BackgroundThe pan-genome of a bacterial species consists of a core and an accessory gene pool. The accessory genome is thought to be an important source of genetic variability in bacterial populations and is gained through lateral gene transfer, allowing subpopulations of bacteria to better adapt to specific niches. Low-cost and high-throughput sequencing platforms have created an exponential increase in genome sequence data and an opportunity to study the pan-genomes of many bacterial species. In this study, we describe a new online pan-genome sequence analysis program, Panseq.ResultsPanseq was used to identify Escherichia coli O157:H7 and E. coli K-12 genomic islands. Within a population of 60 E. coli O157:H7 strains, the existence of 65 accessory genomic regions identified by Panseq analysis was confirmed by PCR. The accessory genome and binary presence/absence data, and core genome and single nucleotide polymorphisms (SNPs) of six L. monocytogenes strains were extracted with Panseq and hierarchically clustered and visualized. The nucleotide core and binary accessory data were also used to construct maximum parsimony (MP) trees, which were compared to the MP tree generated by multi-locus sequence typing (MLST). The topology of the accessory and core trees was identical but differed from the tree produced using seven MLST loci. The Loci Selector module found the most variable and discriminatory combinations of four loci within a 100 loci set among 10 strains in 1 s, compared to the 449 s required to exhaustively search for all possible combinations; it also found the most discriminatory 20 loci from a 96 loci E. coli O157:H7 SNP dataset.ConclusionPanseq determines the core and accessory regions among a collection of genomic sequences based on user-defined parameters. It readily extracts regions unique to a genome or group of genomes, identifies SNPs within shared core genomic regions, constructs files for use in phylogeny programs based on both the presence/absence of accessory regions and SNPs within core regions and produces a graphical overview of the output. Panseq also includes a loci selector that calculates the most variable and discriminatory loci among sets of accessory loci or core gene SNPs.AvailabilityPanseq is freely available online at http://76.70.11.198/panseq. Panseq is written in Perl.
Background: Genetic analysis of Escherichia coli O157:H7 strains has shown divergence into two distinct lineages, lineages I and II, that appear to have distinct ecological characteristics, with lineage I strains more commonly associated with human disease. In this study, microarray-based comparative genomic hybridization (CGH) was used to identify genomic differences among 31 E. coli O157:H7 strains that belong to various phage types (PTs) and different lineage-specific polymorphism assay (LSPA) types.
Abstract:We present a drought reconstruction for north central China based on a tree ring-width chronology developed from two sites of the Chinese pine (Pinus tabulaeformis) in the northern Helan Mountains. The drought reconstruction, spanning 1788-1999 A.D., was developed by calibrating tree-ring data with the Palmer drought severity index (PDSI), an index that describes the regional moisture condition properly. The reconstruction was verified with independent data, and accounts for 45.7% of the actual PDSI variance during their common period . The full reconstruction indicates that the regional drought variability was relatively stable during the nineteenth century, but became more variable and persistent during the twentieth century. The drought epoch in the late 1920s was the most severe one in our reconstruction. In contrast to a wetting trend in the western area of northwest China, a clear drying trend has occurred in north central China since mid-1930s. The multitaper method (MTM) spectral analysis indicates the existence of some decadal (∼11.4 year) and interannual (9.1, 6.8, 4.0, 2.7 and 2.1-2.0 year) cycles, which may potentially be the fingerprints of some proposed climate change forcings.
HAdV-55 has established itself as a major pneumonia pathogen in the Chinese population, and further surveillance and monitoring of this agent as a cause of CAP is warranted.
In this study, the association between genotypic and selected phenotypic characteristics was examined in a collection of Canadian Escherichia coli O157:H7 strains isolated from humans and cattle in the provinces of Alberta, Ontario, Saskatchewan, and Quebec. In a subset of 69 strains selected on the basis of specific phage types (PTs), a strong correlation between the lineage-specific polymorphism assay (LSPA6) genotype and PT was observed with all strains of PTs 4, 14, 21, 31, 33, and 87 belonging to the LSPA6 lineage I (LSPA6-LI) genotype, while those of PTs 23, 45, 67, and 74 belonged to LSPA6 lineage II (LSPA6-LII) genotypes. This correlation was maintained when additional strains of each PT were tested. E. coli O157:H7 strains with the LSPA6-LI genotype were much more common in the collection than were the LSPA6-LII or lineage I/II (LSPA6-LI/II)-related genotypes (82.6, 11.2, and 5.8%, respectively). Of the strains tested, proportionately more LSPA6-LI than LSPA6-LII genotype strains were isolated from humans (52.7% versus 19.7%) than from cattle (47.8% versus 80.2%). In addition, 96.7% of the LSPA6-LII strains carried the stx 2c variant gene, while only 50.0% of LSPA6-LI/II and 2.7% of LSPA6-LI strains carried this gene. LSPA6-LII strains were also significantly more likely to possess the colicin D gene, cda (50.8% versus 23.2%), and have combined resistance to streptomycin, sulfisoxazole, and tetracycline (72.1% versus 0.9%) than were LSPA6-LI strains. The LSPA6 genotype-and PT-related characteristics identified may be important markers of specific ecotypes of E. coli O157:H7 that have unique epidemiological and virulence characteristics.Shiga toxin (Stx)-producing Escherichia coli (STEC) O157:H7 is the leading cause of hemorrhagic colitis and hemolytic-uremic syndrome (HUS) throughout the world (16,23,25). Cattle colonized by E. coli O157:H7 are thought to be the primary reservoir of this bacterium, and its transmission to humans frequently results from the ingestion of contaminated food and water (16,23,35).Results of multiple studies suggest that E. coli O157:H7 strains may differ in their association with human disease. An increasing body of evidence has shown that strains can differ in the type and level of expression of virulence factors (3,28,29,47,48). Similarly, in vivo testing of strains in the gnotobiotic pig model has shown that human isolates caused more severe symptoms than cattle isolates, suggesting that cattle-derived strains may differ in their virulence with respect to those isolated from humans (3). High-resolution genotyping studies on E. coli O157:H7 strains from the United States and Australia using octamer-based genome scanning (OBGS) first demonstrated that the E. coli O157:H7 clonal complex has diverged through two primary lineages, designated lineage I and lineage II, and that these two lineages differ in their frequency of association with human disease (28,29,54). Subsequent studies using a more efficient multiplex PCR assay based on OBGS, the lineage specific polymorphism ass...
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