scholarly journals Genetic Basis of Emerging Vancomycin, Linezolid, and Daptomycin Heteroresistance in a Case of PersistentEnterococcus faeciumBacteremia

2018 ◽  
Vol 62 (4) ◽  
Author(s):  
Kieran I. Chacko ◽  
Mitchell J. Sullivan ◽  
Colleen Beckford ◽  
Deena R. Altman ◽  
Brianne Ciferri ◽  
...  
Keyword(s):  
Fatty Acid Synthase ◽  
Genetic Basis ◽  
Novel Mutation ◽  
Whole Genome ◽  
Multidrug Therapy ◽  
Content Type ◽  
Resistance Determinants ◽  
Progressive Loss ◽  
Plasmid Recombination ◽  
Before And After

ABSTRACTWhole-genome sequencing was used to examine a persistentEnterococcus faeciumbacteremia that acquired heteroresistance to three antibiotics in response to prolonged multidrug therapy. A comparison of the complete genomes before and after each change revealed the emergence of known resistance determinants for vancomycin and linezolid and suggested that a novel mutation infabF, encoding a fatty acid synthase, was responsible for daptomycin nonsusceptibility. Plasmid recombination contributed to the progressive loss of vancomycin resistance after withdrawal of the drug.

scholarly journals Complete Genome Sequence of Streptococcus agalactiae GD201008-001, Isolated in China from Tilapia with Meningoencephalitis

2012 ◽  
Vol 194 (23) ◽  
pp. 6653-6653 ◽  
Author(s):  
Guangjin Liu ◽  
Wei Zhang ◽  
Chengping Lu
Keyword(s):  
Genome Sequence ◽  
Streptococcus Agalactiae ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Genetic Basis ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Content Type ◽  
Host Tropism

ABSTRACTThis work describes a whole-genome sequence ofStreptococcus agalactiaestrain GD201008-001, a pathogen causing meningoencephalitis in cultural tilapia in China. The genome sequence provides opportunities to understand the piscine GBS pathogenicity and its genetic basis associated with host tropism.

scholarly journals Whole-Genome Sequence of Corynebacterium pseudotuberculosis PAT10 Strain Isolated from Sheep in Patagonia, Argentina

2011 ◽  
Vol 193 (22) ◽  
pp. 6420-6421 ◽  
Author(s):  
Louise Teixeira Cerdeira ◽  
Anne Cybelle Pinto ◽  
Maria Paula Cruz Schneider ◽  
Sintia Silva de Almeida ◽  
Anderson Rodrigues dos Santos ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Genetic Basis ◽  
Lung Abscess ◽  
Corynebacterium Pseudotuberculosis ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Content Type

In this work, we report the complete genome sequence of aCorynebacterium pseudotuberculosisPAT10 isolate, collected from a lung abscess in an Argentine sheep in Patagonia, whose pathogen also required an investigation of its pathogenesis. Thus, the analysis of the genome sequence offers a means to better understanding of the molecular and genetic basis of virulence of this bacterium.

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 Whole-Genome Sequence of a Novel Sequence Type 3136 Carbapenem-Resistant Klebsiella pneumoniae Strain Isolated from a Hospitalized Patient in Durban, South Africa

2018 ◽  
Vol 7 (23) ◽  
Author(s):  
Yogandree Ramsamy ◽  
Koleka P. Mlisana ◽  
Mushal Allam ◽  
Arshad Ismail ◽  
Ravesh Singh ◽  
...  
Keyword(s):  
South Africa ◽  
Klebsiella Pneumoniae ◽  
Virulence Factors ◽  
Genome Sequence ◽  
Sequence Type ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Content Type ◽  
Resistance Determinants ◽  
Carbapenem Resistant

Here, we describe the genome sequence of a novel sequence type 3136 (ST3136) Klebsiella pneumoniae strain isolated in South Africa. The 5,574,236-bp genome harbored 23 resistance determinants and 12 virulence factors that are of cardinal importance to infections.

scholarly journals Complete Genome Sequence of a Novel Bioflocculant-Producing Strain, Microbacterium paludicola CC3

2017 ◽  
Vol 5 (38) ◽  
Author(s):  
Weijie Liu ◽  
Cong Liu ◽  
Di Sun
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Genetic Basis ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Content Type

ABSTRACT Microbacterium paludicola CC3 exhibits the capability to produce polysaccharide bioflocculants. Here, we report the whole-genome sequence of M. paludicola CC3, which may be helpful in understanding the genetic basis of the biosynthesis of polysaccharide bioflocculants as well as in promoting its production and application in industrial fields.

scholarly journals Whole-Genome Analysis of Antimicrobial-Resistant and Extraintestinal Pathogenic Escherichia coli in River Water

2016 ◽  
Vol 83 (5) ◽  
Author(s):  
Ryota Gomi ◽  
Tomonari Matsuda ◽  
Yasufumi Matsumura ◽  
Masaki Yamamoto ◽  
Michio Tanaka ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
River Water ◽  
Surface Waters ◽  
Pathogenic Bacteria ◽  
Resistant Bacteria ◽  
Whole Genome ◽  
Whole Genome Analysis ◽  
Content Type ◽  
E Coli ◽  
Resistance Determinants

ABSTRACT Contamination of surface waters by antimicrobial-resistant bacteria and pathogenic bacteria is a great concern. In this study, 531 Escherichia coli isolates obtained from the Yamato River in Japan were evaluated phenotypically for resistance to 25 antimicrobials. Seventy-six isolates (14.3%) were multidrug resistant (MDR), 66 (12.4%) were nonsusceptible to one or two classes of agents, and 389 (73.3%) were susceptible. We performed whole-genome sequencing of selected strains by using Illumina technology. In total, the genome sequences of 155 strains were analyzed for antibiotic resistance determinants and phylogenetic characteristics. More than 50 different resistance determinants, including acquired resistance genes and chromosomal resistance mutations, were detected. Among the sequenced MDR strains (n = 66), sequence type 155 (ST155) complex (n = 9), ST10 complex (n = 9), and ST69 complex (n = 7) were prevalent. Among extraintestinal pathogenic E. coli (ExPEC) strains (n = 58), clinically important clonal groups, namely, ST95 complex (n = 18), ST127 complex (n = 8), ST12 complex (n = 6), ST14 complex (n = 6), and ST131 complex (n = 6), were prevalent, demonstrating the clonal distribution of environmental ExPEC strains. Typing of the fimH (type 1 fimbrial adhesin) gene revealed that ST131 complex strains carried fimH22 or fimH41, and no strains belonging to the fimH30 subgroup were detected. Fine-scale phylogenetic analysis and virulence gene content analysis of strains belonging to the ST95 complex (one of the major clonal ExPEC groups causing community-onset infections) revealed no significant differences between environmental and clinical strains. The results indicate contamination of surface waters by E. coli strains belonging to clinically important clonal groups. IMPORTANCE The prevalence of antimicrobial-resistant and pathogenic E. coli strains in surface waters is a concern because surface waters are used as sources for drinking water, irrigation, and recreational purposes. In this study, MDR and ExPEC strains in river water were characterized by genomic sequencing and analysis. We detected more than 50 resistance determinants and identified clonal groups specific to MDR and ExPEC strains. This study showed contamination of surface waters by E. coli strains belonging to clinically important clonal groups. Overall, this study advances our understanding of environmental MDR and ExPEC strains.

scholarly journals Antimicrobial Susceptibility and Molecular Characterization Using Whole-Genome Sequencing of Clostridioides difficile Collected in 82 Hospitals in Japan between 2014 and 2016

2019 ◽  
Vol 63 (12) ◽  
Author(s):  
Kotaro Aoki ◽  
Shinobu Takeda ◽  
Takashi Miki ◽  
Yoshikazu Ishii ◽  
Kazuhiro Tateda
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Antimicrobial Susceptibility ◽  
Phase Iii ◽  
Molecular Characteristics ◽  
Toxin Gene ◽  
Polymorphism Analysis ◽  
Whole Genome ◽  
Content Type ◽  
Before And After

ABSTRACT We studied the antimicrobial susceptibility and molecular characteristics, using draft whole-genome sequencing, of Clostridioides (Clostridium) difficile strains before and after treatment in adults with C. difficile infection (CDI) enrolled in a phase III, randomized, nationwide study of fidaxomicin versus vancomycin in Japan (ClinicalTrials.gov identifier NCT02179658). C. difficile strains were cultured from stool samples collected before and after standard treatment with either fidaxomicin or vancomycin. Overall, 285 C. difficile strains were recovered, with 188 derived from CDI cases at baseline (87 patients received fidaxomicin, and 101 received vancomycin). No strains isolated from episodes of CDI at baseline were shown to have reduced susceptibilities to fidaxomicin (MIC, ≥1 mg/liter) or resistance to vancomycin and metronidazole. Thirty-three sequence types (STs) were identified, the most common being ST17 (n = 61 [32.4%]), ST8 (n = 26 [13.8%]), and ST2 (n = 21 [11.2%]). Core-genome single-nucleotide polymorphism analysis showed that outbreaks of C. difficile were unlikely to have occurred at each hospital. The predominant toxin gene profile was tcdA+ tcdB+ cdtA-cdtB− (n = 149 [79.3%]). Six of 87 patients who received fidaxomicin harbored C. difficile isolates with reduced fidaxomicin susceptibilities conferred by previously described mutations, Val1143Leu/Gly/Asp in RpoB or Arg89Gly in RpoC or putative mutations, Gln1149Pro in RpoB, or Arg326Cys in RpoC. Allelic exchange studies of these putative mutations were not performed. Prior to fidaxomicin use, we found no C. difficile strains with reduced fidaxomicin susceptibility causing CDI in Japan; however, mutant strains with reduced fidaxomicin susceptibility were detected after fidaxomicin treatment.

scholarly journals Whole-Genome Sequence Analysis of Multidrug-Resistant Campylobacter Isolates: a Focus on Aminoglycoside Resistance Determinants

2018 ◽  
Vol 56 (9) ◽  
Author(s):  
Adrien Fabre ◽  
Monica Oleastro ◽  
Alexandra Nunes ◽  
Andrea Santos ◽  
Elodie Sifré ◽  
...  
Keyword(s):  
Antimicrobial Agents ◽  
Multidrug Resistant ◽  
Whole Genome Sequence ◽  
Rrna Gene ◽  
Whole Genome ◽  
Aminoglycoside Resistance ◽  
Content Type ◽  
Resistance Determinants ◽  
New Genes ◽  
Gentamicin Resistance

ABSTRACT A whole-genome sequencing (WGS) approach was conducted in order to identify the molecular determinants associated with antimicrobial resistance in 12 multidrug-resistant Campylobacter jejuni and Campylobacter coli isolates, with a focus on aminoglycoside resistance determinants. Two variants of a new aminoglycoside phosphotransferase gene [aph(2″)-Ii1 and aph(2″)-Ii2] putatively associated with gentamicin resistance were found. In addition, the following new genes were identified for the first time in Campylobacter: a lincosamide nucleotidyltransferase gene [lnu(G)], likely associated with lincomycin resistance, and two resistance enzyme genes (spw and apmA) similar to those found in Staphylococcus aureus, which may confer spectinomycin and gentamicin resistance, respectively. A C1192T mutation of the 16S rRNA gene that may be involved in spectinomycin resistance was also found in a C. coli isolate. Genes identified in the present study were located either on the bacterial chromosome or on plasmids that could be transferred naturally. Their role in aminoglycoside resistance remains to be supported by genetic studies. Regarding the other antimicrobial agents studied, i.e., ampicillin, ciprofloxacin, erythromycin, and tetracycline, a perfect correlation between antimicrobial phenotypes and genotypes was found. Overall, our data suggest that WGS analysis is a powerful tool for identifying resistance determinants in Campylobacter and can disclose the full genetic elements associated with resistance, including antimicrobial compounds not tested routinely in antimicrobial susceptibility testing.

scholarly journals Whole-Genome Sequencing Identifies Emergence of a Quinolone Resistance Mutation in a Case of Stenotrophomonas maltophilia Bacteremia

2015 ◽  
Vol 59 (11) ◽  
pp. 7117-7120 ◽  
Author(s):  
Theodore R. Pak ◽  
Deena R. Altman ◽  
Oliver Attie ◽  
Robert Sebra ◽  
Camille L. Hamula ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Stenotrophomonas Maltophilia ◽  
De Novo ◽  
Resistance Mutation ◽  
Resistance Mechanisms ◽  
Whole Genome ◽  
Multidrug Efflux ◽  
Content Type ◽  
Before And After

ABSTRACTWhole-genome sequences forStenotrophomonas maltophiliaserial isolates from a bacteremic patient before and after development of levofloxacin resistance were assembledde novoand differed by one single-nucleotide variant insmeT, a repressor for multidrug efflux operonsmeDEF. Along with sequenced isolates from five contemporaneous cases, they displayed considerable diversity compared against all published complete genomes. Whole-genome sequencing and complete assembly can conclusively identify resistance mechanisms emerging inS. maltophiliastrains during clinical therapy.

scholarly journals Expanding U.S. Laboratory Capacity for Neisseria gonorrhoeae Antimicrobial Susceptibility Testing and Whole-Genome Sequencing through the CDC's Antibiotic Resistance Laboratory Network

2020 ◽  
Vol 58 (4) ◽  
Author(s):  
Ellen N. Kersh ◽  
Cau D. Pham ◽  
John R. Papp ◽  
Robert Myers ◽  
Richard Steece ◽  
...  
Keyword(s):  
Public Health ◽  
Antibiotic Resistance ◽  
Neisseria Gonorrhoeae ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Antimicrobial Susceptibility ◽  
Susceptibility Testing ◽  
Whole Genome ◽  
Content Type ◽  
Laboratory Capacity

ABSTRACT U.S. gonorrhea rates are rising, and antibiotic-resistant Neisseria gonorrhoeae (AR-Ng) is an urgent public health threat. Since implementation of nucleic acid amplification tests for N. gonorrhoeae identification, the capacity for culturing N. gonorrhoeae in the United States has declined, along with the ability to perform culture-based antimicrobial susceptibility testing (AST). Yet AST is critical for detecting and monitoring AR-Ng. In 2016, the CDC established the Antibiotic Resistance Laboratory Network (AR Lab Network) to shore up the national capacity for detecting several resistance threats including N. gonorrhoeae. AR-Ng testing, a subactivity of the CDC’s AR Lab Network, is performed in a tiered network of approximately 35 local laboratories, four regional laboratories (state public health laboratories in Maryland, Tennessee, Texas, and Washington), and the CDC’s national reference laboratory. Local laboratories receive specimens from approximately 60 clinics associated with the Gonococcal Isolate Surveillance Project (GISP), enhanced GISP (eGISP), and the program Strengthening the U.S. Response to Resistant Gonorrhea (SURRG). They isolate and ship up to 20,000 isolates to regional laboratories for culture-based agar dilution AST with seven antibiotics and for whole-genome sequencing of up to 5,000 isolates. The CDC further examines concerning isolates and monitors genetic AR markers. During 2017 and 2018, the network tested 8,214 and 8,628 N. gonorrhoeae isolates, respectively, and the CDC received 531 and 646 concerning isolates and 605 and 3,159 sequences, respectively. In summary, the AR Lab Network supported the laboratory capacity for N. gonorrhoeae AST and associated genetic marker detection, expanding preexisting notification and analysis systems for resistance detection. Continued, robust AST and genomic capacity can help inform national public health monitoring and intervention.

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