56 research outputs found
Genotyping and antibiotic resistance of thermophilic Campylobacter isolated from chicken and pig meat in Vietnam
Background Campylobacter species are recognized as the most common cause of
foodborne bacterial gastroenteritis in humans. In this study nine
Campylobacter strains isolated from chicken meat and pork in Hanoi, Vietnam,
were characterized using molecular methods and tested for antibiotic
resistance. Results The nine isolates (eight C. jejuni and one C. coli) were
identified by multiplex PCR, and tested for the presence or absence of 29 gene
loci associated with virulence, lipooligosaccharide (LOS) biosynthesis and
further functions. flaA typing, multilocus sequence typing and microarray
assay investigation showed a high degree of genetic diversity among these
isolates. In all isolates motility genes (flaA, flaB, flhA, fliM),
colonization associated genes (cadF, docB), toxin production genes (cdtA,
cdtB, secD, secF), and the LOS biosynthesis gene pglB were detected. Eight
gene loci (fliY, virB11, Cje1278, Cj1434c, Cj1138, Cj1438c, Cj1440c, Cj1136)
could not be detected by PCR. A differing presence of the gene loci ciaB (22.2
%), Cje1280 (77.8 %), docC (66.7 %), and cgtB (55.6 %) was found. iamA, cdtC,
and the type 6 secretion system were present in all C. jejuni isolates but not
in C. coli. flaA typing resulted in five different genotypes within C. jejuni,
MLST classified the isolates into seven sequence types (ST-5155, ST-6736,
ST-2837, ST-4395, ST-5799, ST-4099 and ST-860). The microarray assay analysis
showed a high genetic diversity within Vietnamese Campylobacter isolates which
resulted in eight different types for C. jejuni. Antibiotic susceptibility
profiles showed that all isolates were sensitive to gentamicin and most
isolates (88.8 %) were sensitive to chloramphenicol, erythromycin and
streptomycin. Resistance rates to nalidixic acid, tetracycline and
ciprofloxacin were 88.9, 77.8 and 66.7 %, respectively. Conclusions To the
best of our knowledge, this study is the first report that shows high genetic
diversity and remarkable antibiotic resistance of Campylobacter strains
isolated from meat in Vietnam which can be considered of high public health
significance. These preliminary data show that large scale screenings are
justified to assess the relevance of Campylobacter infections on human health
in Vietnam
XplorSeq: A software environment for integrated management and phylogenetic analysis of metagenomic sequence data
<p>Abstract</p> <p>Background</p> <p>Advances in automated DNA sequencing technology have accelerated the generation of metagenomic DNA sequences, especially environmental ribosomal RNA gene (rDNA) sequences. As the scale of rDNA-based studies of microbial ecology has expanded, need has arisen for software that is capable of managing, annotating, and analyzing the plethora of diverse data accumulated in these projects.</p> <p>Results</p> <p>XplorSeq is a software package that facilitates the compilation, management and phylogenetic analysis of DNA sequences. XplorSeq was developed for, but is not limited to, high-throughput analysis of environmental rRNA gene sequences. XplorSeq integrates and extends several commonly used UNIX-based analysis tools by use of a Macintosh OS-X-based graphical user interface (GUI). Through this GUI, users may perform basic sequence import and assembly steps (base-calling, vector/primer trimming, contig assembly), perform BLAST (Basic Local Alignment and Search Tool; <abbrgrp><abbr bid="B1">1</abbr><abbr bid="B2">2</abbr><abbr bid="B3">3</abbr></abbrgrp>) searches of NCBI and local databases, create multiple sequence alignments, build phylogenetic trees, assemble Operational Taxonomic Units, estimate biodiversity indices, and summarize data in a variety of formats. Furthermore, sequences may be annotated with user-specified meta-data, which then can be used to sort data and organize analyses and reports. A document-based architecture permits parallel analysis of sequence data from multiple clones or amplicons, with sequences and other data stored in a single file.</p> <p>Conclusion</p> <p>XplorSeq should benefit researchers who are engaged in analyses of environmental sequence data, especially those with little experience using bioinformatics software. Although XplorSeq was developed for management of rDNA sequence data, it can be applied to most any sequencing project. The application is available free of charge for non-commercial use at <url>http://vent.colorado.edu/phyloware</url>.</p
A meta-analysis of N-acetylcysteine in contrast-induced nephrotoxicity: unsupervised clustering to resolve heterogeneity
<p>Abstract</p> <p>Background</p> <p>Meta-analyses of N-acetylcysteine (NAC) for preventing contrast-induced nephrotoxicity (CIN) have led to disparate conclusions. Here we examine and attempt to resolve the heterogeneity evident among these trials.</p> <p>Methods</p> <p>Two reviewers independently extracted and graded the data. Limiting studies to randomized, controlled trials with adequate outcome data yielded 22 reports with 2746 patients.</p> <p>Results</p> <p>Significant heterogeneity was detected among these trials (<it>I</it><sup>2 </sup>= 37%; <it>p </it>= 0.04). Meta-regression analysis failed to identify significant sources of heterogeneity. A modified L'Abbé plot that substituted groupwise changes in serum creatinine for nephrotoxicity rates, followed by model-based, unsupervised clustering resolved trials into two distinct, significantly different (<it>p </it>< 0.0001) and homogeneous populations (<it>I</it><sup>2 </sup>= 0 and <it>p </it>> 0.5, for both). Cluster 1 studies (<it>n </it>= 18; 2445 patients) showed no benefit (relative risk (RR) = 0.87; 95% confidence interval (CI) 0.68–1.12, <it>p </it>= 0.28), while cluster 2 studies (<it>n </it>= 4; 301 patients) indicated that NAC was highly beneficial (RR = 0.15; 95% CI 0.07–0.33, <it>p </it>< 0.0001). Benefit in cluster 2 was unexpectedly associated with NAC-induced decreases in creatinine from baseline (<it>p </it>= 0.07). Cluster 2 studies were relatively early, small and of lower quality compared with cluster 1 studies (<it>p </it>= 0.01 for the three factors combined). Dialysis use across all studies (five control, eight treatment; <it>p </it>= 0.42) did not suggest that NAC is beneficial.</p> <p>Conclusion</p> <p>This meta-analysis does not support the efficacy of NAC to prevent CIN.</p
- …