Candida duobushaemulonii is a drug-resistant yeast that can cause invasive candidiasis. Here, we report the first genome sequence of C. duobushaemulonii, isolate B09383, generated using PacBio sequencing technology. The estimated genome size was 12.5?Mb with a GC content of 46.84%.
Shigella spp. are enteric pathogens that cause shigellosis. We report here the high-quality whole-genome sequences of 59 historical Shigella strains that represent the four species and a variety of serotypes.
Candida haemulonii is an emerging multidrug-resistant yeast that can cause invasive candidiasis. Here, we report the first genome sequence of C. haemulonii (isolate B11899) generated using PacBio sequencing technology. The estimated genome size was 13.3?Mb, with a GC content of 45.19%.
Rhodococcus sp. H-CA8f was isolated from marine sediments obtained from the Comau fjord, located in Northern Chilean Patagonia. Whole-genome sequencing was achieved using PacBio RS II platform, comprising one closed, complete chromosome of 6,19?Mbp with a 62.45% G?+?C content. The chromosome harbours several metabolic pathways providing a wide catabolic potential, where the upper biphenyl route is described. Also, Rhodococcus sp. H-CA8f bears one linear mega-plasmid of 301?Kbp and 62.34% of G?+?C content, where genomic analyses demonstrated that it is constituted mostly by putative ORFs with unknown functions, representing a novel genetic feature. These genetic characteristics provide relevant insights regarding Chilean marine actinobacterial strains.
Increasingly rich metadata are now being linked to samples that have been whole-genome sequenced. However, much of this information is ignored. This is because linking this metadata to genes, or regions of the genome, usually relies on knowing the gene sequence(s) responsible for the particular trait being measured and looking for its presence or absence in that genome. Examples of this would be the spread of antimicrobial resistance genes carried on mobile genetic elements (MGEs). However, although it is possible to routinely identify the resistance gene, identifying the unknown MGE upon which it is carried can be much more difficult if the starting point is short-read whole-genome sequence data. The reason for this is that MGEs are often full of repeats and so assemble poorly, leading to fragmented consensus sequences. Since mobile DNA, which can carry many clinically and ecologically important genes, has a different evolutionary history from the host, its distribution across the host population will, by definition, be independent of the host phylogeny. It is possible to use this phenomenon in a genome-wide association study to identify both the genes associated with the specific trait and also the DNA linked to that gene, for example the flanking sequence of the plasmid vector on which it is encoded, which follows the same patterns of distribution as the marker gene/sequence itself. We present PlasmidTron, which utilizes the phenotypic data normally available in bacterial population studies, such as antibiograms, virulence factors, or geographical information, to identify traits that are likely to be present on DNA that can randomly reassort across defined bacterial populations. It is also possible to use this methodology to associate unknown genes/sequences (e.g. plasmid backbones) with a specific molecular signature or marker (e.g. resistance gene presence or absence) using PlasmidTron. PlasmidTron uses a k-mer-based approach to identify reads associated with a phylogenetically unlinked phenotype. These reads are then assembled de novo to produce contigs in a fast and scalable-to-large manner. PlasmidTron is written in Python 3 and is available under the open source licence GNU GPL3 from https://github.com/sanger-pathogens/plasmidtron.
Escherichia coli O145:H11 strain RM14721 was originally isolated from wildlife feces near a leafy greens-growing region in Yuma, AZ. This strain was initially positive for stx1; however, in subsequent cultures, stx1 was not detected by PCR. Here, we report the complete genome sequence and annotation of RM14721.
Carbapenems are considered last-resort antibiotics used to treat human infections caused by multidrug-resistant bacteria. In 2011, VIM-1 carbapenemase-producing Salmonella enterica subsp. enterica serovar Infantis strains were isolated from livestock for the first time in Germany. Here, we announce the complete genome sequence of the first German blaVIM-1-harboring Salmonella Infantis isolate (15-SA01028) originating from food. Copyright © 2018 Borowiak et al.
Mycobacterium bovis is the causative agent of bovine tuberculosis, an infectious disease that affects both animals and humans and thus presents a risk to public health and the livestock industry. Here, we report the genome sequences of five Mycobacterium bovis strains that represent major genotype clusters observed in farmed animals and wildlife in Canada.© Crown copyright 2018.
Antimonials (Sb) were used for decades for chemotherapy of visceral leishmaniasis (VL). Now abandoned in the Indian subcontinent (ISC) because of Leishmania donovani resistance, this drug offers a unique model for understanding drug resistance dynamics. In a previous phylogenomic study, we found two distinct populations of L. donovani: the core group (CG) in the Gangetic plains and ISC1 in the Nepalese highlands. Sb resistance was only encountered within the CG, and a series of potential markers were identified. Here, we analyzed the development of resistance to trivalent antimonials (SbIII) upon experimental selection in ISC1 and CG strains. We observed that (i) baseline SbIII susceptibility of parasites was higher in ISC1 than in the CG, (ii) time to SbIII resistance was higher for ISC1 parasites than for CG strains, and (iii) untargeted genomic and metabolomic analyses revealed molecular changes along the selection process: these were more numerous in ISC1 than in the CG. Altogether these observations led to the hypothesis that CG parasites are preadapted to SbIII resistance. This hypothesis was experimentally confirmed by showing that only wild-type CG strains could survive a direct exposure to the maximal concentration of SbIII The main driver of this preadaptation was shown to be MRPA, a gene involved in SbIII sequestration and amplified in an intrachromosomal amplicon in all CG strains characterized so far. This amplicon emerged around 1850 in the CG, well before the implementation of antimonials for VL chemotherapy, and we discuss here several hypotheses of selective pressure that could have accompanied its emergence.IMPORTANCE The “antibiotic resistance crisis” is a major challenge for scientists and medical professionals. This steady rise in drug-resistant pathogens also extends to parasitic diseases, with antimony being the first anti-Leishmania drug that fell in the Indian subcontinent (ISC). Leishmaniasis is a major but neglected infectious disease with limited therapeutic options. Therefore, understanding how parasites became resistant to antimonials is of commanding importance. In this study, we experimentally characterized the dynamics of this resistance acquisition and show for the first time that some Leishmania populations of the ISC were preadapted to antimony resistance, likely driven by environmental factors or by drugs used in the 19th century. Copyright © 2018 Dumetz et al.
The genome of Salmonella enterica subsp. enterica serotype Senftenberg N17-509, a strain isolated from desiccated coconut, was sequenced using single-molecule real-time sequencing. It consists of a 5.1-Mbp chromosome and a 29-kb linear plasmid. Copyright © 2018 Stevens et al.
Strains of the ciprofloxacin-resistant (Cipr) Salmonella enterica subsp. enterica serovar Kentucky sequence type 198 (ST198) have rapidly and extensively disseminated globally to become a major food safety and public health concern. Here, we report the complete genome sequence of a CiprS. Kentucky ST198 strain, PU131, isolated from a human patient in Washington State (USA).
The genomes of many strains of Escherichia coli have been sequenced, as this organism is a classic model bacterium. Here, we report the genome sequence of Escherichia coli DH5a, which is resistant to a T4 bacteriophage (CCTCC AB 2015375), while its other homologous E. coli strains, such as E. coli BL21, DH10B, and MG1655, are not resistant to phage invasions. Thus, understanding of the genome of the DH5a strain, along with comparative analysis of its genome sequence along with other sequences of E. coli strains, may help to reveal the bacteriophage resistance mechanism of E. coli. Copyright © 2018 Chen et al.
Escherichia albertii has recently been recognized as an emerging human and bird enteric pathogen. Here, we report the complete chromosome sequence of a clinical isolate of E. albertii strain 1551-2, which may provide information about the pathogenic potential of this new species and the mechanisms of evolution of Escherichia species. Copyright © 2018 Romão et al.
The Burkholderia pseudomallei isolate MSHR1435 is a fully virulent environmental sequence type 131 (ST131) isolate that is epidemiologically associated with a 17.5-year chronic melioidosis infection. The completed genome will serve as a reference for studies of environmental ecology, virulence, and chronic B. pseudomallei infections. Copyright © 2018 Sahl et al.
We report a partial genome sequence for the Coxiella-like endosymbiont strain CLE-RmD, assembled from metagenomics data obtained from the southern cattle tick (Rhipicephalus microplus) Deutsch strain.
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