The mitochondrial genome of the venomous cone snail conus consors

Cone snails are venomous predatory marine neogastropods that belong to the species-rich superfamily of the Conoidea. So far, the mitochondrial genomes of two cone snail species (Conus textile and Conus borgesi) have been described, and these feed on snails and worms, respectively. Here, we report the mitochondrial genome sequence of the fish-hunting cone snail Conus consors and describe a novel putative control region (CR) which seems to be absent in the mitochondrial DNA (mtDNA) of other cone snail species. This possible CR spans about 700 base pairs (bp) and is located between the genes encoding the transfer RNA for phenylalanine (tRNA-Phe, trnF) and cytochrome c oxidase subunit III (cox3). The novel putative CR contains several sequence motifs that suggest a role in mitochondrial replication and transcription

A k-mer-based method for the identification of phenotype-associated genomic biomarkers and predicting phenotypes of sequenced bacteria.

We have developed an easy-to-use and memory-efficient method called PhenotypeSeeker that (a) identifies phenotype-specific k-mers, (b) generates a k-mer-based statistical model for predicting a given phenotype and (c) predicts the phenotype from the sequencing data of a given bacterial isolate. The method was validated on 167 Klebsiella pneumoniae isolates (virulence), 200 Pseudomonas aeruginosa isolates (ciprofloxacin resistance) and 459 Clostridium difficile isolates (azithromycin resistance). The phenotype prediction models trained from these datasets obtained the F1-measure of 0.88 on the K. pneumoniae test set, 0.88 on the P. aeruginosa test set and 0.97 on the C. difficile test set. The F1-measures were the same for assembled sequences and raw sequencing data; however, building the model from assembled genomes is significantly faster. On these datasets, the model building on a mid-range Linux server takes approximately 3 to 5 hours per phenotype if assembled genomes are used and 10 hours per phenotype if raw sequencing data are used. The phenotype prediction from assembled genomes takes less than one second per isolate. Thus, PhenotypeSeeker should be well-suited for predicting phenotypes from large sequencing datasets. PhenotypeSeeker is implemented in Python programming language, is open-source software and is available at GitHub (https://github.com/bioinfo-ut/PhenotypeSeeker/)

Multidrug resistant Pseudomonas aeruginosa in Estonian hospitals

Abstract Background We aimed to identify the main spreading clones, describe the resistance mechanisms associated with carbapenem- and/or multidrug-resistant P. aeruginosa and characterize patients at risk of acquiring these strains in Estonian hospitals. Methods Ninety-two non-duplicated carbapenem- and/or multidrug-resistant P. aeruginosa strains were collected between 27th March 2012 and 30th April 2013. Clinical data of the patients was obtained retrospectively from the medical charts. Clonal relationships of the strains were determined by whole genome sequencing and analyzed by multi-locus sequence typing. The presence of resistance genes and beta-lactamases and their origin was determined. Combined-disk method and PCR was used to evaluate carbapenemase and metallo-beta-lactamase production. Results Forty-three strains were carbapenem-resistant, 11 were multidrug-resistant and 38 were both carbapenem- and multidrug-resistant. Most strains (54%) were isolated from respiratory secretions and caused an infection (74%). Over half of the patients (57%) were ≥ 65 years old and 85% had ≥1 co-morbidity; 96% had contacts with healthcare and/or had received antimicrobial treatment in the previous 90 days. Clinically relevant beta-lactamases (OXA-101, OXA-2 and GES-5) were found in 12% of strains, 27% of which were located in plasmids. No Ambler class B beta-lactamases were detected. Aminoglycoside modifying enzymes were found in 15% of the strains. OprD was defective in 13% of the strains (all with CR phenotype); carbapenem resistance triggering mutations (F170 L, W277X, S403P) were present in 29% of the strains. Ciprofloxacin resistance correlated well with mutations in topoisomerase genes gyrA (T83I, D87N) and parC (S87 L). Almost all strains (97%) with these mutations showed ciprofloxacin-resistant phenotype. Multi-locus sequence type analysis indicated high diversity at the strain level – 36 different sequence types being detected. Two sequence types (ST108 (n = 23) and ST260 (n = 18)) predominated. Whereas ST108 was associated with localized spread in one hospital and mostly carbapenem-resistant phenotype, ST260 strains occurred in all hospitals, mostly with multi-resistant phenotype and carried different resistance genotype/machinery. Conclusions Diverse spread of local rather than international P. aeruginosa strains harboring multiple chromosomal mutations, but not plasmid-mediated Ambler class B beta-lactamases, were found in Estonian hospitals. Trial registration This trial was registered retrospectively in ClinicalTrials.gov (NCT03343119)

Muropeptides Stimulate Growth Resumption from Stationary Phase in Escherichia coli

When nutrients run out, bacteria enter a dormant metabolic state. This low or undetectable metabolic activity helps bacteria to preserve their scant reserves for the future needs, yet it also diminishes their ability to scan the environment for new growth-promoting substrates. However, neighboring microbial growth is a reliable indicator of a favorable environment and can thus serve as a cue for exiting dormancy. Here we report that for Escherichia coli and Pseudomonas aeruginosa this cue is provided by the basic peptidoglycan unit (i.e. muropeptide). We show that several forms of muropeptides from a variety of bacterial species can stimulate growth resumption of dormant cells and the sugar-peptide bond is crucial for this activity. These results, together with previous research that identifies muropeptides as a germination signal for bacterial spores, and their detection by mammalian immune cells, show that muropeptides are a universal cue for bacterial growth

Highly similar segments of the longest non-coding mtDNA region in the neogastropods <i>Conus consors</i> and <i>Terebra dimidiata</i>

<p><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0051528#pone.0051528-Cunha1" target="_blank">[<b>7</b>]</a><b>.</b> CRs in <i>C. consors</i> and <i>T. dimidiata</i> share short and very similar segments, including the 39 bp of the IR2 sequence motif (the second alignment). Sequence alignment was done by MUSCLE <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0051528#pone.0051528-Zuker1" target="_blank">[20]</a>. Sequence similarities are highlighted in green (A), blue (C), yellow (G) and red (T).</p

Predicted secondary structures before IR2 of the mtDNA control region of <i>Conus consors</i> in comparison with <i>C. borgesi</i> and <i>C. textile</i>.

<p>Short inverted repeat IR1 (highlighted with yellow circles) is a common feature of the non-coding region in the mitochondrial genomes of <i>C. consors</i>, <i>C. borgesi</i> and <i>C. textile</i>. Structures and folding energies were predicted with <i>mfold </i><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0051528#pone.0051528-Zuker1" target="_blank">[20]</a>.</p

Analyses of poly(T) and poly(A) motifs in the IR2 sequence of <i>Conus consors</i>.

<p>25 clones representing the first IR2 sequence part (blue bars; primer pair F/R-1.1, PCR product includes poly(T) stretch) and 17 clones representing the second IR2 sequence part (red bars; primer pair F/R-1.3, PCR product includes poly(A) stretch) were sequenced according to Sanger and analyzed. Since, the quality of the poly(A) sequences obtained had been suboptimal, the reverse complement sequences containing a poly(T) stretch instead of the poly(A) motif were analyzed. For both IR2 sequence parts investigated, variations in length due to the phenomenon of strand slippage were observed. Accordingly, it was not possible to determine the exact length of the poly(T) and the poly(A) stretches. Most likely, both homopolymeric sequence motifs are 18 or 19 bp in length.</p