Multiple-locus variable-number tandem-repeat analysis of Streptococcus pneumoniae and comparison with multiple loci sequence typing

Abstract

BackgroundStreptococcus pneumoniae infections remain a major cause of morbidity and mortality worldwide. The diversity of pneumococci was first evidenced by serotyping of their capsular polysaccharides, responsible of virulence, resolving into more than 93 serotypes. Molecular tools have been developed to track the emergence and the spread of resistant, hyper virulent or non-vaccine type clones, particularly DNA-based methods using genetic polymorphism. Pulsed-Field Gel Electrophoresis analysis (PFGE) and Multiple Loci Sequence Typing (MLST) are the most frequently used genotyping techniques for S. pneumoniae. MLST is based on sequence comparison of housekeeping genes clustering isolates within sequence types. The availability of genome sequence data from different S. pneumoniae strains facilitated the search for other class of genetic markers as polymorphic DNA sequences for a Multiple-Locus Variable-Number Tandem-Repeat Analysis (MLVA). This study aims at confirming the relevance of MLVA of S. pneumoniae, comparing MLST and MLVA performances when discriminating subgroups of strains belonging to the same Sequence Type (ST), and defining a restricted but universal set of MLVA markers that has at least the same discriminatory power as MLST for S. pneumoniae by applying marker sets used by different authors on 331 isolates selected in UK.ResultsA minimum spanning tree was built including the serotypes distribution and comparing MLVA and MLST results. 220 MLVA types were determined grouped in 10 Sequence Types (ST). MLVA differentiated ST162 in two clonal complexes. A minimal set was defined: ms 25 and ms37, ms17, ms19, ms33, ms39, and ms40 including two universal markers. The selection was based on MLVA markers with a Diversity Index >0.8 and a selection of others depending of the population tested and the aim of the study. This set of 7 MLVA markers yields strain clusters similar to those obtained by MLST.ConclusionsMLVA can discriminate relevant subgroups among strains belonging to the same ST. MLVA offers the possibility to deduce the ST from the MLVA Type. It permits to investigate local outbreaks or to track the worldwide spread of clones and the emergence of variants.

Molecular characterization, antibiotic resistance pattern and capsular types of invasive Streptococcus pneumonia isolated from clinical samples in Tehran, Iran

“…According to the other studies suggesting high capsular type and genetic diversities in IPD isolates [10,25,33,34], there was important diversity among our isolates base on capsular types and different MLST profiles. In pneumococcal isolates, one of the important factor to selective pressure is use of antibiotics [34,35], so the antibiotic selection pressure may be led to different genetic diversity of IPD isolates that observed in this study [34,35].…”

“…As for capsular type is assumed to be more important than genotype in the ability of an isolate led to invasive disease but also underline the role of genetic background in invasion [30,32,33]. Since pneumococcal isolates with diverse MLST profiles have showed various pathogenicity potential [32].…”

Multilocus Variable-Number-Tandem-Repeats Analysis (MLVA) distinguishes a clonal complex of Clavibacter michiganensis subsp. michiganensis strains isolated from recent outbreaks of bacterial wilt and canker in Belgium

“…However, the final result is group dependent and can vary considerably between different bacterial species. VNTRs have been used to discriminate among individual strains within many food-borne pathogens with little genetic differences, including Escherichia coli O157:H7 [17] and Vibrio cholerae [18] and to study other important human pathogens, such as Neisseria gonorrhoeae [19], Streptococcus pneumoniae [20], and Mycobacterium tuberculosis [21]. MLVA has been extensively used for tracking transmissions of important human and animal pathogens [22,23] and for typing monomorphic bacterial pathogens including Bacillus anthracis [24] and Yersinia pestis [25].…”

Sequence Analysis of 96 Genomic Regions Identifies Distinct Evolutionary Lineages within CC156, the Largest Streptococcus pneumoniae Clonal Complex in the MLST Database

“…Within recent years, the accessibility of sequence analysis tools has increased the diffusion of Streptococcus pneumoniae molecular genotyping methods such as Multi Locus Sequence Typing (MLST) (http://spneumoniae.mlst.net/) [15], [16]. S. pneumoniae MLST is based on sequence data from standardized fragments of seven housekeeping genes; each unique allele is identified by a numerical ID, and the allelic profile at the seven loci is used to classify bacterial isolates into Sequence Types (STs) [17].…”

“…Whole genome sequence analysis has been successfully applied to S. pneumoniae and has provided a clear indication that pneumococcal genomic variability is most likely triggered by homologous recombination events [32], [33]. In addition to whole genome sequencing, other molecular typing methods such as multiple-locus variable number tandem repeat analysis (MLVA), multilocus boxB sequence typing (MLBT) and 96-MLST, able to trace capsular switch or other homologous recombination events, have been proposed [15], [34]–[36].…”