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July 7, 2019

Pseudomonas cerasi sp. nov. (non Griffin, 1911) isolated from diseased tissue of cherry.

Eight isolates of Gram-negative fluorescent bacteria (58(T), 122, 374, 791, 963, 966, 970a and 1021) were obtained from diseased tissue of cherry trees from different regions of Poland. The symptoms resembled those of bacterial canker. Based on an analysis of 16S rDNA sequences the isolates shared the highest over 99.9% similarity with Pseudomonas ficuserectae JCM 2400(T) and P. congelans DSM 14939(T). Phylogenetic analysis using housekeeping genes gyrB, rpoD and rpoB revealed that they form a separate cluster and confirmed their closest relation to P. syringae NCPPB 281(T) and P. congelans LMG 21466(T). DNA-DNA hybridization between the cherry isolate 58(T) and the type strains of these two closely related species revealed relatedness values of 58.2% and 41.9%, respectively. This was further supported by Average Nucleotide Identity (ANIb) and Genome-to-Genome Distance (GGDC) between the whole genome sequences of strain LMG 28609(T) and closely related Pseudomonas species. The major cellular fatty acids are 16:0 and summed feature 3 (16:1 ?7c/15:0 iso 2OH). Phenotypic characteristics differentiated the novel isolates from other closely related species. The G+C content of the genomic DNA of strain 58(T) was 59%. The diversity was proved by PCR MP and BOX PCR, eliminating the possibility that they constitute a clonal population. Based on the evidence of this polyphasic taxonomic study the eight strains are considered to represent a novel species of the genus Pseudomonas for which the name P. cerasi sp. nov. (non Griffin, 1911) is proposed. The type strain of this species is 58(T) (=LMG 28609(T)=CFBP 8305(T)). Copyright © 2016 Elsevier GmbH. All rights reserved.


July 7, 2019

Evaluation of an optimal epidemiologic typing scheme for Legionella pneumophila with whole genome sequence data using validation guidelines.

Sequence-based typing (SBT), analogous to multi-locus sequence typing (MLST), is the current gold-standard typing method for investigation of legionellosis outbreaks caused by Legionella pneumophila However, as common sequence types (STs) cause many infections, some investigations remain unresolved. Here, various whole genome sequencing (WGS)-based methods were evaluated according to published guidelines, including: i) single nucleotide polymorphism (SNP)-based; ii) extended multi-locus sequence typing (MLST) using different numbers of genes; iii) gene presence/absence, and iv) kmer-based. L. pneumophila serogroup 1 isolates (n=106) from the standard “typing panel”, previously used by the European Society for Clinical Microbiology Study Group on Legionella Infections (ESGLI) were tested together with another 229 isolates.Over 98% isolates were considered typable using the mapping- and kmer-based methods. Percentages of isolates with complete extended MLST profiles ranged from 99.1% (50-gene) to 86.8% (1455-gene) whilst only 41.5% produced a full profile with the gene presence/absence scheme. Replicates demonstrated that all methods offer 100% reproducibility. Indices of discrimination range from 0.972 (ribosomal MLST) to 0.999 (SNP-based), and all values are higher than that achieved with SBT (0.940). Epidemiological concordance is generally inversely related to discriminatory power. We propose that an extended MLST scheme with ~50 genes provides optimal epidemiological concordance whilst substantially improving the discrimination offered by SBT, and can be used as part of a hierarchical typing scheme that should maintain backwards compatibility and increase discrimination where necessary. This analysis will be useful for the ESGLI to design a scheme that has the potential to become the new gold standard typing method for L. pneumophila. Copyright © 2016 David et al.


July 7, 2019

Complete genome sequence of cold-adapted enzyme producing Microbulbifer thermotolerans DAU221.

Microbulbifer thermotolerans DAU221 was preliminary isolated from the marine sediment samples in the Republic of Korea. Here, we present the complete genome sequence of M. thermotolerans DAU221, which consisted of 3,938,396 base pairs with a GC content of 56.57%. This genomic information should help us find the industrially useful enzymes. Copyright © 2016 Elsevier B.V. All rights reserved.


July 7, 2019

Horizontal transfer of carbapenemase-encoding plasmids and comparison with hospital epidemiology data.

Carbapenemase-producing organisms have spread worldwide, and infections with these bacteria cause significant morbidity. Horizontal transfer of plasmids that encode carbapenemases plays an important role in the spread of multidrug resistant Gram-negative bacteria. Here we investigate parameters regulating conjugation using an E. coli laboratory strain that lacks plasmids or restriction-enzyme modification systems as a recipient and also using patient isolates as donors and recipients. Because conjugation is tightly regulated, we performed a systematic analysis of the transfer of Klebsiella pneumoniae carbapenemase (blaKPC)-encoding plasmids into multiple strains under different environmental conditions to investigate critical variables. We used four blaKPC-plasmids isolated from patient strains obtained from two hospitals: pKpQIL and pKPC-47e from the National Institutes of Health, and pKPC_UVA01 and pKPC_UVA02 from the University of Virginia. Plasmid transfer frequency differed substantially between different donor and recipient pairs, and was influenced by plasmid content, temperature, and substrate, in addition to donor and recipient strain. pKPC-47e was attenuated in conjugation efficiency across all conditions tested. Despite its presence in multiple clinical species, pKPC_UVA01 had lower conjugation efficiencies than pKpQIL into recipient strains. The conjugation frequency of these plasmids into K. pneumoniae and E. coli patient isolates ranged widely without a clear correlation with clinical epidemiological data. Our results highlight the importance of each variable examined in these controlled experiments. The in vitro models did not reliably predict plasmid mobilization observed in a patient population, indicating that further studies are needed to understand the most important variables affecting horizontal transfer in vivo. Copyright © 2016, American Society for Microbiology. All Rights Reserved.


July 7, 2019

Complete genome sequence of Bacillus subtilis BSD-2, a microbial germicide isolated from cultivated cotton.

Bacillus subtilis BSD-2, isolated from cotton (Gossypium spp.), had strong antagonistic activity to Verticillium dahlia Kleb and Botrytis cinerea. We sequenced and annotated the BSD-2 complete genome to help us the better use of this strain, which has surfactin, bacilysin, bacillibactin, subtilosin A, Tas A and a potential class IV lanthipeptide biosynthetic pathways. Copyright © 2016 Elsevier B.V. All rights reserved.


July 7, 2019

Glutathione-S-transferase FosA6 of Klebsiella pneumoniae origin conferring fosfomycin resistance in ESBL-producing Escherichia coli.

The objectives of this study were to elucidate the genetic context of a novel plasmid-mediated fosA variant, fosA6, conferring fosfomycin resistance and to characterize the kinetic properties of FosA6.The genome of fosfomycin-resistant Escherichia coli strain YD786 was sequenced. Homologues of FosA6 were identified through BLAST searches. FosA6 and FosA(ST258) were purified and characterized using a steady-state kinetic approach. Inhibition of FosA activity was examined with sodium phosphonoformate.Plasmid-encoded glutathione-S-transferase (GST) FosA6 conferring high-level fosfomycin resistance was identified in a CTX-M-2-producing E. coli clinical strain at a US hospital. fosA6 was carried on a self-conjugative, 69 kb IncFII plasmid. The ?lysR-fosA6-?yjiR_1 fragment, located between IS10R and ?IS26, was nearly identical to those on the chromosomes of some Klebsiella pneumoniae strains (MGH78578, PMK1 and KPPR1). FosA6 shared >99% identity with chromosomally encoded FosA(PMK1) in K. pneumoniae of various STs and 98% identity with FosA(ST258), which is commonly found in K. pneumoniae clonal complex (CC) 258 including ST258. FosA6 and FosA(ST258) demonstrated robust GST activities that were comparable to each other. Sodium phosphonoformate, a GST inhibitor, reduced the fosfomycin MICs by 6- to 24-fold for K. pneumoniae and E. coli strains carrying fosA genes on the chromosomes and plasmids, respectively.fosA6, probably captured from the chromosome of K. pneumoniae, conferred high-level fosfomycin resistance in E. coli. FosA6 functioned as a GST and inactivated fosfomycin efficiently. K. pneumoniae may serve as a reservoir of fosfomycin resistance for E. coli.© The Author 2016. Published by Oxford University Press on behalf of the British Society for Antimicrobial Chemotherapy. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.


July 7, 2019

The Solanum demissum R8 late blight resistance gene is an Sw-5 homologue that has been deployed worldwide in late blight resistant varieties.

The potato late blight resistance gene R8 has been cloned. R8 is found in five late blight resistant varieties deployed in three different continents. R8 recognises Avr8 and is homologous to the NB-LRR protein Sw-5 from tomato. The broad spectrum late blight resistance gene R8 from Solanum demissum was cloned based on a previously published coarse map position on the lower arm of chromosome IX. Fine mapping in a recombinant population and bacterial artificial chromosome (BAC) library screening resulted in a BAC contig spanning 170 kb of the R8 haplotype. Sequencing revealed a cluster of at least ten R gene analogues (RGAs). The seven RGAs in the genetic window were subcloned for complementation analysis. Only one RGA provided late blight resistance and caused recognition of Avr8. From these results, it was concluded that the newly cloned resistance gene was indeed R8. R8 encodes a typical intracellular immune receptor with an N-terminal coiled coil, a central nucleotide binding site and 13 C-terminal leucine rich repeats. Phylogenetic analysis of a set of representative Solanaceae R proteins shows that R8 resides in a clearly distinct clade together with the Sw-5 tospovirus R protein from tomato. It was found that the R8 gene is present in late blight resistant potato varieties from Europe (Sarpo Mira), USA (Jacqueline Lee, Missaukee) and China (PB-06, S-60). Indeed, when tested under field conditions, R8 transgenic potato plants showed broad spectrum resistance to the current late blight population in the Netherlands, similar to Sarpo Mira.


July 7, 2019

Complete genome sequence of Mycobacterium chelonae type strain CCUG 47445, a rapidly growing species of nontuberculous mycobacteria.

Mycobacterium chelonae strains are ubiquitous rapidly growing mycobacteria associated with skin and soft tissue infections, cellulitis, abscesses, osteomyelitis, catheter infections, disseminated diseases, and postsurgical infections after implants with prostheses, transplants, and even hemodialysis procedures. Here, we report the complete genome sequence of M. chelonae type strain CCUG 47445. Copyright © 2016 Jaén-Luchoro et al.


July 7, 2019

Complete genome sequence of Mesorhizobium ciceri bv. biserrulae strain WSM1284, an efficient nitrogen-fixing microsymbiont of the pasture legume Biserrula pelecinus.

We report the complete genome sequence of Mesorhizobium ciceri bv. biserrulae strain WSM1284, a nitrogen-fixing microsymbiont of the pasture legume Biserrula pelecinus The genome consists of 6.88 Mb distributed between a single chromosome (6.33 Mb) and a single plasmid (0.55 Mb). Copyright © 2016 Haskett et al.


July 7, 2019

Whole-genome sequence of Hafnia alvei HUMV-5920, a human isolate.

A clinical isolate of Hafnia alvei (strain HUMV-5920) was obtained from a urine sample from an adult patient. We report here its complete genome assembly using PacBio single-molecule real-time (SMRT) sequencing, which resulted in a chromosome with 4.5 Mb and a circular contig of 87 kb. About 4,146 protein-coding genes are predicted from this assembly. Copyright © 2016 Lázaro-Díez et al.


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