scholarly journals CoxBase: an online platform for epidemiological surveillance, visualization, analysis and typing of Coxiella burnetii genomic sequence

2020 ◽  
Author(s):  
Akinyemi. M. Fasemore ◽  
Andrea Helbich ◽  
Mathias. C. Walter ◽  
Thomas Dandekar ◽  
Gilles Vergnaud ◽  
...  
Keyword(s):  
Coxiella Burnetii ◽  
In Silico ◽  
Genomic Sequence ◽  
Control Measure ◽  
Small Ruminants ◽  
Epidemiological Surveillance ◽  
Typing Method ◽  
Country Level ◽  
Central Platform ◽  
Typing Methods

ABSTRACTQ (query) fever is an infectious zoonotic disease, caused by the Gram-negative bacteria Coxiella burnetii, that sometimes is transmitted to humans from small ruminants like sheep, goat and cattle. Although the disease has been studied since decades, it still represents a threat due to sporadic outbreaks across farms in Europe. The reason for this has been linked to the interaction of several dynamic factors including reservoir type and vector diversity. One important control measure we have identified is a central platform for Coxiella typing data management. This is particularly important in the case of an outbreak where the nature of the pathogen and type would need to be rapidly identified and compared to existing isolates as well as further documented and made available for researcher to aid future investigations. The existing platforms are focused on MLVA (multiple locus VNTR analysis) genotyping. We have designed and implemented an online, open, web-based platform called CoxBase (https://coxbase.q-gaps.de), that is capable of in silico genotyping of completely or minimally assembled Coxiella sequences using five different typing methods, included with a database that holds genotyping information of more than 400 Coxiella isolates with their metadata such as host type, source and year of isolation together with further metadata information. Also, it includes a query and submission interface for interrogating existing isolates and depositing new isolates. Attractive visualization features include maps showing the geographical source of the isolates and plots that can be used to summarize isolates metadata on a country level. We tested our in silico typing method on 50 Coxiella genomes downloaded from the RefSeq database and we could type almost all the genomes except for cases where the sequences are poorly assembled. We identified new spacer sequences using our MST in silico typing methods, and could categorize adaA gene phenotypes for all 50 genomes as well as their plasmid types.

scholarly journals C. burnetii Shedding Study In Domestic Animals in Georgia

2019 ◽  
Vol 11 (1) ◽  
Author(s):  
Marine Nikolaishvili
Keyword(s):  
Coxiella Burnetii ◽  
Milk Sample ◽  
Q Fever ◽  
Small Ruminants ◽  
Domestic Animals ◽  
Epidemiological Surveillance ◽  
Bacterial Disease ◽  
Animal Blood ◽  
The Third ◽  
Seropositive Animal

ObjectiveQ fever is poorly understood in Georgia and its prevalence is largely underestimated in both humans and animals.One of the main goal of the project was shedding study in domestic animals – isolation of C. burnetii from suspected seropositive animal blood, milk samples.IntroductionQ fever is a zoonotic bacterial disease resulting from infection by Coxiella burnetii. Domestic ruminants (cattle, sheep, and goats) are considered the main reservoir for the pathogen, which can also infect humans. Q fever is poorly understood in Georgia and its prevalence is largely underestimated in both humans and animals.In Georgia Q fever laboratory diagnostic was started and implemented at the Laboratory of the Ministry of Georgia (LMA) within GG20 ,,Prevalence, Epidemiological Surveillance, and Laboratory Analysis of Coxiella burnetii in Georgia’’.MethodsLMA conducted Coxiella burnetii shedding evaluation in three specific farms from Kvemo Kartli (Tsalka, Dmanisi) and Mtskheta-Mtianeti (Dusheti). Seropositive cattle and small ruminants were sampled per week. Sampling lasted 7 weeks and totally 581 samples samples (blood, milk and swab) were tested. Testing were conducted in a BSL3 laboratory under BSL3 working conditions. ACCM medium was used (2XACCm-2 acidified Citrate Cysteine Medium PH-4.75G N NaOH). The samples were incubated at 37°C using CO2.ResultsAs a result of the study, one culture was bacteriologically isolated from seropositive cattle milk sample ( the sample was taken on the third week of the study in Beshtasheni farm, Tslka, Kvemo Kartli) and confirmed by Molecular biology (PCR).ConclusionsThe study confirmed Q fever existence in Georgia. Traditionally considered an obligate intracellular agent, the requirement to be grown in tissue culture cells, embryonated eggs, or animal hosts has made it difficult to isolate C. Burnetii strains. Within the study one culture was isolated from the seropositive animal milk sample that was collected in the third week of the study. shedding of Coxiella burnetii in milk by infected cows appeared to be the most frequent positive sample for the bacterium. 

scholarly journals Coxiella burnetii Seroprevalence in Small Ruminants in The Gambia

PLoS ONE ◽  
2014 ◽  
Vol 9 (1) ◽  
pp. e85424 ◽  
Author(s):  
Marieke Klaasen ◽  
Hendrik-Jan Roest ◽  
Wim van der Hoek ◽  
Bart Goossens ◽  
Arss Secka ◽  
...  
Keyword(s):  
Coxiella Burnetii ◽  
Small Ruminants ◽  
The Gambia

scholarly journals Active Targeted Surveillance to Identify Sites of Emergence of Hantavirus

2019 ◽  
Vol 70 (3) ◽  
pp. 464-473 ◽  
Author(s):  
Won-Keun Kim ◽  
Jin Sun No ◽  
Daesang Lee ◽  
Jaehun Jung ◽  
Hayne Park ◽  
...  
Keyword(s):  
Genomic Sequence ◽  
Disease Risk ◽  
Hemorrhagic Fever ◽  
Epidemiological Surveillance ◽  
Likelihood Method ◽  
Comparative Genomic ◽  
Novel Approach ◽  
Epidemiological Surveys ◽  
Outbreak Areas ◽  
Complete Sequences

Abstract Background Endemic outbreaks of hantaviruses pose a critical public health threat worldwide. Hantaan orthohantavirus (HTNV) causes hemorrhagic fever with renal syndrome (HFRS) in humans. Using comparative genomic analyses of partial and nearly complete sequences of HTNV from humans and rodents, we were able to localize, with limitations, the putative infection locations for HFRS patients. Partial sequences might not reflect precise phylogenetic positions over the whole-genome sequences; finer granularity of rodent sampling reflects more precisely the circulation of strains. Methods Five HFRS specimens were collected. Epidemiological surveys were conducted with the patients during hospitalization. We conducted active surveillance at suspected HFRS outbreak areas. We performed multiplex polymerase chain reaction–based next-generation sequencing to obtain the genomic sequence of HTNV from patients and rodents. The phylogeny of human- and rodent-derived HTNV was generated using the maximum likelihood method. For phylogeographic analyses, the tracing of HTNV genomes from HFRS patients was defined on the bases of epidemiological interviews, phylogenetic patterns of the viruses, and geographic locations of HTNV-positive rodents. Results The phylogeographic analyses demonstrated genetic clusters of HTNV strains from clinical specimens, with HTNV circulating in rodents at suspected sites of patient infections. Conclusions This study demonstrates a major shift in molecular epidemiological surveillance of HTNV. Active targeted surveillance was performed at sites of suspected infections, allowing the high-resolution phylogeographic analysis to reveal the site of emergence of HTNV. We posit that this novel approach will make it possible to identify infectious sources, perform disease risk assessment, and implement preparedness against vector-borne viruses.

scholarly journals Genetic Characterization of Brucella spp.: Whole Genome Sequencing-Based Approach for the Determination of Multiple Locus Variable Number Tandem Repeat Profiles

2021 ◽  
Vol 12 ◽  
Author(s):  
Ana Pelerito ◽  
Alexandra Nunes ◽  
Teresa Grilo ◽  
Joana Isidro ◽  
Catarina Silva ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
In Silico ◽  
Variable Number Tandem Repeat ◽  
Epidemiological Studies ◽  
Variable Number ◽  
Epidemiological Surveillance ◽  
Future Application ◽  
Whole Genome

Brucellosis is an important zoonosis that is emerging in some regions of the world, gaining increased relevance with the inclusion of the causing agent Brucella spp. in the class B bioterrorism group. Until now, multi-locus VNTR Analysis (MLVA) based on 16 loci has been considered as the gold standard for Brucella typing. However, this methodology is laborious, and, with the rampant release of Brucella genomes, the transition from the traditional MLVA to whole genome sequencing (WGS)-based typing is on course. Nevertheless, in order to avoid a disruptive transition with the loss of massive genetic data obtained throughout the last decade and considering that the transition timings will vary considerably among different countries, it is important to determine WGS-based MLVA alleles of the nowadays sequenced genomes. On this regard, we aimed to evaluate the performance of a Python script that had been previously developed for the rapid in silico extraction of the MLVA alleles, by comparing it to the PCR-based MLVA procedure over 83 strains from different Brucella species. The WGS-based MLVA approach detected 95.3% of all possible 1,328 hits (83 strains×16 loci) and showed an agreement rate with the PCR-based MLVA procedure of 96.4% for MLVA-16. According to our dataset, we suggest the use of a minimal depth of coverage of ~50x and a maximum number of ~200 contigs as guiding “boundaries” for the future application of the script. In conclusion, the evaluated script seems to be a very useful and robust tool for the in silico determination of MLVA profiles of Brucella strains, allowing retrospective and prospective molecular epidemiological studies, which are important for maintaining an active epidemiological surveillance of brucellosis.

scholarly journals Risk factors for Brucella spp. and Coxiella burnetii infection among small ruminants in Eastern India

2020 ◽  
Vol 10 (1) ◽  
pp. 1783091
Author(s):  
Eithne Leahy ◽  
Rajeswari Shome ◽  
Ram Pratim Deka ◽  
Swati Sahay ◽  
Delia Grace ◽  
...  
Keyword(s):  
Risk Factors ◽  
Coxiella Burnetii ◽  
Small Ruminants ◽  
Eastern India

Potential of Three-Way Randomly Amplified Polymorphic DNA Analysis as a Typing Method for TwelveSalmonella Serotypes

1999 ◽  
Vol 65 (11) ◽  
pp. 4830-4836 ◽  
Author(s):  
S. M. Soto ◽  
B. Guerra ◽  
M. A. González-Hevia ◽  
M. C. Mendoza
Keyword(s):  
Dna Analysis ◽  
Phage Typing ◽  
Clinical Samples ◽  
Randomly Amplified Polymorphic Dna ◽  
Typing Method ◽  
Phage Types ◽  
Typing Methods ◽  
In Vitro Stability ◽  
Reference Strains

ABSTRACT The potential of a three-way randomly amplified polymorphic DNA (RAPD) procedure (RAPD typing) for typing Salmonella enterica strains assigned to 12 serotypes was analyzed. The series of organisms used included 235 strains (326 isolates) collected mainly from clinical samples in the Principality of Asturias and 9 reference strains. RAPD typing was performed directly with broth cultures of bacteria by using three selected primers and optimized PCR conditions. The profiles obtained with the three primers were used to define RAPD types and to evaluate the procedure as a typing method at the species and serotype levels. The typeability was 100%; the reproducibility and in vitro stability could be considered good. The concordance of RAPD typing methods with serotyping methods was 100%, but some profiles obtained with two of the three primers were obtained with strains assigned to different serotypes. The discrimination index (DI) within the series of organisms was 0.94, and the DI within serotypes Typhimurium, Enteritidis, and Virchow were 0.72, 0.52, and 0.66, respectively. Within these serotypes the most common RAPD types were differentiated into phage types and vice versa; combining the types identified by the two procedures (RAPD typing and phage typing) resulted in further discrimination (DI, 0.96, 0.74, and 0.87, respectively). The efficiency, rapidity, and flexibility of the RAPD typing method support the conclusion that it can be used as a tool for identifying Salmonella organisms and as a typing method that is complementary to serotyping and phage typing methods.

Rapid Molecular Typing of Methicillin-ResistantStaphylococcus aureusby PCR-RFLP

2001 ◽  
Vol 22 (5) ◽  
pp. 294-298 ◽  
Author(s):  
Thomas A. Wichelhaus ◽  
Klaus-Peter Hunfeld ◽  
Boris Böddinghaus ◽  
Peter Kraiczy ◽  
Volker Schàfer ◽  
...  
Keyword(s):  
Fragment Length Polymorphism ◽  
Restriction Analysis ◽  
Protein A ◽  
Hypervariable Region ◽  
Epidemiological Surveillance ◽  
Typing Method ◽  
Rapid Pcr ◽  
Pcr Rflp ◽  
Polymerase Chain ◽  
Rflp Typing

AbstractObjective:To establish a new, rapid, and reliable genotypic fingerprinting technique for methicillin-resistantStaphylococcus aureus(MRSA) typing in routine epidemiological surveillance.Design:The method is based on polymerase chain reaction (PCR) restriction fragment-length polymorphism (RFLP) followingHaeII digestion of simultaneously amplified parts of the protein A gene, the coagulase gene, and the hypervariable region adjacent tomecA. A total of 46 MRSA initial isolates were analyzed, including 14 isolates from five countries; the six German epidemic strains; 16 isolates from the Frankfurt metropolitan area, which were known to be heterogeneous by pulsed-field gel electrophoresis (PFGE); and 10 isolates obtained during three epidemics, all of which displayed an identical genotype.Results:Restriction analysis by PCR-RFLP permitted discrimination of 10 of 14 international isolates, all six German epidemic strains, and 15 of 16 national isolates. It also confirmed the homogeneous character of the 10 outbreak isolates.Conclusions:This new and rapid PCR-RFLP typing method is an attractive tool in routine epidemiological surveillance. Its impressive characteristics are ease of performance and interpretation, while at the same time guaranteeing good discriminatory power, reproducibility, and typeability.

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