Comparative genomics of quinolone‐resistant and susceptible Campylobacter jejuni of poultry origin from major poultry producing European countries (GENCAMP)

Pimlapas Leekitcharoenphon; Cristina Garcia‐Graells; Nadine Botteldoorn; Katelijne Dierick; Isabelle Kempf; Satu Olkkola; Mirko Rossi; Suvi Nykäsenoja; Burkhard Malorny; Kerstin Stingl; Antonio Battisti; Alessia Franco; Joël Mossong; Kees Veldman; Dik Mevius; Dariusz Wasyl; Kinga Wieczorek; Jacek Osek; Lurdes Clemente; Angela Lacatus; Isabela Nicorescu; Monserrat Agüero García; Cristina De Frutos Escobar; Manuel Duran Ferrer; María Ugarte‐Ruiz; Muna F Anjum; Christopher Teale; Joakim Ågren; Rene S. Hendriksen; Frank M. Aarestrup

doi:10.2903/sp.efsa.2018.en-1398

Comparative genomics of quinolone‐resistant and susceptible Campylobacter jejuni of poultry origin from major poultry producing European countries (GENCAMP)

Pimlapas Leekitcharoenphon, Cristina Garcia‐Graells, Nadine Botteldoorn, Katelijne Dierick, Isabelle Kempf, Satu Olkkola, Mirko Rossi, Suvi Nykäsenoja, Burkhard Malorny, Kerstin Stingl, Antonio Battisti, Alessia Franco, Joël Mossong, Kees Veldman, Dik Mevius, Dariusz Wasyl, Kinga Wieczorek, Jacek Osek, Lurdes Clemente, Angela LacatusIsabela Nicorescu, Monserrat Agüero García, Cristina De Frutos Escobar, Manuel Duran Ferrer, María Ugarte‐Ruiz, Muna F Anjum, Christopher Teale, Joakim Ågren, Rene S. Hendriksen, Frank M. Aarestrup

Research output: Contribution to journal › Article › Academic › peer-review

Abstract

A total of 502 Campylobacter jejuni isolates from poultry in 12 different European countries (10 of them the largest poultry production countries in Europe) were whole genome sequenced to examine the genomic diversity of fluoroquinolone resistant (FQ-R) and susceptible (FQ-S) C. jejuni across the poultry producing European countries and to determine whether the emergence of fluoroquinolone resistance among C. jejuni is related to the transmission through countries or to the selection through fluoroquinolone use in the individual countries. A high genomic diversity was observed. The isolates clustered in four main clusters. All trees revealed that the isolates were clustered according to the presence/absence of the gyrA mutations causing fluoroquinolone resistance and ST-types. The cgMLST trees of only FQ-R and FQ-S isolates showed that isolates from the same country of origin were distributed into multiple clusters similarly to the trees combining FQ-R and FQ-S isolates. The different phylogenetic methods, ranging from single nucleotide polymorphisms analysis to gene-by-gene approaches such as rMLST, cgMLST, wgMLST and core genome tree, provided concordant results, but it is not known which is the most accurate method for identifying the country of origin of the isolates. Allele frequency analysis of isolates under this study and a selection of previously published C. jejuni genomes in ENA showed association of geographical origin of poultry C. jejuni populations between Romania-Poland, Italy-Germany-England, Portugal-The Netherlands and USA-Luxemburg. Allele frequency and phylogenetic analysis indicated that the isolates from Finland were genetically different from C. jejuni populations from other European countries included in this study. Trade pattern and antimicrobial use in livestock were not significantly associated with allele frequency or populations of C. jejuni, but data available to investigate these associations were limited.

Original language	English
Journal	EFSA Supporting Publications
Volume	15
Issue number	5
DOIs	https://doi.org/10.2903/sp.efsa.2018.en-1398
Publication status	Published - 31 May 2018

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10.2903/sp.efsa.2018.en-1398

https://www.mendeley.com/catalogue/435908cf-1900-3fff-b327-17fb037a2655/

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Leekitcharoenphon, P., Garcia‐Graells, C., Botteldoorn, N., Dierick, K., Kempf, I., Olkkola, S., Rossi, M., Nykäsenoja, S., Malorny, B., Stingl, K., Battisti, A., Franco, A., Mossong, J., Veldman, K., Mevius, D., Wasyl, D., Wieczorek, K., Osek, J., Clemente, L., ... Aarestrup, F. M. (2018). Comparative genomics of quinolone‐resistant and susceptible Campylobacter jejuni of poultry origin from major poultry producing European countries (GENCAMP). EFSA Supporting Publications, 15(5). https://doi.org/10.2903/sp.efsa.2018.en-1398

@article{45ddb33820414df6ab9fb6bb4347383a,

title = "Comparative genomics of quinolone‐resistant and susceptible Campylobacter jejuni of poultry origin from major poultry producing European countries (GENCAMP)",

abstract = "A total of 502 Campylobacter jejuni isolates from poultry in 12 different European countries (10 of them the largest poultry production countries in Europe) were whole genome sequenced to examine the genomic diversity of fluoroquinolone resistant (FQ-R) and susceptible (FQ-S) C. jejuni across the poultry producing European countries and to determine whether the emergence of fluoroquinolone resistance among C. jejuni is related to the transmission through countries or to the selection through fluoroquinolone use in the individual countries. A high genomic diversity was observed. The isolates clustered in four main clusters. All trees revealed that the isolates were clustered according to the presence/absence of the gyrA mutations causing fluoroquinolone resistance and ST-types. The cgMLST trees of only FQ-R and FQ-S isolates showed that isolates from the same country of origin were distributed into multiple clusters similarly to the trees combining FQ-R and FQ-S isolates. The different phylogenetic methods, ranging from single nucleotide polymorphisms analysis to gene-by-gene approaches such as rMLST, cgMLST, wgMLST and core genome tree, provided concordant results, but it is not known which is the most accurate method for identifying the country of origin of the isolates. Allele frequency analysis of isolates under this study and a selection of previously published C. jejuni genomes in ENA showed association of geographical origin of poultry C. jejuni populations between Romania-Poland, Italy-Germany-England, Portugal-The Netherlands and USA-Luxemburg. Allele frequency and phylogenetic analysis indicated that the isolates from Finland were genetically different from C. jejuni populations from other European countries included in this study. Trade pattern and antimicrobial use in livestock were not significantly associated with allele frequency or populations of C. jejuni, but data available to investigate these associations were limited.",

author = "Pimlapas Leekitcharoenphon and Cristina Garcia‐Graells and Nadine Botteldoorn and Katelijne Dierick and Isabelle Kempf and Satu Olkkola and Mirko Rossi and Suvi Nyk{\"a}senoja and Burkhard Malorny and Kerstin Stingl and Antonio Battisti and Alessia Franco and Jo{\"e}l Mossong and Kees Veldman and Dik Mevius and Dariusz Wasyl and Kinga Wieczorek and Jacek Osek and Lurdes Clemente and Angela Lacatus and Isabela Nicorescu and Garc{\'i}a, {Monserrat Ag{\"u}ero} and Escobar, {Cristina De Frutos} and Ferrer, {Manuel Duran} and Mar{\'i}a Ugarte‐Ruiz and Anjum, {Muna F} and Christopher Teale and Joakim {\AA}gren and Hendriksen, {Rene S.} and Aarestrup, {Frank M.}",

year = "2018",

month = may,

day = "31",

doi = "10.2903/sp.efsa.2018.en-1398",

language = "English",

volume = "15",

journal = "EFSA Supporting Publications",

issn = "2397-8325",

publisher = "Wiley",

number = "5",

}

Leekitcharoenphon, P, Garcia‐Graells, C, Botteldoorn, N, Dierick, K, Kempf, I, Olkkola, S, Rossi, M, Nykäsenoja, S, Malorny, B, Stingl, K, Battisti, A, Franco, A, Mossong, J, Veldman, K, Mevius, D, Wasyl, D, Wieczorek, K, Osek, J, Clemente, L, Lacatus, A, Nicorescu, I, García, MA, Escobar, CDF, Ferrer, MD, Ugarte‐Ruiz, M, Anjum, MF, Teale, C, Ågren, J, Hendriksen, RS & Aarestrup, FM 2018, 'Comparative genomics of quinolone‐resistant and susceptible Campylobacter jejuni of poultry origin from major poultry producing European countries (GENCAMP)', EFSA Supporting Publications, vol. 15, no. 5. https://doi.org/10.2903/sp.efsa.2018.en-1398

Comparative genomics of quinolone‐resistant and susceptible Campylobacter jejuni of poultry origin from major poultry producing European countries (GENCAMP). / Leekitcharoenphon, Pimlapas; Garcia‐Graells, Cristina; Botteldoorn, Nadine et al.
In: EFSA Supporting Publications, Vol. 15, No. 5, 31.05.2018.

Research output: Contribution to journal › Article › Academic › peer-review

TY - JOUR

T1 - Comparative genomics of quinolone‐resistant and susceptible Campylobacter jejuni of poultry origin from major poultry producing European countries (GENCAMP)

AU - Leekitcharoenphon, Pimlapas

AU - Garcia‐Graells, Cristina

AU - Botteldoorn, Nadine

AU - Dierick, Katelijne

AU - Kempf, Isabelle

AU - Olkkola, Satu

AU - Rossi, Mirko

AU - Nykäsenoja, Suvi

AU - Malorny, Burkhard

AU - Stingl, Kerstin

AU - Battisti, Antonio

AU - Franco, Alessia

AU - Mossong, Joël

AU - Veldman, Kees

AU - Mevius, Dik

AU - Wasyl, Dariusz

AU - Wieczorek, Kinga

AU - Osek, Jacek

AU - Clemente, Lurdes

AU - Lacatus, Angela

AU - Nicorescu, Isabela

AU - García, Monserrat Agüero

AU - Escobar, Cristina De Frutos

AU - Ferrer, Manuel Duran

AU - Ugarte‐Ruiz, María

AU - Anjum, Muna F

AU - Teale, Christopher

AU - Ågren, Joakim

AU - Hendriksen, Rene S.

AU - Aarestrup, Frank M.

PY - 2018/5/31

Y1 - 2018/5/31

N2 - A total of 502 Campylobacter jejuni isolates from poultry in 12 different European countries (10 of them the largest poultry production countries in Europe) were whole genome sequenced to examine the genomic diversity of fluoroquinolone resistant (FQ-R) and susceptible (FQ-S) C. jejuni across the poultry producing European countries and to determine whether the emergence of fluoroquinolone resistance among C. jejuni is related to the transmission through countries or to the selection through fluoroquinolone use in the individual countries. A high genomic diversity was observed. The isolates clustered in four main clusters. All trees revealed that the isolates were clustered according to the presence/absence of the gyrA mutations causing fluoroquinolone resistance and ST-types. The cgMLST trees of only FQ-R and FQ-S isolates showed that isolates from the same country of origin were distributed into multiple clusters similarly to the trees combining FQ-R and FQ-S isolates. The different phylogenetic methods, ranging from single nucleotide polymorphisms analysis to gene-by-gene approaches such as rMLST, cgMLST, wgMLST and core genome tree, provided concordant results, but it is not known which is the most accurate method for identifying the country of origin of the isolates. Allele frequency analysis of isolates under this study and a selection of previously published C. jejuni genomes in ENA showed association of geographical origin of poultry C. jejuni populations between Romania-Poland, Italy-Germany-England, Portugal-The Netherlands and USA-Luxemburg. Allele frequency and phylogenetic analysis indicated that the isolates from Finland were genetically different from C. jejuni populations from other European countries included in this study. Trade pattern and antimicrobial use in livestock were not significantly associated with allele frequency or populations of C. jejuni, but data available to investigate these associations were limited.

AB - A total of 502 Campylobacter jejuni isolates from poultry in 12 different European countries (10 of them the largest poultry production countries in Europe) were whole genome sequenced to examine the genomic diversity of fluoroquinolone resistant (FQ-R) and susceptible (FQ-S) C. jejuni across the poultry producing European countries and to determine whether the emergence of fluoroquinolone resistance among C. jejuni is related to the transmission through countries or to the selection through fluoroquinolone use in the individual countries. A high genomic diversity was observed. The isolates clustered in four main clusters. All trees revealed that the isolates were clustered according to the presence/absence of the gyrA mutations causing fluoroquinolone resistance and ST-types. The cgMLST trees of only FQ-R and FQ-S isolates showed that isolates from the same country of origin were distributed into multiple clusters similarly to the trees combining FQ-R and FQ-S isolates. The different phylogenetic methods, ranging from single nucleotide polymorphisms analysis to gene-by-gene approaches such as rMLST, cgMLST, wgMLST and core genome tree, provided concordant results, but it is not known which is the most accurate method for identifying the country of origin of the isolates. Allele frequency analysis of isolates under this study and a selection of previously published C. jejuni genomes in ENA showed association of geographical origin of poultry C. jejuni populations between Romania-Poland, Italy-Germany-England, Portugal-The Netherlands and USA-Luxemburg. Allele frequency and phylogenetic analysis indicated that the isolates from Finland were genetically different from C. jejuni populations from other European countries included in this study. Trade pattern and antimicrobial use in livestock were not significantly associated with allele frequency or populations of C. jejuni, but data available to investigate these associations were limited.

U2 - 10.2903/sp.efsa.2018.en-1398

DO - 10.2903/sp.efsa.2018.en-1398

M3 - Article

SN - 2397-8325

VL - 15

JO - EFSA Supporting Publications

JF - EFSA Supporting Publications

IS - 5

ER -

Comparative genomics of quinolone‐resistant and susceptible Campylobacter jejuni of poultry origin from major poultry producing European countries (GENCAMP)

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