- Email: [email protected]
The global virome project
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Abstracts / International Journal of Infectious Diseases 53S (2016) 4–163
a growing number of initiatives are focusing on the role of data sharing under these circumstances. Methods & Materials: In this contribution, I am reviewing existing efforts around data sharing in recent public health emergencies from around the globe, focusing on cases where emerging diseases played a major role, as in the ongoing Zika virus outbreak. The underlying project is conducted by way of open notebook science that can be followed and contributed to via https://github.com/Daniel-Mietchen/datascience/blob/master/ emergency-response.md. Results: Data sharing can increase the speed of responses to emerging diseases. It may also affect the quality, the nature or the range of the responses and other variables. Conversely, a lack of adequate data sharing may pose a considerable barrier to effective responses. Conclusion: Data sharing is becoming an important aspect of responses to public health emergencies, and strategies for communicating outbreaks and emerging diseases are evolving around this notion, complementing traditional means of research and public health communication with faster, more transparent, more collaborative and more responsive channels. http://dx.doi.org/10.1016/j.ijid.2016.11.096 18.001 The global virome project P. Daszak a,∗ , D. Carroll b,∗ , N. Wolfe c , J. Mazet d a
EcoHealth Alliance, New York, NY/US USAID, Pandemic Influenza and Other Emerging Threats Unit, Washington, DC/US c Metabiota, San Francisco, CA/US d UC Davis, One Health Institute, Davis, CA/US b
The frequency of pandemics is increasing, driven by rapid demographic and environmental change and globalized trade and travel. Viruses of animal origin are a particular threat and have caused a series of significant recent outbreaks (e.g. SARS, pandemic influenza, MERS, Ebola and Zika). Recent work suggests only an estimated 1% of viral threats have been identified and fewer have had vaccines or counter measures developed. In the future, we will witness spillover from a pool of more than 500,000 currently unknown viruses into human populations. We need to be better informed about these threats to improve preparedness and reduce response times and associated costs. Here, we discuss the scientific and economic rationale, governance and technical framework for a global initiative to identify and characterize every significant viral threat available for spillover from animal reservoirs. We propose that such a step toward ending the pandemic era is achievable over the next ten years at a cost of less than $3.5 billion, and can be scaled up from current projects in a way that will provide rapid benefits to global health. http://dx.doi.org/10.1016/j.ijid.2016.11.097
19.002 Resistance of Streptococcus pneumoniae in Jordanian pediatric carriers, 2015-2016 A. Al-Lahham a,∗ , N. Khanfar b a
German Jordanian University, School of Applied Medical Sciences, Biomedical Engineering, Amman/JO b Private Pediatric Clinic, Amman/JO Purpose: Streptococcus pneumoniae is one of the leading causes of death which disseminates through colonizers to cause seriousnfections. In Jordan, children are majority where colonizers with this bacteria can disseminate and cause infections. Determine pneumococcal carriage rate, resistance, serotype distribution and coverage of pneumococcal Conjugate Vaccines (PCVs) from children attending daily care centers in Jordan. Methods & Materials: Nasopharyngeal swabs were taken from 279 healthy Jordanian children from the capital Amman (n=114) and from Madaba (n=165) with age from 2 to 144 months. Swabs were cultivated and the suspected alpha hemolytic isolates were tested for Optochin sensitivity and bile solubility for identification. Isolates were analyzed for antimicrobial susceptibility, serotyping using the Neufeld Quellung method. Results: Total pneumococcal carriage in Amman and Madaba was 14.0% and 41.2%, respectively. Coverage of PCV7, PCV10 and PCV13 in Amman was 6.3%, 6.3% and 12.5%; whereas in Madaba was 48.5%, 48.5% and 58.8%, respectively. 55 (48.2%) cases taken from Amman were vaccinated between 1-3 PCV injections. Coverage of Multiresistant isolates by PCV7 and PCV13 in Amman and Madaba was 14.3%, 28.6% and 59.5%, 78.4% for Madaba. Rate of carriage for cases below 4 months of age was 60% and can all be covered by the PCV. Carriage in Amman and Madaba was highest in age group 2-6 M (40%) in Amman and 25-36 M (57.1%) in Madaba. Resistance rates in Amman and Madaba was: Penicillin (87.5%; 98.5%), clarithromycin (62.5%; 58.7%), clindamycin (25%; 35.3%), trimethoprim-sulfamethoxazole (32.2%; 52.9%), tetracycline (44%; 55.9%). Multiresistance in Amman and Madaba was 43.8% and 54.4%. 52 isolates were macrolide resistant in both cities, where 63.6% and 36.4% were M-phenotype and cMLSB for Amman and 41.5% and 58.5% for Madaba. Predominant serotypes were 11A (12.5%) and 9N (12.5%) in Amman and for Madaba 23F (16.2%), 19F (11.8%) and 6B (11.8%). Conclusion: There was a significant differences in carriage, but the resistance is high. Localizing specific serotypes is recommended for be better control with the available PCVs. http://dx.doi.org/10.1016/j.ijid.2016.11.098 19.004 Plasmid-mediated colistin-resistance in Escherichia coli isolated from poultry and broiler meat in Austria in 2016 F. Allerberger a,∗ , G. Weissensteiner a , B. Springer a , C. Schlagenhaufen a , H. Lassnig a , W. Ruppitsch b , S. Jelovcan a a
Austrian Agency for Health and Food Safety (AGES), National Reference Laboratory for Antimicrobial Resistance, Graz/AT b Austrian Agency for Health and Food Safety (AGES), Vienna/AT Purpose: Colistin is regarded as a last line defence against infections caused by multidrug-resistant Gram-negative bacteria.
Abstracts / International Journal of Infectious Diseases 53S (2016) 4–163
a growing number of initiatives are focusing on the role of data sharing under these circumstances. Methods & Materials: In this contribution, I am reviewing existing efforts around data sharing in recent public health emergencies from around the globe, focusing on cases where emerging diseases played a major role, as in the ongoing Zika virus outbreak. The underlying project is conducted by way of open notebook science that can be followed and contributed to via https://github.com/Daniel-Mietchen/datascience/blob/master/ emergency-response.md. Results: Data sharing can increase the speed of responses to emerging diseases. It may also affect the quality, the nature or the range of the responses and other variables. Conversely, a lack of adequate data sharing may pose a considerable barrier to effective responses. Conclusion: Data sharing is becoming an important aspect of responses to public health emergencies, and strategies for communicating outbreaks and emerging diseases are evolving around this notion, complementing traditional means of research and public health communication with faster, more transparent, more collaborative and more responsive channels. http://dx.doi.org/10.1016/j.ijid.2016.11.096 18.001 The global virome project P. Daszak a,∗ , D. Carroll b,∗ , N. Wolfe c , J. Mazet d a
EcoHealth Alliance, New York, NY/US USAID, Pandemic Influenza and Other Emerging Threats Unit, Washington, DC/US c Metabiota, San Francisco, CA/US d UC Davis, One Health Institute, Davis, CA/US b
The frequency of pandemics is increasing, driven by rapid demographic and environmental change and globalized trade and travel. Viruses of animal origin are a particular threat and have caused a series of significant recent outbreaks (e.g. SARS, pandemic influenza, MERS, Ebola and Zika). Recent work suggests only an estimated 1% of viral threats have been identified and fewer have had vaccines or counter measures developed. In the future, we will witness spillover from a pool of more than 500,000 currently unknown viruses into human populations. We need to be better informed about these threats to improve preparedness and reduce response times and associated costs. Here, we discuss the scientific and economic rationale, governance and technical framework for a global initiative to identify and characterize every significant viral threat available for spillover from animal reservoirs. We propose that such a step toward ending the pandemic era is achievable over the next ten years at a cost of less than $3.5 billion, and can be scaled up from current projects in a way that will provide rapid benefits to global health. http://dx.doi.org/10.1016/j.ijid.2016.11.097
19.002 Resistance of Streptococcus pneumoniae in Jordanian pediatric carriers, 2015-2016 A. Al-Lahham a,∗ , N. Khanfar b a
German Jordanian University, School of Applied Medical Sciences, Biomedical Engineering, Amman/JO b Private Pediatric Clinic, Amman/JO Purpose: Streptococcus pneumoniae is one of the leading causes of death which disseminates through colonizers to cause seriousnfections. In Jordan, children are majority where colonizers with this bacteria can disseminate and cause infections. Determine pneumococcal carriage rate, resistance, serotype distribution and coverage of pneumococcal Conjugate Vaccines (PCVs) from children attending daily care centers in Jordan. Methods & Materials: Nasopharyngeal swabs were taken from 279 healthy Jordanian children from the capital Amman (n=114) and from Madaba (n=165) with age from 2 to 144 months. Swabs were cultivated and the suspected alpha hemolytic isolates were tested for Optochin sensitivity and bile solubility for identification. Isolates were analyzed for antimicrobial susceptibility, serotyping using the Neufeld Quellung method. Results: Total pneumococcal carriage in Amman and Madaba was 14.0% and 41.2%, respectively. Coverage of PCV7, PCV10 and PCV13 in Amman was 6.3%, 6.3% and 12.5%; whereas in Madaba was 48.5%, 48.5% and 58.8%, respectively. 55 (48.2%) cases taken from Amman were vaccinated between 1-3 PCV injections. Coverage of Multiresistant isolates by PCV7 and PCV13 in Amman and Madaba was 14.3%, 28.6% and 59.5%, 78.4% for Madaba. Rate of carriage for cases below 4 months of age was 60% and can all be covered by the PCV. Carriage in Amman and Madaba was highest in age group 2-6 M (40%) in Amman and 25-36 M (57.1%) in Madaba. Resistance rates in Amman and Madaba was: Penicillin (87.5%; 98.5%), clarithromycin (62.5%; 58.7%), clindamycin (25%; 35.3%), trimethoprim-sulfamethoxazole (32.2%; 52.9%), tetracycline (44%; 55.9%). Multiresistance in Amman and Madaba was 43.8% and 54.4%. 52 isolates were macrolide resistant in both cities, where 63.6% and 36.4% were M-phenotype and cMLSB for Amman and 41.5% and 58.5% for Madaba. Predominant serotypes were 11A (12.5%) and 9N (12.5%) in Amman and for Madaba 23F (16.2%), 19F (11.8%) and 6B (11.8%). Conclusion: There was a significant differences in carriage, but the resistance is high. Localizing specific serotypes is recommended for be better control with the available PCVs. http://dx.doi.org/10.1016/j.ijid.2016.11.098 19.004 Plasmid-mediated colistin-resistance in Escherichia coli isolated from poultry and broiler meat in Austria in 2016 F. Allerberger a,∗ , G. Weissensteiner a , B. Springer a , C. Schlagenhaufen a , H. Lassnig a , W. Ruppitsch b , S. Jelovcan a a
Austrian Agency for Health and Food Safety (AGES), National Reference Laboratory for Antimicrobial Resistance, Graz/AT b Austrian Agency for Health and Food Safety (AGES), Vienna/AT Purpose: Colistin is regarded as a last line defence against infections caused by multidrug-resistant Gram-negative bacteria.