scholarly journals Development and validation of a direct real-time PCR assay for Mycobacterium bovis and implementation into the United States national surveillance program

Author(s):  
Philip E Dykema ◽  
Kevin D Stokes ◽  
Nadine R Beckwith ◽  
James W Mungin ◽  
Lizhe Xu ◽  
...  

Abattoir surveillance for bovine tuberculosis, which consists of identifying and submitting granulomas for histopathology and mycobacterial culture was the primary means for detecting new cases in the United States. Mycobacterial culture is expensive, labor intensive and identifies cases weeks after slaughter, hampering trace back efforts. To address this inefficiency, the United States Department of Agriculture replaced culture with real-time PCR for screening granulomas. The objectives of this paper were to describe the development and validation of this PCR as well as the performance of the assay during the first year of implementation. Using archived culture and histologically positive tissue, the sensitivity was 0.96 (95% CI: 0.89, 0.99) for the Mycobacterium tuberculosis complex primer-probe set and 0.89 (95% CI: 0.80, 0.95) for the Mycobacterium bovis specific primer-probe set. Specificity, estimated during by side by side testing was 0.998 (95% CI: 0.994, 1.000). After implementation, 6124 samples over 54 weeks were tested and all 36 histopathology positive samples were detected including 2 additional cases initially misclassified by histopathology. It appeared that specificity may have declined during post validation testing with 47/6086 signaling positive but not confirmed by either histopathology or culture. While PCR implementation has significantly improved the efficiency of the US slaughter surveillance program, careful attention must be paid to prevent and address cross contamination in the laboratory.

2016 ◽  
Author(s):  
Philip E Dykema ◽  
Kevin D Stokes ◽  
Nadine R Beckwith ◽  
James W Mungin ◽  
Lizhe Xu ◽  
...  

Abattoir surveillance for bovine tuberculosis, which consists of identifying and submitting granulomas for histopathology and mycobacterial culture was the primary means for detecting new cases in the United States. Mycobacterial culture is expensive, labor intensive and identifies cases weeks after slaughter, hampering trace back efforts. To address this inefficiency, the United States Department of Agriculture replaced culture with real-time PCR for screening granulomas. The objectives of this paper were to describe the development and validation of this PCR as well as the performance of the assay during the first year of implementation. Using archived culture and histologically positive tissue, the sensitivity was 0.96 (95% CI: 0.89, 0.99) for the Mycobacterium tuberculosis complex primer-probe set and 0.89 (95% CI: 0.80, 0.95) for the Mycobacterium bovis specific primer-probe set. Specificity, estimated during by side by side testing was 0.998 (95% CI: 0.994, 1.000). After implementation, 6124 samples over 54 weeks were tested and all 36 histopathology positive samples were detected including 2 additional cases initially misclassified by histopathology. It appeared that specificity may have declined during post validation testing with 47/6086 signaling positive but not confirmed by either histopathology or culture. While PCR implementation has significantly improved the efficiency of the US slaughter surveillance program, careful attention must be paid to prevent and address cross contamination in the laboratory.


2000 ◽  
Vol 63 (6) ◽  
pp. 807-809 ◽  
Author(s):  
DAVID J. WALLACE ◽  
THOMAS VAN GILDER ◽  
SUE SHALLOW ◽  
TERRY FIORENTINO ◽  
SUZANNE D. SEGLER ◽  
...  

In 1997, the Foodborne Diseases Active Surveillance Program (FoodNet) conducted active surveillance for culture-confirmed cases of Campylobacter, Escherichia coli O157, Listeria, Salmonella, Shigella, Vibrio, Yersinia, Cyclospora, and Cryptosporidium in five Emerging Infections Program sites. FoodNet is a collaborative effort of the Centers for Disease Control and Prevention's National Center for Infectious Diseases, the United States Department of Agriculture's Food Safety and Inspection Service, the Food and Drug Administration's Center for Food Safety and Applied Nutrition, and state health departments in California, Connecticut, Georgia, Minnesota, and Oregon. The population under active surveillance for food-borne infections was approximately 16.1 million persons or roughly 6% of the United States Population. Through weekly or monthly contact with all clinical laboratories in these sites, 8,576 total isolations were recorded: 2,205 cases of salmonellosis, 1,273 cases of shigellosis, 468 cases of cryptosporidiosis, 340 of E. coli O157:H7 infections, 139 of yersiniosis, 77 of listeriosis, 51 of Vibrio infections, and 49 of cyclosporiasis. Results from 1997 demonstrate that while there are regional and seasonal differences in reported incidence rates of certain bacterial and parasitic diseases, and that some pathogens showed a change in incidence from 1996, the overall incidence of illness caused by pathogens under surveillance was stable. More data over more years are needed to assess if observed variations in incidence reflect yearly fluctuations or true changes in the burden of foodborne illness.


2011 ◽  
Vol 26 (S1) ◽  
pp. s93-s93
Author(s):  
K. Andress

IntroductionHistory is replete with interoperability and resource reporting deficits during disaster that impact medical response and planning. Situational awareness for disaster and emergency medical response includes communicating health hazards as well as infrastructure and resource status, capability and GIS location. The need for actionable, real-time data is crucial to response. Awareness facilitates medical resource placement, response and recovery. A number of internet, web-based disaster resource and situational status reporting applications exist but may be limited or restricted by functional, jurisdictional, proprietary and/or financial requirements. Restrictions prohibit interoperability and inhibit information sharing that could affect health care delivery. Today multiple United States jurisdictions are engaged in infrastructure and resource situation status reporting via “virtual” states and regional projects considered components of “Virtual USA”.MethodsThis report introduces the United States' Department of Homeland Security's “Virtual USA” initiative and demonstrates a health application and interoperability via “Virtual Louisiana's” oil spill related exposure reporting during the 2010, British Petroleum Gulf Horizon catastrophe. Five weekly Louisiana Department of Health and Hospital summary reports from the Louisiana Poison Center; Hospital Surveillance Systems; Public Health Hotline; and Physician Clinic Offices were posted on the Louisiana Office of Homeland Security and Emergency Preparedness's “Virtual Louisiana”.Results227 total spill-related, exposure cases from five reporting weeks were provided by five Louisiana source agencies and reported in Virtual Louisiana. Cases were reported weekly and classified as “workers” or “population”; associated with the parish exposure locations (8), offshore (1), or unknown (1); and shared with four other virtual states.ConclusionsReal-time health and medical situation status, resource awareness, and incident impact could be facilitated through constructs demonstrated by “Virtual USA”.


2018 ◽  
Vol 10 (10) ◽  
pp. 1540 ◽  
Author(s):  
Lingling Liu ◽  
Xiaoyang Zhang ◽  
Yunyue Yu ◽  
Feng Gao ◽  
Zhengwei Yang

Real-time monitoring of crop phenology is critical for assisting farmers managing crop growth and yield estimation. In this study, we presented an approach to monitor in real time crop phenology using timely available daily Visible Infrared Imaging Radiometer Suite (VIIRS) observations and historical Moderate Resolution Imaging Spectroradiometer (MODIS) datasets in the Midwestern United States. MODIS data at a spatial resolution of 500 m from 2003 to 2012 were used to generate the climatology of vegetation phenology. By integrating climatological phenology and timely available VIIRS observations in 2014 and 2015, a set of temporal trajectories of crop growth development at a given time for each pixel were then simulated using a logistic model. The simulated temporal trajectories were used to identify spring green leaf development and predict the occurrences of greenup onset, mid-greenup phase, and maximum greenness onset using curvature change rate. Finally, the accuracy of real-time monitoring from VIIRS observations was evaluated by comparing with summary crop progress (CP) reports of ground observations from the National Agricultural Statistics Service (NASS) of the United States Department of Agriculture (USDA). The results suggest that real-time monitoring of crop phenology from VIIRS observations is a robust tool in tracing the crop progress across regional areas. In particular, the date of mid-greenup phase from VIIRS was significantly correlated to the planting dates reported in NASS CP for both corn and soybean with a consistent lag of 37 days and 27 days on average (p < 0.01), as well as the emergence dates in CP with a lag of 24 days and 16 days on average (p < 0.01), respectively. The real-time monitoring of maximum greenness onset from VIIRS was able to predict the corn silking dates with an advance of 9 days (p < 0.01) and the soybean blooming dates with a lag of 7 days on average (p < 0.01). These findings demonstrate the capability of VIIRS observations to effectively monitor temporal dynamics of crop progress in real time at a regional scale.


2015 ◽  
Author(s):  
◽  
Prashant Singh

Salmonella and Shiga toxin producing Escherichia coli (STEC) are among the most important food pathogens. Increasing use of antibiotics for treatment and as a therapeutic agent on food animals has been proposed as a reason for the emergence of multiple drug resistant (MDR) strains of food pathogens. In this study real-time PCR methods were developed for the detection antibiotic resistant strains of Salmonella, extended-spectrum [beta]-lactam (ESBL) and carbapenem resistant pathogens. The United States Department of Agriculture Food Safety and Inspection Service (USDA-FSIS) declared seven STEC serogroups O157, O26, O45, O103, O111, O121 and O145 as adulterants in ground beef and beef trims. Multiplex real-time PCR melt curve assays with IAC were standardized for the detection of seven STEC serogroups with their virulence genes and Salmonella. The assay was able to detect all STEC strains in 325 g of ground beef and beef trims spiked with 10 CFU.


Plant Disease ◽  
2006 ◽  
Vol 90 (5) ◽  
pp. 603-610 ◽  
Author(s):  
Ronald J. Sayler ◽  
Richard D. Cartwright ◽  
Yinong Yang

Panicle blight of rice (Oryza sativa), caused by the bacterium Burkholderia glumae, is one of the most important new diseases in rice production areas of the southern United States. In this study, pathogenic strains were isolated from diseased panicles in Arkansas rice fields and examined using the Biolog GN microplate system, whole cell fatty acid methyl ester analysis (FAME), rep-polymerase chain reaction (PCR) genomic DNA fingerprinting, and 16S–23S ribosomal DNA (rDNA) intergenic transcribed spacer (ITS) sequence analysis. The B. glumae isolates from Arkansas can be divided into two major groups, but their genetic diversity was relatively low as revealed by 16S–23S rDNA ITS sequence analysis. Since no practical method existed, up to now, for testing the presence of B. glumae in rice seeds, we have developed in this study a real-time PCR method that is effective in detecting and identifying the pathogen in seed lots and in whole plants. The specific PCR primers were designed based on the 16S–23S rDNA ITS sequence of several representative isolates from Arkansas and Japan. This method is highly sensitive, rapid, and reliable, and has great potential for analyzing large numbers of samples without the need for DNA extraction or agarose gel electrophoresis. Although vertical resistance has not been observed among tested rice cultivars, LM-1 and Drew exhibited considerable resistance to B. glumae infection based on disease lesion size and the bacterial growth in planta.


2017 ◽  
Vol 66 (1) ◽  
pp. 1003-1007 ◽  
Author(s):  
Stephen E. Greiman ◽  
Jefferson A. Vaughan ◽  
Rasha Elmahy ◽  
Poom Adisakwattana ◽  
Nguyen Van Ha ◽  
...  

2015 ◽  
Vol 108 (5) ◽  
pp. 2450-2457 ◽  
Author(s):  
M. S. Islam ◽  
N. B. Barr ◽  
W. E. Braswell ◽  
M. Martinez ◽  
L. A. Ledezma ◽  
...  

2019 ◽  
Vol 11 (1) ◽  
Author(s):  
Marissa L. Zwald ◽  
Kristin M. Holland ◽  
Francis Annor ◽  
Aaron Kite-Powell ◽  
Steven A. Sumner ◽  
...  

ObjectiveTo describe epidemiological characteristics of emergency department (ED) visits related to suicidal ideation (SI) or suicidal attempt (SA) using syndromic surveillance data.IntroductionSuicide is a growing public health problem in the United States.1 From 2001 to 2016, ED visit rates for nonfatal self-harm, a common risk factor for suicide, increased 42%.2–4 To improve public health surveillance of suicide-related problems, including SI and SA, the Data and Surveillance Task Force within the National Action Alliance for Suicide Prevention recommended the use of real-time data from hospital ED visits.5 The collection and use of real-time ED visit data on SI and SA could support a more targeted and timely public health response to prevent suicide.5 Therefore, this investigation aimed to monitor ED visits for SI or SA and to identify temporal, demographic, and geographic patterns using data from CDC’s National Syndromic Surveillance Program (NSSP).MethodsCDC’s NSSP data were used to monitor ED visits related to SI or SA among individuals aged 10 years and older from January 1, 2016 through July 31, 2018. A syndrome definition for SI or SA, developed by the International Society for Disease Surveillance’s syndrome definition committee in collaboration with CDC, was used to assess SI or SA-related ED visits. The syndrome definition was based on querying the chief complaint history, discharge diagnosis, and admission reason code and description fields for a combination of symptoms and Boolean operators (for example, hang, laceration, or overdose), as well as ICD-9-CM, ICD-10-CM, and SNOMED diagnostic codes associated with SI or SA. The definition was also developed to include common misspellings of self-harm-related terms and to exclude ED visits in which a patient “denied SI or SA.”The percentage of ED visits involving SI or SA were analyzed by month and stratified by sex, age group, and U.S. region. This was calculated by dividing the number of SI or SA-related ED visits by the total number of ED visits in each month. The average monthly percentage change of SI or SA overall and for each U.S. region was also calculated using the Joinpoint regression software (Surveillance Research Program, National Cancer Institute).6ResultsAmong approximately 259 million ED visits assessed in NSSP from January 2016 to July 2018, a total of 2,301,215 SI or SA-related visits were identified. Over this period, males accounted for 51.2% of ED visits related to SI or SA, and approximately 42.1% of SI or SA-related visits were comprised of patients who were 20-39 years, followed by 40-59 years (29.7%), 10-19 years (20.5%), and ≥60 years (7.7%).During this period, the average monthly percentage of ED visits involving SI or SA significantly increased 1.1%. As shown in Figure 1, all U.S. regions, except for the Southwest region, experienced significant increases in SI or SA ED visits from January 2016 to July 2018. The average monthly increase of SI or SA-related ED visits was 1.9% for the Midwest, 1.5% for the West (1.5%), 1.1% for the Northeast, 0.9% for the Southeast, and 0.5% for the Southwest.ConclusionsED visits for SI or SA increased from January 2016 to June 2018 and varied by U.S. region. In contrast to previous findings reporting data from the National Electronic Injury Surveillance Program – All-Injury Program, we observed different trends in SI or SA by sex, where more ED visits were comprised of patients who were male in our investigation.2 Syndromic surveillance data can fill an existing gap in the national surveillance of suicide-related problems by providing close to real-time information on SI or SA-related ED visits.5 However, our investigation is subject to some limitations. NSSP data is not nationally representative and therefore, these findings are not generalizable to areas not participating in NSSP. The syndrome definition may under-or over-estimate SI or SA based on coding differences and differences in chief complaint or discharge diagnosis data between jurisdictions. Finally, hospital participation in NSSP can vary across months, which could potentially contribute to trends observed in NSSP data. Despite these limitations, states and communities could use this type of surveillance data to detect abnormal patterns at more detailed geographic levels and facilitate rapid response efforts. States and communities can also use resources such as CDC’s Preventing Suicide: A Technical Package of Policy, Programs, and Practices to guide prevention decision-making and implement comprehensive suicide prevention approaches based on the best available evidence.7References1. Stone DM, Simon TR, Fowler KA, et al. Vital Signs: Trends in State Suicide Rates — United States, 1999–2016 and Circumstances Contributing to Suicide — 27 States, 2015. Morb Mortal Wkly Rep. 2018;67(22):617-624.2. CDCs National Center for Injury Prevention and Control. Web-based Injury Statistics Query and Reporting System (WISQARS). https://www.cdc.gov/injury/wisqars/index.html. Published 2018. Accessed September 1, 2018.3. Mercado M, Holland K, Leemis R, Stone D, Wang J. Trends in emergency department visits for nonfatal self-inflicted injuries among youth aged 10 to 24 years in the United States, 2005-2015. J Am Med Assoc. 2017;318(19):1931-1933. doi:10.1001/jama.2017.133174. Olfson M, Blanco C, Wall M, et al. National Trends in Suicide Attempts Among Adults in the United States. JAMA Psychiatry. 2017;10032(11):1095-1103. doi:10.1001/jamapsychiatry.2017.25825. Ikeda R, Hedegaard H, Bossarte R, et al. Improving national data systems for surveillance of suicide-related events. Am J Prev Med. 2014;47(3 SUPPL. 2):S122-S129. doi:10.1016/j.amepre.2014.05.0266. National Cancer Institute. Joinpoint Regression Software. https://surveillance.cancer.gov/joinpoint/. Published 2018. Accessed September 1, 2018.7. Centers for Disease Control and Prevention. Preventing Suicide: A Technical Package of Policy, Programs, and Practices. 


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