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Sunday, July 7, 2019

Complete genome sequence of Escherichia coli AS19, an antibiotic-sensitive variant of E. coli strain B REL606.

The chemically mutagenized Escherichia coli strain AS19 was isolated on the basis of its enhanced sensitivity to different antibiotics, in particular to actinomycin. The strain was later modified to study rRNA modifications that confer antibiotic resistance. Here, we present the genome sequence of the variant E. coli AS19-RrmA. Copyright © 2018 Avalos et al.

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Sunday, July 7, 2019

Complete genome sequence of Staphylococcus haemolyticus type strain SGAir0252.

Staphylococcus haemolyticus is a coagulase-negative staphylococcal species that is part of the skin microbiome and an opportunistic human pathogen. The strain SGAir0252 was isolated from tropical air samples collected in Singapore, and its complete genome comprises one chromosome of 2.63?Mb and one plasmid of 41.6?kb. Copyright © 2018 Premkrishnan et al.

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Sunday, July 7, 2019

First detection of a blaCTX-M-15-carrying plasmid in Vibrio alginolyticus.

Vibrio alginolyticus is a gram-negative halophilic bacterium, widely distributed in sea-water and seafood all over the world and is the main pathogenic bacteria of marine animals such as fish, shrimp and shellfish. Besides, it is also an important human pathogen causing eye, ear and wound infections, as well as gastroenteritis, septicemia, and necrotizing fasciitis [1]. Resistance to extended-spectrum cephalosporins is rarely ob- served in V. alginolyticus. Here, we report for the first time the identification of a foodborne V. alginolyticus strain Vb0506 carrying plasmid encoding blaCTX-M-15.

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Sunday, July 7, 2019

Short genome report of cellulose-producing commensal Escherichia coli 1094.

Bacterial surface colonization and biofilm formation often rely on the production of an extracellular polymeric matrix that mediates cell-cell and cell-surface contacts. In Escherichia coli and many Betaproteobacteria and Gammaproteobacteria cellulose is often the main component of the extracellular matrix. Here we report the complete genome sequence of the cellulose producing strain E. coli 1094 and compare it with five other closely related genomes within E. coli phylogenetic group A. We present a comparative analysis of the regions encoding genes responsible for cellulose biosynthesis and discuss the changes that could have led to the loss of this important adaptive advantage…

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Sunday, July 7, 2019

Complete and assembled genome sequence of an NDM-9- and CTX-M-15-producing Klebsiella pneumoniae ST147 wastewater isolate from Switzerland.

Carbapenem-resistant Klebsiella pneumoniae have emerged worldwide and represent a major threat to human health. Here we report the genome sequence of K. pneumoniae 002SK2, an NDM-9- and CTX-M-15-producing strain isolated from wastewater in Switzerland and belonging to the international high-risk clone sequence type 147 (ST147).Whole-genome sequencing of K. pneumoniae 002SK2 was performed using Pacific Biosciences (PacBio) single-molecule, real-time (SMRT) technology RS2 reads (C4/P6 chemistry). De novo assembly was performed using Canu assembler, and sequences were annotated using the NCBI Prokaryotic Genome Annotation Pipeline (PGAP).The genome of K. pneumoniae 002SK2 consists of a 5.4-Mbp chromosome containing blaSHV-11 and fosA6, a 159-kb…

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Sunday, July 7, 2019

Genome sequences of Shewanella baltica and Shewanella morhuae strains isolated from the gastrointestinal tract of freshwater fish.

We present here the genome sequences of Shewanella baltica strain CW2 and Shewanella morhuae strain CW7, isolated from the gastrointestinal tract of Salvelinus namaycush (lean lake trout) and Coregonus clupeaformis (whitefish), respectively. These genome sequences provide insights into the niche adaptation of these specific species in freshwater systems. Copyright © 2018 Castillo et al.

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Sunday, July 7, 2019

Analysis of resistance genes of clinical Pannonibacter phragmitetus strain 31801 by complete genome sequencing.

To clarify the resistance mechanisms of Pannonibacter phragmitetus 31801, isolated from the blood of a liver abscess patient, at the genomic level, we performed whole genomic sequencing using a PacBio RS II single-molecule real-time long-read sequencer. Bioinformatic analysis of the resulting sequence was then carried out to identify any possible resistance genes. Analyses included Basic Local Alignment Search Tool searches against the Antibiotic Resistance Genes Database, ResFinder analysis of the genome sequence, and Resistance Gene Identifier analysis within the Comprehensive Antibiotic Resistance Database. Prophages, clustered regularly interspaced short palindromic repeats (CRISPR), and other putative virulence factors were also identified using…

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Sunday, July 7, 2019

Low-level antimicrobials in the medicinal leech select for resistant pathogens that spread to patients.

Fluoroquinolones (FQs) and ciprofloxacin (Cp) are important antimicrobials that pollute the environment in trace amounts. Although Cp has been recommended as prophylaxis for patients undergoing leech therapy to prevent infections by the leech gut symbiont Aeromonas, a puzzling rise in Cp-resistant (Cpr) Aeromonas infections has been reported. We report on the effects of subtherapeutic FQ concentrations on bacteria in an environmental reservoir, the medicinal leech, and describe the presence of multiple antibiotic resistance mutations and a gain-of-function resistance gene. We link the rise of CprAeromonas isolates to exposure of the leech microbiota to very low levels of Cp (0.01 to…

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Sunday, July 7, 2019

Pathogenesis of Helicobacter pylori infection

In this review, we highlight progress in the last year in characterizing known virulence factors like flagella and the Cag type IV secretion system with sophisticated struc- tural and biochemical approaches to yield new insight on the assembly and functions of these critical virulence determinants. Several aspects of Helicobacter pylori physi- ology were newly explored this year and evaluated for their functions during stom- ach colonization, including a fascinating role for the essential protease HtrA in allowing access of H. pylori to the basolateral side of the gastric epithelium through cleavage of the tight junction protein E- cadherin to facilitate…

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Sunday, July 7, 2019

Complete genome sequence of herpes simplex virus 2 strain 333.

Herpes simplex virus 2, or human herpesvirus 2, is a ubiquitous human pathogen that causes genital ulcerations and establishes latency in sacral root ganglia. We fully sequenced and manually curated the viral genome sequence of herpes simplex virus 2, strain 333 using Pacific Biosciences and Illumina sequencing technologies.

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Sunday, July 7, 2019

The ß-lactamase gene profile and a plasmid-carrying multiple heavy metal resistance genes of Enterobacter cloacae.

In this work, by high-throughput sequencing, antibiotic resistance genes, including class A (blaCTX-M, blaZ, blaTEM, blaVEB, blaKLUC, and blaSFO), class C (blaSHV, blaDHA, blaMIR, blaAZECL-29, and blaACT), and class D (blaOXA) ß-lactamase genes, were identified among the pooled genomic DNA from 212 clinical Enterobacter cloacae isolates. Six blaMIR-positive E. cloacae strains were identified, and pulsed-field gel electrophoresis (PFGE) showed that these strains were not clonally related. The complete genome of the blaMIR-positive strain (Y546) consisted of both a chromosome (4.78?Mb) and a large plasmid pY546 (208.74?kb). The extended-spectrum ß-lactamases (ESBLs) (blaSHV-12 and blaCTX-M-9a) and AmpC (blaMIR) were encoded on the…

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