Genetic population structure, clonal phylogeny, and pathogenicity of Salmonella paratyphi B

Abstract

Genetic diversity and relationships among 123 strains of Salmonella paratyphi B (serotype 1,4,[5],12:b:[1,2]) were estimated from an assessment of electrophoretically demonstrable allelic variation at 24 chromosomal enzyme gene loci. Fourteen electrophoretic types, marking clones, were distinguished, the phylogeny of the clonal lineages was reconstructed, and biotype and other phenotypic characters were mapped onto this structure. Most d-tartrate-negative strains are members of an abundant, globally distributed clone (Pb 1) that is polymorphic for many biotype characters (including d-tartrate utilization), bacteriophage type, rRNA pattern, and colicin M and phage ES18 sensitivity. This clone is largely responsible for S. paratyphi B enteric fever in humans. In contrast, d-tartrate-positive strains (formerly known as S. java) occurred in all seven of the clonal lineages identified by population genetic analysis, although most d-tartrate-positive isolates belong to only two clones (Pb 3 and Pb 4), which vary in frequency geographically. Monophasic strains represent four closely related clones forming a distinctive phylogenetic lineage. The Kauffmann hypothesis of convergence in serotype among distantly related cell lineages through recombination (via phage transduction or other means) may account for the considerable genotypic diversity among clones of S. paratyphi B. Pb 4, Pb 6, and Pb 7 are more closely allied with clones of S. typhimurium and S. saintpaul than with other clones of S. paratyphi B. Sensitivity or resistance to colicin M and phage ES18 and the electrophoretic pattern of the rRNA, which were incorporated into a recently proposed scheme for the identification of types of S. paratyphi B, individually or in combination fail to mark clones or other meaningful phylogenetic subdivisions.

Limited Genetic Diversity in the Endophytic Sugarcane Bacterium Acetobacter diazotrophicus

“…Despite the low number of isolates analyzed, the results obtained in this study suggest that A. diazotrophicus has a clonal genetic structure on the basis of the wide distribution of one genotype. This type of genetic structure has also been observed for other bacteria (23,32,35,39).…”

“…Four distinctive ETs were identified among the 24 A. diazotrophicus isolates studied (Table 2), and the mean level of genetic diversity for the 11 enzyme loci was found to be 0.064 (Table 1). According to Selander et al (35,36), ETs mark clones; if a particular clone differs from the most frequent clone at a single gene locus, then it is called a subclone. We observed only four ETs.…”

Linkage disequilibrium between minisatellite loci supports clonal evolution of Mycobacterium tuberculosis in a high tuberculosis incidence area

“…Furthermore, in predominantly clonal species, phylogenetic divergence is not clouded by frequent recombination. Therefore, phylogeny can be used as a framework onto which relevant pathogenicity traits of this pathogen can be mapped (Selander et al, 1990).…”

Limitations to estimating bacterial cross‐species transmission using genetic and genomic markers: inferences from simulation modeling

“…Here, we used a simulation model where the true rates of transmission and mutation were known, to evaluate the ability of VNTRs and SNPs to correctly estimate rates of CST between two species (or populations). The clonal population structure of bacteria (Smith et al 1993;Haubold et al 1998) and other pathogens favors the use of a phylogenetic approach to infer bacterial migration patterns between hosts or locations (Selander et al 1990;Spratt and Maiden 1999;Supply et al 2003;Grenfell et al 2004). Several well-studied methods in molecular phylogeny are available to reconstruct a parasite transmission history (Yang and Rannala 2012).…”