scholarly journals Molecular strategy for ‘serotyping’ of human enteroviruses

2001 ◽  
Vol 82 (1) ◽  
pp. 79-91 ◽  
Author(s):  
Valérie Caro ◽  
Sophie Guillot ◽  
Francis Delpeyroux ◽  
Radu Crainic

To explore further the phylogenetic relationships between human enteroviruses and to develop new diagnostic approaches, we designed a pair of generic primers in order to study a 1452 bp genomic fragment (relative to the poliovirus Mahoney genome), including the 3′ end of the VP1-coding region, the 2A- and 2B-coding regions, and the 5′ moiety of the 2C-coding region. Fifty-nine of the 64 prototype strains and 45 field isolates of various origins, involving 21 serotypes and 6 strains untypeable by standard immunological techniques, were successfully amplified with these primers. By determining the nucleotide sequence of the genomic fragment encoding the C-terminal third of the VP1 capsid protein we developed a molecular typing method based on RT–PCR and sequencing. If field isolate sequences were compared to human enterovirus VP1 sequences available in databases, nucleotide identity score was, in each case, highest with the homotypic prototype (74.8 to 89.4%). Phylogenetic trees were generated from alignments of partial VP1 sequences with several phylogeny algorithms. In all cases, the new classification of enteroviruses into five identified species was confirmed and strains of the same serotype were always monophyletic. Analysis of the results confirmed that the 3′ third of the VP1-coding sequence contains serotype-specific information and can be used as the basis of an effective and rapid molecular typing method. Furthermore, the amplification of such a long genomic fragment, including non-structural regions, is straightforward and could be used to investigate genome variability and to identify recombination breakpoints or specific attributes of pathogenicity.

mSphere ◽  
2020 ◽  
Vol 5 (4) ◽  
Author(s):  
Shanshan Liu ◽  
Xiaoliang Li ◽  
Zhenfei Guo ◽  
Hongsheng Liu ◽  
Yu Sun ◽  
...  

ABSTRACT Streptococcus mutans is one of the primary pathogens responsible for the development of dental caries. Recent whole-genome sequencing (WGS)-based core genome multilocus sequence typing (cgMLST) approaches have been employed in epidemiological studies of specific human pathogens. However, this approach has not been reported in studies of S. mutans. Here, we therefore developed a cgMLST scheme for S. mutans. We surveyed 199 available S. mutans genomes as a means of identifying cgMLST targets, developing a scheme that incorporated 594 targets from the S. mutans UA159 reference genome. Sixty-eight sequence types (STs) were identified in this cgMLST scheme (cgSTs) in 80 S. mutans isolates from 40 children that were sequenced in this study, compared to 35 STs identified by multilocus sequence typing (MLST). Fifty-six cgSTs (82.35%) were associated with a single isolate based on our cgMLST scheme, which is significantly higher than in the MLST scheme (11.43%). In addition, 58.06% of all MLST profiles with ≥2 isolates were further differentiated by our cgMLST scheme. Topological analyses of the maximum likelihood phylogenetic trees revealed that our cgMLST scheme was more reliable than the MLST scheme. A minimum spanning tree of 145 S. mutans isolates from 10 countries developed based upon the cgMLST scheme highlighted the diverse population structure of S. mutans. This cgMLST scheme thus offers a new molecular typing method suitable for evaluating the epidemiological distribution of this pathogen and has the potential to serve as a benchmark for future global studies of the epidemiological nature of dental caries. IMPORTANCE Streptococcus mutans is regarded as a major pathogen responsible for the onset of dental caries. S. mutans can transmit among people, especially within families. In this study, we established a new epidemiological approach to S. mutans classification. This approach can effectively differentiate among closely related isolates and offers superior reliability relative to that of the traditional MLST molecular typing method. As such, it has the potential to better support effective public health strategies centered around this bacterium that are aimed at preventing and treating dental caries.


2001 ◽  
Vol 33 (4) ◽  
pp. 453-459 ◽  
Author(s):  
Griselda Tudó ◽  
Julián González ◽  
Josep M. Gatell ◽  
Joan A. Caylà ◽  
Esteban Martínez ◽  
...  

1996 ◽  
Vol 43 (5) ◽  
pp. 34S-34S ◽  
Author(s):  
PHILIPPE M. HAUSER ◽  
DOMINIQUE S. BLANC ◽  
JACQUES BILLE ◽  
AMALIO TELENTI ◽  
PATRICK FRANCIOLI

PLoS ONE ◽  
2015 ◽  
Vol 10 (5) ◽  
pp. e0125763 ◽  
Author(s):  
Maud Gits-Muselli ◽  
Marie-Noelle Peraldi ◽  
Nathalie de Castro ◽  
Véronique Delcey ◽  
Jean Menotti ◽  
...  

1995 ◽  
Vol 115 (3) ◽  
pp. 419-426 ◽  
Author(s):  
N. Kobayashi ◽  
K. Taniguchi ◽  
K. Kojima ◽  
S. Urasawa ◽  
N. Uehara ◽  
...  

SummaryA molecular typing method forStaphylococcus aureusbased on coagulase gene polymorphisms (coagulase gene typing) was evaluated by examining a total of 240 isolates which comprised 210 methicillin-resistantS. aureus(MRSA) and 30 methicillin-susceptibleS. aureus(MSSA) collected from a single hospital. ByAlulrestriction enzyme digestion of the PCR-amplified 3′-end region of the coagulase gene including 81-bp repeated units, the MRSA and MSSA isolates examined were divided into 6 and 12 restriction fragment length polymorphism (RFLP) patterns, respectively, whereas five patterns were commonly detected in MRSA and MSSA. MRSA isolates that showed a particular RFLP pattern were considered to be predominant in the hospital. Coagulase typing with type-specific antisera was also performed for allS. aureusisolates for comparison. Coagulase types II and VII were most frequently detected and included isolates with four and five differentAluIRFLP patterns, respectively, whereas each of the other coagulase types corresponded to a single RFLP pattern. These results indicated that RFLP typing was more discriminatory than serological typing, for typingS. aureusand demonstrated its utility in epidemiologic investigation ofS. aureusinfection in hospitals.


Apmis ◽  
1997 ◽  
Vol 105 (S77) ◽  
pp. 7-10 ◽  
Author(s):  
PHILIPPE M. HAUSER ◽  
DOMINIQUE S. BLANC ◽  
JACQUES BILLE ◽  
AMALIO TELENTI ◽  
PATRICK FRANCIOLI

1999 ◽  
Vol 150 (5) ◽  
pp. 317-322 ◽  
Author(s):  
Isabelle Noppe-Leclercq ◽  
Frédéric Wallet ◽  
Stephanie Haentjens ◽  
René Courcol ◽  
Michel Simonet

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