scholarly journals Phylogenomic analysis for Campylobacter fetus ocurring in Argentina

2021 ◽  
pp. 1165-1179
Author(s):  
Pablo Daniel Farace ◽  
José Matías Irazoqui ◽  
Claudia Graciela Morsella ◽  
Juan Agustín García ◽  
María Alejandra Méndez ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Core Genome ◽  
Global Analysis ◽  
Local Maximum ◽  
Economic Losses ◽  
Phylogenomic Analysis ◽  
Local Strains ◽  
Campylobacter Fetus ◽  
New Variant ◽  
Pampas Region

Background and Aim: Campylobacter fetus is one of the most important pathogens that severely affects livestock industry worldwide. C. fetus mediated bovine genital campylobacteriosis infection in cattle has been associated with significant economic losses in livestock production in the Pampas region, the most productive area of Argentina. The present study aimed to establish the genomic relationships between C. fetus strains, isolated from the Pampas region, at local and global levels. The study also explored the utility of multi-locus sequence typing (MLST) as a typing technique for C. fetus. Materials and Methods: For pangenome and phylogenetic analysis, whole genome sequences for 34 C. fetus strains, isolated from cattle in Argentina were downloaded from GenBank. A local maximum likelihood (ML) tree was constructed and linked to a Microreact project. In silico analysis based on MLST was used to obtain information regarding sequence type (ST) for each strain. For global phylogenetic analysis, a core genome ML-tree was constructed using genomic dataset for 265 C. fetus strains, isolated from various sources obtained from 20 countries. Results: The local core genome phylogenetic tree analysis described the presence of two major clusters (A and B) and one minor cluster (C). The occurrence of 82% of the strains in these three clusters suggested a clonal population structure for C. fetus. The MLST analysis for the local strains revealed that 31 strains were ST4 type and one strain was ST5 type. In addition, a new variant was identified that was assigned a novel ST, ST70. In the present case, ST4 was homogenously distributed across all the regions and clusters. The global analysis showed that most of the local strains clustered in the phylogenetic groups that comprised exclusively of the strains isolated from Argentina. Interestingly, three strains showed a close genetic relationship with bovine strains obtained from Uruguay and Brazil. The ST5 strain grouped in a distant cluster, with strains obtained from different sources from various geographic locations worldwide. Two local strains clustered in a phylogenetic group comprising intercontinental Campylobacter fetus venerealis strains. Conclusion: The results of the study suggested active movement of animals, probably due to economic trade between different regions of the country as well as with neighboring countries. MLST results were partially concordant with phylogenetic analysis. Thus, this method did not qualify as a reliable subtyping method to assess C. fetus diversity in Argentina. The present study provided a basic platform to conduct future research on C. fetus, both at local and international levels.

scholarly journals Characterization of Winter Dysentery Bovine Coronavirus Isolated from Cattle in Israel

Viruses ◽  
2021 ◽  
Vol 13 (6) ◽  
pp. 1070
Author(s):  
Dan David ◽  
Nick Storm ◽  
Waksman Ilan ◽  
Asaf Sol
Keyword(s):  
Phylogenetic Analysis ◽  
Genetic Variants ◽  
Dairy Farms ◽  
Molecular Data ◽  
Economic Losses ◽  
Bovine Coronavirus ◽  
Local Strains ◽  
Esterase Gene ◽  
Winter Dysentery

Bovine coronavirus (BCoV) is the causative agent of winter dysentery (WD). In adult dairy cattle, WD is characterized by hemorrhagic diarrhea and a reduction in milk production. Therefore, WD leads to significant economic losses in dairy farms. In this study, we aimed to isolate and characterize local BCoV strains. BCoV positive samples, collected during 2017–2021, were used to amplify and sequence the S1 domain of S glycoprotein and the full hemagglutinin esterase gene. Based on our molecular analysis, local strains belong to different genetic variants circulating in dairy farms in Israel. Phylogenetic analysis revealed that all local strains clustered together and in proximity to other BCoV circulating in the area. Additionally, we found that local strains are genetically distant from the reference enteric strain Mebus. To our knowledge, this is the first report providing molecular data on BCoV circulating in Israel.

scholarly journals Detection of Rhodococcus fascians, the Causative Agent of Lily Fasciation in South Korea

Pathogens ◽  
2021 ◽  
Vol 10 (2) ◽  
pp. 241
Author(s):  
Joon Moh Park ◽  
Jachoon Koo ◽  
Se Won Kang ◽  
Sung Hee Jo ◽  
Jeong Mee Park
Keyword(s):  
Phylogenetic Analysis ◽  
South Korea ◽  
Nicotiana Benthamiana ◽  
Economic Value ◽  
Virulence Gene ◽  
Economic Losses ◽  
Herbaceous Perennials ◽  
Rhodococcus Fascians ◽  
Different Strains

Rhodococcus fascians is an important pathogen that infects various herbaceous perennials and reduces their economic value. In this study, we examined R. fascians isolates carrying a virulence gene from symptomatic lily plants grown in South Korea. Phylogenetic analysis using the nucleotide sequences of 16S rRNA, vicA, and fasD led to the classification of the isolates into four different strains of R. fascians. Inoculation of Nicotiana benthamiana with these isolates slowed root growth and resulted in symptoms of leafy gall. These findings elucidate the diversification of domestic pathogenic R. fascians and may lead to an accurate causal diagnosis to help reduce economic losses in the bulb market.

scholarly journals Diversity unearthed by the estimated molecular phylogeny and ecologically quantitative characteristics of uncultured Ehrlichia bacteria in Haemaphysalis ticks, Japan

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Hongru Su ◽  
Eri Onoda ◽  
Hitoshi Tai ◽  
Hiromi Fujita ◽  
Shigetoshi Sakabe ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
Core Genome ◽  
Phylogenetic Analyses ◽  
Taxonomic Status ◽  
Housekeeping Genes ◽  
Pcr Screening ◽  
Taxonomic Profiling ◽  
Quantitative Characteristics

AbstractEhrlichia species are obligatory intracellular bacteria transmitted by arthropods, and some of these species cause febrile diseases in humans and livestock. Genome sequencing has only been performed with cultured Ehrlichia species, and the taxonomic status of such ehrlichiae has been estimated by core genome-based phylogenetic analysis. However, many uncultured ehrlichiae exist in nature throughout the world, including Japan. This study aimed to conduct a molecular-based taxonomic and ecological characterization of uncultured Ehrlichia species or genotypes from ticks in Japan. We first surveyed 616 Haemaphysalis ticks by p28-PCR screening and analyzed five additional housekeeping genes (16S rRNA, groEL, gltA, ftsZ, and rpoB) from 11 p28-PCR-positive ticks. Phylogenetic analyses of the respective genes showed similar trees but with some differences. Furthermore, we found that V1 in the V1–V9 regions of Ehrlichia 16S rRNA exhibited the greatest variability. From an ecological viewpoint, the amounts of ehrlichiae in a single tick were found to equal approx. 6.3E+3 to 2.0E+6. Subsequently, core-partial-RGGFR-based phylogenetic analysis based on the concatenated sequences of the five housekeeping loci revealed six Ehrlichia genotypes, which included potentially new Ehrlichia species. Thus, our approach contributes to the taxonomic profiling and ecological quantitative analysis of uncultured or unidentified Ehrlichia species or genotypes worldwide.

scholarly journals Biological and Genomic Characterization of a Novel Jumbo Bacteriophage, vB_VhaM_pir03 with Broad Host Lytic Activity against Vibrio harveyi

Pathogens ◽  
2020 ◽  
Vol 9 (12) ◽  
pp. 1051
Author(s):  
Gerald N. Misol ◽  
Constantina Kokkari ◽  
Pantelis Katharios
Keyword(s):  
Phage Therapy ◽  
Vibrio Harveyi ◽  
Burst Size ◽  
Disease Outbreaks ◽  
Artemia Salina ◽  
Open Reading Frames ◽  
Lytic Activity ◽  
Economic Losses ◽  
Phylogenomic Analysis ◽  
Antibiotic Resistant

Vibrio harveyi is a Gram-negative marine bacterium that causes major disease outbreaks and economic losses in aquaculture. Phage therapy has been considered as a potential alternative to antibiotics however, candidate bacteriophages require comprehensive characterization for a safe and practical phage therapy. In this work, a lytic novel jumbo bacteriophage, vB_VhaM_pir03 belonging to the Myoviridae family was isolated and characterized against V. harveyi type strain DSM19623. It had broad host lytic activity against 31 antibiotic-resistant strains of V. harveyi, V. alginolyticus, V. campbellii and V. owensii. Adsorption time of vB_VhaM_pir03 was determined at 6 min while the latent-phase was at 40 min and burst-size at 75 pfu/mL. vB_VhaM_pir03 was able to lyse several host strains at multiplicity-of-infections (MOI) 0.1 to 10. The genome of vB_VhaM_pir03 consists of 286,284 base pairs with 334 predicted open reading frames (ORFs). No virulence, antibiotic resistance, integrase encoding genes and transducing potential were detected. Phylogenetic and phylogenomic analysis showed that vB_VhaM_pir03 is a novel bacteriophage displaying the highest similarity to another jumbo phage, vB_BONAISHI infecting Vibrio coralliilyticus. Experimental phage therapy trial using brine shrimp, Artemia salina infected with V. harveyi demonstrated that vB_VhaM_pir03 was able to significantly reduce mortality 24 h post infection when administered at MOI 0.1 which suggests that it can be an excellent candidate for phage therapy.

scholarly journals Molecular characterization of porcine epidemic diarrhoea virus (PEDV) in Poland reveals the presence of swine enteric coronavirus (SeCoV) sequence in S gene

PLoS ONE ◽  
2021 ◽  
Vol 16 (10) ◽  
pp. e0258318
Author(s):  
Marta Antas ◽  
Monika Olech ◽  
Anna Szczotka-Bochniarz
Keyword(s):  
Phylogenetic Analysis ◽  
Molecular Characterization ◽  
Rna Virus ◽  
Economic Losses ◽  
High Morbidity ◽  
Antigenic Analysis ◽  
S Gene ◽  
Porcine Epidemic Diarrhoea Virus ◽  
Diarrhoea Virus

Porcine epidemic diarrhoea (PED) is a highly contagious enteric viral disease of pigs with a high morbidity and mortality rate, which ultimately results in huge economic losses in the pig production sector. The etiological agent of this disease is the porcine epidemic diarrhoea virus (PEDV) which is an enveloped, positive single-stranded RNA virus. The aim of this study was to perform molecular characterization of PEDV to identify the strains circulating in Poland. In this study, 662 faecal samples from 2015 to 2021 were tested with reverse transcription quantitative real-time PCR (RT-qPCR) and the results showed that 3.8% of the tested samples revealed a positive result for PEDV. A phylogenetic analysis of the complete genome and complete S gene sequences showed that Polish PEDV strains belonged to the G1b (S-INDEL) subgroup and were closely related to the European PEDV strains isolated from 2014 to 2019. Furthermore, RDP4 analysis revealed that the Polish PEDV strains harboured a recombinant fragment of ~400 nt in the 5’ end of S gene with PEDV and swine enteric coronavirus (SeCoV) being the major and minor parents, respectively. Antigenic analysis showed that the aa sequences of neutralizing epitopes were conserved among the Polish PEDV strains. Only one strain, #0100/5P, had a unique substitution in the COE epitope. However, Polish PEDV strains showed several substitutions, especially in the COE antigen, as compared to the classical strain CV777. To the best of our knowledge, this is the first report concerning the molecular characterization of porcine epidemic diarrhoea virus strains, as well as the first phylogenetic analysis for PEDV in Poland.

scholarly journals Usefulness of High-Quality Core Genome Single-Nucleotide Variant Analysis for Subtyping the Highly Clonal and the Most Prevalent Salmonella enterica Serovar Heidelberg Clone in the Context of Outbreak Investigations

2015 ◽  
Vol 54 (2) ◽  
pp. 289-295 ◽  
Author(s):  
S. Bekal ◽  
C. Berry ◽  
A. R. Reimer ◽  
G. Van Domselaar ◽  
G. Beaudry ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Salmonella Enterica ◽  
Core Genome ◽  
Phage Type ◽  
Epidemiological Data ◽  
Single Nucleotide Variant ◽  
High Quality ◽  
Typing Method ◽  
Single Nucleotide ◽  
Content Type

Salmonella entericaserovar Heidelberg is the second most frequently occurring serovar in Quebec and the third-most prevalent in Canada. Given that conventional pulsed-field gel electrophoresis (PFGE) subtyping for commonSalmonellaserovars, such asS. Heidelberg, yields identical subtypes for the majority of isolates recovered, public health laboratories are desperate for new subtyping tools to resolve highly clonalS. Heidelberg strains involved in outbreak events. As PFGE was unable to discriminate isolates from three epidemiologically distinct outbreaks in Quebec, this study was conducted to evaluate whole-genome sequencing (WGS) and phylogenetic analysis as an alternative to conventional subtyping tools. Genomes of 46 isolates from 3 Quebec outbreaks (2012, 2013, and 2014) supported by strong epidemiological evidence were sequenced and analyzed using a high-quality core genome single-nucleotide variant (hqSNV) bioinformatics approach (SNV phylogenomics [SNVphyl] pipeline). Outbreaks were indistinguishable by conventional PFGE subtyping, exhibiting the same PFGE pattern (SHEXAI.0001/SHEBNI.0001). Phylogenetic analysis based on hqSNVs extracted from WGS separated the outbreak isolates into three distinct groups, 100% concordant with the epidemiological data. The minimum and maximum number of hqSNVs between isolates from the same outbreak was 0 and 4, respectively, while >59 hqSNVs were measured between 2 previously indistinguishable outbreaks having the same PFGE and phage type, thus corroborating their distinction as separate unrelated outbreaks. This study demonstrates that despite the previously reported high clonality of this serovar, the WGS-based hqSNV approach is a superior typing method, capable of resolving events that were previously indistinguishable using classic subtyping tools.

Molecular characterization and phylogenetic analysis of Taenia multiceps from China

2018 ◽  
Vol 63 (4) ◽  
pp. 721-727 ◽  
Author(s):  
L. Tan ◽  
A.B. Wang ◽  
S.Q. Zheng ◽  
X.L. Zhang ◽  
C.J. Huang ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Dna Sequences ◽  
Hunan Province ◽  
Biological Study ◽  
Economic Losses ◽  
Molecular Characteristics ◽  
12S Rrna ◽  
Intermediate Hosts ◽  
Taenia Multiceps ◽  
Coenurus Cerebralis

Abstract Taenia multiceps, one of the most widely distributed zoonotic tapeworm parasites, is able to parasitize the small intestine of canids. The metacestode of T.multiceps is fatal to ruminants and causes important economic losses in livestock. However, molecular characteristics of T.multiceps and coenurus in China are still unclear. In this study, 36 goat isolates of the coenurus stage and 18 dog isolates of the adult stage of T.multiceps were obtained from three geographical areas in China and the isolated parasite above were analyzed by amplifying the partial of cytochrome coxidase subunit 1(pcox1), 12S ribosomal RNA (12S rRNA) from mitochondrial DNA (mtDNA) regions and an internal transcribed spacer (ITS) of ribosomal DNA (rDNA). These DNA sequences obtained from T.multiceps and coenurus were employed to evaluate the nucleotide diversity and confirm the relationship between T.multiceps and coenurus. Sequences variation were 0–1.4%, 0–1.5%, 0–4.2% for pcox1, 12S rRNA and ITS, respectively, among T.multiceps and coenurus isolates obtained in this study. In Sichuan province, sequence variations for Coenurus cerebralis isolated from Yaan city were 0–1.4% for pcox1, 0–1.0% for 12S rRNA and 0–2.1% for ITS. In Hunan province, variations were 0–1.0%, 0–1.5% and 0–3.3% for corresponding genes for non-coenurus cerebralis isolated from Changsha city, while variations of T.multiceps isolates from Xiangxi autonomous prefecture were 0–1.0%, 0–1.1% and 0–3.4% for pcox1, 12S rRNA and ITS, respectively. Phylogenetic analysis based on pcox1 sequences indicated that all cerebral and noncerebral metacestodes belong to T.multiceps. These results provide reference values for future molecular epidemiological and biological study on T.multiceps in dogs and intermediate hosts.

scholarly journals Campylobacter fetus subspecies fetus spondylodiscitis

2010 ◽  
Vol 59 (12) ◽  
pp. 1505-1508 ◽  
Author(s):  
Antoine Chaillon ◽  
Gaelle Baty ◽  
Marie Agnès Lauvin ◽  
Jean Marc Besnier ◽  
Alain Goudeau ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
Rrna Gene ◽  
Gastrointestinal Infections ◽  
Systemic Complications ◽  
Campylobacter Fetus ◽  
Common Causes ◽  
Vertebral Biopsy ◽  
The 16S Rrna Gene ◽  
Predisposing Conditions

Campylobacter spp. are common causes of gastrointestinal infections. Campylobacter fetus is a much rarer pathogen in humans, and usually causes bacteraemia and systemic complications in patients with predisposing conditions. We report a case of spondylodiscitis caused by C. fetus subsp. fetus as revealed by vertebral biopsy culture. This identification was confirmed by sequencing the 16S rRNA gene and by phylogenetic analysis. Treatment consisted of 6 weeks antimicrobial therapy combined with a strict initial immobilization, followed by a re-education program. The patient's recovery was uneventful.

scholarly journals Phylogenetic analysis of a partial L1 gene from bovine papillomavirus type 1 isolated from naturally occurring papilloma cases in the northwestern region of Turkey

2017 ◽  
Vol 84 (1) ◽  
Author(s):  
M. Ozkan Timurkan ◽  
M. Eray Alcigir
Keyword(s):  
Phylogenetic Analysis ◽  
Histopathological Examination ◽  
Control Measures ◽  
Economic Losses ◽  
Bovine Papillomavirus ◽  
Sequencing Analysis ◽  
Molecular Characterisation ◽  
Northwestern Turkey ◽  
Northwestern Region

This study was aimed at the molecular characterisation of bovine papillomavirus type 1 (BPV-1) isolated from papilloma cases in the northwestern region of Turkey. BPV-1 is a widely occurring oncogenic virus in cattle and is associated with benign epithelial neoplasia which causes significant economic losses in dairy and beef cattle because of treatment costs. In this study, 29 suspected papilloma specimens were collected from cattle in northwestern Turkey. These samples underwent molecular characterisation via the polymerase chain reaction (PCR) and sequencing analysis as well as macroscopic and histopathological examination. The histopathological examinations confirmed papilloma as the main lesion type in the specimens. Of the 29 papilloma-like tissue samples that were collected, 11 (i.e. 37.93%) were detected as positive and determined as containing BPV-1 (11 of 11, 100%). Using a partial sequence for the L1 gene acquired from GenBank, phylogenetic analysis confirmed the presence of BPV-1 and revealed that the infection might have originated in cross bred domestic and imported cattle. This study provides potentially useful information on the origin and spread of this disease. Its results can potentially aid in the development of appropriate control measures and therapeutic or vaccination strategies against the BPV-1 strain of bovine papillomatosis.

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