Additional file 4: of Whole-genome epidemiology, characterisation, and phylogenetic reconstruction of Staphylococcus aureus strains in a paediatric hospital

Supplementary Table 2: List of Staphylococcus aureus genomes used for the version 1(19 genomes) and version 2 (an additional 21 genomes) for constructing the SNP pattern file used in this study.

Sandeep Joseph (821068)

November 2015

Supplementary Table 2: List of Staphylococcus aureus genomes used for the version 1(19 g...

Additional file 3: Table S1. of Preliminary comparative genomics revealed pathogenic potential and international spread of Staphylococcus argenteus

Dao-Feng Zhang (4529971)
Xiao-Yang Zhi (405438)
Jing Zhang (23775)
George Paoli (4529974)
Yan Cui (9885)
Chunlei Shi (301020)
Xianming Shi (301021)

October 2017

Complete list of homologous gene families in S. aureus complex (SAC) genomes. Fifty-one SAC genomes ...

Additional file 1: of USA300 Staphylococcus aureus persists on multiple body sites following an infection

Timothy Read (333405)
Robert Petit (6055523)
Zachary Yin (6055526)
Tuyaa Montgomery (6055529)
Moira McNulty (6055532)
Michael David (35198)

December 2018

Patient metadata. Breakdown of all metadata fields collected and summary of genetic results. Include...

Additional file 1: of Whole-genome epidemiology, characterisation, and phylogenetic reconstruction of Staphylococcus aureus strains in a paediatric hospital

Serena Manara (5961503)
Edoardo Pasolli (3155043)
Daniela Dolce (727996)
Novella Ravenni (5961506)
Silvia Campana (5961509)
Federica Armanini (4176511)
Francesco Asnicar (5198411)
Alessio Mengoni (619628)
Luisa Galli (304813)
Carlotta Montagnani (634645)
Elisabetta Venturini (5961512)
Omar Rota-Stabelli (847806)
Guido Grandi (120744)
Giovanni Taccetti (727999)
Nicola Segata (103809)

November 2018

Table S1. Characteristics of the single isolates, including collection details, genome assembly stat...

Additional file 5: of Whole-genome epidemiology, characterisation, and phylogenetic reconstruction of Staphylococcus aureus strains in a paediatric hospital

Serena Manara (5961503)
Edoardo Pasolli (3155043)
Daniela Dolce (727996)
Novella Ravenni (5961506)
Silvia Campana (5961509)
Federica Armanini (4176511)
Francesco Asnicar (5198411)
Alessio Mengoni (619628)
Luisa Galli (304813)
Carlotta Montagnani (634645)
Elisabetta Venturini (5961512)
Omar Rota-Stabelli (847806)
Guido Grandi (120744)
Giovanni Taccetti (727999)
Nicola Segata (103809)

November 2018

Table S4. Most relevant clones represented in the cohort and their abundance. (XLSX 9Â kb

Additional file 3: of Whole-genome epidemiology, characterisation, and phylogenetic reconstruction of Staphylococcus aureus strains in a paediatric hospital

Serena Manara (5961503)
Edoardo Pasolli (3155043)
Daniela Dolce (727996)
Novella Ravenni (5961506)
Silvia Campana (5961509)
Federica Armanini (4176511)
Francesco Asnicar (5198411)
Alessio Mengoni (619628)
Luisa Galli (304813)
Carlotta Montagnani (634645)
Elisabetta Venturini (5961512)
Omar Rota-Stabelli (847806)
Guido Grandi (120744)
Giovanni Taccetti (727999)
Nicola Segata (103809)

November 2018

Table S2. Presence/absence profile of virulence and antibiotic resistance genes in the cohort. (XLSX...

Additional file 2: Figure S1. of Complete genome of Staphylococcus aureus Tager 104 provides evidence of its relation to modern systemic hospital-acquired strains

Richard Davis (26945)
Andrew Brannen (3571868)
Mohammad Hossain (591858)
Scott Monsma (813166)
Paul Bock (3571865)
Matthias Nahrendorf (172537)
David Mead (103432)
Michael Lodes (813170)
Mark Liles (3571871)
Peter Panizzi (249587)

March 2016

Complete Phylogenetic Tree of S. aureus Reference Strains. Whole-genome phylogenetic analysis of all...

Additional file 1: of Genomic exploration of sequential clinical isolates reveals a distinctive molecular signature of persistent Staphylococcus aureus bacteraemia

Stefano Giulieri (5626835)
Sarah Baines (5626838)
Romain Guerillot (5626841)
Torsten Seemann (85973)
Anders Gonรงalves da Silva (5626844)
Mark Schultz (5626847)
Ruth Massey (5534384)
Natasha Holmes (4913263)
Timothy Stinear (7853)
Benjamin Howden (4913269)

August 2018

Table S1. Microbiological data and sequence metrics of S. aureus isolates included in the study. (XL...

Additional file 3: of Genomic exploration of sequential clinical isolates reveals a distinctive molecular signature of persistent Staphylococcus aureus bacteraemia

Stefano Giulieri (5626835)
Sarah Baines (5626838)
Romain Guerillot (5626841)
Torsten Seemann (85973)
Anders Gonรงalves da Silva (5626844)
Mark Schultz (5626847)
Ruth Massey (5534384)
Natasha Holmes (4913263)
Timothy Stinear (7853)
Benjamin Howden (4913269)

August 2018

Table S2. List of 182 variants identified in 32 isolates (after excluding unrelated strains). (XLSX ...

Additional file 4: of Genomic exploration of sequential clinical isolates reveals a distinctive molecular signature of persistent Staphylococcus aureus bacteraemia

Stefano Giulieri (5626835)
Sarah Baines (5626838)
Romain Guerillot (5626841)
Torsten Seemann (85973)
Anders Gonรงalves da Silva (5626844)
Mark Schultz (5626847)
Ruth Massey (5534384)
Natasha Holmes (4913263)
Timothy Stinear (7853)
Benjamin Howden (4913269)

August 2018

Table S3. List of 81 mutations with predicted modification of protein sequences with COG annotation....

Additional file 3: of USA300 Staphylococcus aureus persists on multiple body sites following an infection

Timothy Read (333405)
Robert Petit (6055523)
Zachary Yin (6055526)
Tuyaa Montgomery (6055529)
Moira McNulty (6055532)
Michael David (35198)

December 2018

Additional figures and tables. Table S1. agr frameshifts. Figure S1. Provenance of strains sequenced...

Additional file 1: of Complete genome sequencing of three human clinical isolates of Staphylococcus caprae reveals virulence factors similar to those of S. epidermidis and S. capitis

Shinya Watanabe (3092)
Yoshifumi Aiba (5948150)
Xin-Ee Tan (5948153)
Feng-Yu Li (5948156)
Tanit Boonsiri (5948159)
Kanate Thitiananpakorn (5948162)
Bintao Cui (5948165)
Yusuke Satoâo (5948171)
Kotaro Kiga (693099)
Teppei Sasahara (159779)
Longzhu Cui (5948168)

November 2018

Table S1. List of Staphylococcus strains used in phylogenetic analysis (XLSX 14 kb

Additional file 2: of Regional outbreak of community-associated methicillin-resistant Staphylococcus aureus ST834 in Japanese children

Yuki Uehara (6192830)
Takashi Sasaki (263542)
Tadashi Baba (230966)
Yujie Lu (2257369)
Eri Imajo (6192833)
Yuka Sato (2182424)
Shigeru Tanno (6192836)
Munehiro Furuichi (790083)
Miki Kawada (31404)
Keiichi Hiramatsu (230971)

January 2019

Table S2. Detailed results of whole genome sequencing a SNPs, single nucleotide polymorphisms. (XLSX...

Additional file 3: Figure S2. of Prophages and adaptation of Staphylococcus aureus ST398 to the human clinic

Seydina Diene (3721954)
Anna Corvaglia (3721951)
Patrice François (22568)
Nathalie van der Mee-Marquet (20483)

February 2017

Comparative genomics for the identified prophages from three groups: φ3, MR11-like and others. The g...

Additional file 4: of USA300 Staphylococcus aureus persists on multiple body sites following an infection

Timothy Read (333405)
Robert Petit (6055523)
Zachary Yin (6055526)
Tuyaa Montgomery (6055529)
Moira McNulty (6055532)
Michael David (35198)

December 2018

Antibiotic resistance phenotypes. Table of phenotypic antibiotic results for the initial infection i...

Supplementary Table 2: List of Staphylococcus aureus genomes used for the version 1(19 genomes) and version 2 (an additional 21 genomes) for constructing the SNP pattern file used in this study.

Sandeep Joseph (821068)

November 2015

Supplementary Table 2: List of Staphylococcus aureus genomes used for the version 1(19 g...

Additional file 3: Table S1. of Preliminary comparative genomics revealed pathogenic potential and international spread of Staphylococcus argenteus

Dao-Feng Zhang (4529971)
Xiao-Yang Zhi (405438)
Jing Zhang (23775)
George Paoli (4529974)
Yan Cui (9885)
Chunlei Shi (301020)
Xianming Shi (301021)

October 2017

Complete list of homologous gene families in S. aureus complex (SAC) genomes. Fifty-one SAC genomes ...

Additional file 1: of USA300 Staphylococcus aureus persists on multiple body sites following an infection

Timothy Read (333405)
Robert Petit (6055523)
Zachary Yin (6055526)
Tuyaa Montgomery (6055529)
Moira McNulty (6055532)
Michael David (35198)

December 2018

Patient metadata. Breakdown of all metadata fields collected and summary of genetic results. Include...

Additional file 1: of Whole-genome epidemiology, characterisation, and phylogenetic reconstruction of Staphylococcus aureus strains in a paediatric hospital

Serena Manara (5961503)
Edoardo Pasolli (3155043)
Daniela Dolce (727996)
Novella Ravenni (5961506)
Silvia Campana (5961509)
Federica Armanini (4176511)
Francesco Asnicar (5198411)
Alessio Mengoni (619628)
Luisa Galli (304813)
Carlotta Montagnani (634645)
Elisabetta Venturini (5961512)
Omar Rota-Stabelli (847806)
Guido Grandi (120744)
Giovanni Taccetti (727999)
Nicola Segata (103809)

November 2018

Table S1. Characteristics of the single isolates, including collection details, genome assembly stat...

Additional file 5: of Whole-genome epidemiology, characterisation, and phylogenetic reconstruction of Staphylococcus aureus strains in a paediatric hospital

Serena Manara (5961503)
Edoardo Pasolli (3155043)
Daniela Dolce (727996)
Novella Ravenni (5961506)
Silvia Campana (5961509)
Federica Armanini (4176511)
Francesco Asnicar (5198411)
Alessio Mengoni (619628)
Luisa Galli (304813)
Carlotta Montagnani (634645)
Elisabetta Venturini (5961512)
Omar Rota-Stabelli (847806)
Guido Grandi (120744)
Giovanni Taccetti (727999)
Nicola Segata (103809)

November 2018

Table S4. Most relevant clones represented in the cohort and their abundance. (XLSX 9Â kb

Additional file 3: of Whole-genome epidemiology, characterisation, and phylogenetic reconstruction of Staphylococcus aureus strains in a paediatric hospital

Serena Manara (5961503)
Edoardo Pasolli (3155043)
Daniela Dolce (727996)
Novella Ravenni (5961506)
Silvia Campana (5961509)
Federica Armanini (4176511)
Francesco Asnicar (5198411)
Alessio Mengoni (619628)
Luisa Galli (304813)
Carlotta Montagnani (634645)
Elisabetta Venturini (5961512)
Omar Rota-Stabelli (847806)
Guido Grandi (120744)
Giovanni Taccetti (727999)
Nicola Segata (103809)

November 2018

Table S2. Presence/absence profile of virulence and antibiotic resistance genes in the cohort. (XLSX...

Additional file 2: Figure S1. of Complete genome of Staphylococcus aureus Tager 104 provides evidence of its relation to modern systemic hospital-acquired strains

Richard Davis (26945)
Andrew Brannen (3571868)
Mohammad Hossain (591858)
Scott Monsma (813166)
Paul Bock (3571865)
Matthias Nahrendorf (172537)
David Mead (103432)
Michael Lodes (813170)
Mark Liles (3571871)
Peter Panizzi (249587)

March 2016

Complete Phylogenetic Tree of S. aureus Reference Strains. Whole-genome phylogenetic analysis of all...

Additional file 1: of Genomic exploration of sequential clinical isolates reveals a distinctive molecular signature of persistent Staphylococcus aureus bacteraemia

Stefano Giulieri (5626835)
Sarah Baines (5626838)
Romain Guerillot (5626841)
Torsten Seemann (85973)
Anders Gonรงalves da Silva (5626844)
Mark Schultz (5626847)
Ruth Massey (5534384)
Natasha Holmes (4913263)
Timothy Stinear (7853)
Benjamin Howden (4913269)

August 2018

Table S1. Microbiological data and sequence metrics of S. aureus isolates included in the study. (XL...

Additional file 3: of Genomic exploration of sequential clinical isolates reveals a distinctive molecular signature of persistent Staphylococcus aureus bacteraemia

Stefano Giulieri (5626835)
Sarah Baines (5626838)
Romain Guerillot (5626841)
Torsten Seemann (85973)
Anders Gonรงalves da Silva (5626844)
Mark Schultz (5626847)
Ruth Massey (5534384)
Natasha Holmes (4913263)
Timothy Stinear (7853)
Benjamin Howden (4913269)

August 2018

Table S2. List of 182 variants identified in 32 isolates (after excluding unrelated strains). (XLSX ...

Additional file 4: of Genomic exploration of sequential clinical isolates reveals a distinctive molecular signature of persistent Staphylococcus aureus bacteraemia

Stefano Giulieri (5626835)
Sarah Baines (5626838)
Romain Guerillot (5626841)
Torsten Seemann (85973)
Anders Gonรงalves da Silva (5626844)
Mark Schultz (5626847)
Ruth Massey (5534384)
Natasha Holmes (4913263)
Timothy Stinear (7853)
Benjamin Howden (4913269)

August 2018

Table S3. List of 81 mutations with predicted modification of protein sequences with COG annotation....

Additional file 3: of USA300 Staphylococcus aureus persists on multiple body sites following an infection

Timothy Read (333405)
Robert Petit (6055523)
Zachary Yin (6055526)
Tuyaa Montgomery (6055529)
Moira McNulty (6055532)
Michael David (35198)

December 2018

Additional figures and tables. Table S1. agr frameshifts. Figure S1. Provenance of strains sequenced...

Additional file 1: of Complete genome sequencing of three human clinical isolates of Staphylococcus caprae reveals virulence factors similar to those of S. epidermidis and S. capitis

Shinya Watanabe (3092)
Yoshifumi Aiba (5948150)
Xin-Ee Tan (5948153)
Feng-Yu Li (5948156)
Tanit Boonsiri (5948159)
Kanate Thitiananpakorn (5948162)
Bintao Cui (5948165)
Yusuke Satoâo (5948171)
Kotaro Kiga (693099)
Teppei Sasahara (159779)
Longzhu Cui (5948168)

November 2018

Table S1. List of Staphylococcus strains used in phylogenetic analysis (XLSX 14 kb

Additional file 2: of Regional outbreak of community-associated methicillin-resistant Staphylococcus aureus ST834 in Japanese children

Yuki Uehara (6192830)
Takashi Sasaki (263542)
Tadashi Baba (230966)
Yujie Lu (2257369)
Eri Imajo (6192833)
Yuka Sato (2182424)
Shigeru Tanno (6192836)
Munehiro Furuichi (790083)
Miki Kawada (31404)
Keiichi Hiramatsu (230971)

January 2019

Table S2. Detailed results of whole genome sequencing a SNPs, single nucleotide polymorphisms. (XLSX...

Additional file 3: Figure S2. of Prophages and adaptation of Staphylococcus aureus ST398 to the human clinic

Seydina Diene (3721954)
Anna Corvaglia (3721951)
Patrice François (22568)
Nathalie van der Mee-Marquet (20483)

February 2017

Comparative genomics for the identified prophages from three groups: φ3, MR11-like and others. The g...

Additional file 4: of USA300 Staphylococcus aureus persists on multiple body sites following an infection

Timothy Read (333405)
Robert Petit (6055523)
Zachary Yin (6055526)
Tuyaa Montgomery (6055529)
Moira McNulty (6055532)
Michael David (35198)

December 2018

Antibiotic resistance phenotypes. Table of phenotypic antibiotic results for the initial infection i...

Supplementary Table 2: List of Staphylococcus aureus genomes used for the version 1(19 genomes) and version 2 (an additional 21 genomes) for constructing the SNP pattern file used in this study.

Sandeep Joseph (821068)

November 2015

Supplementary Table 2: List of Staphylococcus aureus genomes used for the version 1(19 g...

Additional file 3: Table S1. of Preliminary comparative genomics revealed pathogenic potential and international spread of Staphylococcus argenteus

Dao-Feng Zhang (4529971)
Xiao-Yang Zhi (405438)
Jing Zhang (23775)
George Paoli (4529974)
Yan Cui (9885)
Chunlei Shi (301020)
Xianming Shi (301021)

October 2017

Complete list of homologous gene families in S. aureus complex (SAC) genomes. Fifty-one SAC genomes ...

Additional file 1: of USA300 Staphylococcus aureus persists on multiple body sites following an infection

Timothy Read (333405)
Robert Petit (6055523)
Zachary Yin (6055526)
Tuyaa Montgomery (6055529)
Moira McNulty (6055532)
Michael David (35198)

December 2018

Patient metadata. Breakdown of all metadata fields collected and summary of genetic results. Include...

Additional file 4: of Whole-genome epidemiology, characterisation, and phylogenetic reconstruction of Staphylococcus aureus strains in a paediatric hospital

Abstract

Extracted data

Additional file 4: of Whole-genome epidemiology, characterisation, and phylogenetic reconstruction of Staphylococcus aureus strains in a paediatric hospital

Abstract

Extracted data

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