Prevalence of Staphylococcus aureus and methicillin-resistant S aureus on environmental surfaces in Ohio nursing homes.

BACKGROUND: Methicillin-resistant Staphylococcus aureus (MRSA) is common in medical institutions. We sought to examine the prevalence of S aureus on environmental surfaces in nursing homes and to obtain molecular information on contaminating strains. METHODS: A total of 259 environmental samples were collected from 7 different nursing homes in Northeast Ohio (NEO), from suburban, urban, and rural settings. The presence of the mecA and PVL genes was determined, and spa typing was performed in order to identify molecular types. RESULTS: The prevalence of S aureus was 28.6% (74/259). The prevalence of MRSA and methicillin-susceptible S aureus was 20.1% (52/259) and 8.5% (22/259), respectively. S aureus contamination in suburban, urban, and rural sites was 25.7% (38/148), 45.9% (34/74), and 5.4% (2/37), respectively. MRSA was detected in 16.9% (25/148) of suburban samples and 36.5% (27/74) of urban samples. No MRSA was found in rural samples. Nursing homes from urban areas had a significantly higher (P < .001) prevalence of S aureus compared to nursing homes from suburban and rural sites. Areas with high nurse touch rates were the most commonly contaminated. CONCLUSIONS: We found differences in the prevalence of S aureus and MRSA in nursing homes in different regions of NEO. Part of these differences may result from transfers from hospitals; the urban nursing homes had 4 to 15 hospitals nearby, whereas suburban and rural locations had 1 to 3 hospitals within the area.

Gypsum-DL: an open-source program for preparing small-molecule libraries for structure-based virtual screening.

Computational techniques such as structure-based virtual screening require carefully prepared 3D models of potential small-molecule ligands. Though powerful, existing commercial programs for virtual-library preparation have restrictive and/or expensive licenses. Freely available alternatives, though often effective, do not fully account for all possible ionization, tautomeric, and ring-conformational variants. We here present Gypsum-DL, a free, robust open-source program that addresses these challenges. As input, Gypsum-DL accepts virtual compound libraries in SMILES or flat SDF formats. For each molecule in the virtual library, it enumerates appropriate ionization, tautomeric, chiral, cis/trans isomeric, and ring-conformational forms. As output, Gypsum-DL produces an SDF file containing each molecular form, with 3D coordinates assigned. To demonstrate its utility, we processed 1558 molecules taken from the NCI Diversity Set VI and 56,608 molecules taken from a Distributed Drug Discovery (D3) combinatorial virtual library. We also used 4463 high-quality protein-ligand complexes from the PDBBind database to show that Gypsum-DL processing can improve virtual-screening pose prediction. Gypsum-DL is available free of charge under the terms of the Apache License, Version 2.0.

Genome Sequences of Gordonia Phages BaxterFox, Kita, Nymphadora, and Yeezy.

Gordonia phages BaxterFox, Kita, Nymphadora, and Yeezy are newly characterized phages of Gordonia terrae, isolated from soil samples in Pittsburgh, Pennsylvania. These phages have genome lengths between 50,346 and 53,717 bp, and encode on average 84 predicted proteins. All have G+C content of 66.6%.

Genome Sequences of Gordonia Bacteriophages Obliviate, UmaThurman, and Guacamole.

We describe three newly isolated phages-Obliviate, UmaThurman, and Guacamole-that infect Gordonia terrae 3612. The three genomes are related to one another but are not closely related to other previously sequenced phages or prophages. The three phages are predicted to use integration-dependent immunity systems as described in several mycobacteriophages.

Genome Sequences of Gordonia terrae Phages Benczkowski14 and Katyusha.

Bacteriophages Katyusha and Benczkowski14 are newly isolated phages that infect Gordonia terrae 3612. Both have siphoviral morphologies with isometric heads and long tails (500 nm). The genomes are 75,380 bp long and closely related, and the tape measure genes (9 kbp) are among the largest to be identified.

Genome Sequences of Cluster G Mycobacteriophages Cambiare, FlagStaff, and MOOREtheMARYer.

Mycobacteriophages Cambiare, FlagStaff, and MOOREtheMARYer are newly isolated phages of Mycobacterium smegmatis mc(2) 155 recovered from soil samples in Pittsburgh, PA. All three genomes are closely related to cluster G mycobacteriophages but differ sufficiently in nucleotide sequence and gene content to warrant division of cluster G into several subclusters.