Identification of Major Sequence Types among Multidrug-Resistant Staphylococcus epidermidis Strains Isolated from Infected Eyes and Healthy Conjunctiva.

We examined the presence of virulence and antibiotic resistance genes, SCCmec types and determined the genomic diversity among ocular S. epidermidis isolates (patients-23, healthy controls-29). PCR determined the presence of antibiotic resistance genes, virulence genes and SCCmec types among all isolates. MLST and PFGE determined the genomic relatedness among them. All isolates of S. epidermidis showed resistance to at least one class of antibiotics of which 48 isolates were multidrug resistant and carried ARGs. Thirty-five isolates were methicillin resistant and carried mecA gene. Majority of the isolates were resistant to fluoroquinolones and showed mutation in gyrA, parC, and parE genes, however, few isolates showed additional novel mutations in parC gene. Of the MRSE strains, 17 strains carried SCCmec type IV, four type V, two type II, and two UT4. Seven strains carried novel combination of ccr complex and SCCmercury element, not reported earlier. All the S. epidermidis strains harbored icaA and icaD genes, 47 carried ACME operon, and 50 contained IS256. A noteworthy finding was the presence of ST179 among 43% of infected eye isolates an observation rarely reported among S. epidermidis. PFGE and MLST analysis showed genomic diversity among them. Statistical analysis suggests that few healthy conjunctiva isolates had characteristics similar to infected eye isolates. S. epidermidis strains carrying mecA gene are multidrug resistant, virulent and diverse irrespective of sources of isolation. IS256 cannot be used as marker to differentiate isolates of infected eye from healthy conjunctiva.

ChloroMitoCU: Codon patterns across organelle genomes for functional genomics and evolutionary applications.

Organelle genomes are widely thought to have arisen from reduction events involving cyanobacterial and archaeal genomes, in the case of chloroplasts, or α-proteobacterial genomes, in the case of mitochondria. Heterogeneity in base composition and codon preference has long been the subject of investigation of topics ranging from phylogenetic distortion to the design of overexpression cassettes for transgenic expression. From the overexpression point of view, it is critical to systematically analyze the codon usage patterns of the organelle genomes. In light of the importance of codon usage patterns in the development of hyper-expression organelle transgenics, we present ChloroMitoCU, the first-ever curated, web-based reference catalog of the codon usage patterns in organelle genomes. ChloroMitoCU contains the pre-compiled codon usage patterns of 328 chloroplast genomes (29,960 CDS) and 3,502 mitochondrial genomes (49,066 CDS), enabling genome-wide exploration and comparative analysis of codon usage patterns across species. ChloroMitoCU allows the phylogenetic comparison of codon usage patterns across organelle genomes, the prediction of codon usage patterns based on user-submitted transcripts or assembled organelle genes, and comparative analysis with the pre-compiled patterns across species of interest. ChloroMitoCU can increase our understanding of the biased patterns of codon usage in organelle genomes across multiple clades. ChloroMitoCU can be accessed at: http://chloromitocu.cgu.edu.tw/.

Thiomonas bhubaneswarensis sp. nov., an obligately mixotrophic, moderately thermophilic, thiosulfate-oxidizing bacterium.

A novel aerobic, obligately mixotrophic, moderately thermophilic, thiosulfate-oxidizing bacterium, S10T, was isolated from hot-spring sediment samples collected from Atri, Bhubaneswar, India. The cells of this isolate stained Gram-negative and were strictly aerobic, non-sporulating, rod-shaped and motile with a single polar flagellum. Strain S10T was positive for oxidase and catalase activities. It was capable of utilizing thiosulfate under mixotrophic growth conditions. Mixotrophic growth was observed at pH 6.0-8.5 and 25-45 degrees C; optimum growth occurred at pH 7.5-8.0 and 30-37 degrees C. The major cellular fatty acids were C12:0 3-OH, C16:1omega7c, C16:0, C17:0 cyclo, C18:1omega7c and C19:0 cyclo omega8c. The DNA G+C content of strain S10T was 64.8 mol%. 16S rRNA gene sequence analysis indicated that the bacterium clustered within the radiation of the genus Thiomonas and showed 98.0% similarity with Thiomonas perometabolis ATCC 23370T and Thiomonas intermedia ATCC 15466T. However, DNA-DNA reassociation values of strain S10T with Thiomonas perometabolis JCM 20426T and Thiomonas intermedia JCM 20425T, its nearest phylogenetic relatives, were 46 and 39%, respectively. On the basis of phenotypic, physiological and chemotaxonomic properties, 16S rRNA gene sequence analysis and DNA-DNA reassociation studies, it is proposed that strain S10T represents a novel species of the genus Thiomonas, Thiomonas bhubaneswarensis sp. nov.; the type strain is S10T (=DSM 18181T=JCM 14806T).

Thiosulfate oxidation by Comamonas sp. S23 isolated from a sulfur spring.

A bacterial isolate S23 capable of oxidizing thiosulfate was isolated from a sulfur spring. Strain S23 is gram-negative, aerobic, and motile. The G + C content of DNA is 61.4 mol%. The fatty acid composition and phylogenetic analysis of the 16S rRNA gene sequence of strain S23 showed that it is related to the members of the genus Comamonas, and most closely related to Comamonas testosteroni (99.9% sequence similarity). The isolate S23 exhibited thiosulfate oxidation under a mixotrophic growth condition. Polymerase chain reaction (PCR) using soxB-specific primers and DNA sequencing showed the presence of the soxB gene. This is the first report in Comamonas sp. showing thiosulfate oxidation under a mixotrophic growth condition.

Mutational bias and gene expression level shape codon usage in Thermobifida fusca YX.

In this study major factors shaping codon and amino acid usage variation in Thermobifida fusca YX are reported. It is a major degrader of plant cell walls. It produces spores that can be allergenic and has been associated with a condition called farmers lung. For comparison, two other closely related Actinobacteria, S. coelicolor and N. farcinica were considered. Correspondence analysis on RSCU (Relative Synonymous Codon Usage) showed significant correlation between the major trend of codon usage variation and gene expression level assessed by the "Codon Adaptation Index" (CAI) values. The result was further confirmed from distribution of genes along the first axis. In addition, N_{c} (effective number of codons) plot, SCUO (synonymous codon usage order) plot and correlation analyses showed that base composition and mutational bias have a dominant role in codon usage variation. Furthermore, gene expression level, hydrophobicity and aromaticity have played a significant role in the source of variations for amino acid usage. In addition, codon preference for genes at higher expression level was found to be similar among three different genera. Notably, 14 codons optimally used by Thermobifida fusca YX and its comparative study with S. coelicolor and N. farcinica might provide some useful information for their further study of molecular evolution and genetic engineering.