scholarly journals An Outpatient Clinic as a Potential Site of Transmission for an Outbreak of New Delhi Metallo-β-Lactamase–producing Klebsiella pneumoniae Sequence Type 716: A Study Using Whole-genome Sequencing

2018 ◽  
Vol 68 (6) ◽  
pp. 993-1000 ◽  
Author(s):  
Amélie Heinrichs ◽  
Maria Angeles Argudín ◽  
Ricardo De Mendonça ◽  
Ariane Deplano ◽  
Sandrine Roisin ◽  
...  
Keyword(s):  
Klebsiella Pneumoniae ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Outpatient Clinic ◽  
Sequence Type ◽  
New Delhi ◽  
Whole Genome ◽  
Potential Site

scholarly journals Whole Genome Sequencing detects Inter-Facility Transmission of Carbapenem-resistant Klebsiella pneumoniae

2019 ◽  
Vol 78 (3) ◽  
pp. 187-199 ◽  
Author(s):  
Melanie D. Spencer ◽  
Kathryn Winglee ◽  
Catherine Passaretti ◽  
Ashlee M. Earl ◽  
Abigail L. Manson ◽  
...  
Keyword(s):  
Klebsiella Pneumoniae ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Whole Genome ◽  
Carbapenem Resistant

scholarly journals Tracking a hospital outbreak of KPC-producing ST11 Klebsiella pneumoniae with whole genome sequencing

2015 ◽  
Vol 21 (11) ◽  
pp. 1001-1007 ◽  
Author(s):  
Y. Jiang ◽  
Z. Wei ◽  
Y. Wang ◽  
X. Hua ◽  
Y. Feng ◽  
...  
Keyword(s):  
Klebsiella Pneumoniae ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Whole Genome ◽  
Hospital Outbreak

Molecular Detection of Class 1 Integron-Associated Gene Cassettes in KPC-2-Producing Klebsiella pneumoniae Clones by Whole-Genome Sequencing

2019 ◽  
Vol 25 (8) ◽  
pp. 1127-1131 ◽  
Author(s):  
Bruna Fuga ◽  
Sabrina Royer ◽  
Paola Amaral de Campos ◽  
Melina Lorraine Ferreira ◽  
Iara Rossi ◽  
...  
Keyword(s):  
Klebsiella Pneumoniae ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Molecular Detection ◽  
Whole Genome ◽  
Class 1 Integron ◽  
Gene Cassettes ◽  
Class 1

scholarly journals High-Resolution Analysis by Whole-Genome Sequencing of an International Lineage (Sequence Type 111) of Pseudomonas aeruginosa Associated with Metallo-Carbapenemases in the United Kingdom

2015 ◽  
Vol 53 (8) ◽  
pp. 2622-2631 ◽  
Author(s):  
Jane F. Turton ◽  
Laura Wright ◽  
Anthony Underwood ◽  
Adam A. Witney ◽  
Yuen-Ting Chan ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
United Kingdom ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Sequence Type ◽  
Polymorphism Analysis ◽  
Whole Genome ◽  
Evolutionary Analysis ◽  
Accessory Gene ◽  
The United Kingdom

Whole-genome sequencing (WGS) was carried out on 87 isolates of sequence type 111 (ST-111) of Pseudomonas aeruginosa collected between 2005 and 2014 from 65 patients and 12 environmental isolates from 24 hospital laboratories across the United Kingdom on an Illumina HiSeq instrument. Most isolates (73) carried VIM-2, but others carried IMP-1 or IMP-13 (5) or NDM-1 (1); one isolate had VIM-2 and IMP-18, and 7 carried no metallo-beta-lactamase (MBL) gene. Single nucleotide polymorphism analysis divided the isolates into distinct clusters; the NDM-1 isolate was an outlier, and the IMP isolates and 6/7 MBL-negative isolates clustered separately from the main set of 73 VIM-2 isolates. Within the VIM-2 set, there were at least 3 distinct clusters, including a tightly clustered set of isolates from 3 hospital laboratories consistent with an outbreak from a single introduction that was quickly brought under control and a much broader set dominated by isolates from a long-running outbreak in a London hospital likely seeded from an environmental source, requiring different control measures; isolates from 7 other hospital laboratories in London and southeast England were also included. Bayesian evolutionary analysis indicated that all the isolates shared a common ancestor dating back ∼50 years (1960s), with the main VIM-2 set separating approximately 20 to 30 years ago. Accessory gene profiling revealed blocks of genes associated with particular clusters, with some having high similarity (≥95%) to bacteriophage genes. WGS of widely found international lineages such as ST-111 provides the necessary resolution to inform epidemiological investigations and intervention policies.

scholarly journals Enterobacter cloacae Complex Sequence Type 171 Isolates Expressing KPC-4 Carbapenemase Recovered from Canine Patients in Ohio

2018 ◽  
Vol 62 (12) ◽  
Author(s):  
Joshua B. Daniels ◽  
Liang Chen ◽  
Susan V. Grooters ◽  
Dixie F. Mollenkopf ◽  
Dimitria A. Mathys ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Companion Animals ◽  
Enterobacter Cloacae ◽  
Sequence Type ◽  
Resistant Bacteria ◽  
Whole Genome ◽  
Content Type ◽  
Complex Sequence ◽  
Enterobacter Cloacae Complex

ABSTRACT Companion animals are likely relevant in the transmission of antimicrobial-resistant bacteria. Enterobacter xiangfangensis sequence type 171 (ST171), a clone that has been implicated in clusters of infections in humans, was isolated from two dogs with clinical disease in Ohio. The canine isolates contained IncHI2 plasmids encoding blaKPC-4. Whole-genome sequencing was used to put the canine isolates in phylogenetic context with available human ST171 sequences, as well as to characterize their blaKPC-4 plasmids.

scholarly journals Comparative Genome Analysis of Extended-Spectrum-β-Lactamase-Producing Escherichia coli Sequence Type 131 Strains from Nepal and Japan

mSphere ◽  
2016 ◽  
Vol 1 (5) ◽  
Author(s):  
Tohru Miyoshi-Akiyama ◽  
Jatan Bahadur Sherchan ◽  
Yohei Doi ◽  
Maki Nagamatsu ◽  
Jeevan B. Sherchand ◽  
...  
Keyword(s):  
Molecular Epidemiology ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Sequence Type ◽  
Whole Genome ◽  
Asian Countries ◽  
Content Type ◽  
E Coli ◽  
Global Spread ◽  
Low Prevalence

ABSTRACT The global spread of ESBL-E. coli has been driven in large part by pandemic sequence type 131 (ST131). A recent study suggested that, within E. coli ST131, certain sublineages have disseminated worldwide with little association with their geographical origin, highlighting the complexity of the epidemiology of this pandemic clone. ST131 bacteria have also been classified into four virotypes based on the distribution of certain virulence genes. Information on virotype distribution in Asian ST131 strains is limited. We conducted whole-genome sequencing of ESBL-E. coli ST131 strains collected in Nepal and Japan, two Asian countries with a high and low prevalence of ESBL-E. coli, respectively. We systematically compared these ST131 genomes with those reported from other regions to gain insights into the molecular epidemiology of their spread and found the distinct phylogenetic characteristics of the spread of ESBL-E. coli ST131 in these two geographical areas of Asia. The global spread of extended-spectrum-β-lactamase (ESBL)-producing Escherichia coli (ESBL-E. coli) has largely been driven by the pandemic sequence type 131 (ST131). This study aimed to determine the molecular epidemiology of their spread in two Asian countries with contrasting prevalence. We conducted whole-genome sequencing (WGS) of ESBL-E. coli ST131 strains collected prospectively from Nepal and Japan, two countries in Asia with a high and low prevalence of ESBL-E. coli, respectively. We also systematically compared these genomes with those reported from other regions using publicly available WGS data for E. coli ST131 strains. Further, we conducted phylogenetic analysis of these isolates and all genome sequence data for ST131 strains to determine sequence diversity. One hundred five unique ESBL-E. coli isolates from Nepal (February 2013 to July 2013) and 76 isolates from Japan (October 2013 to September 2014) were included. Of these isolates, 54 (51%) isolates from Nepal and 11 (14%) isolates from Japan were identified as ST131 by WGS. Phylogenetic analysis based on WGS suggested that the majority of ESBL-E. coli ST131 isolates from Nepal clustered together, whereas those from Japan were more diverse. Half of the ESBL-E. coli ST131 isolates from Japan belonged to virotype C, whereas half of the isolates from Nepal belonged to a virotype other than virotype A, B, C, D, or E (A/B/C/D/E). The dominant sublineage of E. coli ST131 was H30Rx, which was most prominent in ESBL-E. coli ST131 isolates from Nepal. Our results revealed distinct phylogenetic characteristics of ESBL-E. coli ST131 spread in the two geographical areas of Asia, indicating the involvement of multiple factors in its local spread in each region. IMPORTANCE The global spread of ESBL-E. coli has been driven in large part by pandemic sequence type 131 (ST131). A recent study suggested that, within E. coli ST131, certain sublineages have disseminated worldwide with little association with their geographical origin, highlighting the complexity of the epidemiology of this pandemic clone. ST131 bacteria have also been classified into four virotypes based on the distribution of certain virulence genes. Information on virotype distribution in Asian ST131 strains is limited. We conducted whole-genome sequencing of ESBL-E. coli ST131 strains collected in Nepal and Japan, two Asian countries with a high and low prevalence of ESBL-E. coli, respectively. We systematically compared these ST131 genomes with those reported from other regions to gain insights into the molecular epidemiology of their spread and found the distinct phylogenetic characteristics of the spread of ESBL-E. coli ST131 in these two geographical areas of Asia.

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