
Zhirong Li ◽  
Xiaolei Liu ◽  
Jianhong Zhao ◽  
Kaiyue Xu ◽  
Tiantian Tian ◽  
...  
Keyword(s):  
Clostridium Difficile ◽  
Multilocus Sequence Typing ◽  
Typing Methods
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