scispace - formally typeset
Search or ask a question
Journal Article•DOI•

Whole-genome typing and characterization of blaVIM19-harbouring ST383 Klebsiella pneumoniae by PFGE, whole-genome mapping and WGS

Julia Sabirova1, Basil Britto Xavier1, Jasmine Coppens1, Olympia Zarkotou, Christine Lammens1, Lore Janssens1, Ronald Burggrave, Trevor Wagner, Herman Goossens1, Surbhi Malhotra-Kumar1 •
University of Antwerp1
01 Jun 2016-Journal of Antimicrobial Chemotherapy (Oxford University Press)-Vol. 71, Iss: 6, pp 1501-1509
TL;DR: This study demonstrates the application of WGM to understanding the epidemiology of hospital-associated K. pneumoniae and presents the first longitudinal genomic characterization of the highly dynamic carbapenem-resistant ST383 K.neumoniae clone that is rapidly gaining importance in Europe.
Abstract: Objectives We utilized whole-genome mapping (WGM) and WGS to characterize 12 clinical carbapenem-resistant Klebsiella pneumoniae strains (TGH1-TGH12). Methods All strains were screened for carbapenemase genes by PCR, and typed by MLST, PFGE (XbaI) and WGM (AflII) (OpGen, USA). WGS (Illumina) was performed on TGH8 and TGH10. Reads were de novo assembled and annotated [SPAdes, Rapid Annotation Subsystem Technology (RAST)]. Contigs were aligned directly, and after in silico AflII restriction, with corresponding WGMs (MapSolver, OpGen; BioNumerics, Applied Maths). Results All 12 strains were ST383. Of the 12 strains, 11 were carbapenem resistant, 7 harboured blaKPC-2 and 11 harboured blaVIM-19. Varying the parameters for assigning WGM clusters showed that these were comparable to STs and to the eight PFGE types or subtypes (difference of three or more bands). A 95% similarity coefficient assigned all 12 WGMs to a single cluster, whereas a 99% similarity coefficient (or ≥10 unmatched-fragment difference) assigned the 12 WGMs to eight (sub)clusters. Based on a difference of three or more bands between PFGE profiles, the Simpson's diversity indices (SDIs) of WGM (0.94, Jackknife pseudo-values CI: 0.883-0.996) and PFGE (0.93, Jackknife pseudo-values CI: 0.828-1.000) were similar (P = 0.649). However, the discriminatory power of WGM was significantly higher (SDI: 0.94, Jackknife pseudo-values CI: 0.883-0.996) than that of PFGE profiles typed on a difference of seven or more bands (SDI: 0.53, Jackknife pseudo-values CI: 0.212-0.849) (P = 0.007). Conclusions This study demonstrates the application of WGM to understanding the epidemiology of hospital-associated K. pneumoniae. Utilizing a combination of WGM and WGS, we also present here the first longitudinal genomic characterization of the highly dynamic carbapenem-resistant ST383 K. pneumoniae clone that is rapidly gaining importance in Europe.

Summary (1 min read)

Jump to: [Introduction] – [Strain collection 84] – [Antimicrobial resistance profiling 88] and [MLST and PFGE 95]

Introduction

  • These can be utilized to develop in 70 silico restriction maps using the same enzymes as used for experimentally-generated WGMs, 71 allowing comparison of restriction patterns and eventual identification of the genetic content of the 72 variable regions in the strains of interest.
  • 5 73 In this study, the authors demonstrate the utility of WGM in conjunction with WGS for typing, 74 characterizing, and dissecting the genomic features of carbapenem-resistant K. pneumoniae 75 isolated at the Tzaneio General (TG) hospital, Piraeus, Greece.

Strain collection 84

  • Twelve K. pneumoniae (TGH1-TGH12), harbouring blaVIM and/or blaKPC, and isolated from 85 patients admitted to the intensive care unit (n=8) or surgical ward (n=4) at the TG hospital during 86 2010-2013 were studied.
  • Clinical data and strain characteristics are outlined in Table 1. 87.

Antimicrobial resistance profiling 88

  • All 12 strains were screened for resistance to 17 antibiotics, including β-lactams with and without 89 β-lactamase inhibitors, by disk diffusion (Table 1).
  • MICs of carbapenems (ertapenem, imipenem 90 and meropenem) were determined by Etest (bioMérieux Inc., Durham, NC), and results 91 interpreted according to CLSI cut-offs.
  • 11 Strains were screened for presence of extended-spectrum 92 β-lactamase (ESBL) and carbapenemase genes by PCR and Sanger sequencing as described 93 previously.

MLST and PFGE 95

  • MLST was performed as described previously for seven marker genes (gapA, infB, mdh, pgi, 96 phoE, rpoB, tonB), 15 and sequence types were assigned using the Institute Pasteur database 97 (www.pasteur.fr/mlst).
  • Both parameters showed 186 similar (sub) clustering of WGMs, identifying two clusters, C1 and C2, and two singletons, C3 187 and C4 , with C1 and C2 each divided into two sub clusters and a singleton .

Did you find this useful? Give us your feedback

Content maybe subject to copyright    Report

This item is the archived peer-reviewed author-version of:
Whole-genome typing and characterization of -harbouring ST383
Klebsiella pneumoniae by PFGE, whole-genome mapping and WGS
Reference:
Sabirova Julia, Xavier Basil Britto, Coppens Jasmine, Zarkotou Olympia, Lammens Christine, Janssens Lore, Burggrave
Ronald, Wagner Trevor, Goossens Herman, Malhotra Surbhi.- Whole-genome typing and characterization of -
harbouring ST383 Klebsiella pneumoniae by PFGE, whole-genome mapping and WGS
The journal of antimicrobial chemotherapy - ISSN 1460-2091 - (2016), p. 1-9
Full text (Publishers DOI): http://dx.doi.org/doi:10.1093/JAC/DKW003
To cite this reference: http://hdl.handle.net/10067/1318080151162165141
Institutional repository IRUA
Whole genome typing and characterisation of bla
VIM19
-harbouring
1
ST383 Klebsiella pneumoniae by PFGE, whole genome mapping and
2
sequencing
3
4
5
Julia S. Sabirova
a*
, Basil Britto Xavier
a*
, Jasmine Coppens
a
, Olympia Zarkotou
b
, Christine
6
Lammens
a
, Lore Janssens
a
, Ronald Burggrave
c
, Trevor Wagner
c
, Herman Goossens
a
, Surbhi
7
Malhotra-Kumar
a#
8
a
Department of Medical Microbiology, Vaccine & Infectious Disease Institute, Universiteit Antwerpen,
9
Antwerp, Belgium
a
; Department of Microbiology, Tzaneio General Hospital, Piraeus, Greece
b
; OpGen,
10
Inc., Gaithersburg, Maryland, USA
c
.
11
12
Running Title: bla
VIM19
-harbouring ST383 K. pneumoniae
13
14
Key words: Whole genome sequencing, class 1 integron, integrase, ICEPm1, ST383, optical
15
mapping, whole genome maps, PFGE
16
Text word count: 3749
17
Synopsis word count: 248
18
19
*Equal contribution authors
20
#
Corresponding author mailing address: Department of Medical Microbiology, Campus Drie
21
Eiken, University of Antwerp, S6, Universiteitsplein 1, B-2610 Wilrijk, Belgium. Phone: 32-3-
22
265-27-52. Fax: 32-3-265-26-63. E-mail: surbhi.malhotra@uantwerpen.be
23
Synopsis
24
Objectives: We utilized whole-genome mapping (WGM) and WGS to characterize 12 clinical
25
carbapenem-resistant Klebsiella pneumoniae (TGH1-TGH12).
26
Methods: All strains were screened for carbapenemase genes by PCR, and typed by MLST, PFGE
27
(XbaI), and WGM (AflII) (Opgen, USA). WGS (Illumina) was performed on TGH8 and TGH10.
28
Reads were denovo assembled and annotated (SPAdes, RAST). Contigs were aligned directly, and
29
after in silico AflII restriction, with corresponding WGMs (MapSolver, OpGen; BioNumerics,
30
Applied Maths).
31
Results: All 12 strains were ST383. Eleven of the 12 strains were carbapenem-resistant and 7
32
harboured bla
KPC-2,
and 11, bla
VIM-19 .
Varying the parameters for assigning WGM clusters showed
33
that these were comparable to ST types, and to the 8 PFGE (sub)types (≥ 3-band difference). A
34
95% similarity coefficient assigned all 12 WGMs to a single cluster while a 99% similarity
35
coefficient (or ≥ 10 unmatched-fragment difference) assigned the 12 WGMs to 8 (sub)clusters.
36
Based on a ≥ 3-band difference between PFGE profiles, the Simpson’s diversity index (SDI) of
37
WGM (0.94, Jackknife pseudo-values CI: 0.883-0.996) and PFGE (0.93, CI: 0.828-1.000) were
38
similar (p=0.649). However, discriminatory power of WGM was significantly higher (SDI: 0.94,
39
CI: 0.883-0.996) than PFGE profiles typed on a ≥7-band difference (SDI: 0.53, CI: 0.212-0.849)
40
(p=0.007).
41
Conclusions: This study demonstrates the application of whole-genome mapping to understanding
42
the epidemiology of hospital-associated K. pneumoniae. Utilizing a combination of WGM and
43
WGS, we also present here the first longitudinal genomic characterization of the highly dynamic
44
carbapenem-resistant ST383 K. pneumoniae clone that is rapidly gaining importance in Europe.
45
INTRODUCTION
46
The spread of multidrug-resistant K. pneumoniae strains in hospitals constitutes a pressing global
47
health problem. The increasing prevalence of plasmid-encoded carbapenem-hydrolysing enzymes
48
in K. pneumoniae is of particular concern due to their ability to hydrolyse almost all β-lactam
49
antibiotics, as well as their genetic association with transferable multidrug resistance.
1-3
Infections
50
due to carbapenem-resistant K. pneumoniae are not only difficult to treat due to limited therapeutic
51
options, but such clones could potentially cause hospital epidemics if not promptly detected and
52
contained.
4
53
Molecular typing techniques are effective surveillance tools to monitor the dynamics of multidrug-
54
resistant clones circulating in hospitals during non-outbreak situations and to detect early signs of
55
an outbreak. Currently used techniques are based on amplification of marker genes followed by
56
sequencing (MLST), or targeting entire genomes by PFGE or by whole genome mapping (WGM),
57
with the restriction fragments analysed on a gel or in a microfluidic device, respectively. Of the
58
three techniques, MLST is most commonly utilized for bacteria strain typing. While it is highly
59
reproducible and relatively inexpensive, the resolution achieved by clustering strains based on
60
sequenced segments of seven or more housekeeping genes is not high enough to study inter- and
61
intra-clonal genetic diversity. Compared to PFGE, WGM has the advantage of being less labour
62
intensive and, importantly, allowing inter-lab reproducibility and comparison of results that has
63
been a major shortcoming of PFGE typing. WGM is also far less technologically challenging than
64
whole genome sequencing (WGS) and does not require bioinformatics expertise. Furthermore,
65
results can be generated on the same day with WGM that offers a distinct advantage for
66
microbiology laboratories undertaking outbreak investigations. Notwithstanding instrument costs,
67
the cost of running a single strain for PFGE < WGM ≤ WGS. Also with WGM, the genetic
68
content of the detected variable genome regions can be extracted and identified by utilizing the
69
vast number of publicly available whole genome sequences. These can be utilized to develop in
70
silico restriction maps using the same enzymes as used for experimentally-generated WGMs,
71
allowing comparison of restriction patterns and eventual identification of the genetic content of the
72
variable regions in the strains of interest.
5
73
In this study, we demonstrate the utility of WGM in conjunction with WGS for typing,
74
characterizing, and dissecting the genomic features of carbapenem-resistant K. pneumoniae
75
isolated at the Tzaneio General (TG) hospital, Piraeus, Greece. Carbapenem-resistant K.
76
pneumoniae producing VIM-type metallo-β-lactamases have been endemic in Greek hospitals
77
since the early 2000s.
6
Many strains with VIM-1–producing K. pneumoniae have also been
78
described.
7
From 2007, KPC-type carbapenemases became prevalent and even caused outbreaks,
8,
79
9
followed by emergence of strains coproducing KPC and VIM.
10
We studied VIM- and KPC-
80
+VIM-producing K. pneumoniae isolated from colonized or infected patients during 2010-2013 at
81
the TG hospital.
82
Citations
More filters
SPAdes, a new genome assembly algorithm and its applications to single-cell sequencing ( 7th Annual SFAF Meeting, 2012)

[...]

Glenn Tesler
01 Jun 2012
TL;DR: SPAdes as mentioned in this paper is a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler and on popular assemblers Velvet and SoapDeNovo (for multicell data).
Abstract: The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

10,124 citations

Journal Article•DOI•
Evidence of Sharing of Klebsiella pneumoniae Strains between Healthy Companion Animals and Cohabiting Humans.

[...]

Cátia Marques1, Adriana Belas1, Catarina Aboim1, Patrícia Cavaco-Silva, Graça Trigueiro, Luis Telo da Gama1, Constança Pomba1 •
University of Lisbon1
24 May 2019-Journal of Clinical Microbiology
TL;DR: The results highlight the potential role of dogs as a reservoir of K. pneumoniae to humans and vice versa and to the best knowledge, this is the first report of healthy humans and dogs sharing K. influenza pneumoniae strains that were undistinguishable by PFGE/MLST.
Abstract: This study aimed to characterize the fecal colonization and sharing of Klebsiella pneumoniae strains between companion animals and humans living in close contact. Fecal samples were collected from 50 healthy participants (24 humans, 18 dogs, and 8 cats) belonging to 18 households. Samples were plated onto MacConkey agar (MCK) plates with and without cefotaxime or meropenem supplementation. Up to five K. pneumoniae colonies per participant were compared by pulsed-field gel electrophoresis (PFGE) after XbaI restriction. K. pneumoniae strains with unique pulse types from each participant were characterized for antimicrobial susceptibility, virulence genes, and multilocus sequence type (MLST). Fecal K. pneumoniae pulse types were compared to those of clinical K. pneumoniae strains from animal and human patients with urinary tract infections (n = 104). K. pneumoniae colonization was detected in nonsupplemented MCK in around 38% of dogs (n = 7) and humans (n = 9). K. pneumoniae strains isolated from dogs belonged to sequence type 17 (ST17), ST188, ST252, ST281, ST423, ST1093, ST1241, ST3398, and ST3399. None of the K. pneumoniae strains were multidrug resistant or hypervirulent. Two households included multiple colonized participants. Notably, two colonized dogs within household 15 (H15) shared a strain each (ST252 and ST1241) with one coliving human. One dog from H16 shared one PFGE-undistinguishable K. pneumoniae ST17 strain with two humans from different households; however, the antimicrobial susceptibility phenotypes of these three strains differed. Two main virulence genotypes were detected, namely fimH-1 mrkD ycfM entB kfu and fimH-1 mrkD ycfM entB kpn. These results highlight the potential role of dogs as a reservoir of K. pneumoniae to humans and vice versa. Furthermore, to our best knowledge, this is the first report of healthy humans and dogs sharing K. pneumoniae strains that were undistinguishable by PFGE/MLST.

50 citations

Cites methods from "Whole-genome typing and characteriz..."

  • ...tent with the PFGE and MLST data combined, especially in strains differing in less than 3 bands (37, 38)....

    [...]

Journal Article•DOI•
Monitoring microevolution of OXA-48-producing Klebsiella pneumoniae ST147 in a hospital setting by SMRT sequencing.

[...]

Andreas E. Zautner1, Boyke Bunk2, Yvonne Pfeifer3, Cathrin Spröer2, Utz Reichard1, Helmut Eiffert1, Simone Scheithauer1, Uwe Groß1, Jörg Overmann2, Wolfgang Bohne1 •
University of Göttingen1, Leibniz Association2, Robert Koch Institute3
01 Oct 2017-Journal of Antimicrobial Chemotherapy
TL;DR: Single molecule real-time sequencing allowed monitoring of the genetic and epigenetic microevolution of MDR OXA-48-producing K. pneumoniae and revealed in addition to SNPs, complex rearrangements of genetic elements.
Abstract: Objectives Carbapenemase-producing Klebsiella pneumoniae pose an increasing risk for healthcare facilities worldwide. A continuous monitoring of ST distribution and its association with resistance and virulence genes is required for early detection of successful K. pneumoniae lineages. In this study, we used WGS to characterize MDR blaOXA-48-positive K. pneumoniae isolated from inpatients at the University Medical Center Gottingen, Germany, between March 2013 and August 2014. Methods Closed genomes for 16 isolates of carbapenemase-producing K. pneumoniae were generated by single molecule real-time technology using the PacBio RSII platform. Results Eight of the 16 isolates showed identical XbaI macrorestriction patterns and shared the same MLST, ST147. The eight ST147 isolates differed by only 1-25 SNPs of their core genome, indicating a clonal origin. Most of the eight ST147 isolates carried four plasmids with sizes of 246.8, 96.1, 63.6 and 61.0 kb and a novel linear plasmid prophage, named pKO2, of 54.6 kb. The blaOXA-48 gene was located on a 63.6 kb IncL plasmid and is part of composite transposon Tn1999.2. The ST147 isolates expressed the yersinabactin system as a major virulence factor. The comparative whole-genome analysis revealed several rearrangements of mobile genetic elements and losses of chromosomal and plasmidic regions in the ST147 isolates. Conclusions Single molecule real-time sequencing allowed monitoring of the genetic and epigenetic microevolution of MDR OXA-48-producing K. pneumoniae and revealed in addition to SNPs, complex rearrangements of genetic elements.

33 citations

Journal Article•DOI•
Whole-Genome Comparative Analysis of Two Carbapenem-Resistant ST-258 Klebsiella pneumoniae Strains Isolated during a North-Eastern Ohio Outbreak: Differences within the High Heterogeneity Zones.

[...]

Maria Soledad Ramirez1, Gang Xie2, German Matias Traglia3, Shannon L. Johnson2, Karen W. Davenport2, David van Duin4, Azam Ramazani5, Azam Ramazani1, Federico Perez6, Michael R. Jacobs7, David J. Sherratt5, Robert A. Bonomo6, Robert A. Bonomo7, Patrick S.G. Chain3, Marcelo E. Tolmasky1 •
California State University, Fullerton1, Los Alamos National Laboratory2, University of Buenos Aires3, University of North Carolina at Chapel Hill4, University of Oxford5, United States Department of Veterans Affairs6, Case Western Reserve University7
01 Jun 2016-Genome Biology and Evolution
TL;DR: The potential value of the high heterogeneity zone (HHZ) as a potential marker for K. pneumoniae clinical and epidemiological studies is identified.
Abstract: Klebsiella pneumoniae has become one of the most dangerous causative agents of hospital infections due to the acquisition of resistance to carbapenems, one of the last resort families of antibiotics. Resistance is usually mediated by carbapenemases coded for by different classes of genes. A prolonged outbreak of carbapenem-resistant K. pneumoniae infections has been recently described in northeastern Ohio. Most strains isolated from patients during this outbreak belong to MLST sequence type 258 (ST258). To understand more about this outbreak two isolates (strains 140 and 677), one of them responsible for a fatal infection, were selected for genome comparison analyses. Whole genome map and sequence comparisons demonstrated that both strains are highly related showing 99% average nucleotide identity. However, the genomes differ at the so-called high heterogeneity zone (HHZ) and other minor regions. This study identifies the potential value of the HHZ as a potential marker for K. pneumoniae clinical and epidemiological studies.

21 citations

Cites result from "Whole-genome typing and characteriz..."

  • ...This was not surprising because as others and we have previously observed comparing other K. pneumoniae strains (Deleo et al. 2014; Ramirez et al. 2014b; Sabirova et al. 2016), the genomes of this bacterium seem to be quite homogeneous....

    [...]

  • ...We propose that this zone of the K. pneumoniae genome can be used as a signature for epidemiology analysis....

    [...]

Journal Article•DOI•
Emergence of VIM-producing <i>Enterobacter cloacae</i> complex in France between 2015 and 2018

[...]

Laurent Dortet1•
CNR de la Résistance aux Antibiotiques1
19 Jan 2022-Journal of Antimicrobial Chemotherapy
TL;DR: In this paper , the authors performed WGS, species determination, MLST, clonal relationship and genetic characterization on 149 VIM-producing ECC isolates recovered in France from 2015 to 2018.
Abstract: To genetically characterize VIM-producing Enterobacter cloacae complex (ECC) isolates recovered in France from 2015 to 2018.WGS, species determination, MLST, clonal relationship and genetic characterization were performed on 149 VIM-producing ECC isolates.Among VIM-producing Enterobacterales, the prevalence of ECC increased drastically from 6% in 2012 to 52% in 2018. The most prevalent species were Enterobacter hormaechei subsp. hoffmannii (40.9%), E. hormaechei subsp. steigerwaltii (21.5%), E. hormaechei subsp. xiangfangensis (14.8%) and ECC clade S (17.4%). Major STs were ST-873 (17.5%), ST-66 (12.1%), ST-78 (9.4%), ST-419 (8.1%), ST-145 (4.7%), ST-50 (4.0%), ST-118 (4.0%) and ST-168 (4.0%). Finally, six different integrons were identified, with some being specific to a given blaVIM variant (In916 with blaVIM-1-aacA4'-aphA15-aadA1-catB2 and In416 with blaVIM-4-aacA7-dfrA1b-aadA1b-smr2 genes).This study demonstrated the genetic diversity among VIM-producing ECC isolates, indicating that their spread is not linked to a single clone.

6 citations

References
More filters
Journal Article•DOI•
Basic Local Alignment Search Tool

[...]

Stephen F. Altschul1, Warren Gish1, Webb Miller2, Eugene W. Myers3, David J. Lipman1 •
National Institutes of Health1, Pennsylvania State University2, University of Arizona3
01 Oct 1990-Journal of Molecular Biology
TL;DR: A new approach to rapid sequence comparison, basic local alignment search tool (BLAST), directly approximates alignments that optimize a measure of local similarity, the maximal segment pair (MSP) score.

88,255 citations

Journal Article•DOI•
SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

[...]

Anton Bankevich1, Sergey Nurk, Dmitry Antipov, Alexey Gurevich, Mikhail Dvorkin, Alexander S. Kulikov, Valery M. Lesin, Sergey I. Nikolenko, Son Pham, Andrey D. Prjibelski, Alexey V. Pyshkin, Alexander Sirotkin, Nikolay Vyahhi, Glenn Tesler, Max A. Alekseyev, Pavel A. Pevzner •
Saint Petersburg Academic University1
07 May 2012-Journal of Computational Biology
TL;DR: SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies.
Abstract: The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V−SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online (http://bioinf.spbau.ru/spades). It is distributed as open source software.

16,859 citations

SPAdes, a new genome assembly algorithm and its applications to single-cell sequencing ( 7th Annual SFAF Meeting, 2012)

[...]

Glenn Tesler
01 Jun 2012
TL;DR: SPAdes as mentioned in this paper is a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler and on popular assemblers Velvet and SoapDeNovo (for multicell data).
Abstract: The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

10,124 citations

Journal Article•DOI•
The RAST Server: Rapid Annotations using Subsystems Technology

[...]

Ramy K. Aziz1, Ramy K. Aziz2, Daniela Bartels3, Aaron A. Best4, Matthew DeJongh4, Terrence Disz5, Terrence Disz3, Robert Edwards5, Kevin Formsma4, Svetlana Gerdes, Elizabeth M. Glass5, Michael Kubal3, Folker Meyer3, Folker Meyer5, Gary J. Olsen6, Gary J. Olsen5, Robert Olson3, Robert Olson5, Andrei L. Osterman7, Ross Overbeek, Leslie Klis McNeil6, Daniel Paarmann3, Tobias Paczian3, Bruce Parrello, Gordon D. Pusch3, Claudia I. Reich6, Rick Stevens5, Rick Stevens3, Olga Vassieva, Veronika Vonstein, Andreas Wilke3, Olga Zagnitko •
University of Tennessee Health Science Center1, Cairo University2, University of Chicago3, Hope College4, Argonne National Laboratory5, University of Illinois at Urbana–Champaign6, Sanford-Burnham Institute for Medical Research7
08 Feb 2008-BMC Genomics
TL;DR: A fully automated service for annotating bacterial and archaeal genomes that identifies protein-encoding, rRNA and tRNA genes, assigns functions to the genes, predicts which subsystems are represented in the genome, uses this information to reconstruct the metabolic network and makes the output easily downloadable for the user.
Abstract: The number of prokaryotic genome sequences becoming available is growing steadily and is growing faster than our ability to accurately annotate them. We describe a fully automated service for annotating bacterial and archaeal genomes. The service identifies protein-encoding, rRNA and tRNA genes, assigns functions to the genes, predicts which subsystems are represented in the genome, uses this information to reconstruct the metabolic network and makes the output easily downloadable for the user. In addition, the annotated genome can be browsed in an environment that supports comparative analysis with the annotated genomes maintained in the SEED environment. The service normally makes the annotated genome available within 12–24 hours of submission, but ultimately the quality of such a service will be judged in terms of accuracy, consistency, and completeness of the produced annotations. We summarize our attempts to address these issues and discuss plans for incrementally enhancing the service. By providing accurate, rapid annotation freely to the community we have created an important community resource. The service has now been utilized by over 120 external users annotating over 350 distinct genomes.

9,397 citations

Journal Article•DOI•
Interpreting chromosomal DNA restriction patterns produced by pulsed-field gel electrophoresis: criteria for bacterial strain typing.

[...]

Fred C. Tenover1, Robert D. Arbeit1, Richard V. Goering1, P. A. Mickelsen1, Barbara E Murray1, D. H. Persing1, B. Swaminathan1 •
Centers for Disease Control and Prevention1
01 Sep 1995-Journal of Clinical Microbiology
TL;DR: This research presents a novel, scalable and scalable approach that allows for real-time assessment of the severity of the infection and its impact on patients’ health.
Abstract: FRED C. TENOVER,* ROBERT D. ARBEIT, RICHARD V. GOERING, PATRICIA A. MICKELSEN, BARBARA E. MURRAY, DAVID H. PERSING, AND BALA SWAMINATHAN National Center for Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia 30333; Veterans Affairs Medical Center, Boston, Massachusetts 02130; Creighton University, Omaha, Nebraska 68178; Stanford University Medical Center, Stanford, California 94305; University of Texas Medical School, Houston, Texas 77030; and Mayo Clinic, Rochester, Minnesota 55905

7,784 citations

Related Papers (5)
Tracking a hospital outbreak of KPC-producing ST11 Klebsiella pneumoniae with whole genome sequencing

[...]

01 Nov 2015-Clinical Microbiology and Infection
Yan Jiang, Z. Wei, Yanfei Wang, Xiaoting Hua, Ye Feng, Ye Feng, Yunsong Yu 
Multilocus Sequence Typing of Klebsiella pneumoniae Nosocomial Isolates

[...]

01 Aug 2005-Journal of Clinical Microbiology
Laure Diancourt, Virginie Passet, Jan Verhoef, Patrick A. D. Grimont, Sylvain Brisse 
Molecular Epidemiology of KPC-Producing Klebsiella pneumoniae Isolates in the United States: Clonal Expansion of Multilocus Sequence Type 258

[...]

01 Aug 2009-Antimicrobial Agents and Chemotherapy
Brandon Kitchel, J. Kamile Rasheed, Jean B. Patel, Arjun Srinivasan, Shiri Navon-Venezia, Yehuda Carmeli, Alma Brolund, Christian G. Giske 
Phylogenetic diversity of Klebsiella pneumoniae and Klebsiella oxytoca clinical isolates revealed by randomly amplified polymorphic DNA, gyrA and parC genes sequencing and automated ribotyping.

[...]

01 May 2001-International Journal of Systematic and Evolutionary Microbiology
Sylvain Brisse, Jan Verhoef
MALDI-TOF mass spectrometry and blakpc gene phylogenetic analysis of an outbreak of carbapenem-resistant K. pneumoniae strains.

[...]

01 Oct 2015-New Microbiologica
Silvia Angeletti, Giordano Dicuonzo, Lo Presti A, Eleonora Cella, Francesca Crea, Alessandra Avola, Massimiliano Andrea Vitali, Fagioni M, De Florio L 
Frequently Asked Questions (1)
Q1. What contributions have the authors mentioned in the paper "Whole-genome typing and characterization of -harbouring st383 klebsiella pneumoniae by pfge, whole-genome mapping and wgs reference:" ?

In this paper, a whole-genome typing and characterization of harboring ST383 Klebsiella pneumoniae by PFGE, wholegenome mapping and WGS is presented.