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

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Si-Hyeon Kim ◽  
Yong-Kuk Kwon ◽  
Choi-Kyu Park ◽  
Hye-Ryoung Kim
Keyword(s):  
Campylobacter Jejuni ◽  
High Throughput Sequencing ◽  
De Novo ◽  
Disease Diagnosis ◽  
Chlamydia Psittaci ◽  
Campylobacter Coli ◽  
Severe Diarrhea ◽  
Pet Birds ◽  
Nymphicus Hollandicus ◽  
The Republic

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.

scholarly journals Identification of Campylobacter Jejuni and Chlamydia Psittaci From cockatiel (Nymphicus Hollandicus) Using Metagenomics

2021 ◽  
Author(s):  
Si-Hyeon Kim ◽  
Yong-Kuk Kwon ◽  
Choi-Kyu Park ◽  
Hye-Ryoung Kim
Keyword(s):  
Campylobacter Jejuni ◽  
High Throughput Sequencing ◽  
De Novo ◽  
Disease Diagnosis ◽  
Chlamydia Psittaci ◽  
Campylobacter Coli ◽  
Severe Diarrhea ◽  
Pet Birds ◽  
Nymphicus Hollandicus ◽  
The Republic

Abstract BackgroundIn 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. MethodsWe 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).ResultsSequence 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. ConclusionC. 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.

scholarly journals Prevalence and Genotyping ofCryptosporidiumInfection in Pet Parrots in North China

2015 ◽  
Vol 2015 ◽  
pp. 1-6 ◽  
Author(s):  
Xiao-Xuan Zhang ◽  
Nian-Zhang Zhang ◽  
Guang-Hui Zhao ◽  
Quan Zhao ◽  
Xing-Quan Zhu
Keyword(s):  
Enzyme Linked Immunosorbent Assay ◽  
Sequencing Analysis ◽  
Fecal Samples ◽  
Severe Diarrhea ◽  
Pet Birds ◽  
Nymphicus Hollandicus ◽  
Flotation Technique ◽  
And Control ◽  
Sugar Flotation ◽  
Genotype V

Cryptosporidiosis is a worldwide zoonosis caused byCryptosporidiumspp., sometimes leading to severe diarrhea in humans and animals. In the present study, 311 parrots, belonging to four species, namely, Budgerigars (Melopsittacus undulatus), Lovebirds (Agapornissp.), Alexandrine parakeets (Psittacula eupatria), and Cockatiel (Nymphicus hollandicus), from Beijing and Weifang cities, were examined forCryptosporidiumspp. infection. Blood samples of each bird were examined using enzyme linked immunosorbent assay (ELISA) and fecal samples were examined by Sheather’s sugar flotation technique. Prevalence ofCryptosporidiuminfection were 3.22% (10/311) and 0.64% (2/311) by ELISA and Sheather’s sugar flotation technique, respectively. Seroprevalence ofCryptosporidiuminfection in different breeds varied from 0 to 15.39%. Sequencing analysis showed that both positive samples from fecal samples belonged toCryptosporidiumavian genotype V. This is the first report ofCryptosporidiumavian genotype V in Budgerigars. The results of the present study provided foundation-data for prevention and control of cryptosporidiosis in pet birds in China.

Prevalence of Campylobacter and Salmonella in Raw Chicken on Retail Sale in the Republic of Ireland

2011 ◽  
Vol 74 (11) ◽  
pp. 1912-1916 ◽  
Author(s):  
ROBERT H. MADDEN ◽  
LYNN MORAN ◽  
PAM SCATES ◽  
JANE MCBRIDE ◽  
CARMEL KELLY
Keyword(s):  
Campylobacter Jejuni ◽  
Campylobacter Coli ◽  
Retail Sale ◽  
Salmonella Infection ◽  
Republic Of Ireland ◽  
The United Kingdom ◽  
Human Salmonellosis ◽  
The Republic ◽  
On Farm ◽  
Campylobacter Spp

To assess the current risks to consumers from Campylobacter and Salmonella in raw chicken products sold in the Republic of Ireland, a retail survey was undertaken to define their prevalence. Samples (n = 510) were analyzed using protocols based on ISO 10272-1:2006 and ISO 6579:2002. Processor codes on pack labels showed that 67% of samples were produced in the Republic of Ireland and 25% in the United Kingdom. Salmonella was present in 5.1% of samples, but the eight serovars found caused less than 7% of human salmonellosis reported in the Republic of Ireland. The results suggest that on-farm controls to limit Salmonella infection of broilers have been successful and that in Ireland raw chicken is not a significant cause of salmonellosis in humans. The overall prevalence of Campylobacter spp. was 84.3%. Isolation by the ISO method found 52.7% of samples to be positive, but overgrowth by contaminants was frequently evident. Therefore, in addition to enrichment, an homogenized sample was plated directly onto modified charcoal cefoperazone deoxycholate agar, and this detected a further 31.6%. Speciation of isolates (n = 426) determined that 67% were Campylobacter jejuni and 32% were Campylobacter coli. These species are the most common cause of campylobacteriosis in man. The results indicate that there is a need for poultry producers to introduce interventions to minimize the exposure of consumers in the Republic of Ireland to Campylobacter spp., as has been successfully done for Salmonella.

Campylobacter coli bacteraemia: how common is it?

2020 ◽  
Vol 13 (12) ◽  
pp. e236634
Author(s):  
Sindhura Pisipati ◽  
Adnan Zafar ◽  
Yousaf Zafar
Keyword(s):  
Liver Cirrhosis ◽  
Campylobacter Jejuni ◽  
Unusual Case ◽  
Campylobacter Coli ◽  
Decompensated Liver Cirrhosis ◽  
The Past

Campylobacter species are known to cause enteritis. However, over the past 40–50 years, there have been reports of varying presentations, such as cellulitis, spondylodiscitis and bacteraemia. Of the Campylobacter species, Campylobacter jejuni is the most common culprit for causing bacteraemia, however, Campylobacter coli bacteraemia is becoming more prevalent. Here, we discuss an unusual case of C. coli bacteraemia in a patient with decompensated liver cirrhosis.

scholarly journals HP1 drives de novo 3D genome reorganization in early Drosophila embryos

Nature ◽  
2021 ◽  
Author(s):  
Fides Zenk ◽  
Yinxiu Zhan ◽  
Pavel Kos ◽  
Eva Löser ◽  
Nazerke Atinbayeva ◽  
...  
Keyword(s):  
Genome Organization ◽  
Molecular Mechanisms ◽  
High Throughput Sequencing ◽  
De Novo ◽  
Early Embryo ◽  
Heterochromatin Protein ◽  
Chromosome Conformation ◽  
3D Genome ◽  
Genome Reorganization

AbstractFundamental features of 3D genome organization are established de novo in the early embryo, including clustering of pericentromeric regions, the folding of chromosome arms and the segregation of chromosomes into active (A-) and inactive (B-) compartments. However, the molecular mechanisms that drive de novo organization remain unknown1,2. Here, by combining chromosome conformation capture (Hi-C), chromatin immunoprecipitation with high-throughput sequencing (ChIP–seq), 3D DNA fluorescence in situ hybridization (3D DNA FISH) and polymer simulations, we show that heterochromatin protein 1a (HP1a) is essential for de novo 3D genome organization during Drosophila early development. The binding of HP1a at pericentromeric heterochromatin is required to establish clustering of pericentromeric regions. Moreover, HP1a binding within chromosome arms is responsible for overall chromosome folding and has an important role in the formation of B-compartment regions. However, depletion of HP1a does not affect the A-compartment, which suggests that a different molecular mechanism segregates active chromosome regions. Our work identifies HP1a as an epigenetic regulator that is involved in establishing the global structure of the genome in the early embryo.

scholarly journals Whole genome-based characterisation of antimicrobial resistance and genetic diversity in Campylobacter jejuni and Campylobacter coli from ruminants

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Medelin Ocejo ◽  
Beatriz Oporto ◽  
José Luis Lavín ◽  
Ana Hurtado
Keyword(s):  
Genetic Diversity ◽  
Antimicrobial Resistance ◽  
Campylobacter Jejuni ◽  
Resistance Genes ◽  
Campylobacter Coli ◽  
Whole Genome ◽  
Northern Spain ◽  
Sequence Alignments ◽  
Phenotypic Data ◽  
Wide Range

AbstractCampylobacter, a leading cause of gastroenteritis in humans, asymptomatically colonises the intestinal tract of a wide range of animals.Although antimicrobial treatment is restricted to severe cases, the increase of antimicrobial resistance (AMR) is a concern. Considering the significant contribution of ruminants as reservoirs of resistant Campylobacter, Illumina whole-genome sequencing was used to characterise the mechanisms of AMR in Campylobacter jejuni and Campylobacter coli recovered from beef cattle, dairy cattle, and sheep in northern Spain. Genome analysis showed extensive genetic diversity that clearly separated both species. Resistance genotypes were identified by screening assembled sequences with BLASTn and ABRicate, and additional sequence alignments were performed to search for frameshift mutations and gene modifications. A high correlation was observed between phenotypic resistance to a given antimicrobial and the presence of the corresponding known resistance genes. Detailed sequence analysis allowed us to detect the recently described mosaic tet(O/M/O) gene in one C. coli, describe possible new alleles of blaOXA-61-like genes, and decipher the genetic context of aminoglycoside resistance genes, as well as the plasmid/chromosomal location of the different AMR genes and their implication for resistance spread. Updated resistance gene databases and detailed analysis of the matched open reading frames are needed to avoid errors when using WGS-based analysis pipelines for AMR detection in the absence of phenotypic data.

scholarly journals Antimicrobial Activity of Sorghum Phenolic Extract on Bovine Foodborne and Mastitis-Causing Pathogens

Antibiotics ◽  
2021 ◽  
Vol 10 (5) ◽  
pp. 594
Author(s):  
Sydney E. Schnur ◽  
Raghavendra G. Amachawadi ◽  
Giovanna Baca ◽  
Sarah Sexton-Bowser ◽  
Davina H. Rhodes ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Phenolic Compounds ◽  
Enterococcus Faecalis ◽  
Campylobacter Jejuni ◽  
Bacterial Pathogens ◽  
Klebsiella Oxytoca ◽  
Bovine Mastitis ◽  
Campylobacter Coli ◽  
Foodborne Illnesses ◽  
Phenolic Extract

Antimicrobial resistance in bacterial pathogens associated with bovine mastitis and human foodborne illnesses from contaminated food and water have an impact on animal and human health. Phenolic compounds have antimicrobial properties and some specialty sorghum grains are high in phenolic compounds, and the grain extract may have the potential as a natural antimicrobial alternative. The study’s objective was to determine antimicrobial effects of sorghum phenolic extract on bacterial pathogens that cause bovine mastitis and human foodborne illnesses. Bacterial pathogens tested included Escherichia coli, Salmonella Typhimurium, Campylobacter jejuni, Campylobacter coli, Pseudomonas aeruginosa, Klebsiella pneumoniae, Klebsiella oxytoca, Staphylococcus aureus, and Enterococcus faecalis. Antibacterial activities of sorghum phenolic extracts were determined by agar-well diffusion assay. Sorghum phenolic extract was added to the wells in concentrations of 0, 100, 200, 500, 1000, or 4000 µg/mL. The control wells did not receive phenolic extract. Plates were incubated for 18–24 h, and the diameter of each zone of inhibition was measured. The results indicated that sorghum phenolic extract had inhibitory effects on Staphylococcus aureus, Enterococcus faecalis, Campylobacter jejuni, and Campylobacter coli.

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