Additional file 2: of Whole genome sequencing analysis of multiple Salmonella serovars provides insights into phylogenetic relatedness, antimicrobial resistance, and virulence markers across humans, food animals and agriculture environmental sources

Suchawan Pornsukarom (3226743)
Arnoud van Vliet (5940479)
Siddhartha Thakur (137473)

Publication date

November 2018

DOI

10.6084/m9.figshare.7305770.v1

Abstract

Table S1. Salmonella isolates that were sequenced and constructed for this research. Table S2. AMR, plasmid, and virulence genes. (XLSX 253 kb

Extracted data

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Additional file 2: of Whole genome sequencing analysis of multiple Salmonella serovars provides insights into phylogenetic relatedness, antimicrobial resistance, and virulence markers across humans, food animals and agriculture environmental sources

Suchawan Pornsukarom (3226743)
Arnoud van Vliet (5940479)
Siddhartha Thakur (137473)

Open link

Publication date

November 2018

DOI

10.6084/m9.figshare.7305770.v1

Abstract

Table S1. Salmonella isolates that were sequenced and constructed for this research. Table S2. AMR, plasmid, and virulence genes. (XLSX 253 kb

Extracted data

Jing Xie (180526)
Fuli Wu (1608274)
Xuebin Xu (2230003)
Xiaoxia Yang (625366)
Rongtao Zhao (1610134)
Qiuxia Ma (3072051)
Peng Li (69518)
Ligui Wang (417691)
Rongzhang Hao (417687)
Leiji Jia (5480357)
Xinying Du (181777)
Shaofu Qiu (417685)
Hongbin Song (340782)

July 2018

Table S1. Reference strains for phs operon sequence analysis. Table S2. GenBank accession numbers fo...

MOESM3 of Genome divergence and increased virulence of outbreak associated Salmonella enterica subspecies enterica serovar Heidelberg

Linto Antony (4605940)
Melissa Behr (6116618)
Donald Sockett (6116621)
Dale Miskimins (6116624)
Nicole Aulik (6116627)
Jane Christopher-Hennings (4984700)
Eric Nelson (2959734)
Marc Allard (281187)
Joy Scaria (74080)

December 2018

Additional file 3: Table S3A. List of antimicrobial resistance genes identified in Salmonella ser. H...

Whole genome sequencing analysis of multiple Salmonella serovars provides insights into phylogenetic relatedness, antimicrobial resistance, and virulence markers across humans, food animals and agriculture environmental sources

Pornsukarom, Suchawan
van Vliet, Arnoud H M
Thakur, Siddhartha

September 2019

Background Salmonella enterica is a significant foodborne pathogen, which can be transmitted via sev...

Additional file 1: of Whole genome sequencing analysis of multiple Salmonella serovars provides insights into phylogenetic relatedness, antimicrobial resistance, and virulence markers across humans, food animals and agriculture environmental sources

Suchawan Pornsukarom (3226743)
Arnoud van Vliet (5940479)
Siddhartha Thakur (137473)

November 2018

Figure S1. Distribution of phenotypic antimicrobial resistance of Salmonella isolates based on FFPry...

Additional file 2: of Next generation genome sequencing reveals phylogenetic clades with different level of virulence among Salmonella Typhimurium clinical human isolates in Hong Kong

Chi Cheng (1688212)
Man Cheung (3456749)
Wenyan Nong (276765)
Patrick Law (3456752)
Jing Qin (41397)
Julia Ling (3456755)
Kai Kam (3456761)
William Cheung (151192)
Hoi Kwan (3456758)

September 2015

Maximum-parsimony phylogenetic tree of 92â S. Typhimurium genomes based on SNPs identified by mapp...

Additional file 2: of Antimicrobial resistance profiles and virulence genotyping of Salmonella enterica serovars recovered from broiler chickens and chicken carcasses in Egypt

Rasha Elkenany (6642806)
Mona Elsayed (6642809)
Amira Zakaria (6642812)
Shimaa El-sayed (6642815)
Mohamed Rizk (6237824)

April 2019

Table S1. Primers sequences, target genes, amplicon sizes and cycling conditions for virulence facto...

Additional file 1: of Next generation genome sequencing reveals phylogenetic clades with different level of virulence among Salmonella Typhimurium clinical human isolates in Hong Kong

Chi Cheng (1688212)
Man Cheung (3456749)
Wenyan Nong (276765)
Patrick Law (3456752)
Jing Qin (41397)
Julia Ling (3456755)
Kai Kam (3456761)
William Cheung (151192)
Hoi Kwan (3456758)

September 2015

Maximum-parsimony phylogenetic tree of 47â S. Typhimurium genomes with bootstrap values reported o...

MOESM2 of Genome divergence and increased virulence of outbreak associated Salmonella enterica subspecies enterica serovar Heidelberg

Linto Antony (4605940)
Melissa Behr (6116618)
Donald Sockett (6116621)
Dale Miskimins (6116624)
Nicole Aulik (6116627)
Jane Christopher-Hennings (4984700)
Eric Nelson (2959734)
Marc Allard (281187)
Joy Scaria (74080)

December 2018

Additional file 2: Table S2A. List of virulence factors identified in Salmonella ser. Heidelberg iso...

Additional file 5: of Genome analysis of Salmonella enterica subsp. diarizonae isolates from invasive human infections reveals enrichment of virulence-related functions in lineage ST1256

Joaquín Giner-Lamia (6286118)
Pablo Vinuesa (269485)
Laura Betancor (3582353)
Claudia Silva (751465)
Julieta Bisio (4710242)
Lorena Soleto (6286121)
José Chabalgoity (3563168)
José Puente (6286124)
Francisco García-del Portillo (478385)

January 2019

Table S4. S. enterica subsp. diarizonae draft genomes used in the phylogenomic analyses (XLSX 30 kb

Additional file 11: of Genome analysis of Salmonella enterica subsp. diarizonae isolates from invasive human infections reveals enrichment of virulence-related functions in lineage ST1256

Joaquín Giner-Lamia (6286118)
Pablo Vinuesa (269485)
Laura Betancor (3582353)
Claudia Silva (751465)
Julieta Bisio (4710242)
Lorena Soleto (6286121)
José Chabalgoity (3563168)
José Puente (6286124)
Francisco García-del Portillo (478385)

January 2019

Table S8. Virulence factors proteins encoded by S. enterica subsp. diarizonae genomes and representa...

Additional file 6: of Genome analysis of Salmonella enterica subsp. diarizonae isolates from invasive human infections reveals enrichment of virulence-related functions in lineage ST1256

Joaquín Giner-Lamia (6286118)
Pablo Vinuesa (269485)
Laura Betancor (3582353)
Claudia Silva (751465)
Julieta Bisio (4710242)
Lorena Soleto (6286121)
José Chabalgoity (3563168)
José Puente (6286124)
Francisco García-del Portillo (478385)

January 2019

Table S5. S. enterica subsp. diarizonae genomes of strains isolated from diverse sources that were f...

Additional file 3: of Next generation genome sequencing reveals phylogenetic clades with different level of virulence among Salmonella Typhimurium clinical human isolates in Hong Kong

Chi Cheng (1688212)
Man Cheung (3456749)
Wenyan Nong (276765)
Patrick Law (3456752)
Jing Qin (41397)
Julia Ling (3456755)
Kai Kam (3456761)
William Cheung (151192)
Hoi Kwan (3456758)

September 2015

Maximum-parsimony phylogenetic tree of 92â S. Typhimurium genomes with bootstrap values reported o...

Additional file 8: of Genome analysis of Salmonella enterica subsp. diarizonae isolates from invasive human infections reveals enrichment of virulence-related functions in lineage ST1256

Joaquín Giner-Lamia (6286118)
Pablo Vinuesa (269485)
Laura Betancor (3582353)
Claudia Silva (751465)
Julieta Bisio (4710242)
Lorena Soleto (6286121)
José Chabalgoity (3563168)
José Puente (6286124)
Francisco García-del Portillo (478385)

January 2019

Table S6. Genomic islands (GI) found in S. enterica subsp. diarizonae SBO13 (XLSX 43 kb

Additional file 14: of Genome analysis of Salmonella enterica subsp. diarizonae isolates from invasive human infections reveals enrichment of virulence-related functions in lineage ST1256

Joaquín Giner-Lamia (6286118)
Pablo Vinuesa (269485)
Laura Betancor (3582353)
Claudia Silva (751465)
Julieta Bisio (4710242)
Lorena Soleto (6286121)
José Chabalgoity (3563168)
José Puente (6286124)
Francisco García-del Portillo (478385)

January 2019

Table S11. Virulence determinants distribution along S. enterica subsp. diarizonae ST associated and...

Additional file 13: of Genome analysis of Salmonella enterica subsp. diarizonae isolates from invasive human infections reveals enrichment of virulence-related functions in lineage ST1256

Joaquín Giner-Lamia (6286118)
Pablo Vinuesa (269485)
Laura Betancor (3582353)
Claudia Silva (751465)
Julieta Bisio (4710242)
Lorena Soleto (6286121)
José Chabalgoity (3563168)
José Puente (6286124)
Francisco García-del Portillo (478385)

January 2019

Table S10. S. enterica subsp. diarizonae isolates statistically associated with human infections (% ...

Additional file 1: of Antibiotic resistance and molecular characterization of the hydrogen sulfide-negative phenotype among diverse Salmonella serovars in China

Jing Xie (180526)
Fuli Wu (1608274)
Xuebin Xu (2230003)
Xiaoxia Yang (625366)
Rongtao Zhao (1610134)
Qiuxia Ma (3072051)
Peng Li (69518)
Ligui Wang (417691)
Rongzhang Hao (417687)
Leiji Jia (5480357)
Xinying Du (181777)
Shaofu Qiu (417685)
Hongbin Song (340782)

July 2018

Table S1. Reference strains for phs operon sequence analysis. Table S2. GenBank accession numbers fo...

MOESM3 of Genome divergence and increased virulence of outbreak associated Salmonella enterica subspecies enterica serovar Heidelberg

Linto Antony (4605940)
Melissa Behr (6116618)
Donald Sockett (6116621)
Dale Miskimins (6116624)
Nicole Aulik (6116627)
Jane Christopher-Hennings (4984700)
Eric Nelson (2959734)
Marc Allard (281187)
Joy Scaria (74080)

December 2018

Additional file 3: Table S3A. List of antimicrobial resistance genes identified in Salmonella ser. H...

Pornsukarom, Suchawan
van Vliet, Arnoud H M
Thakur, Siddhartha

September 2019

Background Salmonella enterica is a significant foodborne pathogen, which can be transmitted via sev...

Suchawan Pornsukarom (3226743)
Arnoud van Vliet (5940479)
Siddhartha Thakur (137473)

November 2018

Figure S1. Distribution of phenotypic antimicrobial resistance of Salmonella isolates based on FFPry...

Additional file 2: of Next generation genome sequencing reveals phylogenetic clades with different level of virulence among Salmonella Typhimurium clinical human isolates in Hong Kong

Chi Cheng (1688212)
Man Cheung (3456749)
Wenyan Nong (276765)
Patrick Law (3456752)
Jing Qin (41397)
Julia Ling (3456755)
Kai Kam (3456761)
William Cheung (151192)
Hoi Kwan (3456758)

September 2015

Maximum-parsimony phylogenetic tree of 92â S. Typhimurium genomes based on SNPs identified by mapp...

Additional file 2: of Antimicrobial resistance profiles and virulence genotyping of Salmonella enterica serovars recovered from broiler chickens and chicken carcasses in Egypt

Rasha Elkenany (6642806)
Mona Elsayed (6642809)
Amira Zakaria (6642812)
Shimaa El-sayed (6642815)
Mohamed Rizk (6237824)

April 2019

Table S1. Primers sequences, target genes, amplicon sizes and cycling conditions for virulence facto...

Additional file 1: of Next generation genome sequencing reveals phylogenetic clades with different level of virulence among Salmonella Typhimurium clinical human isolates in Hong Kong

Chi Cheng (1688212)
Man Cheung (3456749)
Wenyan Nong (276765)
Patrick Law (3456752)
Jing Qin (41397)
Julia Ling (3456755)
Kai Kam (3456761)
William Cheung (151192)
Hoi Kwan (3456758)

September 2015

Maximum-parsimony phylogenetic tree of 47â S. Typhimurium genomes with bootstrap values reported o...

MOESM2 of Genome divergence and increased virulence of outbreak associated Salmonella enterica subspecies enterica serovar Heidelberg

Linto Antony (4605940)
Melissa Behr (6116618)
Donald Sockett (6116621)
Dale Miskimins (6116624)
Nicole Aulik (6116627)
Jane Christopher-Hennings (4984700)
Eric Nelson (2959734)
Marc Allard (281187)
Joy Scaria (74080)

December 2018

Additional file 2: Table S2A. List of virulence factors identified in Salmonella ser. Heidelberg iso...

Additional file 5: of Genome analysis of Salmonella enterica subsp. diarizonae isolates from invasive human infections reveals enrichment of virulence-related functions in lineage ST1256

Joaquín Giner-Lamia (6286118)
Pablo Vinuesa (269485)
Laura Betancor (3582353)
Claudia Silva (751465)
Julieta Bisio (4710242)
Lorena Soleto (6286121)
José Chabalgoity (3563168)
José Puente (6286124)
Francisco García-del Portillo (478385)

January 2019

Table S4. S. enterica subsp. diarizonae draft genomes used in the phylogenomic analyses (XLSX 30 kb

Additional file 11: of Genome analysis of Salmonella enterica subsp. diarizonae isolates from invasive human infections reveals enrichment of virulence-related functions in lineage ST1256

Joaquín Giner-Lamia (6286118)
Pablo Vinuesa (269485)
Laura Betancor (3582353)
Claudia Silva (751465)
Julieta Bisio (4710242)
Lorena Soleto (6286121)
José Chabalgoity (3563168)
José Puente (6286124)
Francisco García-del Portillo (478385)

January 2019

Table S8. Virulence factors proteins encoded by S. enterica subsp. diarizonae genomes and representa...

Additional file 6: of Genome analysis of Salmonella enterica subsp. diarizonae isolates from invasive human infections reveals enrichment of virulence-related functions in lineage ST1256

Joaquín Giner-Lamia (6286118)
Pablo Vinuesa (269485)
Laura Betancor (3582353)
Claudia Silva (751465)
Julieta Bisio (4710242)
Lorena Soleto (6286121)
José Chabalgoity (3563168)
José Puente (6286124)
Francisco García-del Portillo (478385)

January 2019

Table S5. S. enterica subsp. diarizonae genomes of strains isolated from diverse sources that were f...

Additional file 3: of Next generation genome sequencing reveals phylogenetic clades with different level of virulence among Salmonella Typhimurium clinical human isolates in Hong Kong

Chi Cheng (1688212)
Man Cheung (3456749)
Wenyan Nong (276765)
Patrick Law (3456752)
Jing Qin (41397)
Julia Ling (3456755)
Kai Kam (3456761)
William Cheung (151192)
Hoi Kwan (3456758)

September 2015

Maximum-parsimony phylogenetic tree of 92â S. Typhimurium genomes with bootstrap values reported o...

Additional file 8: of Genome analysis of Salmonella enterica subsp. diarizonae isolates from invasive human infections reveals enrichment of virulence-related functions in lineage ST1256

Joaquín Giner-Lamia (6286118)
Pablo Vinuesa (269485)
Laura Betancor (3582353)
Claudia Silva (751465)
Julieta Bisio (4710242)
Lorena Soleto (6286121)
José Chabalgoity (3563168)
José Puente (6286124)
Francisco García-del Portillo (478385)

January 2019

Table S6. Genomic islands (GI) found in S. enterica subsp. diarizonae SBO13 (XLSX 43 kb

Additional file 14: of Genome analysis of Salmonella enterica subsp. diarizonae isolates from invasive human infections reveals enrichment of virulence-related functions in lineage ST1256

Joaquín Giner-Lamia (6286118)
Pablo Vinuesa (269485)
Laura Betancor (3582353)
Claudia Silva (751465)
Julieta Bisio (4710242)
Lorena Soleto (6286121)
José Chabalgoity (3563168)
José Puente (6286124)
Francisco García-del Portillo (478385)

January 2019

Table S11. Virulence determinants distribution along S. enterica subsp. diarizonae ST associated and...

Additional file 13: of Genome analysis of Salmonella enterica subsp. diarizonae isolates from invasive human infections reveals enrichment of virulence-related functions in lineage ST1256

Joaquín Giner-Lamia (6286118)
Pablo Vinuesa (269485)
Laura Betancor (3582353)
Claudia Silva (751465)
Julieta Bisio (4710242)
Lorena Soleto (6286121)
José Chabalgoity (3563168)
José Puente (6286124)
Francisco García-del Portillo (478385)

January 2019

Table S10. S. enterica subsp. diarizonae isolates statistically associated with human infections (% ...

Additional file 1: of Antibiotic resistance and molecular characterization of the hydrogen sulfide-negative phenotype among diverse Salmonella serovars in China

Jing Xie (180526)
Fuli Wu (1608274)
Xuebin Xu (2230003)
Xiaoxia Yang (625366)
Rongtao Zhao (1610134)
Qiuxia Ma (3072051)
Peng Li (69518)
Ligui Wang (417691)
Rongzhang Hao (417687)
Leiji Jia (5480357)
Xinying Du (181777)
Shaofu Qiu (417685)
Hongbin Song (340782)

July 2018

Table S1. Reference strains for phs operon sequence analysis. Table S2. GenBank accession numbers fo...

MOESM3 of Genome divergence and increased virulence of outbreak associated Salmonella enterica subspecies enterica serovar Heidelberg

Linto Antony (4605940)
Melissa Behr (6116618)
Donald Sockett (6116621)
Dale Miskimins (6116624)
Nicole Aulik (6116627)
Jane Christopher-Hennings (4984700)
Eric Nelson (2959734)
Marc Allard (281187)
Joy Scaria (74080)

December 2018

Additional file 3: Table S3A. List of antimicrobial resistance genes identified in Salmonella ser. H...

Pornsukarom, Suchawan
van Vliet, Arnoud H M
Thakur, Siddhartha

September 2019

Background Salmonella enterica is a significant foodborne pathogen, which can be transmitted via sev...

Additional file 2: of Whole genome sequencing analysis of multiple Salmonella serovars provides insights into phylogenetic relatedness, antimicrobial resistance, and virulence markers across humans, food animals and agriculture environmental sources

Abstract

Extracted data

Additional file 2: of Whole genome sequencing analysis of multiple Salmonella serovars provides insights into phylogenetic relatedness, antimicrobial resistance, and virulence markers across humans, food animals and agriculture environmental sources

Abstract

Extracted data

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