The complete circularized genome sequences of selected specimens from the largest known Elizabethkingia anophelis outbreak to date are described here. Genomic rearrangements observed among the outbreak strains are discussed. Copyright © 2016 Nicholson et al.
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.
The recent discovery of a plasmid-borne colistin resistance gene, mcr-1, in China heralds the emergence of truly pan-drug-resistant bacteria (1). The gene has been found primarily in Escherichia coli but has also been identified in other members of the Enterobacteriaceae in human, animal, food, and environmental samples on every continent (2–5). In response to this threat, starting in May 2016, all extended-spectrum-ß-lactamase (ESBL)-producing E. coli clinical isolates submitted to the clinical microbiology laboratory at the Walter Reed National Military Medical Center (WRNMMC) have been tested for resistance to colistin by Etest. Here we report the presence of mcr-1 in an E. coli strain cultured from a patient with a urinary tract infection (UTI) in the United States. The strain was resistant to colistin, but it remained susceptible to several other agents, including amikacin, piperacillin-tazobactam, all carbapenems, and nitrofurantoin (Table 1).
The zoonotic pathogen Borrelia hermsii bears its multiple paralogous genes for variable antigens on several linear plasmids. Application of combined long-read and short-read next-generation sequencing provided complete sequences for antigen-encoding plasmids as well as other linear and circular plasmids and the linear chromosome of the genome. Copyright © 2016 Barbour.
The blaIMP-14 carbapenem resistance gene has largely previously been observed in Pseudomonas aeruginosa and Acinetobacter spp. As part of global surveillance and sequencing of carbapenem-resistant E. coli, we identified an ST131 strain harboring blaIMP-14 within a class 1 integron, itself nested within a ~54kb multi-drug resistance region on an epidemic IncA/C2 plasmid. The emergence of blaIMP-14 in this context in the ST131 lineage is of potential clinical concern. Copyright © 2016 Stoesser et al.
We report here the complete genome sequence of Enterobacter asburiae strain ENIPBJ-CG1, isolated from a bone marrow transplant patient. The size of the genome sequence is approximately 4.65 Mb, with a G+C content of 55.76%, and it is predicted to contain 4,790 protein-coding genes. Copyright © 2016 Liu et al.
Salmonella enterica is an important pathogen transmitted by numerous vectors. Genomic comparisons of Salmonella strains from disparate hosts have the potential to further our understanding of mechanisms underlying host specificities and virulence. Here, we present the closed genome and plasmid sequences of 10 Salmonella enterica subsp. enterica serovar Anatum isolates from bovine and human sources. Copyright © 2016 Nguyen et al.
Sequencing of the blaKPC-positive strain Proteus mirabilis AOUC-001 was performed using both the MiSeq and PacBio RS II platforms and yielded a single molecule of 4,272,433 bp, representing the complete chromosome. Genome analysis showed the presence of several acquired resistance determinants, including two copies of blaKPC-2 carried on a fragment of a KPC-producing plasmid previously described in Klebsiella pneumoniae. Copyright © 2016 Di Pilato et al.
All eukaryotic genomes encode multiple members of the heat shock protein 70 (HSP70) family, which evolved distinctive structural and functional features in response to specific environmental constraints. Phylogenetic analysis of this protein family thus can inform on genetic and molecular mechanisms that drive species-specific environmental adaptation. Here we use the eukaryotic pathogen Leishmania spp. as a model system to investigate the evolution of the HSP70 protein family in an early-branching eukaryote that is prone to gene amplification and adapts to cytotoxic host environments by stress-induced and chaperone-dependent stage differentiation. Combining phylogenetic and comparative analyses of trypanosomatid genomes, draft genome of Paratrypanosoma and recently published genome sequences of 204 L. donovani field isolates, we gained unique insight into the evolutionary dynamics of the Leishmania HSP70 protein family. We provide evidence for (i) significant evolutionary expansion of this protein family in Leishmania through gene amplification and functional specialization of highly conserved canonical HSP70 members, (ii) evolution of trypanosomatid-specific, non-canonical family members that likely gained ATPase-independent functions, and (iii) loss of one atypical HSP70 member in the Trypanosoma genus. Finally, we reveal considerable copy number variation of canonical cytoplasmic HSP70 in highly related L. donovani field isolates, thus identifying this locus as a potential hot spot of environment-genotype interaction. Our data draw a complex picture of the genetic history of HSP70 in trypanosomatids that is driven by the remarkable plasticity of the Leishmania genome to undergo massive intra-chromosomal gene amplification to compensate for the absence of regulated transcriptional control in these parasites. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.
Acinetobacter baumannii has emerged as a dangerous nosocomial pathogen, particularly for severely ill patients in intensive care units and patients with hematologic malignancies. Here, we present the complete genome sequence of a multidrug-resistant A. baumannii isolate, recovered from a Mexican hospital and classified as sequence type 422 according to the multilocus sequence typing Pasteur scheme. Copyright © 2016 Castro-Jaimes et al.
Lysinibacillus sphaericus is a species that contains strains widely used in the biological control of mosquitoes. Here, we present the complete 4.67-Mb genome of the WHO entomopathogenic reference strain L. sphaericus 2362, which is probably one of the most commercialized and studied strains. Genes coding for mosquitocidal toxin proteins were detected. Copyright © 2016 Hernández-Santana et al.
Vibrio vulnificus, a resident in the human gut, is frequently found in seafood, causing food-borne illnesses including gastroenteritis and severe septicemia. While V. vulnificus has been known to be one of the major food-borne pathogens, pathogenicity and virulence factors are not fully understood yet. To extend our understanding of the pathogenesis of V. vulnificus at the genomic level, the genome of V. vulnificus FORC_017 isolated from a female patient experiencing a hemorrhagic rash was completely sequenced and analyzed.Three discontinuous contigs were generated from a hybrid assembly using Illumina MiSeq and PacBio platforms, revealing that the genome of the FORC_017 consists of two circular chromosomes and a plasmid. Chromosome I consists of 3,253,417-bp (GC content 46.49 %) containing 2943 predicted open reading frames (ORFs) and chromosome II of 1,905,745-bp (GC content 46.90 %) containing 1638 ORFs. The plasmid pFORC17 consists of 70,069-bp (GC content 43.77 %) containing 84 ORFs. The average nucleotide identity (ANI) value of the FORC_017 and CMCP6 strains was 98.53, suggesting that they are closely related.Pathogenesis-associated genes including vvhA, rtx gene cluster, and various hemolysin genes were present in FORC_017. In addition, three complete secretion systems (Type I, II and VI) as well as iron uptake-related genes for virulence of the FORC_017 were detected, suggesting that this strain is pathogenic. Further comparative genome analysis revealed that FORC_017 and CMCP6 share major toxin genes including vvhA and rtx for pathogenesis activities. The genome information of the FORC_017 provides novel insights into pathogenicity and virulence factors of V. vulnificus.
Shiga toxin-producing Escherichia coli (STEC) is a foodborne pathogen. We report here the high-quality draft whole-genome sequences of five STEC strains isolated from clinical cases in the United States. This report is for STEC of serotypes O55:H7, O79:H7, O91:H14, O153:H2, and O156:H25. Copyright © 2016 Lindsey et al.
Here, a complete genome sequence of Wohlfahrtiimonas chitiniclastica strain BM-Y is presented. The whole genome is 2.18-Mb and contains a blaVEB-1 gene cassette which endows it with resistance to ceftazidime, ampicillin, tetracycline, etc. To our knowledge, this is the first time that an extended spectrum beta-lactamase (ESBL) type W. chitiniclastica strain has been found. Copyright © 2016 Zhou et al.
Chloroplasts play a crucial role in sustaining life on earth. The availability of over 800 sequenced chloroplast genomes from a variety of land plants has enhanced our understanding of chloroplast biology, intracellular gene transfer, conservation, diversity, and the genetic basis by which chloroplast transgenes can be engineered to enhance plant agronomic traits or to produce high-value agricultural or biomedical products. In this review, we discuss the impact of chloroplast genome sequences on understanding the origins of economically important cultivated species and changes that have taken place during domestication. We also discuss the potential biotechnological applications of chloroplast genomes.
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