Complete Genome Sequence of sp. Strain W8901, a Human Clinical Specimen, Assembled Using MiSeq and MinION Sequence Data.

sp. strain W8901 is a Gram-positive, aerobic, mycolic acid-containing coccobacillus obtained from a patient with acute lymphocytic leukemia. Here, we report on the complete, circular genome sequence obtained using Illumina MiSeq and Oxford Nanopore Technologies MinION reads in order to better resolve the phylogeny of a rare pathogen.

Complete and Circularized Bacterial Genome Sequence of sp. Strain X0973.

sp. strain X0973 is a Gram-positive, weakly acid-fast, aerobic actinomycete obtained from a human abscess with NBRC 100433 as its closest phylogenetic neighbor. Here, we report using Illumina MiSeq and PacBio reads to assemble the complete and circular genome sequence of 3.

Complete and Circularized Genome Assemblies of the Kroppenstedtia eburnea Genus Type Strain and the Kroppenstedtia pulmonis Species Type Strain with MiSeq and MinION Sequence Data.

DSM 45196 and W9323 are aerobic, Gram-positive, filamentous, chemoorganotrophic thermoactinomycetes. Here, we report on the complete and circular genome assemblies generated using Illumina MiSeq and Oxford Nanopore Technologies MinION reads. Putative gene clusters predicted to be involved in the production of secondary metabolites were also identified.

Draft Genome Sequence of Kroppenstedtia sanguinis X0209, a Clinical Isolate Recovered from Human Blood.

X0209, a thermoactinomycete, was isolated from the blood of a patient in Sweden. We report on the draft genome sequence obtained with an Illumina MiSeq instrument. The assembled genome totaled 3.

Streptacidiphilus bronchialis sp. nov., a ciprofloxacin-resistant bacterium from a human clinical specimen; reclassification of Streptomyces griseoplanus as Streptacidiphilus griseoplanus comb. nov. and emended description of the genus Streptacidiphilus.

The taxonomic position of strain 15-057A, an acidophilic actinobacterium isolated from the bronchial lavage of an 80-year-old male, was determined using a polyphasic approach incorporating morphological, phenotypic, chemotaxonomic and genomic analyses. Pairwise 16S rRNA gene sequence similarities calculated using the GGDC web server between strain 15-057A and its closest phylogenetic neighbours, Streptomyces griseoplanus NBRC 12779 and Streptacidiphilus oryzae TH49, were 99.7 and 97.

Complete Genome Sequence of Nocardia farcinica W6977 Obtained by Combining Illumina and PacBio Reads.

The complete genome sequence of the Nocardia farcinica type strain was obtained by combining Illumina HiSeq and PacBio reads, producing a single 6.29-Mb chromosome and 2 circular plasmids. Bioinformatic analysis identified 5,991 coding sequences, including putative genes for virulence, microbial resistance, transposons, and biosynthesis gene clusters.

Complete Genome Sequence of Streptacidiphilus sp. Strain 15-057A, Obtained from Bronchial Lavage Fluid.

Streptacidiphilus sp. strain 15-057A was isolated from a bronchial lavage sample and represents the only member of the genus not isolated from acidic soils. A single circular chromosome of 7.

Kroppenstedtia pulmonis sp. nov. and Kroppenstedtia sanguinis sp. nov., isolated from human patients.

Three human clinical strains (W9323(T), X0209(T) and X0394) isolated from a lung biopsy, blood and cerebral spinal fluid, respectively, were characterised using a polyphasic taxonomic approach. Comparative analysis of the 16S rRNA gene sequences showed the three strains belong to two novel branches within the genus Kroppenstedtia: 16S rRNA gene sequence analysis of W9323(T) showed close sequence similarity to Kroppenstedtia eburnea JFMB-ATE(T) (95.3 %), Kroppenstedtia guangzhouensis GD02(T) (94.

Nocardia arizonensis sp. nov., obtained from human respiratory specimens.

In 2008, three clinical isolates (W9405(T), W9409 and W9575) were obtained from bronchial wash or sputum specimens from patients from the state of Arizona and characterised by polyphasic analysis. All three clinical isolates 16S rRNA gene sequences were found to be 100% identical to each other and showed the strains belong in the genus Nocardia. BLASTn searches in the GenBank database of near full-length 16S rRNA gene sequences showed the highest sequence similarities to the type strains of Nocardia takedensis (98.

Nocardia vulneris sp. nov., isolated from wounds of human patients in North America.

Nocardia species are ubiquitous in the environment with an increasing number of species isolated from clinical sources. From 2005 to 2009, eight isolates (W9042, W9247, W9290, W9319, W9846, W9851T, W9865, and W9908) were obtained from eight patients from three states in the United States and Canada; all were from males ranging in age from 47 to 81 years old; and all were obtained from finger (n = 5) or leg (n = 3) wounds. Isolates were characterized by polyphasic analysis using molecular, phenotypic, morphologic and chemotaxonomic methods.

Genotyping of Candida parapsilosis from three neonatal intensive care units (NICUs) using a panel of five multilocus microsatellite markers: broad genetic diversity and a cluster of related strains in one NICU.

Candida parapsilosis (CP) (n = 40) isolated from an unselected patient population in the neonatal intensive care units (NICUs) of three US hospitals were collected over periods of 3.5-9 years. Two previously published microsatellite markers and three additional trinucleotide markers were used to produce multiplex genotypes, which revealed broad strain diversity among the NICU isolates with a combined index of discrimination (D) = 0.

Nocardia amikacinitolerans sp. nov., an amikacin-resistant human pathogen.

Five nocardioform isolates from human clinical sources were evaluated. Analysis of the nearly full-length 16S rRNA gene showed 99.9-100 % similarity among the strains.

Nocardia cyriacigeorgica infections attributable to unlicensed cosmetic procedures--an emerging public health problem?

We describe an outbreak of Nocardia cyriacigeorgica soft-tissue infections attributable to unlicensed cosmetic injections and the first report using multilocus sequence typing sequence data for determining Nocardia strain relatedness in an outbreak. All 8 cases identified had a common source exposure and required hospitalization, surgical debridement, and prolonged antimicrobial therapy.

Gordonia bronchialis bacteremia and pleural infection: case report and review of the literature.

Gordonia species are aerobic actinomycetes recently recognized as causing human disease, often in the setting of intravascular catheter-related infections. We describe a case of Gordonia bronchialis bacteremia and pleural space infection in the absence of an indwelling intravascular catheter and review the breadth of reported infections with this emerging pathogen.

Mutant selection window and characterization of allelic diversity for ciprofloxacin-resistant mutants of Rhodococcus equi.

The mutant prevention concentration (MPC) for ciprofloxacin was determined for two Rhodococcus equi strains. The MPC for both strains was 32 mug/ml, which is above the peak serum concentration of ciprofloxacin obtainable by oral administration in humans. Nine single nucleotide changes corresponding to eight amino acid substitutions in the quinolone resistance-determining regions of DNA gyrase subunits A and B were characterized.

Investigation of an apparent outbreak of Rhodococcus equi bacteremia.

During January to April 2007, hospital staff reported 3 patients with Rhodococcus equi bloodstream infections. Isolates were analyzed at the Centers for Disease Control and Prevention, Atlanta, GA, to confirm identification and to assess strain relatedness; 2 were R. equi but genetically distinct, and 1 was identified as Gordonia polyisoprenivorans.

Nocardia niwae sp. nov., isolated from human pulmonary sources.

Members of the genus Nocardia are responsible for cutaneous, pulmonary and disseminated human infections. From 2003 to 2008, four nocardioform strains (W8027, W8681, W9071 and W9241(T)) were isolated from patients in the state of Florida, USA. Ribosomal gene sequencing analysis suggested that a novel species of the genus Nocardia had been isolated.

Nocardia mikamii sp. nov., isolated from human pulmonary infections in the USA.

Four nocardioform bacterial strains isolated from clinical respiratory sources were characterized using a polyphasic taxonomic approach. On the basis of 16S rRNA gene sequence analyses, these strains were found to be 100 % similar to each other and were shown to belong to the genus Nocardia. Chemotaxonomic data [major menaquinone: ω-cyclic isoprene side chain MK-8(H₄(cycl)); major polar lipids: diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and phosphatidylinositol mannosides; major fatty acids: monounsaturated fatty acids with a considerable amount of tuberculostearic acid; and mycolic acids (52-62 carbon atoms)] were consistent with the assignment of the novel strains to the genus Nocardia.

Gordonia araii infection associated with an orthopedic device and review of the literature on medical device-associated Gordonia infections.

Gordonia infections in humans are rare and usually affect immunocompromised patients. We present the first case of Gordonia araii infection associated with a medical device in an immunocompetent patient. Sequencing was required for conclusive identification.

Molecular epidemiology of Candida parapsilosis sepsis from outbreak investigations in neonatal intensive care units.

The DNA probe, Cp3-13, was used in a Southern blot assay for genotyping Candida parapsilosis (CP) from 3 fungemia outbreaks in neonatal intensive care units (NICUs) in the southeastern U.S. Genotyping, in 2 outbreaks, supplied evidence of horizontal transmission of CP.

Utility of a microsatellite assay for identifying clonally related outbreak isolates of Aspergillus fumigatus.

A microsatellite assay based on short tandem repeats (STRAf) has been recently described as a discriminatory, high throughput assay for fingerprinting Aspergillus fumigatus isolates. However, the STRAf assay has not been tested for its utility in outbreak settings where it is critical to distinguish clonal clusters from genetically unrelated genotypes. In the present study, employing a panel of epidemiologically linked A.

Characterization of a novel gene for strain typing reveals substructuring of Aspergillus fumigatus across North America.

Fifty-five epidemiologically linked Aspergillus fumigatus isolates obtained from six nosocomial outbreaks of invasive aspergillosis were subtyped by sequencing the polymorphic region of the gene encoding a putative cell surface protein, Afu3g08990 (denoted as CSP). Comparative sequence analysis showed that genetic diversity was generated in the coding region of this gene by both tandem repeats and point mutations. Each unique sequence in an outbreak cluster was assigned an arbitrary number or CSP sequence type.

Nucleotide sequence-based analysis for determining the molecular epidemiology of Penicillium marneffei.

The dimorphic fungus, Penicillium marneffei, is an emerging opportunistic pathogen endemic in Southeast Asia, especially for those with impaired cellular immunity such as human immunodeficiency virus-infected persons. A discriminatory and reproducible method based on the analysis of nucleotide sequences would facilitate epidemiologic investigations of this fungus. Twenty-four clinical or environmental isolates of P.

Comparison of multilocus sequence typing and Ca3 fingerprinting for molecular subtyping epidemiologically-related clinical isolates of Candida albicans.

Southern hybridization with the complex probe Ca3 is a well established tool for molecular subtyping of Candida albicans. Multilocus sequence typing (MLST) is a DNA sequence-based subtyping method recently applied to C. albicans and shown to have a high degree of intraspecies discriminatory power.