Comparative Antibiotic Resistance of Diarrheal Pathogens from Vietnam and Thailand, 1996-1999

Antimicrobial resistance rates for shigella, campylobacter, nontyphoidal salmonella, and enterotoxigenic Escherichia coli were compared for Vietnam and Thailand from 1996 to 1999. Resistance to trimethoprim-sulfamethoxazole, ampicillin, chloramphenicol, and tetracycline was common. Quinolone resistance remains low in both countries, except among campylobacter and salmonella organisms in Thailand. Nalidixic acid resistance among salmonellae has more than doubled since 1995 (to 21%) in Thailand but is not yet documented in Vietnam. Resistance to quinolones correlated with resistance to azithromycin in both campylobacter and salmonella in Thailand. This report describes the first identification of this correlation and its epidemiologic importance among clinical isolates. These data illustrate the growing magnitude of antibiotic resistance and important differences between countries in Southeast Asia

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