Plasmids and genes contributing to high-level quinolone resistance in Escherichia coli.

Introduction: The importance of plasmid-mediated quinolone resistance (PMQR) in Enterobacterales and its high incidence has been emphasised many times. However, a clinical strain carrying more than two PMQR genes is rare. This study sequenced plasmid transconjugants from a donor strain carrying four different PMQR genes to establish their genetic locations.

Community-acquired in name only: A cluster of carbapenem-resistant in a burn intensive care unit and beyond.

Objective: To describe an investigation into 5 clinical cases of carbapenem-resistant Acinetobacter baumannii (CRAB).

Design: Epidemiological investigation supplemented by whole-genome sequencing (WGS) of clinical and environmental isolates.

Setting: A tertiary-care academic health center in Boston, Massachusetts.

Low O level enhances CH-derived carbon flow into microbial communities in landfill cover soils.

CH oxidation in landfill cover soils plays a significant role in mitigating CH release to the atmosphere. Oxygen availability and the presence of co-contaminants are potentially important factors affecting CH oxidation rate and the fate of CH-derived carbon. In this study, microbial populations that oxidize CH and the subsequent conversion of CH-derived carbon into CO, soil organic C and biomass C were investigated in landfill cover soils at two O tensions, i.

Anaerobic oxidation of methane by aerobic methanotrophs in sub-Arctic lake sediments.

Anaerobic oxidation of methane (AOM) is a biological process that plays an important role in reducing the CH emissions from a wide range of ecosystems. Arctic and sub-Arctic lakes are recognized as significant contributors to global methane (CH) emission, since CH production is increasing as permafrost thaws and provides fuels for methanogenesis. Methanotrophy, including AOM, is critical to reducing CH emissions.

Genomic Methods and Microbiological Technologies for Profiling Novel and Extreme Environments for the Extreme Microbiome Project (XMP).

The Extreme Microbiome Project (XMP) is a project launched by the Association of Biomolecular Resource Facilities Metagenomics Research Group (ABRF MGRG) that focuses on whole genome shotgun sequencing of extreme and unique environments using a wide variety of biomolecular techniques. The goals are multifaceted, including development and refinement of new techniques for the following: 1) the detection and characterization of novel microbes, 2) the evaluation of nucleic acid techniques for extremophilic samples, and 3) the identification and implementation of the appropriate bioinformatics pipelines. Here, we highlight the different ongoing projects that we have been working on, as well as details on the various methods we use to characterize the microbiome and metagenome of these complex samples.

Phylogenetic and ecological analyses of soil and sporocarp DNA sequences reveal high diversity and strong habitat partitioning in the boreal ectomycorrhizal genus Russula (Russulales; Basidiomycota).

*Although critical for the functioning of ecosystems, fungi are poorly known in high-latitude regions. Here, we provide the first genetic diversity assessment of one of the most diverse and abundant ectomycorrhizal genera in Alaska: Russula. *We analyzed internal transcribed spacer rDNA sequences from sporocarps and soil samples using phylogenetic methods, operational taxonomic unit (OTU) delimitations and ordinations to compare species composition in various types of boreal forest.

Increasing ecological inference from high throughput sequencing of fungi in the environment through a tagging approach.

High throughput sequencing methods are widely used in analyses of microbial diversity, but are generally applied to small numbers of samples, which precludes characterization of patterns of microbial diversity across space and time. We have designed a primer-tagging approach that allows pooling and subsequent sorting of numerous samples, which is directed to amplification of a region spanning the nuclear ribosomal internal transcribed spacers and partial large subunit from fungi in environmental samples. To test the method for phylogenetic biases, we constructed a controlled mixture of four taxa representing the Chytridiomycota, Zygomycota, Ascomycota and Basidiomycota.

TOPO TA is A-OK: a test of phylogenetic bias in fungal environmental clone library construction.

TA cloning methods are widely used in analyses of environmental microbial diversity, yet the potential of TA methods to yield phylogenetically biased results has received little attention. To test for a TA bias, we constructed clone libraries of fungal amplicons spanning the ribosomal internally transcribed spacer (ITS) and partial large subunit (LSU) from 92 boreal forest soil DNA extracts using two contrasting methods: the Invitrogen TOPO-TA system and the Lucigen PCR-SMART system. The Lucigen system utilizes blunt-ended rather than TA cloning and transcription terminators to reduce biases due to toxicity of expressed inserts.