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July 7, 2019

Escherichia coli harboring mcr-1 and blaCTX-M on a novel IncF plasmid: first report of mcr-1 in the United States.

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).


July 7, 2019

First report of blaIMP-14 on a plasmid harboring multiple drug resistance genes in Escherichia coli ST131.

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.


July 7, 2019

Complete and closed genome sequences of 10 Salmonella enterica subsp. enterica serovar Anatum isolates from human and bovine sources.

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.


July 7, 2019

Expression and purification of the modification-dependent restriction enzyme BisI and its homologous enzymes.

The methylation-dependent restriction endonuclease (REase) BisI (G(m5)C???NGC) is found in Bacillus subtilis T30. We expressed and purified the BisI endonuclease and 34 BisI homologs identified in bacterial genomes. 23 of these BisI homologs are active based on digestion of (m5)C-modified substrates. Two major specificities were found among these BisI family enzymes: Group I enzymes cut GCNGC containing two to four (m5)C in the two strands, or hemi-methylated sites containing two (m5)C in one strand; Group II enzymes only cut GCNGC sites containing three to four (m5)C, while one enzyme requires all four cytosines to be modified for cleavage. Another homolog, Esp638I cleaves GCS???SGC (relaxed specificity RCN???NGY, containing at least four (m5)C). Two BisI homologs show degenerate specificity cleaving unmodified DNA. Many homologs are small proteins ranging from 150 to 190 amino acid (aa) residues, but some homologs associated with mobile genetic elements are larger and contain an extra C-terminal domain. More than 156 BisI homologs are found in >60 bacterial genera, indicating that these enzymes are widespread in bacteria. They may play an important biological function in restricting pre-modified phage DNA.


July 7, 2019

Complete genome sequence of Dyella thiooxydans ATSB10, a thiosulfate-oxidizing bacterium isolated from sunflower fields in South Korea.

Dyella thiooxydans ATSB10 (KACC 12756(T) = LMG 24673(T)) is a thiosulfate-oxidizing bacterium isolated from rhizosphere soils of sunflower plants. In this study, we completely sequenced the genome of D. thiooxydans ATSB10 and identified the genes involved in thiosulfate oxidation and the metabolism of aromatic intermediates. Copyright © 2016 Hwangbo et al.


July 7, 2019

High-quality permanent draft genome sequence of Ensifer sp. PC2, isolated from a nitrogen-fixing root nodule of the legume tree (Khejri) native to the Thar Desert of India.

Ensifer sp. PC2 is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated from a nitrogen-fixing nodule of the tree legume P. cineraria (L.) Druce (Khejri), which is a keystone species that grows in arid and semi-arid regions of the Indian Thar desert. Strain PC2 exists as a dominant saprophyte in alkaline soils of Western Rajasthan. It is fast growing, well-adapted to arid conditions and is able to form an effective symbiosis with several annual crop legumes as well as species of mimosoid trees and shrubs. Here we describe the features of Ensifer sp. PC2, together with genome sequence information and its annotation. The 8,458,965 bp high-quality permanent draft genome is arranged into 171 scaffolds of 171 contigs containing 8,344 protein-coding genes and 139 RNA-only encoding genes, and is one of the rhizobial genomes sequenced as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) project proposal.


July 7, 2019

Complete genome sequence of the first KPC-type carbapenemase-positive Proteus mirabilis strain from a bloodstream infectio

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.


July 7, 2019

Draft genome sequences of two strains of Paenibacillus glucanolyticus with the ability to degrade lignocellulose.

Paenibacillus glucanolyticus 5162, a bacterium isolated from soil, and Paenibacillus glucanolyticus SLM1, a bacterium isolated from pulp mill waste, can utilize cellulose, hemicellulose and lignin as sole carbon sources for growth. These two strains of Paenibacillus glucanolyticus were sequenced using PacBio and Illumina MiSeq technologies. Copyright © 2016 Mathews et al.


July 7, 2019

Bacillus pumilus SAFR-032 genome revisited: sequence update and re-annotation.

Bacillus pumilus strain SAFR-032 is a non-pathogenic spore-forming bacterium exhibiting an anomalously high persistence in bactericidal environments. In its dormant state, it is capable of withstanding doses of ultraviolet (UV) radiation or hydrogen peroxide, which are lethal for the vast majority of microorganisms. This unusual resistance profile has made SAFR-032 a reference strain for studies of bacterial spore resistance. The complete genome sequence of B. pumilus SAFR-032 was published in 2007 early in the genomics era. Since then, the SAFR-032 strain has frequently been used as a source of genetic/genomic information that was regarded as representative of the entire B. pumilus species group. Recently, our ongoing studies of conservation of gene distribution patterns in the complete genomes of various B. pumilus strains revealed indications of misassembly in the B. pumilus SAFR-032 genome. Synteny-driven local genome resequencing confirmed that the original SAFR-032 sequence contained assembly errors associated with long sequence repeats. The genome sequence was corrected according to the new findings. In addition, a significantly improved annotation is now available. Gene orders were compared and portions of the genome arrangement were found to be similar in a wide spectrum of Bacillus strains.


July 7, 2019

Complete genome sequence of a multidrug-resistant Acinetobacter baumannii isolate obtained from a Mexican hospital (sequence type 422).

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.


July 7, 2019

Comparative genomics of Campylobacter fetus from reptiles and mammals reveals divergent evolution in host-associated lineages.

Campylobacter fetus currently comprises three recognized subspecies, which display distinct host association. Campylobacter fetus subsp. fetus and C fetus subsp. venerealis are both associated with endothermic mammals, primarily ruminants, whereas C fetus subsp. testudinum is primarily associated with ectothermic reptiles. Both C. fetus subsp. testudinum and C. fetus subsp. fetus have been associated with severe infections, often with a systemic component, in immunocompromised humans. To study the genetic factors associated with the distinct host dichotomy in C. fetus, whole-genome sequencing and comparison of mammal- and reptile-associated C fetus was performed. The genomes of C fetus subsp. testudinum isolated from either reptiles or humans were compared with elucidate the genetic factors associated with pathogenicity in humans. Genomic comparisons showed conservation of gene content and organization among C fetus subspecies, but a clear distinction between mammal- and reptile-associated C fetus was observed. Several genomic regions appeared to be subspecies specific, including a putative tricarballylate catabolism pathway, exclusively present in C fetus subsp. testudinum strains. Within C fetus subsp. testudinum, sapA, sapB, and sapAB type strains were observed. The recombinant locus iamABC (mlaFED) was exclusively associated with invasive C fetus subsp. testudinum strains isolated from humans. A phylogenetic reconstruction was consistent with divergent evolution in host-associated strains and the existence of a barrier to lateral gene transfer between mammal- and reptile-associated C fetus Overall, this study shows that reptile-associated C fetus subsp. testudinum is genetically divergent from mammal-associated C fetus subspecies. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.


July 7, 2019

Complete genome sequence of Lysinibacillus sphaericus WHO reference strain 2362.

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.


July 7, 2019

Complete genome sequence of Vibrio vulnificus FORC_017 isolated from a patient with a hemorrhagic rash after consuming raw dotted gizzard shad.

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.


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