Molecular Epidemiology of Campylobacter jejuni in the Genomic Era

Sara Maaria Kovanen

Forskningsoutput: AvhandlingDoktorsavhandlingSamling av artiklar

Sammanfattning

Campylobacter jejuni is a leading cause of human bacterial gastroenteritis worldwide. This zoonotic pathogen transmits to humans mainly indirectly, via consumption of contaminated food or drinking water or from various environmental sources. In Finland, ~4500 confirmed campylobacteriosis cases are registered annually and most of the infections occur in the summer. Poultry has been generally identified as a major reservoir and source of human campylobacteriosis. Molecular epidemiology of C. jejuni has been widely studied. Especially multilocus sequence typing (MLST), which assigns isolates to sequence types (STs) and clonal complexes (CCs), has provided valuable information about existing C. jejuni genotypes in different sources worldwide. While MLST has advantages to compare larger data worldwide, it has limitations in further distinguishing isolates within STs for epidemiological purposes. Whole-genome sequencing (WGS) enables the investigation of whole bacterial genomes instead of few selected genes. Aim of this thesis was to study C. jejuni isolates in domestic human infections, poultry and water using MLST and further whole-genome (wg) MLST. The most commonly found STs belonged to ST-45 CC, ST-21 CC, ST-283 CC and ST-677 CC. In this thesis, we further explored C. jejuni isolates within same STs, using highly discriminatory wgMLST and also considering the temporal relationship between the isolates from humans and chickens in summer 2012. We were able to recognize human isolates that were both genetically and epidemiologically related, thus most likely sharing the same infection source. We also identified the association between C. jejuni isolates from chicken slaughter batches and human patients. Although 79% of MLST types of human C. jejuni isolates overlapped with the isolates from chickens, only 24% of domestic human infections were related to chickens using both wgMLST and temporal association. Hence, the origin of more than 70% of the infections remained unidentified suggesting other potential transmission routes such as other domestic animals or environment-associated sources. In addition, we used WGS data to characterize genomic features among C. jejuni ST-677 CC isolates. We recognized several genetic characteristics, which are typical for this lineage that has been frequently detected among Finnish patients and associated also with bacteremia.
Originalspråkengelska
Tilldelande institution
  • Helsingfors universitet
Handledare
  • Hänninen, Marja-Liisa, Handledare
  • Kivistö, Rauni, Handledare
Tilldelningsdatum22 sep 2017
UtgivningsortHelsinki
Förlag
Tryckta ISBN978-951-51-3653-4
Elektroniska ISBN978-951-51-3654-1
StatusPublicerad - 22 sep 2017
MoE-publikationstypG5 Doktorsavhandling (artikel)

Vetenskapsgrenar

  • 413 Veterinärvetenskap

Citera det här

Kovanen, S. M. (2017). Molecular Epidemiology of Campylobacter jejuni in the Genomic Era. Helsinki: University of Helsinki.
Kovanen, Sara Maaria. / Molecular Epidemiology of Campylobacter jejuni in the Genomic Era. Helsinki : University of Helsinki, 2017. 147 s.
@phdthesis{26dd518a8135441c86cae97db5b44de8,
title = "Molecular Epidemiology of Campylobacter jejuni in the Genomic Era",
abstract = "Campylobacter jejuni is a leading cause of human bacterial gastroenteritis worldwide. This zoonotic pathogen transmits to humans mainly indirectly, via consumption of contaminated food or drinking water or from various environmental sources. In Finland, ~4500 confirmed campylobacteriosis cases are registered annually and most of the infections occur in the summer. Poultry has been generally identified as a major reservoir and source of human campylobacteriosis. Molecular epidemiology of C. jejuni has been widely studied. Especially multilocus sequence typing (MLST), which assigns isolates to sequence types (STs) and clonal complexes (CCs), has provided valuable information about existing C. jejuni genotypes in different sources worldwide. While MLST has advantages to compare larger data worldwide, it has limitations in further distinguishing isolates within STs for epidemiological purposes. Whole-genome sequencing (WGS) enables the investigation of whole bacterial genomes instead of few selected genes. Aim of this thesis was to study C. jejuni isolates in domestic human infections, poultry and water using MLST and further whole-genome (wg) MLST. The most commonly found STs belonged to ST-45 CC, ST-21 CC, ST-283 CC and ST-677 CC. In this thesis, we further explored C. jejuni isolates within same STs, using highly discriminatory wgMLST and also considering the temporal relationship between the isolates from humans and chickens in summer 2012. We were able to recognize human isolates that were both genetically and epidemiologically related, thus most likely sharing the same infection source. We also identified the association between C. jejuni isolates from chicken slaughter batches and human patients. Although 79{\%} of MLST types of human C. jejuni isolates overlapped with the isolates from chickens, only 24{\%} of domestic human infections were related to chickens using both wgMLST and temporal association. Hence, the origin of more than 70{\%} of the infections remained unidentified suggesting other potential transmission routes such as other domestic animals or environment-associated sources. In addition, we used WGS data to characterize genomic features among C. jejuni ST-677 CC isolates. We recognized several genetic characteristics, which are typical for this lineage that has been frequently detected among Finnish patients and associated also with bacteremia.",
keywords = "413 Veterinary science",
author = "Kovanen, {Sara Maaria}",
year = "2017",
month = "9",
day = "22",
language = "English",
isbn = "978-951-51-3653-4",
series = "Dissertationes Schola Doctoralis Scientiae Circumiectalis, Alimentariae, Biologicae",
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Kovanen, SM 2017, 'Molecular Epidemiology of Campylobacter jejuni in the Genomic Era', Helsingfors universitet, Helsinki.

Molecular Epidemiology of Campylobacter jejuni in the Genomic Era. / Kovanen, Sara Maaria.

Helsinki : University of Helsinki, 2017. 147 s.

Forskningsoutput: AvhandlingDoktorsavhandlingSamling av artiklar

TY - THES

T1 - Molecular Epidemiology of Campylobacter jejuni in the Genomic Era

AU - Kovanen, Sara Maaria

PY - 2017/9/22

Y1 - 2017/9/22

N2 - Campylobacter jejuni is a leading cause of human bacterial gastroenteritis worldwide. This zoonotic pathogen transmits to humans mainly indirectly, via consumption of contaminated food or drinking water or from various environmental sources. In Finland, ~4500 confirmed campylobacteriosis cases are registered annually and most of the infections occur in the summer. Poultry has been generally identified as a major reservoir and source of human campylobacteriosis. Molecular epidemiology of C. jejuni has been widely studied. Especially multilocus sequence typing (MLST), which assigns isolates to sequence types (STs) and clonal complexes (CCs), has provided valuable information about existing C. jejuni genotypes in different sources worldwide. While MLST has advantages to compare larger data worldwide, it has limitations in further distinguishing isolates within STs for epidemiological purposes. Whole-genome sequencing (WGS) enables the investigation of whole bacterial genomes instead of few selected genes. Aim of this thesis was to study C. jejuni isolates in domestic human infections, poultry and water using MLST and further whole-genome (wg) MLST. The most commonly found STs belonged to ST-45 CC, ST-21 CC, ST-283 CC and ST-677 CC. In this thesis, we further explored C. jejuni isolates within same STs, using highly discriminatory wgMLST and also considering the temporal relationship between the isolates from humans and chickens in summer 2012. We were able to recognize human isolates that were both genetically and epidemiologically related, thus most likely sharing the same infection source. We also identified the association between C. jejuni isolates from chicken slaughter batches and human patients. Although 79% of MLST types of human C. jejuni isolates overlapped with the isolates from chickens, only 24% of domestic human infections were related to chickens using both wgMLST and temporal association. Hence, the origin of more than 70% of the infections remained unidentified suggesting other potential transmission routes such as other domestic animals or environment-associated sources. In addition, we used WGS data to characterize genomic features among C. jejuni ST-677 CC isolates. We recognized several genetic characteristics, which are typical for this lineage that has been frequently detected among Finnish patients and associated also with bacteremia.

AB - Campylobacter jejuni is a leading cause of human bacterial gastroenteritis worldwide. This zoonotic pathogen transmits to humans mainly indirectly, via consumption of contaminated food or drinking water or from various environmental sources. In Finland, ~4500 confirmed campylobacteriosis cases are registered annually and most of the infections occur in the summer. Poultry has been generally identified as a major reservoir and source of human campylobacteriosis. Molecular epidemiology of C. jejuni has been widely studied. Especially multilocus sequence typing (MLST), which assigns isolates to sequence types (STs) and clonal complexes (CCs), has provided valuable information about existing C. jejuni genotypes in different sources worldwide. While MLST has advantages to compare larger data worldwide, it has limitations in further distinguishing isolates within STs for epidemiological purposes. Whole-genome sequencing (WGS) enables the investigation of whole bacterial genomes instead of few selected genes. Aim of this thesis was to study C. jejuni isolates in domestic human infections, poultry and water using MLST and further whole-genome (wg) MLST. The most commonly found STs belonged to ST-45 CC, ST-21 CC, ST-283 CC and ST-677 CC. In this thesis, we further explored C. jejuni isolates within same STs, using highly discriminatory wgMLST and also considering the temporal relationship between the isolates from humans and chickens in summer 2012. We were able to recognize human isolates that were both genetically and epidemiologically related, thus most likely sharing the same infection source. We also identified the association between C. jejuni isolates from chicken slaughter batches and human patients. Although 79% of MLST types of human C. jejuni isolates overlapped with the isolates from chickens, only 24% of domestic human infections were related to chickens using both wgMLST and temporal association. Hence, the origin of more than 70% of the infections remained unidentified suggesting other potential transmission routes such as other domestic animals or environment-associated sources. In addition, we used WGS data to characterize genomic features among C. jejuni ST-677 CC isolates. We recognized several genetic characteristics, which are typical for this lineage that has been frequently detected among Finnish patients and associated also with bacteremia.

KW - 413 Veterinary science

M3 - Doctoral Thesis

SN - 978-951-51-3653-4

T3 - Dissertationes Schola Doctoralis Scientiae Circumiectalis, Alimentariae, Biologicae

PB - University of Helsinki

CY - Helsinki

ER -

Kovanen SM. Molecular Epidemiology of Campylobacter jejuni in the Genomic Era. Helsinki: University of Helsinki, 2017. 147 s. (Dissertationes Schola Doctoralis Scientiae Circumiectalis, Alimentariae, Biologicae; 18).