Additional file 5: of Comparative genomics and biological characterization of sequential Pseudomonas aeruginosa isolates from persistent airways infection

Additional file 4: Table S3. of Genomic characterisation of clinical and environmental Pseudomonas putida group strains and determination of their role in the transfer of antimicrobial resistance genes to Pseudomonas aeruginosa

Ossowski, Stephan
Dörfel, Daniela
Peter, Silke
Dinkelacker, Ariane
Willmann, Matthias
Vogel, Wichard
Schüle, Leonard
Oberhettinger, Philipp
Liese, Jan
Marschal, Matthias
Bezdan, Daniela
University of Tübingen

November 2017

Average of the nucleotide identity of the P. putida study strains and closely related species. (XLSX...

Comparative genomics and biological characterization of sequential Pseudomonas aeruginosa isolates from persistent airways infection

Bianconi, Irene
Jeukens, Julie
Freschi, Luca
Alcalá-Franco, Beatriz
Facchini, Marcella
Boyle, Brian
Molinaro, Antonio
Kukavica-Ibrulj, Irena
Tümmler, Burkhard
Levesque, Roger C.
Bragonzi, Alessandra

January 2015

Background: Pseudomonas aeruginosa establishes life-long chronic airway infections in cystic fibrosi...

Comparative genomics and biological characterization of sequential Pseudomonas aeruginosa isolates from persistent airways infection

Bianconi, Irene
Jeukens, Julie
Freschi, Luca
Alcalá-Franco, Beatriz
Facchini, Marcella
Boyle, Brian
Molinaro, Antonio
Kukavica-Ibrulj, Irena
Tümmler, Burkhard
Levesque, Roger C.
Bragonzi, Alessandra

January 2015

Background: Pseudomonas aeruginosa establishes life-long chronic airway infections in cystic fibrosi...

Additional file 3: of Comparative genomics and biological characterization of sequential Pseudomonas aeruginosa isolates from persistent airways infection

Irene Bianconi (108469)
Julie Jeukens (520628)
Luca Freschi (513340)
Beatriz AlcalĂĄ-Franco (3544031)
Marcella Facchini (2461264)
Brian Boyle (276326)
Antonio Molinaro (255584)
Irena Kukavica-Ibrulj (300135)
Burkhard TĂźmmler (3544028)
Roger Levesque (3487352)
Alessandra Bragonzi (108447)

December 2015

Genomic features of RP strains compared to others complete P. aeruginosa genomes [ 4 , 12 , 19 , 23 ...

Additional file 5: Table S5. of Is genotyping of single isolates sufficient for population structure analysis of Pseudomonas aeruginosa in cystic fibrosis airways?

Lea Sommer (3465434)
Rasmus Marvig (3465443)
Adela LujĂĄn (3465431)
Anna Koza (2550025)
Tacjana Pressler (3465440)
SĂ¸ren Molin (3465446)
Helle Johansen (3465437)

August 2016

Detailed overview of SNPs found in single isolates and the rediscovery in the metagenomic reads. For...

RESEARCH ARTICLE Open Access Comparative

Irene Bianconi
Julie Jeukens
Luca Freschi
Beatriz Alcalá-franco
Marcella Facchini
Brian Boyle
Antonio Molinaro
Irena Kukavica-ibrulj
Burkhard Tümmler
Roger C. Levesque
Ra Bragonzi

August 2016

genomics and biological characterization of sequential Pseudomonas aeruginosa isolates from persiste...

Additional file 1: of Whole genome sequencing reveals the emergence of a Pseudomonas aeruginosa shared strain sub-lineage among patients treated within a single cystic fibrosis centre

Bryan Wee (3473117)
Anna Tai (4569634)
Laura Sherrard (4569637)
Nouri Ben Zakour (5704643)
Kirt Hanks (5704646)
Timothy Kidd (4569640)
Kay Ramsay (4569643)
Iain Lamont (5704649)
David Whiley (171092)
Scott Bell (3475514)
Scott Beatson (5704652)

September 2018

Table S1. Details of Pseudomonas aeruginosa isolates and genome assembly metrics used in this study....

Additional file 9: of Whole genome sequencing reveals the emergence of a Pseudomonas aeruginosa shared strain sub-lineage among patients treated within a single cystic fibrosis centre

Bryan Wee (3473117)
Anna Tai (4569634)
Laura Sherrard (4569637)
Nouri Ben Zakour (5704643)
Kirt Hanks (5704646)
Timothy Kidd (4569640)
Kay Ramsay (4569643)
Iain Lamont (5704649)
David Whiley (171092)
Scott Bell (3475514)
Scott Beatson (5704652)

September 2018

Table S5. Table of variants (SNPs and indels) that vary across 37Â M3L7 genomes and 1Â M3L1 (AUS970)...

Additional file 9: Figure S3. of Comparative genomics of Pseudomonas fluorescens subclade III strains from human lungs

Brittan Scales (3401519)
John Erb-Downward (3401513)
Ian Huffnagle (3401525)
John LiPuma (3401522)
Gary Huffnagle (3401516)

December 2015

Phylogenetic tree inferred from the nucleotide acid sequences of vasH homologues from representative...

Additional file 5: of Whole genome sequencing reveals the emergence of a Pseudomonas aeruginosa shared strain sub-lineage among patients treated within a single cystic fibrosis centre

Bryan Wee (3473117)
Anna Tai (4569634)
Laura Sherrard (4569637)
Nouri Ben Zakour (5704643)
Kirt Hanks (5704646)
Timothy Kidd (4569640)
Kay Ramsay (4569643)
Iain Lamont (5704649)
David Whiley (171092)
Scott Bell (3475514)
Scott Beatson (5704652)

September 2018

Table S3. Details of co-pathogens in people with M3L7/M3L1 infection at time of isolation and in the...

Additional file 8: of Whole genome sequencing reveals the emergence of a Pseudomonas aeruginosa shared strain sub-lineage among patients treated within a single cystic fibrosis centre

Bryan Wee (3473117)
Anna Tai (4569634)
Laura Sherrard (4569637)
Nouri Ben Zakour (5704643)
Kirt Hanks (5704646)
Timothy Kidd (4569640)
Kay Ramsay (4569643)
Iain Lamont (5704649)
David Whiley (171092)
Scott Bell (3475514)
Scott Beatson (5704652)

September 2018

Table S4. Position and details of non-synonymous SNPs (nâ=â35) and indels (nâ=â9) that chara...

Additional file 4: Table S3. of Genomic characterisation of clinical and environmental Pseudomonas putida group strains and determination of their role in the transfer of antimicrobial resistance genes to Pseudomonas aeruginosa

Ossowski, Stephan
Dörfel, Daniela
Peter, Silke
Dinkelacker, Ariane
Willmann, Matthias
Vogel, Wichard
Schüle, Leonard
Oberhettinger, Philipp
Liese, Jan
Marschal, Matthias
Bezdan, Daniela
University of Tübingen

November 2017

Average of the nucleotide identity of the P. putida study strains and closely related species. (XLSX...

Additional file 4: Table S3. of Genomic characterisation of clinical and environmental Pseudomonas putida group strains and determination of their role in the transfer of antimicrobial resistance genes to Pseudomonas aeruginosa

Ossowski, Stephan
Dörfel, Daniela
Peter, Silke
Dinkelacker, Ariane
Willmann, Matthias
Vogel, Wichard
Schüle, Leonard
Oberhettinger, Philipp
Liese, Jan
Marschal, Matthias
Bezdan, Daniela
University of Tübingen

November 2017

Average of the nucleotide identity of the P. putida study strains and closely related species. (XLSX...

Additional file 4: Table S3. of Genomic characterisation of clinical and environmental Pseudomonas putida group strains and determination of their role in the transfer of antimicrobial resistance genes to Pseudomonas aeruginosa

Ossowski, Stephan
Dörfel, Daniela
Peter, Silke
Dinkelacker, Ariane
Willmann, Matthias
Vogel, Wichard
Schüle, Leonard
Oberhettinger, Philipp
Liese, Jan
Marschal, Matthias
Bezdan, Daniela
University of Tübingen

November 2017

Average of the nucleotide identity of the P. putida study strains and closely related species. (XLSX...

Additional file 2: of Genome plasticity favours double chromosomal Tn4401b-blaKPC-2 transposon insertion in the Pseudomonas aeruginosa ST235 clone

Deisy Abril (6385460)
Ricaurte Marquez-Ortiz (3706963)
Betsy Castro-Cardozo (6385463)
José Moncayo-Ortiz (6385466)
Narda Olarte Escobar (6385469)
Zayda Corredor Rozo (6385472)
Niradiz Reyes (3706978)
Catalina Tovar (3706969)
Héctor Sánchez (6385475)
Jaime Castellanos (2841758)
Yina Guaca-González (6385478)
Carmen Llanos-Uribe (6385481)
Natasha Vanegas Gómez (6385484)
Javier Escobar-Pérez (6385487)

February 2019

Figure S1. Genetic relationship by PFGE of the carbapenem-resistant P. aeruginosa isolates identifie...

Additional file 4: Table S3. of Genomic characterisation of clinical and environmental Pseudomonas putida group strains and determination of their role in the transfer of antimicrobial resistance genes to Pseudomonas aeruginosa

Ossowski, Stephan
Dörfel, Daniela
Peter, Silke
Dinkelacker, Ariane
Willmann, Matthias
Vogel, Wichard
Schüle, Leonard
Oberhettinger, Philipp
Liese, Jan
Marschal, Matthias
Bezdan, Daniela
University of Tübingen

November 2017

Average of the nucleotide identity of the P. putida study strains and closely related species. (XLSX...

Comparative genomics and biological characterization of sequential Pseudomonas aeruginosa isolates from persistent airways infection

Bianconi, Irene
Jeukens, Julie
Freschi, Luca
Alcalá-Franco, Beatriz
Facchini, Marcella
Boyle, Brian
Molinaro, Antonio
Kukavica-Ibrulj, Irena
Tümmler, Burkhard
Levesque, Roger C.
Bragonzi, Alessandra

January 2015

Background: Pseudomonas aeruginosa establishes life-long chronic airway infections in cystic fibrosi...

Comparative genomics and biological characterization of sequential Pseudomonas aeruginosa isolates from persistent airways infection

Bianconi, Irene
Jeukens, Julie
Freschi, Luca
Alcalá-Franco, Beatriz
Facchini, Marcella
Boyle, Brian
Molinaro, Antonio
Kukavica-Ibrulj, Irena
Tümmler, Burkhard
Levesque, Roger C.
Bragonzi, Alessandra

January 2015

Background: Pseudomonas aeruginosa establishes life-long chronic airway infections in cystic fibrosi...

Additional file 3: of Comparative genomics and biological characterization of sequential Pseudomonas aeruginosa isolates from persistent airways infection

Irene Bianconi (108469)
Julie Jeukens (520628)
Luca Freschi (513340)
Beatriz AlcalĂĄ-Franco (3544031)
Marcella Facchini (2461264)
Brian Boyle (276326)
Antonio Molinaro (255584)
Irena Kukavica-Ibrulj (300135)
Burkhard TĂźmmler (3544028)
Roger Levesque (3487352)
Alessandra Bragonzi (108447)

December 2015

Genomic features of RP strains compared to others complete P. aeruginosa genomes [ 4 , 12 , 19 , 23 ...

Additional file 5: Table S5. of Is genotyping of single isolates sufficient for population structure analysis of Pseudomonas aeruginosa in cystic fibrosis airways?

Lea Sommer (3465434)
Rasmus Marvig (3465443)
Adela LujĂĄn (3465431)
Anna Koza (2550025)
Tacjana Pressler (3465440)
SĂ¸ren Molin (3465446)
Helle Johansen (3465437)

August 2016

Detailed overview of SNPs found in single isolates and the rediscovery in the metagenomic reads. For...

RESEARCH ARTICLE Open Access Comparative

Irene Bianconi
Julie Jeukens
Luca Freschi
Beatriz Alcalá-franco
Marcella Facchini
Brian Boyle
Antonio Molinaro
Irena Kukavica-ibrulj
Burkhard Tümmler
Roger C. Levesque
Ra Bragonzi

August 2016

genomics and biological characterization of sequential Pseudomonas aeruginosa isolates from persiste...

Additional file 1: of Whole genome sequencing reveals the emergence of a Pseudomonas aeruginosa shared strain sub-lineage among patients treated within a single cystic fibrosis centre

Bryan Wee (3473117)
Anna Tai (4569634)
Laura Sherrard (4569637)
Nouri Ben Zakour (5704643)
Kirt Hanks (5704646)
Timothy Kidd (4569640)
Kay Ramsay (4569643)
Iain Lamont (5704649)
David Whiley (171092)
Scott Bell (3475514)
Scott Beatson (5704652)

September 2018

Table S1. Details of Pseudomonas aeruginosa isolates and genome assembly metrics used in this study....

Additional file 9: of Whole genome sequencing reveals the emergence of a Pseudomonas aeruginosa shared strain sub-lineage among patients treated within a single cystic fibrosis centre

Bryan Wee (3473117)
Anna Tai (4569634)
Laura Sherrard (4569637)
Nouri Ben Zakour (5704643)
Kirt Hanks (5704646)
Timothy Kidd (4569640)
Kay Ramsay (4569643)
Iain Lamont (5704649)
David Whiley (171092)
Scott Bell (3475514)
Scott Beatson (5704652)

September 2018

Table S5. Table of variants (SNPs and indels) that vary across 37Â M3L7 genomes and 1Â M3L1 (AUS970)...

Additional file 9: Figure S3. of Comparative genomics of Pseudomonas fluorescens subclade III strains from human lungs

Brittan Scales (3401519)
John Erb-Downward (3401513)
Ian Huffnagle (3401525)
John LiPuma (3401522)
Gary Huffnagle (3401516)

December 2015

Phylogenetic tree inferred from the nucleotide acid sequences of vasH homologues from representative...

Additional file 5: of Whole genome sequencing reveals the emergence of a Pseudomonas aeruginosa shared strain sub-lineage among patients treated within a single cystic fibrosis centre

Bryan Wee (3473117)
Anna Tai (4569634)
Laura Sherrard (4569637)
Nouri Ben Zakour (5704643)
Kirt Hanks (5704646)
Timothy Kidd (4569640)
Kay Ramsay (4569643)
Iain Lamont (5704649)
David Whiley (171092)
Scott Bell (3475514)
Scott Beatson (5704652)

September 2018

Table S3. Details of co-pathogens in people with M3L7/M3L1 infection at time of isolation and in the...

Additional file 8: of Whole genome sequencing reveals the emergence of a Pseudomonas aeruginosa shared strain sub-lineage among patients treated within a single cystic fibrosis centre

Bryan Wee (3473117)
Anna Tai (4569634)
Laura Sherrard (4569637)
Nouri Ben Zakour (5704643)
Kirt Hanks (5704646)
Timothy Kidd (4569640)
Kay Ramsay (4569643)
Iain Lamont (5704649)
David Whiley (171092)
Scott Bell (3475514)
Scott Beatson (5704652)

September 2018

Table S4. Position and details of non-synonymous SNPs (nâ=â35) and indels (nâ=â9) that chara...

Additional file 4: Table S3. of Genomic characterisation of clinical and environmental Pseudomonas putida group strains and determination of their role in the transfer of antimicrobial resistance genes to Pseudomonas aeruginosa

Ossowski, Stephan
Dörfel, Daniela
Peter, Silke
Dinkelacker, Ariane
Willmann, Matthias
Vogel, Wichard
Schüle, Leonard
Oberhettinger, Philipp
Liese, Jan
Marschal, Matthias
Bezdan, Daniela
University of Tübingen

November 2017

Average of the nucleotide identity of the P. putida study strains and closely related species. (XLSX...

Additional file 4: Table S3. of Genomic characterisation of clinical and environmental Pseudomonas putida group strains and determination of their role in the transfer of antimicrobial resistance genes to Pseudomonas aeruginosa

Ossowski, Stephan
Dörfel, Daniela
Peter, Silke
Dinkelacker, Ariane
Willmann, Matthias
Vogel, Wichard
Schüle, Leonard
Oberhettinger, Philipp
Liese, Jan
Marschal, Matthias
Bezdan, Daniela
University of Tübingen

November 2017

Average of the nucleotide identity of the P. putida study strains and closely related species. (XLSX...

Additional file 4: Table S3. of Genomic characterisation of clinical and environmental Pseudomonas putida group strains and determination of their role in the transfer of antimicrobial resistance genes to Pseudomonas aeruginosa

Ossowski, Stephan
Dörfel, Daniela
Peter, Silke
Dinkelacker, Ariane
Willmann, Matthias
Vogel, Wichard
Schüle, Leonard
Oberhettinger, Philipp
Liese, Jan
Marschal, Matthias
Bezdan, Daniela
University of Tübingen

November 2017

Average of the nucleotide identity of the P. putida study strains and closely related species. (XLSX...

Additional file 2: of Genome plasticity favours double chromosomal Tn4401b-blaKPC-2 transposon insertion in the Pseudomonas aeruginosa ST235 clone

Deisy Abril (6385460)
Ricaurte Marquez-Ortiz (3706963)
Betsy Castro-Cardozo (6385463)
José Moncayo-Ortiz (6385466)
Narda Olarte Escobar (6385469)
Zayda Corredor Rozo (6385472)
Niradiz Reyes (3706978)
Catalina Tovar (3706969)
Héctor Sánchez (6385475)
Jaime Castellanos (2841758)
Yina Guaca-González (6385478)
Carmen Llanos-Uribe (6385481)
Natasha Vanegas Gómez (6385484)
Javier Escobar-Pérez (6385487)

February 2019

Figure S1. Genetic relationship by PFGE of the carbapenem-resistant P. aeruginosa isolates identifie...

Additional file 4: Table S3. of Genomic characterisation of clinical and environmental Pseudomonas putida group strains and determination of their role in the transfer of antimicrobial resistance genes to Pseudomonas aeruginosa

Ossowski, Stephan
Dörfel, Daniela
Peter, Silke
Dinkelacker, Ariane
Willmann, Matthias
Vogel, Wichard
Schüle, Leonard
Oberhettinger, Philipp
Liese, Jan
Marschal, Matthias
Bezdan, Daniela
University of Tübingen

November 2017

Average of the nucleotide identity of the P. putida study strains and closely related species. (XLSX...

Comparative genomics and biological characterization of sequential Pseudomonas aeruginosa isolates from persistent airways infection

Bianconi, Irene
Jeukens, Julie
Freschi, Luca
Alcalá-Franco, Beatriz
Facchini, Marcella
Boyle, Brian
Molinaro, Antonio
Kukavica-Ibrulj, Irena
Tümmler, Burkhard
Levesque, Roger C.
Bragonzi, Alessandra

January 2015

Background: Pseudomonas aeruginosa establishes life-long chronic airway infections in cystic fibrosi...

Comparative genomics and biological characterization of sequential Pseudomonas aeruginosa isolates from persistent airways infection

Bianconi, Irene
Jeukens, Julie
Freschi, Luca
Alcalá-Franco, Beatriz
Facchini, Marcella
Boyle, Brian
Molinaro, Antonio
Kukavica-Ibrulj, Irena
Tümmler, Burkhard
Levesque, Roger C.
Bragonzi, Alessandra

January 2015

Background: Pseudomonas aeruginosa establishes life-long chronic airway infections in cystic fibrosi...

Additional file 5: of Comparative genomics and biological characterization of sequential Pseudomonas aeruginosa isolates from persistent airways infection

Abstract

Extracted data

Additional file 5: of Comparative genomics and biological characterization of sequential Pseudomonas aeruginosa isolates from persistent airways infection

Abstract

Extracted data

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