scholarly journals Tracking brucellosis–a re-emerging disease

2021 ◽  
Vol 854 (1) ◽  
pp. 012080
Author(s):  
J Schaeffer ◽  
S Revilla-Fernández ◽  
E Hofer ◽  
V Djordjevic ◽  
B Lakicevic ◽  
...  
Keyword(s):  
Public Health ◽  
Dairy Products ◽  
Whole Genome ◽  
Prevention Of Infection ◽  
Effective Strategies ◽  
Sequencing Technologies ◽  
Source Of Infection ◽  
Risks Factors ◽  
Time Periods ◽  
Undercooked Meat

Abstract Brucellosis caused by members of the genus Brucella is of major concern for animal and public health and is recognized as a re-emerging zoonotic disease. Brucellosis causes flu-like symptoms like fever, sweats, weakness, pain in muscles, joint and back, with some symptoms persisting for longer time periods. Infections occur through consumption of unpasteurized dairy products or undercooked meat, inhalation, and contact with animals. Human-to-human transmission is rare. Surveillance of this disease in animals and humans and prevention of infection risks factors are the most effective strategies to prevent brucellosis. With the progress in sequencing technologies, whole genome sequencing (WGS) has become an effective tool in surveillance, tracking of pathogens and in outbreak investigation. WGS allows identification of the source of infection and to elucidation of transmission chains, which enables authorities to implement timely and appropriate interventions.

scholarly journals Introduction of Ebola virus into a remote border district of Sierra Leone, 2014: use of field epidemiology and RNA sequencing to describe chains of transmission

2019 ◽  
Vol 147 ◽  
Author(s):  
M. B. DeSilva ◽  
T. Styles ◽  
C. Basler ◽  
F. L. Moses ◽  
F. Husain ◽  
...  
Keyword(s):  
Public Health ◽  
West Africa ◽  
Sierra Leone ◽  
Genome Sequencing ◽  
Ebola Virus ◽  
Virus Disease ◽  
Whole Genome ◽  
Geographic Isolation ◽  
Source Of Infection ◽  
Field Response

AbstractIn early October 2014, 7 months after the 2014–2015 Ebola epidemic in West Africa began, a cluster of reported deaths in Koinadugu, a remote district of Sierra Leone, was the first evidence of Ebola virus disease (Ebola) in the district. Prior to this event, geographic isolation was thought to have prevented the introduction of Ebola to this area. We describe our initial investigation of this cluster of deaths and subsequent public health actions after Ebola was confirmed, and present challenges to our investigation and methods of overcoming them. We present a transmission tree and results of whole genome sequencing of selected isolates to identify the source of infection in Koinadugu and demonstrate transmission between its villages. Koinadugu's experience highlights the danger of assuming that remote location and geographic isolation can prevent the spread of Ebola, but also demonstrates how deployment of rapid field response teams can help limit spread once Ebola is detected.

scholarly journals Comparison of Molecular and In Silico Salmonella Serotyping for Salmonella Surveillance

2021 ◽  
Vol 9 (5) ◽  
pp. 955
Author(s):  
Linda Chui ◽  
Christina Ferrato ◽  
Vincent Li ◽  
Sara Christianson
Keyword(s):  
Public Health ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Dna Microarray ◽  
In Silico ◽  
Whole Genome ◽  
Sequencing Technology ◽  
Outbreak Management ◽  
Sequencing Technologies ◽  
Processing Cost

Salmonella surveillance and outbreak management is a key function of public health. Laboratories are shifting from antigenic serotype determination to molecular methods including microarray or whole genome sequencing technologies. The objective of this study was to compare the Check&Trace Salmonella™ DNA microarray (CTS), a commercially available assay with the Salmonella in silico typing resource (SISTR), which uses whole genome sequencing technology for serotyping clinical Salmonella strains in Alberta, Canada, collected over an 18-month period. A high proportion of isolates (96.3%) were successfully typed by both systems. SISTR is a powerful tool for laboratories which already have a WGS infrastructure in place, whereas smaller laboratories can benefit from a commercial microarray system and reduce the processing cost per isolate compared to traditional serotyping.

EPEGENTIC TOXICOLOGY: PERSPECTIVES OF THE DEVELOPMENT

2018 ◽  
pp. 2-7
Author(s):  
G. A. Sofronov ◽  
E. L. Patkin
Keyword(s):  
Public Health ◽  
Life Cycle ◽  
Human Health ◽  
Chronic Exposure ◽  
Environmental Pollutants ◽  
Epigenetic Mechanisms ◽  
Epigenetic Changes ◽  
Mechanism Of Formation ◽  
Health Disorders ◽  
Time Periods

One of the complex problems of modern experimental toxicology remains the molecular mechanism of formation of human health disorders separated at different time periods from acute or chronic exposure to toxic environmental pollutants (ecotoxicants). Identifying and understanding what epigenetic changes are induced by the environment, and how they can lead to unfavorable outcome, are vital for protecting public health. Therefore, we consider it important a modern understanding of epigenetic mechanisms involved in the life cycle of mammals and assess available data on the environmentally caused epigenetic toxicity and, accordingly fledging epigenenomic (epigenetic) regulatory toxicology.

scholarly journals Expanding U.S. Laboratory Capacity for Neisseria gonorrhoeae Antimicrobial Susceptibility Testing and Whole-Genome Sequencing through the CDC's Antibiotic Resistance Laboratory Network

2020 ◽  
Vol 58 (4) ◽  
Author(s):  
Ellen N. Kersh ◽  
Cau D. Pham ◽  
John R. Papp ◽  
Robert Myers ◽  
Richard Steece ◽  
...  
Keyword(s):  
Public Health ◽  
Antibiotic Resistance ◽  
Neisseria Gonorrhoeae ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Antimicrobial Susceptibility ◽  
Susceptibility Testing ◽  
Whole Genome ◽  
Content Type ◽  
Laboratory Capacity

ABSTRACT U.S. gonorrhea rates are rising, and antibiotic-resistant Neisseria gonorrhoeae (AR-Ng) is an urgent public health threat. Since implementation of nucleic acid amplification tests for N. gonorrhoeae identification, the capacity for culturing N. gonorrhoeae in the United States has declined, along with the ability to perform culture-based antimicrobial susceptibility testing (AST). Yet AST is critical for detecting and monitoring AR-Ng. In 2016, the CDC established the Antibiotic Resistance Laboratory Network (AR Lab Network) to shore up the national capacity for detecting several resistance threats including N. gonorrhoeae. AR-Ng testing, a subactivity of the CDC’s AR Lab Network, is performed in a tiered network of approximately 35 local laboratories, four regional laboratories (state public health laboratories in Maryland, Tennessee, Texas, and Washington), and the CDC’s national reference laboratory. Local laboratories receive specimens from approximately 60 clinics associated with the Gonococcal Isolate Surveillance Project (GISP), enhanced GISP (eGISP), and the program Strengthening the U.S. Response to Resistant Gonorrhea (SURRG). They isolate and ship up to 20,000 isolates to regional laboratories for culture-based agar dilution AST with seven antibiotics and for whole-genome sequencing of up to 5,000 isolates. The CDC further examines concerning isolates and monitors genetic AR markers. During 2017 and 2018, the network tested 8,214 and 8,628 N. gonorrhoeae isolates, respectively, and the CDC received 531 and 646 concerning isolates and 605 and 3,159 sequences, respectively. In summary, the AR Lab Network supported the laboratory capacity for N. gonorrhoeae AST and associated genetic marker detection, expanding preexisting notification and analysis systems for resistance detection. Continued, robust AST and genomic capacity can help inform national public health monitoring and intervention.

scholarly journals Comprehensive identification of transposable element insertions using multiple sequencing technologies

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Chong Chu ◽  
Rebeca Borges-Monroy ◽  
Vinayak V. Viswanadham ◽  
Soohyun Lee ◽  
Heng Li ◽  
...  
Keyword(s):  
Transposable Element ◽  
Structure And Function ◽  
Endogenous Retroviruses ◽  
Whole Genome Sequencing Data ◽  
Whole Genome ◽  
Sequencing Data ◽  
Short Read ◽  
Sequencing Technologies ◽  
Long Read ◽  
And Function

AbstractTransposable elements (TEs) help shape the structure and function of the human genome. When inserted into some locations, TEs may disrupt gene regulation and cause diseases. Here, we present xTea (x-Transposable element analyzer), a tool for identifying TE insertions in whole-genome sequencing data. Whereas existing methods are mostly designed for short-read data, xTea can be applied to both short-read and long-read data. Our analysis shows that xTea outperforms other short read-based methods for both germline and somatic TE insertion discovery. With long-read data, we created a catalogue of polymorphic insertions with full assembly and annotation of insertional sequences for various types of retroelements, including pseudogenes and endogenous retroviruses. Notably, we find that individual genomes have an average of nine groups of full-length L1s in centromeres, suggesting that centromeres and other highly repetitive regions such as telomeres are a significant yet unexplored source of active L1s. xTea is available at https://github.com/parklab/xTea.

scholarly journals Rapid whole-genome mutational profiling using next-generation sequencing technologies

2008 ◽  
Vol 18 (10) ◽  
pp. 1638-1642 ◽  
Author(s):  
D. R. Smith ◽  
A. R. Quinlan ◽  
H. E. Peckham ◽  
K. Makowsky ◽  
W. Tao ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Whole Genome ◽  
Next Generation ◽  
Sequencing Technologies ◽  
Mutational Profiling ◽  
Generation Sequencing

scholarly journals Prevalence assessment of ectoparasitic arthropods among commonly consumed wildlife in Nsukka, southeast Nigeria

2021 ◽  
Vol 45 (1) ◽  
Author(s):  
Kingsley Uchenna Ozioko ◽  
Chris Ikem Okoye ◽  
Patience Obiageli Ubachukwu ◽  
Raymond Awudu Agbu ◽  
Bede Izuchukwu Ezewudo ◽  
...  
Keyword(s):  
Public Health ◽  
Control Measures ◽  
Wild Game ◽  
Wildlife Reservoirs ◽  
Source Of Infection ◽  
Ixodes Holocyclus ◽  
Public Health Significance ◽  
Physical Examinations ◽  
Health Significance ◽  
Vector Borne

Abstract Background Wildlife reservoirs not only act as a source of infection for vectors but also serve as hosts for the vectors themselves, supporting their populations. Their public health significance in developing countries is of growing importance as a result of zoonotic and enzootic diseases associated with the pathogens they transmit. Therefore, a study was carried out to determine the prevalence of ectoparasites of wild game in Nsukka, southeast Nigeria. Physical examinations were carried out on 143 wildlife, and laboratory identification was employed on the ectoparasites. The collected ectoparasites were identified in the laboratory using literature and with the help of a taxonomist. Results Out of the 143 game examined, 114 was infected with at least one parasite representing about 98.6% of an infestation. Among the parasites identified, Amblyomma spp. showed the highest prevalence of 24.5% at 95% confidential intervals of CI (1.45–3.19)–24.5% (p ≤ 0.05). No difference was observed in the prevalence of the ectoparasites according to sex, except for Ixodes holocyclus. Similarly, no difference was observed in prevalence with reference to age except for Rhipicephalus spp. and Polyplax spinulosa which showed differences. Conclusions The present study provides basic data about the most prevalent ectoparasitic arthropod among game in Nsukka, southeast Nigeria, which requires an evaluation of its zoonotic control measures. This work can elicit the risk of possible transmission of some zoonotic and enzootic diseases via game. Improving awareness among local people and bushmeat dealers about the risk of contracting a vector-borne disease through wildlife is crucial.

scholarly journals MUM&Co: accurate detection of all SV types through whole-genome alignment

2020 ◽  
Vol 36 (10) ◽  
pp. 3242-3243 ◽  
Author(s):  
Samuel O’Donnell ◽  
Gilles Fischer
Keyword(s):  
De Novo ◽  
Supplementary Information ◽  
Genome Alignment ◽  
Whole Genome ◽  
Structural Variations ◽  
Sequencing Technologies ◽  
Third Generation Sequencing ◽  
Human Genomes ◽  
Whole Genome Alignment ◽  
Primary Output

Abstract Summary MUM&Co is a single bash script to detect structural variations (SVs) utilizing whole-genome alignment (WGA). Using MUMmer’s nucmer alignment, MUM&Co can detect insertions, deletions, tandem duplications, inversions and translocations greater than 50 bp. Its versatility depends upon the WGA and therefore benefits from contiguous de-novo assemblies generated by third generation sequencing technologies. Benchmarked against five WGA SV-calling tools, MUM&Co outperforms all tools on simulated SVs in yeast, plant and human genomes and performs similarly in two real human datasets. Additionally, MUM&Co is particularly unique in its ability to find inversions in both simulated and real datasets. Lastly, MUM&Co’s primary output is an intuitive tabulated file containing a list of SVs with only necessary genomic details. Availability and implementation https://github.com/SAMtoBAM/MUMandCo. Supplementary information Supplementary data are available at Bioinformatics online.

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