scholarly journals Homologous Recombination within Large Chromosomal Regions Facilitates Acquisition of β-Lactam and Vancomycin Resistance in Enterococcus faecium

2016 ◽  
Vol 60 (10) ◽  
pp. 5777-5786 ◽  
Author(s):  
Mónica García-Solache ◽  
Francois Lebreton ◽  
Robert E. McLaughlin ◽  
James D. Whiteaker ◽  
Michael S. Gilmore ◽  
...  
Keyword(s):  
Enterococcus Faecium ◽  
Genomic Dna ◽  
Large Scale ◽  
Vancomycin Resistance ◽  
Whole Genome ◽  
Whole Genome Analysis ◽  
Single Nucleotide ◽  
Content Type ◽  
Donor Chromosome ◽  
Vancomycin Resistant

ABSTRACTThe transfer of DNA betweenEnterococcus faeciumstrains has been characterized both by the movement of well-defined genetic elements and by the large-scale transfer of genomic DNA fragments. In this work, we report on the whole-genome analysis of transconjugants resulting from mating events between the vancomycin-resistantE. faeciumC68 strain and the vancomycin-susceptible D344RRF strain to discern the mechanism by which the transferred regions enter the recipient chromosome. Vancomycin-resistant transconjugants from five independent matings were analyzed by whole-genome sequencing. In all cases but one, the penicillin binding protein 5 (pbp5) gene and the Tn5382vancomycin resistance transposon were transferred together and replaced the correspondingpbp5region of D344RRF. In one instance, Tn5382inserted independently downstream of the D344RRFpbp5gene. Single nucleotide variant (SNV) analysis suggested that entry of donor DNA into the recipient chromosome occurred by recombination across regions of homology between donor and recipient chromosomes, rather than through insertion sequence-mediated transposition. The transfer of genomic DNA was also associated with the transfer of C68 plasmid pLRM23 and another putative plasmid. Our data are consistent with the initiation of transfer by cointegration of a transferable plasmid with the donor chromosome, with subsequent circularization of the plasmid-chromosome cointegrant in the donor prior to transfer. Entry into the recipient chromosome most commonly occurred across regions of homology between donor and recipient chromosomes.

scholarly journals Identification of VanN-Type Vancomycin Resistance in an Enterococcus faecium Isolate from Chicken Meat in Japan

2012 ◽  
Vol 56 (12) ◽  
pp. 6389-6392 ◽  
Author(s):  
Takahiro Nomura ◽  
Koichi Tanimoto ◽  
Keigo Shibayama ◽  
Yoshichika Arakawa ◽  
Shuhei Fujimoto ◽  
...  
Keyword(s):  
Enterococcus Faecium ◽  
Gel Electrophoresis ◽  
Vancomycin Resistance ◽  
Pulsed Field Gel Electrophoresis ◽  
Chicken Meat ◽  
Large Plasmid ◽  
Content Type ◽  
Vancomycin Resistant ◽  
Faecium Isolate ◽  
Level Resistance

ABSTRACTFive VanN-type vancomycin-resistantEnterococcus faeciumstrains were isolated from a sample of domestic chicken meat in Japan. All isolates showed low-level resistance to vancomycin (MIC, 12 mg/liter) and had the same pulsed-field gel electrophoresis profile. The vancomycin resistance was encoded on a large plasmid (160 kbp) and was expressed constitutively. The VanN-type resistance operon was identical to the first resistance operon to be reported, with the exception of a 1-bp deletion invanTNand a 1-bp substitution invanSN.

scholarly journals Whole-Genome Analysis of a Daptomycin-Susceptible Enterococcus faecium Strain and Its Daptomycin-Resistant Variant Arising during Therapy

2012 ◽  
Vol 57 (1) ◽  
pp. 261-268 ◽  
Author(s):  
Truc T. Tran ◽  
Diana Panesso ◽  
Hongyu Gao ◽  
Jung H. Roh ◽  
Jose M. Munita ◽  
...  
Keyword(s):  
Enterococcus Faecium ◽  
Fatty Acid Synthase ◽  
Cell Envelope ◽  
Phospholipid Metabolism ◽  
Clinical Strain ◽  
Cyclopropane Fatty Acid ◽  
Whole Genome ◽  
Whole Genome Analysis ◽  
Resistant Variant ◽  
Content Type

ABSTRACTDevelopment of daptomycin (DAP) resistance inEnterococcus faecalishas recently been associated with mutations in genes encoding proteins with two main functions: (i) control of the cell envelope stress response to antibiotics and antimicrobial peptides (LiaFSR system) and (ii) cell membrane phospholipid metabolism (glycerophosphoryl diester phosphodiesterase and cardiolipin synthase [cls]). However, the genetic bases for DAP resistance inEnterococcus faeciumare unclear. We performed whole-genome comparative analysis of a clinical strain pair, DAP-susceptibleE. faeciumS447 and its DAP-resistant derivative R446, which was recovered from a single patient during DAP therapy. By comparative whole-genome sequencing, DAP resistance in R446 was associated with changes in 8 genes. Two of these genes encoded proteins involved in phospholipid metabolism: (i) an R218Q substitution in Cls and (ii) an A292G reversion in a putative cyclopropane fatty acid synthase enzyme. The DAP-resistant derivative R446 also exhibited an S333L substitution in the putative histidine kinase YycG, a member of the YycFG system, which, similar to LiaFSR, has been involved in cell envelope homeostasis and DAP resistance in other Gram-positive cocci. Additional changes identified inE. faeciumR446 (DAP resistant) included two putative proteins involved in transport (one for carbohydrate and one for sulfate) and three enzymes predicted to play a role in general metabolism. Exchange of the “susceptible”clsallele from S447 for the “resistant” one belonging to R446 did not affect DAP susceptibility. Our results suggest that, apart from the LiaFSR system, the essential YycFG system is likely to be an important mediator of DAP resistance in someE. faeciumstrains.

scholarly journals Tenacibaculum piscium sp. nov., isolated from skin ulcers of sea-farmed fish, and description of Tenacibaculum finnmarkense sp. nov. with subdivision into genomovars finnmarkense and ulcerans

2020 ◽  
Vol 70 (12) ◽  
pp. 6079-6090 ◽  
Author(s):  
Anne Berit Olsen ◽  
Bjørn Spilsberg ◽  
Hanne K. Nilsen ◽  
Karin Lagesen ◽  
Snorre Gulla ◽  
...  
Keyword(s):  
Type Strain ◽  
Type Species ◽  
Large Scale ◽  
Whole Genome ◽  
Farmed Fish ◽  
Whole Genome Analysis ◽  
Content Type ◽  
Link Type ◽  
Phylogenetic Lineages ◽  
Genome Analyses

Results of previous multilocus sequence and whole-genome-based analyses have suggested that a homogeneous group of isolates belonging to the genus Tenacibaculum , represented by strain TNO020T and associated with skin ulcer development in sea-farmed fish, represents an as-yet-undescribed species. Comparative whole-genome analysis performed in the present study clustered five isolates, including TNO020T, in a distinct lineage within the genus Tenacibaculum . Phenotypic differences, high intra-cluster average nucleotide identity (ANI) values and low ANI values with other Tenacibaculum species support the proposal of a novel species, for which we propose the name Tenacibaculum piscium sp. nov. with strain TNO020T (=CCUG 73833T=NCIMB 15240T) as the type strain. Further, large-scale genome analyses confirmed the existence of two different phylogenetic lineages within ‘ T. finnmarkense ’, a species effectively but not validly published previously. ANI values just above the species delineation threshold of 95–96 % confirmed that both lineages belong to the same species. This result was also supported by DNA–DNA hybridization values. Phenotypically, the two conspecific lineages are distinguishable by differences in growth temperature range and ability to degrade l-proline. For the group of isolates already commonly known as ‘ T. finnmarkense ’, we propose the name Tenacibaculum finnmarkense sp. nov., with strain TNO006T (=CCUG 73831T=NCIMB 15238T) as the type strain. We further propose the subdivision of T. finnmarkense sp. nov. into two genomovars, T. finnmarkense genomovar finnmarkense with strain TNO006T (=CCUG 73831T=NCIMB 15238T) as the type strain and T. finnmarkense genomovar ulcerans with strain TNO010T (=CCUG 73832T=NCIMB 15239T) as the type strain.

scholarly journals Genotypic and Phenotypic Evaluation of the Evolution of High-Level Daptomycin Nonsusceptibility in Vancomycin-Resistant Enterococcus faecium

2012 ◽  
Vol 56 (11) ◽  
pp. 6051-6053 ◽  
Author(s):  
Romney M. Humphries ◽  
Theodoros Kelesidis ◽  
Ryan Tewhey ◽  
Warren E. Rose ◽  
Nicholas Schork ◽  
...  
Keyword(s):  
Enterococcus Faecium ◽  
Open Reading Frames ◽  
Vancomycin Resistant Enterococcus ◽  
Single Nucleotide Variants ◽  
Phosphotransferase System ◽  
Single Nucleotide ◽  
Content Type ◽  
Vancomycin Resistant ◽  
High Level ◽  
Reading Frames

ABSTRACTWhole-genome sequencing and cell membrane studies of three clonalEnterococcus faeciumstrains with daptomycin MICs of 4, 32, and 192 μg/ml were performed, revealing nonsynonymous single nucleotide variants in eight open reading frames, including those predicted to encode a phosphoenolpyruvate-dependent, mannose-specific phosphotransferase system, cardiolipin synthetase, and EzrA. Membrane studies revealed a higher net surface charge among the daptomycin-nonsusceptible isolates and increased septum formation in the isolate with a daptomycin MIC of 192 μg/ml.

Whole-genome analysis of vancomycin-resistant Enterococcus faecium causing nosocomial outbreaks suggests the occurrence of few endemic clonal lineages in Bavaria, Germany

2020 ◽  
Vol 75 (6) ◽  
pp. 1398-1404 ◽  
Author(s):  
David Eisenberger ◽  
Christian Tuschak ◽  
Markus Werner ◽  
Christian Bogdan ◽  
Thomas Bollinger ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genome Analysis ◽  
Enterococcus Faecium ◽  
Treatment Options ◽  
Health Concern ◽  
Snp Analysis ◽  
Whole Genome ◽  
Vancomycin Resistant Enterococcus ◽  
Whole Genome Analysis ◽  
Vancomycin Resistant

Abstract Objectives Infections caused by vancomycin-resistant Enterococcus faecium (VREfm) represent a major public health concern due to limited treatment options. Among invasive isolates of VREfm, ST117, ST80 and ST78 represent the most frequently detected STs by MLST in Germany. In this study, we investigated the genetic diversity of isolates of VREfm recovered from different nosocomial outbreaks in Bavaria, Germany, by WGS. Methods Between January 2018 and April 2019, 99 non-replicate isolates of VREfm originating from nosocomial outbreaks at eight different hospitals in Bavaria were investigated for genetic diversity by WGS. In detail, complex types (CTs) were identified by core-genome MLST. Furthermore, an SNP analysis was performed for all VREfm strains. Results Most of the isolates of this study (76%) belonged to three major clonal groups, which occurred in at least three hospitals: ST80/CT1065 vanB (n = 45; six hospitals), ST117/CT71 vanB (n = 11; four hospitals) and ST78/CT894like vanA (n = 19; three hospitals). Moreover, isolates of the predominant lineage ST80/CT1065 vanB showed a maximum difference of 36 SNPs as revealed by SNP analysis. Conclusions Whole-genome analysis of VREfm causing nosocomial outbreaks suggests the occurrence of few endemic clonal lineages in Bavarian hospital settings, namely ST80/CT1065 vanB, ST117/CT71 vanB and ST78/CT894like vanA. Further studies are needed for a better understanding of the factors affecting the successful spread of the above-mentioned lineages.

scholarly journals Persistence of Vancomycin Resistance in Multiple Clones of Enterococcus faecium Isolated from Danish Broilers 15 Years after the Ban of Avoparcin

2015 ◽  
Vol 59 (5) ◽  
pp. 2926-2929 ◽  
Author(s):  
Valeria Bortolaia ◽  
Manuela Mander ◽  
Lars B. Jensen ◽  
John E. Olsen ◽  
Luca Guardabassi
Keyword(s):  
Enterococcus Faecium ◽  
Vancomycin Resistance ◽  
Sequence Type ◽  
Content Type ◽  
Selective Enrichment ◽  
Vancomycin Resistant

ABSTRACTThe occurrence and diversity of vancomycin-resistantEnterococcus faecium(VREF) were investigated in 100 Danish broiler flocks 15 years after the avoparcin ban. VREF occurred in 47 flocks at low fecal concentrations detectable only by selective enrichment. Vancomycin resistance was prevalently associated with a transferable nontypeable plasmid lineage occurring in multipleE. faeciumclones. Coselection of sequence type 842 by tetracycline use only partly explained the persistence of vancomycin resistance in the absence of detectable plasmid coresistance and toxin-antitoxin systems.

scholarly journals Genomic Comparison of Campylobacter spp. and Their Potential for Zoonotic Transmission between Birds, Primates, and Livestock

2016 ◽  
Vol 82 (24) ◽  
pp. 7165-7175 ◽  
Author(s):  
Allison M. Weis ◽  
Dylan B. Storey ◽  
Conor C. Taff ◽  
Andrea K. Townsend ◽  
Bihua C. Huang ◽  
...  
Keyword(s):  
Host Species ◽  
Large Scale ◽  
Genomic Variation ◽  
Zoonotic Transmission ◽  
Fluoroquinolone Resistance ◽  
Whole Genome ◽  
Whole Genome Analysis ◽  
Pathogenic Potential ◽  
Content Type ◽  
New Genes

ABSTRACTCampylobacteris the leading cause of human gastroenteritis worldwide. Wild birds, including American crows, are abundant in urban, suburban, and agricultural settings and are likely zoonotic vectors ofCampylobacter. Their proximity to humans and livestock increases the potential spreading ofCampylobactervia crows between the environment, livestock, and humans. However, no studies have definitively demonstrated that crows are a vector for pathogenicCampylobacter. We used genomics to evaluate the zoonotic and pathogenic potential ofCampylobacterfrom crows to other animals with 184 isolates obtained from crows, chickens, cows, sheep, goats, humans, and nonhuman primates. Whole-genome analysis uncovered two distinct clades ofCampylobacter jejunigenotypes; the first contained genotypes found only in crows, while a second genotype contained “generalist” genomes that were isolated from multiple host species, including isolates implicated in human disease, primate gastroenteritis, and livestock abortion. Two major β-lactamase genes were observed frequently in these genomes (oxa-184, 55%, andoxa-61, 29%), whereoxa-184was associated only with crows andoxa-61was associated with generalists. Mutations ingyrA, indicative of fluoroquinolone resistance, were observed in 14% of the isolates. Tetracycline resistance (tetO) was present in 22% of the isolates, yet it occurred in 91% of the abortion isolates. Virulence genes were distributed throughout the genomes; however,cdtCalleles recapitulated the crow-only and generalist clades. A specificcdtCallele was associated with abortion in livestock and was concomitant withtetO. These findings indicate that crows harboring a generalistC. jejunigenotype may act as a vector for the zoonotic transmission ofCampylobacter.IMPORTANCEThis study examined the link between public health and the genomic variation ofCampylobacterin relation to disease in humans, primates, and livestock. Use of large-scale whole-genome sequencing enabled population-level assessment to find new genes that are linked to livestock disease. With 184Campylobactergenomes, we assessed virulence traits, antibiotic resistance susceptibility, and the potential for zoonotic transfer to observe that there is a “generalist” genotype that may move between host species.

scholarly journals Whole-Genome Single-Nucleotide-Polymorphism Analysis for Discrimination of Clostridium botulinum Group I Strains

2014 ◽  
Vol 80 (7) ◽  
pp. 2125-2132 ◽  
Author(s):  
Narjol Gonzalez-Escalona ◽  
Ruth Timme ◽  
Brian H. Raphael ◽  
Donald Zink ◽  
Shashi K. Sharma
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Clostridium Botulinum ◽  
Toxin Gene ◽  
Polymorphism Analysis ◽  
Snp Analysis ◽  
Whole Genome ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Content Type ◽  
Group I

ABSTRACTClostridium botulinumis a genetically diverse Gram-positive bacterium producing extremely potent neurotoxins (botulinum neurotoxins A through G [BoNT/A-G]). The complete genome sequences of three strains harboring only the BoNT/A1 nucleotide sequence are publicly available. Although these strains contain a toxin cluster (HA+OrfX−) associated with hemagglutinin genes, little is known about the genomes of subtype A1 strains (termed HA−OrfX+) that lack hemagglutinin genes in the toxin gene cluster. We sequenced the genomes of three BoNT/A1-producingC. botulinumstrains: two strains with the HA+OrfX−cluster (69A and 32A) and one strain with the HA−OrfX+cluster (CDC297). Whole-genome phylogenic single-nucleotide-polymorphism (SNP) analysis of these strains along with other publicly availableC. botulinumgroup I strains revealed five distinct lineages. Strains 69A and 32A clustered with theC. botulinumtype A1 Hall group, and strain CDC297 clustered with theC. botulinumtype Ba4 strain 657. This study reports the use of whole-genome SNP sequence analysis for discrimination ofC. botulinumgroup I strains and demonstrates the utility of this analysis in quickly differentiatingC. botulinumstrains harboring identical toxin gene subtypes. This analysis further supports previous work showing that strains CDC297 and 657 likely evolved from a common ancestor and independently acquired separate BoNT/A1 toxin gene clusters at distinct genomic locations.

scholarly journals Whole-Genome Phylogenomic Heterogeneity of Neisseria gonorrhoeae Isolates with Decreased Cephalosporin Susceptibility Collected in Canada between 1989 and 2013

2014 ◽  
Vol 53 (1) ◽  
pp. 191-200 ◽  
Author(s):  
Walter Demczuk ◽  
Tarah Lynch ◽  
Irene Martin ◽  
Gary Van Domselaar ◽  
Morag Graham ◽  
...  
Keyword(s):  
Neisseria Gonorrhoeae ◽  
Large Scale ◽  
Epidemiological Studies ◽  
23S Rrna ◽  
Genome Comparison ◽  
Whole Genome ◽  
Content Type ◽  
Genomic Epidemiology ◽  
High Level ◽  
Sequence Types

A large-scale, whole-genome comparison of CanadianNeisseria gonorrhoeaeisolates with high-level cephalosporin MICs was used to demonstrate a genomic epidemiology approach to investigate strain relatedness and dynamics. Although current typing methods have been very successful in tracing short-chain transmission of gonorrheal disease, investigating the temporal evolutionary relationships and geographical dissemination of highly clonal lineages requires enhanced resolution only available through whole-genome sequencing (WGS). Phylogenomic cluster analysis grouped 169 Canadian strains into 12 distinct clades. While someN. gonorrhoeaemultiantigen sequence types (NG-MAST) agreed with specific phylogenomic clades or subclades, other sequence types (ST) and closely related groups of ST were widely distributed among clades. Decreased susceptibility to extended-spectrum cephalosporins (ESC-DS) emerged among a group of diverse strains in Canada during the 1990s with a variety of nonmosaicpenAalleles, followed in 2000/2001 with thepenAmosaic X allele and then in 2007 with ST1407 strains with thepenAmosaic XXXIV allele. Five genetically distinct ESC-DS lineages were associated withpenAmosaic X, XXXV, and XXXIV alleles and nonmosaic XII and XIII alleles. ESC-DS with coresistance to azithromycin was observed in 5 strains with 23S rRNA C2599T or A2143G mutations. As the costs associated with WGS decline and analysis tools are streamlined, WGS can provide a more thorough understanding of strain dynamics, facilitate epidemiological studies to better resolve social networks, and improve surveillance to optimize treatment for gonorrheal infections.

scholarly journals Clonal Lineages of Erysipelothrix rhusiopathiae Responsible for Acute Swine Erysipelas in Japan Identified by Using Genome-Wide Single-Nucleotide Polymorphism Analysis

2017 ◽  
Vol 83 (11) ◽  
Author(s):  
Yohsuke Ogawa ◽  
Kazumasa Shiraiwa ◽  
Yoshitoshi Ogura ◽  
Tadasuke Ooka ◽  
Sayaka Nishikawa ◽  
...  
Keyword(s):  
Polymorphism Analysis ◽  
Whole Genome ◽  
Sequencing Analysis ◽  
Erysipelothrix Rhusiopathiae ◽  
Single Nucleotide ◽  
Content Type ◽  
Genome Wide ◽  
Wide Range ◽  
Swine Erysipelas ◽  
Lineage Iv

ABSTRACTErysipelothrix rhusiopathiaecauses swine erysipelas, an important infectious disease in the swine industry. In Japan, the incidence of acute swine erysipelas due toE. rhusiopathiaeserovar 1a has recently increased markedly. To study the genetic relatedness of the strains from the recent cases, we analyzed 34E. rhusiopathiaeserovar 1a swine isolates collected between 1990 and 2011 and further investigated the possible association of the live Koganei 65-0.15 vaccine strain (serovar 1a) with the increase in cases. Pulsed-field gel electrophoresis analysis revealed no marked variation among the isolates; however, sequencing analysis of a hypervariable region in the surface-protective antigen A gene (spaA) revealed that the strains isolated after 2007 exhibited the samespaAgenotype and could be differentiated from older strains. Phylogenetic analysis based on genome-wide single-nucleotide polymorphisms (SNPs) revealed that the Japanese strains examined were closely related, showing a relatively small number of SNPs among them. The strains were classified into four major lineages, with Koganei 65-0.15 (lineage III) being phylogenetically separated from the other three lineages. The strains isolated after 2007 and the two older strains constituted one major lineage (lineage IV) with a specificspaAgenotype (M203/I257-SpaA), while the recent isolates were further divided into two geographic groups. The remaining older isolates belonged to either lineage I, with the I203/L257-SpaA type, or lineage II, with the I203/I257-SpaA type. These results indicate that the recent increased incidence of acute swine erysipelas in Japan is associated with two sublineages of lineage IV, which have independently evolved in two different geographic regions.IMPORTANCEUsing large-scale whole-genome sequence data fromErysipelothrix rhusiopathiaeisolates from a wide range of hosts and geographic origins, a recent study clarified the existence of three distinct clades (clades 1, 2, and 3) that are found across multiple continents and host species, representing both livestock and wildlife, and an “intermediate” clade between clade 2 and the dominant clade 3 within the species. In this study, we found that theE. rhusiopathiaeJapanese strains examined exhibited remarkably low levels of genetic diversity and confirmed that all of the Japanese and Chinese swine isolates examined in this study belong to clonal lineages within the intermediate clade. We report thatspaAgenotyping ofE. rhusiopathiaestrains is a practical alternative to whole-genome sequencing analysis of theE. rhusiopathiaeisolates from eastern Asian countries.

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