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1.  Evaluation of the point-of-care Becton Dickinson Veritor™ Rapid influenza diagnostic test in Kenya, 2013–2014 
We evaluated the performance of the Becton Dickinson Veritor™ System Flu A + B rapid influenza diagnostic test (RIDT) to detect influenza viruses in respiratory specimens from patients enrolled at five surveillance sites in Kenya, a tropical country where influenza seasonality is variable.
Nasal swab (NS) and nasopharyngeal (NP)/oropharyngeal (OP) swabs were collected from patients with influenza like illness and/or severe acute respiratory infection. The sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) of the RIDT using NS specimens were evaluated against nasal swabs tested by real time reverse transcription polymerase chain reaction (rRT-PCR). The performance parameter results were expressed as 95% confidence intervals (CI) calculated using binomial exact methods, with P < 0.05 considered significant. Two-sample Z tests were used to test for differences in sample proportions. Analysis was performed using SAS software version 9.3.
From July 2013 to July 2014, 3,569 patients were recruited, of which 78.7% were aged <5 years. Overall, 14.4% of NS specimens were influenza-positive by RIDT. RIDT overall sensitivity was 77.1% (95% CI 72.8–81.0%) and specificity was 94.9% (95% CI 94.0–95.7%) compared to rRT-PCR using NS specimens. RIDT sensitivity for influenza A virus compared to rRT-PCR using NS specimens was 71.8% (95% CI 66.7–76.4%) and was significantly higher than for influenza B which was 43.8% (95% CI 33.8–54.2%). PPV ranged from 30%–80% depending on background prevalence of influenza.
Although the variable seasonality of influenza in tropical Africa presents unique challenges, RIDTs may have a role in making influenza surveillance sustainable in more remote areas of Africa, where laboratory capacity is limited.
PMCID: PMC5225564  PMID: 28077093
Influenza; Rapid influenza test; Sensitivity and specificity; Kenya
2.  On the relative role of different age groups in influenza epidemics 
Epidemics  2015;13:10-16.
The identification of key “driver” groups in influenza epidemics is of much interest for the implementation of effective public health response strategies, including vaccination programs. However, the relative importance of different age groups in propagating epidemics is uncertain.
During a communicable disease outbreak, some groups may be disproportionately represented during the outbreak’s ascent due to increased susceptibility and/or contact rates. Such groups or subpopulations can be identified by considering the proportion of cases within the subpopulation occurring before (Bp) and after the epidemic peak (Ap) to calculate the subpopulation’s relative risk, RR=Bp/Ap. We estimated RR for several subpopulations (age groups) using data on laboratory-confirmed US influenza hospitalizations during epidemics between 2009–2014. Additionally, we simulated various influenza outbreaks in an age-stratified population, relating the RR to the impact of vaccination in each subpopulation on the epidemic’s initial effective reproductive number R_e(0).
We found that children aged 5–17 had the highest estimates of RR during the five largest influenza A outbreaks, though the relative magnitude of RR in this age group compared to other age groups varied, being highest for the 2009 A/H1N1 pandemic. For the 2010–2011 and 2012–2013 influenza B epidemics, adults aged 18–49, and 0–4 year-olds had the highest estimates of RR respectively.
For 83% of simulated epidemics, the group with the highest RR was also the group for which initial distribution of a given quantity of vaccine would result in the largest reduction of R_e(0). In the largest 40% of simulated outbreaks, the group with the highest RR and the largest vaccination impact was children 5–17.
While the relative importance of different age groups in propagating influenza outbreaks varies, children aged 5–17 play the leading role during the largest influenza A epidemics. Extra vaccination efforts for this group may contribute to reducing the epidemic’s impact in the whole community.
PMCID: PMC4469206  PMID: 26097505
3.  Does Influenza Vaccination Modify Influenza Severity? Data on Older Adults Hospitalized With Influenza During the 2012−2013 Season in the United States 
The Journal of Infectious Diseases  2015;212(8):1200-1208.
Background. Some studies suggest that influenza vaccination might be protective against severe influenza outcomes in vaccinated persons who become infected. We used data from a large surveillance network to further investigate the effect of influenza vaccination on influenza severity in adults aged ≥50 years who were hospitalized with laboratory-confirmed influenza.
Methods. We analyzed influenza vaccination and influenza severity using Influenza Hospitalization Surveillance Network (FluSurv-NET) data for the 2012−2013 influenza season. Intensive care unit (ICU) admission, death, diagnosis of pneumonia, and hospital and ICU lengths of stay served as measures of disease severity. Data were analyzed by multivariable logistic regression, parametric survival models, and propensity score matching (PSM).
Results. Overall, no differences in severity were observed in the multivariable logistic regression model. Using PSM, adults aged 50−64 years (but not other age groups) who were vaccinated against influenza had a shorter length of ICU stay than those who were unvaccinated (hazard ratio for discharge, 1.84; 95% confidence interval, 1.12−3.01).
Conclusions. Our findings show a modest effect of influenza vaccination on disease severity. Analysis of data from seasons with different predominant strains and higher estimates of vaccine effectiveness are needed.
PMCID: PMC4683374  PMID: 25821227
influenza; influenza vaccine; adults; severe illness
4.  Crop management as a driving force of plant growth promoting rhizobacteria physiology 
SpringerPlus  2016;5(1):1574.
Crop management systems influence plant productivity and nutrient use efficiency, as well as plant growth-promoting rhizobacteria (PGPR), which are known to influence the growth of plants via phytohormone production, phosphate solubilization, nitrogen (N) fixation and antimicrobial activity. The objective of this study was to compare the influence of two crop management system on microbial PGPR features. PGPR isolated from the rhizospheres of Carica papaya L. grown under two distinct management systems (conventional and organic) were identified and characterized. The 12 strains most efficient in solubilizing inorganic phosphate belonged to the genera Burkholderia, Klebsiella, and Leclercia. N fixation was observed in the strains B. vietnamiensis from the conventional farming system and B. vietnamiensis, B. cepacia and Leclercia sp. from the organic farming system. The B. vietnamiensis, B. cepacia, Klebsiella sp. and Klebsiella sp. isolates showed antifungal activity, while Leclercia sp. did not. The strains B. vietnamiensis and Enterobcter sp. (isolated from the conventional farming system) and Klebsiella sp. (isolated from the organic farming system) were efficient at solubilizing phosphate, producing phytohormones and siderophores, and inhibiting the mycelial growth of various phytopathogenic fungi (Botrytis cinerea, Pestalotia sp., Alternaria sp., Phoma sp., Fusarium culmorum, Geotrichum candidum). Physiological differences between the isolates from the two crop management regimes were distinguishable after 10 years of distinct management.
PMCID: PMC5025401  PMID: 27652147
Biocontrol; Organic farming; Conventional farming; Fungi; Nitrogen fixation; Rhizosphere
5.  Survey of influenza and other respiratory viruses diagnostic testing in US hospitals, 2012–2013 
Little is known about laboratory capacity to routinely diagnose influenza and other respiratory viruses at clinical laboratories and hospitals.
We sought to assess diagnostic practices for influenza and other respiratory virus in a survey of hospitals and laboratories participating in the US Influenza Hospitalization Surveillance Network in 2012–2013.
Materials and Methods
All hospitals and their associated laboratories participating in the Influenza Hospitalization Surveillance Network (FluSurv‐NET) were included in this evaluation. The network covers more than 80 counties in 15 states, CA, CO, CT, GA, MD, MN, NM, NY, OR, TN, IA, MI, OH, RI, and UT, with a catchment population of ~28 million people. We administered a standardized questionnaire to key personnel, including infection control practitioners and laboratory departments, at each hospital through telephone interviews.
Of the 240 participating laboratories, 67% relied only on commercially available rapid influenza diagnostic tests to diagnose influenza. Few reported the availability of molecular diagnostic assays for detection of influenza (26%) and other viral pathogens (≤20%) in hospitals and commercial laboratories.
Reliance on insensitive assays to detect influenza may detract from optimal clinical management of influenza infections in hospitals.
PMCID: PMC4746564  PMID: 26505742
EIP; FluSurv‐NET; influenza; laboratory capacity; respiratory viruses
6.  Respiratory Viral Testing and Influenza Antiviral Prescriptions During Hospitalization for Acute Respiratory Illnesses 
Open Forum Infectious Diseases  2016;3(1):ofv216.
We examined respiratory viral testing and influenza antiviral prescriptions at a US tertiary care hospital. During the 2010–11 to 2012–13 influenza seasons, antiviral prescriptions among acute respiratory illness (ARI) hospitalizations were associated with viral testing (rate ratio = 15.0), and empiric prescriptions were rare (<1% of ARI hospitalizations).
PMCID: PMC4751920  PMID: 26885545
influenza; influenza antivirals; respiratory virus testing; acute respiratory illness hospitalizations
7.  Influenza-Related Hospitalization and ED Visits in Children Less Than 5 Years: 2000–2011 
Pediatrics  2015;135(1):e66-e74.
In the United States, recommendations for annual influenza vaccination gradually expanded from 2004 to 2008, to include all children aged ≥6 months. The effects of these policies on vaccine uptake and influenza-associated health care encounters are unclear. The objectives of the study were to examine the annual incidence of influenza-related health care encounters and vaccine uptake among children age 6 to 59 months from 2000–2001 through 2010–2011 in Davidson County, TN.
We estimated the proportion of laboratory-confirmed influenza-related hospitalizations and emergency department (ED) visits by enrolling and testing children with acute respiratory illness or fever. We estimated influenza-related health care encounters by multiplying these proportions by the number of acute respiratory illness/fever hospitalizations and ED visits for county residents. We assessed temporal trends in vaccination coverage, and influenza-associated hospitalizations and ED visit rates.
The proportion of fully vaccinated children increased from 6% in 2000–2001 to 38% in 2010–2011 (P < .05). Influenza-related hospitalizations ranged from 1.9 to 16.0 per 10 000 children (median 4.5) per year. Influenza-related ED visits ranged from 89 to 620 per 10 000 children (median 143) per year. Significant decreases in hospitalizations (P < .05) and increases in ED visits (P < .05) over time were not clearly related to vaccination trends. Influenza-related encounters were greater when influenza A(H3N2) circulated than during other years with median rates of 8.2 vs 3.2 hospitalizations and 307 vs 143 ED visits per 10 000 children, respectively.
Influenza vaccination increased over time; however, the proportion of fully vaccinated children remained <50%. Influenza was associated with a substantial illness burden particularly when influenza A(H3N2) predominated.
PMCID: PMC4279064  PMID: 25489015
influenza; hospitalization; rate; ratio; vaccination coverage
8.  Improving Accuracy of Influenza-Associated Hospitalization Rate Estimates 
Emerging Infectious Diseases  2015;21(9):1595-1601.
Adjusting for diagnostic test sensitivity enables more accurate and timely comparisons over time.
Diagnostic test sensitivity affects rate estimates for laboratory-confirmed influenza–associated hospitalizations. We used data from FluSurv-NET, a national population-based surveillance system for laboratory-confirmed influenza hospitalizations, to capture diagnostic test type by patient age and influenza season. We calculated observed rates by age group and adjusted rates by test sensitivity. Test sensitivity was lowest in adults >65 years of age. For all ages, reverse transcription PCR was the most sensitive test, and use increased from <10% during 2003–2008 to ≈70% during 2009–2013. Observed hospitalization rates per 100,000 persons varied by season: 7.3–50.5 for children <18 years of age, 3.0–30.3 for adults 18–64 years, and 13.6–181.8 for adults >65 years. After 2009, hospitalization rates adjusted by test sensitivity were ≈15% higher for children <18 years, ≈20% higher for adults 18–64 years, and ≈55% for adults >65 years of age. Test sensitivity adjustments improve the accuracy of hospitalization rate estimates.
PMCID: PMC4550134  PMID: 26292017
influenza; hospitalizations; sensitivity; diagnostic tests; viruses
9.  The US Influenza Hospitalization Surveillance Network  
Emerging Infectious Diseases  2015;21(9):1543-1550.
This network has helped determine risk, define outbreak severity, and guide recommendations for treatment and vaccination programs.
In 2003, surveillance for influenza in hospitalized persons was added to the Centers for Disease Control and Prevention Emerging Infections Program network. This surveillance enabled monitoring of the severity of influenza seasons and provided a platform for addressing priority questions associated with influenza. For enhanced surveillance capacity during the 2009 influenza pandemic, new sites were added to this platform. The combined surveillance platform is called the Influenza Hospitalization Surveillance Network (FluSurv-NET). FluSurv-NET has helped to determine the risk for influenza-associated illness in various segments of the US population, define the severity of influenza seasons and the 2009 pandemic, and guide recommendations for treatment and vaccination programs.
PMCID: PMC4550140  PMID: 26291121
Influenza; influenza hospitalizations; population-based surveillance; Emerging Infections Program; EIP; viruses; US Influenza Hospitalization Surveillance Network; FluSurv-NET
10.  Effect of Culture-Independent Diagnostic Tests on Future Emerging Infections Program Surveillance 
Emerging Infectious Diseases  2015;21(9):1582-1588.
Use of such tests in clinical settings presents opportunities and challenges.
The Centers for Disease Control and Prevention Emerging Infections Program (EIP) network conducts population-based surveillance for pathogens of public health importance. Central to obtaining estimates of disease burden and tracking microbiological characteristics of these infections is accurate laboratory detection of pathogens. The use of culture-independent diagnostic tests (CIDTs) in clinical settings presents both opportunities and challenges to EIP surveillance. Because CIDTs offer better sensitivity than culture and are relatively easy to perform, their use could potentially improve estimates of disease burden. However, changes in clinical testing practices, use of tests with different sensitivities and specificities, and changes to case definitions make it challenging to monitor trends. Isolates are still needed for performing strain typing, antimicrobial resistance testing, and identifying other molecular characteristics of organisms. In this article, we outline current and future EIP activities to address issues associated with adoption of CIDTs, which may apply to other public health surveillance.
PMCID: PMC4550165  PMID: 26291736
culture-independent diagnostics; surveillance; molecular testing; antigen-based testing; Emerging Infections Program; EIP
11.  Estimating Influenza Disease Burden from Population-Based Surveillance Data in the United States 
PLoS ONE  2015;10(3):e0118369.
Annual estimates of the influenza disease burden provide information to evaluate programs and allocate resources. We used a multiplier method with routine population-based surveillance data on influenza hospitalization in the United States to correct for under-reporting and estimate the burden of influenza for seasons after the 2009 pandemic. Five sites of the Influenza Hospitalization Surveillance Network (FluSurv-NET) collected data on the frequency and sensitivity of influenza testing during two seasons to estimate under-detection. Population-based rates of influenza-associated hospitalization and Intensive Care Unit admission from 2010–2013 were extrapolated to the U.S. population from FluSurv-NET and corrected for under-detection. Influenza deaths were calculated using a ratio of deaths to hospitalizations. We estimated that influenza-related hospitalizations were under-detected during 2010-11 by a factor of 2.1 (95%CI 1.7–2.9) for age < 18 years, 3.1 (2.4–4.5) for ages 18-64 years, and 5.2 (95%CI 3.8–8.3) for age 65+. Results were similar in 2011-12. Extrapolated estimates for 3 seasons from 2010–2013 included: 114,192–624,435 hospitalizations, 18,491–95,390 ICU admissions, and 4,915–27,174 deaths per year; 54–70% of hospitalizations and 71–85% of deaths occurred among adults aged 65+. Influenza causes a substantial disease burden in the U.S. that varies by age and season. Periodic estimation of multipliers across multiple sites and age groups improves our understanding of influenza detection in sentinel surveillance systems. Adjusting surveillance data using a multiplier method is a relatively simple means to estimate the impact of influenza and the subsequent value of interventions to prevent influenza.
PMCID: PMC4349859  PMID: 25738736
12.  Statin Treatment and Mortality: Propensity Score-Matched Analyses of 2007–2008 and 2009–2010 Laboratory-Confirmed Influenza Hospitalizations 
Open Forum Infectious Diseases  2015;2(1):ofv028.
Background. Annual influenza epidemics are responsible for substantial morbidity and mortality. The use of immunomodulatory agents such as statins to target host inflammatory responses in influenza virus infection has been suggested as an adjunct treatment, especially during pandemics, when antiviral quantities are limited or vaccine production can be delayed.
Methods. We used population-based, influenza hospitalization surveillance data, propensity score-matched analysis, and Cox regression to determine whether there was an association between mortality (within 30 days of a positive influenza test) and statin treatment among hospitalized cohorts from 2 influenza seasons (October 1, 2007 to April 30, 2008 and September 1, 2009 to April 31, 2010).
Results. Hazard ratios for death within the 30-day follow-up period were 0.41 (95% confidence interval [CI], .25–.68) for a matched sample from the 2007–2008 season and 0.77 (95% CI, .43–1.36) for a matched sample from the 2009 pandemic.
Conclusions. The analysis suggests a protective effect against death from influenza among patients hospitalized in 2007–2008 but not during the pandemic. Sensitivity analysis indicates the findings for 2007–2008 may be influenced by unmeasured confounders. This analysis does not support using statins as an adjunct treatment for preventing death among persons hospitalized for influenza.
PMCID: PMC4438907  PMID: 26034777
immunomodulatory agents; influenza; influenza mortality; pandemic; pandemic H1N1; statins
13.  The Burden of Influenza in Young Children, 2004–2009 
Pediatrics  2013;131(2):207-216.
To characterize the health care burden of influenza from 2004 through 2009, years when influenza vaccine recommendations were expanded to all children aged ≥6 months.
Population-based surveillance for laboratory-confirmed influenza was performed among children aged <5 years presenting with fever and/or acute respiratory illness to inpatient and outpatient settings during 5 influenza seasons in 3 US counties. Enrolled children had nasal/throat swabs tested for influenza by reverse transcriptase-polymerase chain reaction and their medical records reviewed. Rates of influenza hospitalizations per 1000 population and proportions of outpatients (emergency department and clinic) with influenza were computed.
The study population comprised 2970, 2698, and 2920 children from inpatient, emergency department, and clinic settings, respectively. The single-season influenza hospitalization rates were 0.4 to 1.0 per 1000 children aged <5 years and highest for infants <6 months. The proportion of outpatient children with influenza ranged from 10% to 25% annually. Among children hospitalized with influenza, 58% had physician-ordered influenza testing, 35% had discharge diagnoses of influenza, and 2% received antiviral medication. Among outpatients with influenza, 7% were tested for influenza, 7% were diagnosed with influenza, and <1% had antiviral treatment. Throughout the 5 study seasons, <45% of influenza-negative children ≥6 months were fully vaccinated against influenza.
Despite expanded vaccination recommendations, many children are insufficiently vaccinated, and substantial influenza burden remains. Antiviral use was low. Future studies need to evaluate trends in use of vaccine and antiviral agents and their impact on disease burden and identify strategies to prevent influenza in young infants.
PMCID: PMC3557405  PMID: 23296444
influenza; epidemiology; influenza vaccine; hospitalization; ambulatory care
14.  Photoprotective Bioactivity Present in a Unique Marine Bacteria Collection from Portuguese Deep Sea Hydrothermal Vents 
Marine Drugs  2013;11(5):1506-1523.
Interesting biological activities have been found for numerous marine compounds. In fact, screening of phylogenetically diverse marine microorganisms from extreme environments revealed to be a rational approach for the discovery of novel molecules with relevant bioactivities for industries such as pharmaceutical and cosmeceutical. Nevertheless, marine sources deliverables are still far from the expectations and new extreme sources of microbes should be explored. In this work, a marine prokaryotic collection from four Mid-Atlantic Ridge (MAR) deep sea hydrothermal vents near the Azores Islands, Portugal, was created, characterized and tested for its photoprotective capacity. Within 246 isolates, a polyphasic approach, using chemotaxonomic and molecular typing methods, identified 23-related clusters of phenetically similar isolates with high indexes of diversity. Interestingly, 16S rRNA gene sequencing suggested the presence of 43% new prokaryotic species. A sub-set of 139 isolates of the prokaryotic collection was selected for biotechnological exploitation with 484 bacterial extracts prepared in a sustainable upscalling manner. 22% of the extracts showed an industrially relevant photoprotective activity, with two extracts, belonging to new strains of the species Shewanella algae and Vibrio fluvialis, uniquely showing UV-A, UV-B and UV-C protective capacity. This clearly demonstrates the high potential of the bacteria MAR vents collection in natural product synthesis with market applications.
PMCID: PMC3707158  PMID: 23665957
deep sea; marine bacteria; natural products; MAR hydrothermal vents; photoprotection
15.  Diversity and Impact of Prokaryotic Toxins on Aquatic Environments: A Review 
Toxins  2010;2(10):2359-2410.
Microorganisms are ubiquitous in all habitats and are recognized by their metabolic versatility and ability to produce many bioactive compounds, including toxins. Some of the most common toxins present in water are produced by several cyanobacterial species. As a result, their blooms create major threats to animal and human health, tourism, recreation and aquaculture. Quite a few cyanobacterial toxins have been described, including hepatotoxins, neurotoxins, cytotoxins and dermatotoxins. These toxins are secondary metabolites, presenting a vast diversity of structures and variants. Most of cyanobacterial secondary metabolites are peptides or have peptidic substructures and are assumed to be synthesized by non-ribosomal peptide synthesis (NRPS), involving peptide synthetases, or NRPS/PKS, involving peptide synthetases and polyketide synthases hybrid pathways. Besides cyanobacteria, other bacteria associated with aquatic environments are recognized as significant toxin producers, representing important issues in food safety, public health, and human and animal well being. Vibrio species are one of the most representative groups of aquatic toxin producers, commonly associated with seafood-born infections. Some enterotoxins and hemolysins have been identified as fundamental for V. cholerae and V. vulnificus pathogenesis, but there is evidence for the existence of other potential toxins. Campylobacter spp. and Escherichia coli are also water contaminants and are able to produce important toxins after infecting their hosts. Other bacteria associated with aquatic environments are emerging as toxin producers, namely Legionella pneumophila and Aeromonas hydrophila, described as responsible for the synthesis of several exotoxins, enterotoxins and cytotoxins. Furthermore, several Clostridium species can produce potent neurotoxins. Although not considered aquatic microorganisms, they are ubiquitous in the environment and can easily contaminate drinking and irrigation water. Clostridium members are also spore-forming bacteria and can persist in hostile environmental conditions for long periods of time, contributing to their hazard grade. Similarly, Pseudomonas species are widespread in the environment. Since P. aeruginosa is an emergent opportunistic pathogen, its toxins may represent new hazards for humans and animals. This review presents an overview of the diversity of toxins produced by prokaryotic microorganisms associated with aquatic habitats and their impact on environment, life and health of humans and other animals. Moreover, important issues like the availability of these toxins in the environment, contamination sources and pathways, genes involved in their biosynthesis and molecular mechanisms of some representative toxins are also discussed.
PMCID: PMC3153167  PMID: 22069558
diversity of toxins; impact of toxins; prokaryotes; aquatic; molecular mechanisms
16.  Chickenpox Exposure and Herpes Zoster Disease Incidence in Older Adults in the U.S. 
Public Health Reports  2007;122(2):155-159.
Exposure to varicella zoster virus through close contact with people with chickenpox was suggested to boost specific immunity, reducing the risk of herpes zoster (HZ). Since the introduction of the varicella immunization program in the U.S. in 1995, varicella morbidity has decreased substantially. This article examines incidence and risk factors associated with self-reported HZ disease and whether exposure to chickenpox within the previous decade reduces the risk of shingles in this age group.
In 2004, a national random-digit dial telephone survey was used to obtain information on self-reported HZ disease, demographic characteristics, and exposure to children with chickenpox in the past decade. National estimates of the incidence of shingles disease were calculated.
Incidence rate of self-reported HZ was 19 per 1,000 population per year. White individuals were 3.5 times more likely to report shingles than Hispanic individuals (p<0.01). Previous exposure to chickenpox did not protect against HZ disease in this population. Seven percent of adults ≥65 years of age reported exposure to children with chickenpox in the past decade.
Incidence of HZ among individuals ≥65 years of age in the U.S. may be higher than previously described in the literature, with whites being at higher risk for the disease. Currently, the potential contribution of exposure to chickenpox as a mechanism for maintaining cell-mediated immunity against HZ may be limited to a small percentage of the population. Vaccination against HZ may represent the best means of decreasing this disease burden.
PMCID: PMC1820439  PMID: 17357357
17.  Norovirus and Foodborne Disease, United States, 1991–2000 
Emerging Infectious Diseases  2005;11(1):95-102.
Analysis of foodborne outbreaks shows how advances in viral diagnostics are clarifying the causes of foodborne outbreaks and determining the high impact of norovirus infections.
Efforts to prevent foodborne illness target bacterial pathogens, yet noroviruses (NoV) are suspected to be the most common cause of gastroenteritis. New molecular assays allow for better estimation of the role of NoV in foodborne illness. We analyzed 8,271 foodborne outbreaks reported to the Centers for Disease Control and Prevention from 1991 to 2000 and additional data from 6 states. The proportion of NoV-confirmed outbreaks increased from 1% in 1991 to 12% in 2000. However, from 1998 to 2000, 76% of NoV outbreaks were reported by only 11 states. In 2000, an estimated 50% of foodborne outbreaks in 6 states were attributable to NoV. NoV outbreaks were larger than bacterial outbreaks (median persons affected: 25 versus 15), and 10% of affected persons sought medical care; 1% were hospitalized. More widespread use of molecular assays will permit better estimates of the role of NoV illness and help direct efforts to control foodborne illness.
PMCID: PMC3294339  PMID: 15705329
research; food; norovirus; disease outbreaks; burden of illness
18.  Automated, Laboratory-based System Using the Internet for Disease Outbreak Detection, the Netherlands 
Emerging Infectious Diseases  2003;9(9):1046-1052.
Rapid detection of outbreaks is recognized as crucial for effective control measures and has particular relevance with the recently increased concern about bioterrorism. Automated analysis of electronically collected laboratory data can result in rapid detection of widespread outbreaks or outbreaks of pathogens with common signs and symptoms. In the Netherlands, an automated outbreak detection system for all types of pathogens has been developed within an existing electronic laboratory-based surveillance system called ISIS. Features include the use of a flexible algorithm for daily analysis of data and presentation of signals on the Internet for interpretation by health professionals. By 2006, the outbreak detection system will analyze laboratory-reported data on all pathogens and will cover 35% of the Dutch population.
PMCID: PMC3016793  PMID: 14519238
Disease outbreaks; algorithms; Internet; laboratories; data collection
19.  Epidemiology of Urban Canine Rabies, Santa Cruz, Bolivia, 1972–1997 
Emerging Infectious Diseases  2002;8(5):458-461.
We analyzed laboratory data from 1972 to 1997 from Santa Cruz, Bolivia, to determine risk factors for laboratory canine samples’ testing positive for Rabies virus (RABV). Of 9,803 samples, 50.7% tested positive for RABV; the number of cases and the percentage positive has dropped significantly since 1978. A 5- to 6-year cycle in rabies incidence was clearly apparent, though no seasonality was noted. Male dogs had significantly increased odds of testing positive for RABV (odds ratio [OR]=1.14), as did 1- to 2-year-old dogs (OR=1.73); younger and older dogs were at lower risk. Samples submitted from the poorer suburbs of the city were more likely to test positive for RABV (OR=1.71). We estimated the distribution of endemic canine rabies in an urban environment to facilitate control measures in a resource-poor environment.
PMCID: PMC2732486  PMID: 11996678
Epidemiology; rabies; Bolivia; urban health; risk factors; canine
20.  Assessment of Metronidazole Susceptibility in Helicobacter pylori: Statistical Validation and Error Rate Analysis of Breakpoints Determined by the Disk Diffusion Test 
Journal of Clinical Microbiology  1999;37(5):1628-1631.
Metronidazole susceptibility of 100 Helicobacter pylori strains was assessed by determining the inhibition zone diameters by disk diffusion test and the MICs by agar dilution and PDM Epsilometer test (E test). Linear regression analysis was performed, allowing the definition of significant linear relations, and revealed correlations of disk diffusion results with both E-test and agar dilution results (r2 = 0.88 and 0.81, respectively). No significant differences (P = 0.84) were found between MICs defined by E test and those defined by agar dilution, taken as a standard. Reproducibility comparison between E-test and disk diffusion tests showed that they are equivalent and with good precision. Two interpretative susceptibility schemes (with or without an intermediate class) were compared by an interpretative error rate analysis method. The susceptibility classification scheme that included the intermediate category was retained, and breakpoints were assessed for diffusion assay with 5-μg metronidazole disks. Strains with inhibition zone diameters less than 16 mm were defined as resistant (MIC > 8 μg/ml), those with zone diameters equal to or greater than 16 mm but less than 21 mm were considered intermediate (4 μg/ml < MIC ≤ 8 μg/ml), and those with zone diameters of 21 mm or greater were regarded as susceptible (MIC ≤ 4 μg/ml). Error rate analysis applied to this classification scheme showed occurrence frequencies of 1% for major errors and 7% for minor errors, when the results were compared to those obtained by agar dilution. No very major errors were detected, suggesting that disk diffusion might be a good alternative for determining the metronidazole sensitivity of H. pylori strains.
PMCID: PMC84858  PMID: 10203543

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