Alignment of Tandem Repeats with Excision, Duplication, Substitution and Indels (EDSI). In: Casadio R, Myers G, editors. Algorithms in Bioinformatics. Berlin: Springer Berlin Heidelberg; 2005. pp. 276-90. [DOI: 10.1007/11557067_23]

Graph-based modeling of tandem repeats improves global multiple sequence alignment

Tandem repeats (TRs) are often present in proteins with crucial functions, responsible for resistance, pathogenicity and associated with infectious or neurodegenerative diseases. This motivates numerous studies of TRs and their evolution, requiring accurate multiple sequence alignment. TRs may be lost or inserted at any position of a TR region by replication slippage or recombination, but current methods assume fixed unit boundaries, and yet are of high complexity. We present a new global graph-based alignment method that does not restrict TR unit indels by unit boundaries. TR indels are modeled separately and penalized using the phylogeny-aware alignment algorithm. This ensures enhanced accuracy of reconstructed alignments, disentangling TRs and measuring indel events and rates in a biologically meaningful way. Our method detects not only duplication events but also all changes in TR regions owing to recombination, strand slippage and other events inserting or deleting TR units. We evaluate our method by simulation incorporating TR evolution, by either sampling TRs from a profile hidden Markov model or by mimicking strand slippage with duplications. The new method is illustrated on a family of type III effectors, a pathogenicity determinant in agriculturally important bacteria Ralstonia solanacearum. We show that TR indel rate variation contributes to the diversification of this protein family.

Molecular characterization of clinical methicillin-resistant Staphylococcus aureus isolates in South Africa

Eighty-two percent of 320 clinical methicillin-resistant Staphylococcus aureus (MRSA) isolates from various infection sites collected throughout South Africa were separated into five major globally prevalent clusters by SmaI pulsed-field gel electrophoresis, spa, and SCCmec typing. Only one Panton-Valentine leukocidin-positive isolate was detected. This is the first detailed MRSA epidemiology study for the whole country.

Evolutionary relationships between sporadic and epidemic strains of healthcare-associated methicillin-resistant Staphylococcus aureus

National surveillance of healthcare-associated methicillin-resistant Staphylococcus aureus (HA-MRSA) isolates by pulsed-field gel electrophoresis (PFGE) typing allowed identification of rarely occurring 'sporadic' isolates with patterns significantly distinct from those of major epidemic clones of methicillin-resistant S. aureus (MRSA) circulating in Belgian hospitals. The aim of the present study was to compare the genetic background, antibiotic susceptibility profile and in vitro growth rates of 36 MRSA isolates with either 'epidemic' or 'sporadic' PFGE profiles to identify factors that could be involved in the epidemic behaviour of S. aureus. Sequence analysis of seven housekeeping genes (multilocus sequence typing) and seven surface-associated genes, combined with staphylococcal cassette chromosome mec (SCCmec) typing and spa typing results, segregated sporadic isolates into four groups: (1) isolates phylogenetically distant from epidemic HA-MRSA clones that possessed several properties of community-acquired MRSA strains; (2) isolates derived from the same methicillin-susceptible S. aureus ancestor as epidemic isolates but possessing a distinct type of SCCmec; and (3) and (4) isolates that were closely related to epidemic strains, either as recent descendants of these or as intermediate evolutionary steps between epidemic HA-MRSA strains and their putative ancestors. Sporadic isolates did not show slower growth in vitro than epidemic isolates. These findings suggest that the SCCmec type and insertion/deletion of other mobile genetic elements may be involved in modulating the epidemic behaviour of MRSA strains of similar genetic background, independently of fitness cost.

Global distribution of Panton-Valentine leukocidin--positive methicillin-resistant Staphylococcus aureus, 2006

We determined the agr type, multilocus sequence type, protein A gene type (spa typing), toxin gene profile, and antimicrobial drug resistance profile of 469 isolates of Panton-Valentine leukocidin-positive community-acquired methicillin-resistant Staphylococcus aureus isolates (PVL-positive CA-MRSA). The isolates had been collected from around the world from 1999 through 2005 by the French National Reference Center for Staphylococci. We found that some continent-specific clones described in 2003, such as clone ST8, have now spread all over the world. Likewise, some PVL-positive CA-MRSA have spread to several countries on various continents. New clones have emerged (e.g., ST377) on new genetic backgrounds. PVL-positive CA-MRSA that were usually susceptible to most antistaphylococcal antimicrobial agents have acquired new resistance determinants (e.g., to gentamicin) in certain countries. The major trait shared by all these clones is a short staphylococcal chromosomal cassette mec element of type IV or V.

Comparing tandem repeats with duplications and excisions of variable degree

Traditional sequence comparison by alignment employs a mutation model comprised of two events, substitutions and indels (insertions or deletions) of single positions. However, modern genetic analysis knows a variety of more complex mutation events (e.g., duplications, excisions, and rearrangements), especially regarding DNA. With ever more DNA sequence data becoming available, the need to accurately compare sequences which have clearly undergone more complicated types of mutational processes is becoming critical. Herein we introduce a new method for pairwise alignment and comparison of sequences with respect to the special evolution of tandem repeats: substitutions and indels of single positions and, additionally, duplications and excisions of variable degree (i.e., of one or more repeat copies simultaneously) are taken into account. To evaluate our method, we apply it to the spa VNTR (variable number of tandem repeats) cluster of Staphylococcus aureus, a bacterium of high medical importance.