scholarly journals Development and Application of a gp60-Based Subtyping Tool for Cryptosporidium bovis

2021 ◽  
Vol 9 (10) ◽  
pp. 2067
Author(s):  
Weijian Wang ◽  
Muchun Wan ◽  
Fang Yang ◽  
Na Li ◽  
Lihua Xiao ◽  
...  
Keyword(s):  
Dairy Cattle ◽  
Genetic Recombination ◽  
Transmission Characteristics ◽  
Typical Structure ◽  
Sequence Patterns ◽  
Geographic Differences ◽  
Sequence Types ◽  
Sequence Characteristics ◽  
Multiple Episodes ◽  
Subtyping Tool

Cryptosporidium bovis is a common enteric pathogen in bovine animals. The research on transmission characteristics of the pathogen is hampered by the lack of subtyping tools. In this study, we retrieve the nucleotide sequence of the 60 kDa glycoprotein (GP60) from the whole genome sequences of C. bovis we obtained previously and analyze its sequence characteristics. Despite a typical structure of the GP60 protein, the GP60 of C. bovis had only 19.3–45.3% sequence identity to those of other Cryptosporidium species. On the basis of the gene sequence, a subtype typing tool was developed for C. bovis and used in the analysis of 486 C. bovis samples from dairy cattle, yaks, beef cattle, and water buffalos from China. Sixty-eight sequence types were identified from 260 subtyped samples, forming six subtype families, namely XXVIa to XXVIf. The mosaic sequence patterns among subtype families and the 121 potential recombination events identified among the sequences both suggest the occurrence of genetic recombination at the locus. No obvious host adaptation and geographic differences in the distribution of subtype families were observed. Most farms with more extensive sampling had more than one subtype family, and the dominant subtype families on a farm appeared to differ between pre- and post-weaned calves, indicating the likely occurrence of multiple episodes of C. bovis infections. There was an association between XXVId infection and occurrence of moderate diarrhea in dairy cattle. The subtyping tool developed and the data generated in the study might improve our knowledge of the genetic diversity and transmission of C. bovis.

scholarly journals Subtyping Cryptosporidium xiaoi, a Common Pathogen in Sheep and Goats

Pathogens ◽  
2021 ◽  
Vol 10 (7) ◽  
pp. 800
Author(s):  
Yingying Fan ◽  
Xitong Huang ◽  
Sheng Guo ◽  
Fang Yang ◽  
Xin Yang ◽  
...  
Keyword(s):  
Genetic Recombination ◽  
Furin Cleavage ◽  
Sheep And Goats ◽  
Gp60 Gene ◽  
Furin Cleavage Site ◽  
Glycosylation Sites ◽  
Sequence Patterns ◽  
Established Species ◽  
Sequence Types ◽  
Subtyping Tool

Cryptosporidiosis is a significant cause of diarrhea in sheep and goats. Among the over 40 established species of Cryptosporidium, Cryptosporidium xiaoi is one of the dominant species infecting ovine and caprine animals. The lack of subtyping tools makes it impossible to examine the transmission of this pathogen. In the present study, we identified and characterized the 60-kDa glycoprotein (gp60) gene by sequencing the genome of C. xiaoi. The GP60 protein of C. xiaoi had a signal peptide, a furin cleavage site of RSRR, a glycosylphosphatidylinositol anchor, and over 100 O-glycosylation sites. Based on the gp60 sequence, a subtyping tool was developed and used in characterizing C. xiaoi in 355 positive samples from sheep and goats in China. A high sequence heterogeneity was observed in the gp60 gene, with 94 sequence types in 12 subtype families, namely XXIIIa to XXIIIl. Co-infections with multiple subtypes were common in these animals, suggesting that genetic recombination might be responsible for the high diversity within C. xiaoi. This was supported by the mosaic sequence patterns among the subtype families. In addition, a potential host adaptation was identified within this species, reflected by the exclusive occurrence of XXIIIa, XXIIIc, XXIIIg, and XXIIIj in goats. This subtyping tool should be useful in studies of the genetic diversity and transmission dynamics of C. xiaoi.

scholarly journals Development of a Subtyping Tool for Zoonotic Pathogen Cryptosporidium Canis

2020 ◽  
Author(s):  
Wen Jiang ◽  
Dawn M. Roellig ◽  
Yaqiong Guo ◽  
Na Li ◽  
Yaoyu Feng ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Zoonotic Transmission ◽  
Similar Distribution ◽  
Transmission Characteristics ◽  
Nucleotide Level ◽  
Zoonotic Pathogen ◽  
Subtyping Tool

Cryptosporidium canis is an important cause of cryptosporidiosis in canines and humans. Studies of the transmission characteristics of C. canis are currently hampered by lack of suitable subtyping tools. In this study, we conducted a genomic survey of the pathogen and developed a subtyping tool targeting the partial 60-kDa glycoprotein (gp60) gene. Seventy-six isolates previously identified as C. canis were analyzed using the new subtyping tool. Amplicons of expected size were obtained from 49 isolates, and phylogenetic analysis identified 10 subtypes clustered in five distinct groups (XXa–XXe). The largest group XXa contained 43 isolates from four subtypes that differed slightly from each other at the nucleotide level, while groups XXb–XXe contain one to three isolates each. The similar distribution of subtypes in humans and canines suggests that zoonotic transmission might play an important role in the epidemiology of C. canis. In addition, a suspected zoonotic transmission of C. canis between dogs and humans in a household was confirmed using the subtyping tool. The subtyping tool and data generated in this study might improve our understanding of the transmission of this zoonotic pathogen.

scholarly journals Identification of the Plasmid-Mediated Colistin Resistance Gene mcr-1 in Escherichia coli Isolates From Migratory Birds in Guangdong, China

2021 ◽  
Vol 12 ◽  
Author(s):  
Yan Zhang ◽  
Xu Kuang ◽  
Juan Liu ◽  
Ruan-Yang Sun ◽  
Xing-Ping Li ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Antibiotic Resistance ◽  
Migratory Birds ◽  
Antibiotic Resistance Genes ◽  
Sequencing Analysis ◽  
Transmission Characteristics ◽  
Colistin Resistance ◽  
Anser Indicus ◽  
Sequence Types ◽  
Plasmid Backbone

We determined the prevalence and transmission characteristics of mcr-1-positive Escherichia coli (MCRPEC) isolates from migratory birds Anser indicus in Guangdong, China. We identified 22 MCRPEC from 303 A. indicus fecal samples (7.3%) in Guangzhou, Zhaoqing, and Futian. The mcr-1 gene coexisted with 24 other types of antibiotic resistance genes (ARG), and 11 ARGs were highly prevalent at levels >50%. The MCRPEC displayed a diversity of sequence types (ST), and 19 distinct STs were identified with ST10, ST1146, and ST1147 as the most prevalent. In addition, these MCRPEC from birds were closely related phylogenetically to those from other sources in China. Whole-genome sequencing analysis demonstrated that mcr-1 was located on IncX4 (n=9, 40.9%), IncI2 (n=5, 22.7%) and IncP (n=1, 4.5%) plasmids and the latter shared an identical plasmid backbone with other sources. These results highlight the significance of migratory birds in the transmission of antibiotic resistance and provide powerful evidence that migratory birds are potential transmitters of antibiotic resistance.

Detection of potentially human infectious assemblages of Giardia duodenalis in fecal samples from beef and dairy cattle in Scotland

Parasitology ◽  
2018 ◽  
Vol 146 (9) ◽  
pp. 1123-1130 ◽  
Author(s):  
Paul M. Bartley ◽  
Beeke K. Roehe ◽  
Sarah Thomson ◽  
Hannah J. Shaw ◽  
Frederieke Peto ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Beef Cattle ◽  
Dairy Cattle ◽  
Age Groups ◽  
Giardia Duodenalis ◽  
Host Age ◽  
Fecal Samples ◽  
Different Ages ◽  
Sequence Types ◽  
Assemblage B

AbstractThis study aimed to determine the prevalence and assemblages of Giardia duodenalis present in Scottish beef and dairy cattle at different ages, to try to ascertain if cattle could play a role in the spread of zoonotic assemblages of Giardia. A total of 388 fecal samples (128 beef and 253 dairy, seven of unknown breed) were collected from 19 farms in Scotland. Samples were sub-divided by host age, 1, 2, 3, 4, 5 and 6, 7–24 and ⩾25 weeks. DNA was extracted and tested by PCR to detect G. duodenalis DNA. Of the 388 samples, 126 tested positive, giving an overall prevalence of 32.5%, with positive samples being observed in all age groups tested. The prevalence in dairy cattle was 44.7% (113/235), which was significantly higher (P < 0.001) than the prevalence in beef cattle 10.1% (13/128). Sequence analysis demonstrated the presence of assemblage E (77.2%, sequence types E-S1–E-S5), assemblage B (18.2%) and assemblage A (sub-assemblages AI-AII) (4.6%). These data demonstrate that G. duodenalis is found routinely in both dairy and beef cattle throughout Scotland; the presence of assemblages A and B also indicates that cattle may play a role in the spread of potentially zoonotic assemblages of Giardia.

scholarly journals Genetic recombination of bovine viral diarrhea virus subgenotype -1a and -1c in persistently infected dairy cattle

2020 ◽  
Vol 25 (2) ◽  
pp. 120
Author(s):  
Sri Handayani Irianingsih ◽  
Bagoes Poermadjaja ◽  
Hastari Wuryastuti ◽  
Raden Wasito
Keyword(s):  
Phylogenetic Analysis ◽  
Dairy Cattle ◽  
Bovine Viral Diarrhea Virus ◽  
Genetic Recombination ◽  
Bovine Viral Diarrhea ◽  
Viral Pathogen ◽  
Persistently Infected ◽  
Diarrhea Virus ◽  
Viral Diarrhea ◽  
Viral Diarrhea Virus

The bovine viral diarrhea virus (BVDV) is a major viral pathogen in cattle worldwide. In Indonesia,  diversity in subgenotypes of BVDV-1 has been observed, with the highest proportion of subgenotype -1a, followed by -1c, -1b, and -1d. So far, phylogenetic analysis of BVDV-1 is based on nucleotide sequences of the 5′ UTR and partial NS5B regions. Accuracy in identifying the subgenotype and antigenic type is critical for vaccine development and effective vaccination. The aim of this study was to determine genetic recombination of BVDV through phylogenetic analysis of five different regions (5′ UTR, NPro, E2, NS3, and NS5B) of BVDV in persistently infected dairy cattle. Five isolates were sequenced using next-generation sequencing, and data were analyzed with the CLC Genomic Workbench 9.0 and MEGA-X programs. Phylogenetic analysis based on the 5′ UTR (275 nt), NPro (504 nt), E2 (1,122 nt), NS3 (2,049 nt), and NS5B (2,157 nt) regions indicated  that one BVDV isolate from Banyumas, Central Java, could be classified into different subgenotypes based on the E2 region (-1c), but the same subgenotype based on the other four regions (-1a), suggesting  the presence of genetic recombination of the BVDV subgenotypes -1a and -1c in persistently infected dairy cattle.

scholarly journals Molecular Epidemiology of Dairy Cattle-AssociatedEscherichia coliCarryingblaCTX-MGenes in Washington State

2018 ◽  
Vol 84 (6) ◽  
Author(s):  
Josephine A. Afema ◽  
Sara Ahmed ◽  
Thomas E. Besser ◽  
Lisa P. Jones ◽  
William M. Sischo ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Dairy Cattle ◽  
Molecular Epidemiology ◽  
Washington State ◽  
M Gene ◽  
Antimicrobial Drugs ◽  
Content Type ◽  
E Coli ◽  
Plasmid Replicon ◽  
Sequence Types

ABSTRACTAn increase in the prevalence of commensalEscherichia colicarryingblaCTX-Mgenes among dairy cattle was observed between 2008 and 2012 in Washington State. To study the molecular epidemiology of this change, we selected 126blaCTX-M-positive and 126blaCTX-M-negative isolates for determinations of the multilocus sequence types (MLSTs) and antibiotic resistance phenotypes fromE. coliobtained during a previous study. For 99 isolates, we also determined theblaCTX-Malleles using PCR and sequencing and identified the replicon types ofblaCTX-M-carrying plasmids. TheblaCTX-M-negativeE. coliisolates comprised 76 sequence types (STs) compared with 32 STs inblaCTX-M-positiveE. coliisolates. TheblaCTX-M-positiveE. coliisolates formed three MLST clonal complexes, accounting for 83% of these isolates; 52% ofblaCTX-M-negativeE. coliisolates clustered into 10 clonal complexes, and the remainder were singletons. Overall,blaCTX-M-negativeE. coliisolates had more diverse genotypes that were distinct to farms, whereasblaCTX-M-positiveE. coliisolates had a clonal population structure and were widely disseminated on farms in both regions included in the study. Plasmid replicon types included IncI1 which predominated, followed by IncFIB and IncFIA/FIB.blaCTX-M-15was the predominant CTX-M gene allele, followed byblaCTX-M-27andblaCTX-M-14. There was no significant association between plasmid replicon types and bacterial STs, and neither clonal complexes nor major plasmid groups were associated with two discrete dairy-farming regions of Washington State.IMPORTANCEInfections caused by extended-spectrum β-lactamase (ESBL)-producingEscherichia colioccur globally and present treatment challenges because of their resistance to multiple antimicrobial drugs. Cattle are potential reservoirs of ESBL-producingEnterobacteriaceae, and so understanding the causes of successful dissemination ofblaCTX-Mgenes in commensal bacteria will inform future approaches for the prevention of antibiotic-resistant pathogen emergence.

scholarly journals Subtyping Cryptosporidium ryanae: A Common Pathogen in Bovine Animals

2020 ◽  
Vol 8 (8) ◽  
pp. 1107 ◽  
Author(s):  
Xin Yang ◽  
Ni Huang ◽  
Wen Jiang ◽  
Xinrui Wang ◽  
Na Li ◽  
...  
Keyword(s):  
Dairy Cattle ◽  
Sequence Data ◽  
Southern China ◽  
Eastern China ◽  
Whole Genome Sequence ◽  
Furin Cleavage ◽  
Genetic Characteristics ◽  
Water Buffaloes ◽  
Furin Cleavage Site ◽  
Subtyping Tool

Cryptosporidium ryanae is one of the most common species for cryptosporidiosis in cattle. However, little is known of the genetic characteristics of C. ryanae due to the lack of subtyping tools. In the present study, the 60-kDa glycoprotein (gp60) gene of C. ryanae was identified in whole genome sequence data and analyzed for sequence characteristics using bioinformatics tools. The protein it encodes had some of the typical characteristics of GP60 proteins, with a signal peptide, a furin cleavage site, and a glycosylphosphatidylinositol anchor at the C terminus of the protein, and numerous O-glycosylation sites. The gene sequence was used in the development of a subtyping tool, which was used in characterizing C. ryanae from 110 specimens from dairy cattle, 2 from beef cattle, 6 from yaks, and 4 from water buffaloes in China. Altogether, 17 subtypes from 8 subtype families were recognized, namely XXIa to XXIh. Possible host adaption was identified within this species, reflected by the unique occurrence of XXIa, XXIc, and XXIh in dairy cattle, yaks, and water buffaloes, respectively. Some geographical differences were detected in the distribution of subtype families in dairy cattle; specimens from southern China showed higher genetic diversity than from northern China, and the XXIa subtype family was only seen in dairy cattle in southern and eastern China. The gp60-based subtyping tool should be useful in molecular epidemiological studies of the transmission of C. ryanae.

Detection of Babesia DNA in blood and spleen samples from Eurasian badgers (Meles meles) in Scotland

Parasitology ◽  
2017 ◽  
Vol 144 (9) ◽  
pp. 1203-1210 ◽  
Author(s):  
PAUL M. BARTLEY ◽  
CARI WILSON ◽  
ELISABETH A. INNES ◽  
FRANK KATZER
Keyword(s):  
Sequence Analysis ◽  
Genetic Recombination ◽  
Meles Meles ◽  
18S Rrna Gene ◽  
Babesia Microti ◽  
Rrna Gene ◽  
Initial Sequence ◽  
Babesia Annae ◽  
Distinct Sequence ◽  
Sequence Types

SUMMARYBabesia are intraerythrocytic parasites of importance worldwide within the fields of human and veterinary medicine, as some Babesia sp., including Babesia microti are potentially zoonotic and can cause fatal disease in both humans and animals. The aims of this study were to use a nested PCR (amplifying the 18S rRNA gene) to determine the presence and species of Babesia parasite DNA found in blood (n = 47) and spleen (n = 47) samples collected from Eurasian badgers (Meles meles) in Scotland. The results showed 28/47 (59·6%) blood and 14/47 (29·8%) spleen samples tested positive for the presence of Babesia DNA. Initial sequence analysis of the Babesia DNA identified three distinct sequence types (submitted to GenBank KX528553, KX528554 and KX528555), which demonstrated ⩾99% identity to Babesia sp. parasites previously identified in badgers in Spain (KT223484 and KT223485). Phylogenetic analysis showed that the three isolates are closely related to Babesia annae, B. microti and other Piroplasmida species found in wildlife. Further sequence analysis of the samples demonstrated that the badgers were routinely infected with more than one parasite isolate and there was also evidence of genetic recombination between the Babesia parasite isolates (submitted to GenBank KY250472 – KY250477)

Simulation Study of Partial Discharge UHF Wave Transmission Characteristic in GIS Typical Structure

2014 ◽  
Vol 672-674 ◽  
pp. 787-792
Author(s):  
Jing Gang Yang ◽  
Yong Yong Jia ◽  
Ke Zhao ◽  
Shan Gao
Keyword(s):  
Electromagnetic Wave ◽  
Electromagnetic Waves ◽  
Single Phase ◽  
Partial Discharge ◽  
Simulation Models ◽  
Propagation Characteristic ◽  
Transmission Characteristics ◽  
Typical Structure ◽  
The Waves ◽  
Difference Time

Defects inside the gas-insulated switchgear (GIS) will produce ultra-high frequency (UHF) electromagnetic waves. The waves will be affected by the shell of GIS when propagating inside the GIS cavity. In the 0-3GHz frequency range, propagation characteristic of electromagnetic which is excited by partial discharge in GIS is simulated based on the method of finite difference time domain (FDTD). This paper designs the GIS simulation models with and without insulator according to the size of a 220kV single phase GIS bus and sets a metal protrusion defect on the bus as the PD source. The transmission characteristics of model waves inside typical GIS structures, and the influence of the insulator to the propagation of electromagnetic wave was studied via setting the different directions of electromagnetic, comparing the time and frequency domain results of electromagnetic wave in different structures and measurement angles.

Electron Microscopy and image analysis of nucleo-protein complexes

1994 ◽  
Vol 52 ◽  
pp. 88-89
Author(s):  
E. H. Egelman ◽  
X. Yu
Keyword(s):  
Electron Microscopy ◽  
Image Analysis ◽  
Normal Cell ◽  
Genetic Recombination ◽  
Protein Complexes ◽  
Chromosomal Rearrangements ◽  
Reca Protein ◽  
E Coli ◽  
Helical Polymer ◽  
Specific Protease

The RecA protein of E. coli has been shown to mediate genetic recombination, regulate its own synthesis, control the expression of other genes, act as a specific protease, form a helical polymer and have an ATPase activity, among other observed properties. The unusual filament formed by the RecA protein on DNA has not previously been shown to exist outside of bacteria. Within this filament, the 36 Å pitch of B-form DNA is extended to about 95 Å, the pitch of the RecA helix. We have now establishedthat similar nucleo-protein complexes are formed by bacteriophage and yeast proteins, and availableevidence suggests that this structure is universal across all of biology, including humans. Thus, understanding the function of the RecA protein will reveal basic mechanisms, in existence inall organisms, that are at the foundation of general genetic recombination and repair.Recombination at this moment is assuming an importance far greater than just pure biology. The association between chromosomal rearrangements and neoplasms has become stronger and stronger, and these rearrangements are most likely products of the recombinatory apparatus of the normal cell. Further, damage to DNA appears to be a major cause of cancer.

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