Identification of Campylobacter jejuni and Chlamydia psittaci from cockatiel (Nymphicus hollandicus) using metagenomics

Abstract Background In July 2015, the carcasses of 11 cockatiels were submitted for disease diagnosis to the Avian Disease Division of the Animal and Plant Quarantine Agency of Korea. The cockatiels, which appeared dehydrated and underweight, had exhibited severe diarrhea and 22 % mortality over 2 w...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Si-Hyeon Kim, Yong-Kuk Kwon, Choi-Kyu Park, Hye-Ryoung Kim
Formato:	article
Lenguaje:	EN
Publicado:	BMC 2021
Materias:	Pet birds Cockatiel Metagenomics Chlamydiosis Campylobacteriosis Recombination Biotechnology TP248.13-248.65 Genetics QH426-470
Acceso en línea:	https://doaj.org/article/9773f76bb2674713b5d0f002cb435b75
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:9773f76bb2674713b5d0f002cb435b75
record_format	dspace
spelling	oai:doaj.org-article:9773f76bb2674713b5d0f002cb435b752021-11-08T10:57:29ZIdentification of Campylobacter jejuni and Chlamydia psittaci from cockatiel (Nymphicus hollandicus) using metagenomics10.1186/s12864-021-08122-y1471-2164https://doaj.org/article/9773f76bb2674713b5d0f002cb435b752021-11-01T00:00:00Zhttps://doi.org/10.1186/s12864-021-08122-yhttps://doaj.org/toc/1471-2164Abstract Background In July 2015, the carcasses of 11 cockatiels were submitted for disease diagnosis to the Avian Disease Division of the Animal and Plant Quarantine Agency of Korea. The cockatiels, which appeared dehydrated and underweight, had exhibited severe diarrhea and 22 % mortality over 2 weeks. Traditional diagnosis did not reveal the causes of these symptoms. Methods We conducted metagenomics analysis on intestines and livers from the dead cockatiels using Illumina high-throughput sequencing. To obtain more accurate and longer contigs, which are required for further genetic characterization, we compared the results of three de novo assembly tools (metaSPAdes, MEGAHIT, and IDBA-UD). Results Sequence reads of Campylobacter jejuni (C. jejuni) and Chlamydia psittaci (C. psittaci) were present in most of the cockatiel samples. Either of these bacteria could cause the reported symptoms in psittaciformes. metaSPAdes (ver.3.14.1) identified the 1152 bp flaA gene of C. jejuni and the 1096 bp ompA gene of C. psittaci. Genetic analysis revealed that flaA of C. jejuni was recombinant between C. jejuni and Campylobacter coli, and that ompA of C. psittaci isolated from cockatiel was closely related to strains isolated from humans. Conclusions C. jejuni and C. psittaci were detected in cockatiels in the Republic of Korea using metagenomic analysis. This approach is useful for understanding pathogens of pet birds. Three de novo assemblers were compared to obtain accurate contigs from large quantities of reads, and sequences of C. jejuni and C. psittaci generated by metaSPAdes were analyzed.Si-Hyeon KimYong-Kuk KwonChoi-Kyu ParkHye-Ryoung KimBMCarticlePet birdsCockatielMetagenomicsChlamydiosisCampylobacteriosisRecombinationBiotechnologyTP248.13-248.65GeneticsQH426-470ENBMC Genomics, Vol 22, Iss 1, Pp 1-10 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Pet birds Cockatiel Metagenomics Chlamydiosis Campylobacteriosis Recombination Biotechnology TP248.13-248.65 Genetics QH426-470
spellingShingle	Pet birds Cockatiel Metagenomics Chlamydiosis Campylobacteriosis Recombination Biotechnology TP248.13-248.65 Genetics QH426-470 Si-Hyeon Kim Yong-Kuk Kwon Choi-Kyu Park Hye-Ryoung Kim Identification of Campylobacter jejuni and Chlamydia psittaci from cockatiel (Nymphicus hollandicus) using metagenomics
description	Abstract Background In July 2015, the carcasses of 11 cockatiels were submitted for disease diagnosis to the Avian Disease Division of the Animal and Plant Quarantine Agency of Korea. The cockatiels, which appeared dehydrated and underweight, had exhibited severe diarrhea and 22 % mortality over 2 weeks. Traditional diagnosis did not reveal the causes of these symptoms. Methods We conducted metagenomics analysis on intestines and livers from the dead cockatiels using Illumina high-throughput sequencing. To obtain more accurate and longer contigs, which are required for further genetic characterization, we compared the results of three de novo assembly tools (metaSPAdes, MEGAHIT, and IDBA-UD). Results Sequence reads of Campylobacter jejuni (C. jejuni) and Chlamydia psittaci (C. psittaci) were present in most of the cockatiel samples. Either of these bacteria could cause the reported symptoms in psittaciformes. metaSPAdes (ver.3.14.1) identified the 1152 bp flaA gene of C. jejuni and the 1096 bp ompA gene of C. psittaci. Genetic analysis revealed that flaA of C. jejuni was recombinant between C. jejuni and Campylobacter coli, and that ompA of C. psittaci isolated from cockatiel was closely related to strains isolated from humans. Conclusions C. jejuni and C. psittaci were detected in cockatiels in the Republic of Korea using metagenomic analysis. This approach is useful for understanding pathogens of pet birds. Three de novo assemblers were compared to obtain accurate contigs from large quantities of reads, and sequences of C. jejuni and C. psittaci generated by metaSPAdes were analyzed.
format	article
author	Si-Hyeon Kim Yong-Kuk Kwon Choi-Kyu Park Hye-Ryoung Kim
author_facet	Si-Hyeon Kim Yong-Kuk Kwon Choi-Kyu Park Hye-Ryoung Kim
author_sort	Si-Hyeon Kim
title	Identification of Campylobacter jejuni and Chlamydia psittaci from cockatiel (Nymphicus hollandicus) using metagenomics
title_short	Identification of Campylobacter jejuni and Chlamydia psittaci from cockatiel (Nymphicus hollandicus) using metagenomics
title_full	Identification of Campylobacter jejuni and Chlamydia psittaci from cockatiel (Nymphicus hollandicus) using metagenomics
title_fullStr	Identification of Campylobacter jejuni and Chlamydia psittaci from cockatiel (Nymphicus hollandicus) using metagenomics
title_full_unstemmed	Identification of Campylobacter jejuni and Chlamydia psittaci from cockatiel (Nymphicus hollandicus) using metagenomics
title_sort	identification of campylobacter jejuni and chlamydia psittaci from cockatiel (nymphicus hollandicus) using metagenomics
publisher	BMC
publishDate	2021
url	https://doaj.org/article/9773f76bb2674713b5d0f002cb435b75
work_keys_str_mv	AT sihyeonkim identificationofcampylobacterjejuniandchlamydiapsittacifromcockatielnymphicushollandicususingmetagenomics AT yongkukkwon identificationofcampylobacterjejuniandchlamydiapsittacifromcockatielnymphicushollandicususingmetagenomics AT choikyupark identificationofcampylobacterjejuniandchlamydiapsittacifromcockatielnymphicushollandicususingmetagenomics AT hyeryoungkim identificationofcampylobacterjejuniandchlamydiapsittacifromcockatielnymphicushollandicususingmetagenomics
_version_	1718442449813110784

Identification of Campylobacter jejuni and Chlamydia psittaci from cockatiel (Nymphicus hollandicus) using metagenomics

Ejemplares similares