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1. Pneumococcal lineages associated with serotype replacement and antibiotic resistance in childhood invasive pneumococcal disease in the post-PCV13 era: an international whole-genome sequencing study

Author

Brooks, Abdullah W, Corso, Alejandra, Davydov, Alexander, Maguire, Alison, Pollard, Andrew, Kiran, Anmol, Skoczynska, Anna, Moiane, Benild, Beall, Bernard, Sigauque, Betuel, Aanensen, David, Lehmann, Deborah, Faccone, Diego, Foster-Nyarko, Ebenezer, Bojang, Ebrima, Egorova, Ekaterina, Voropaeva, Elena, Sampane-Donkor, Eric, Sadowy, Ewa, Bigogo, Godfrey, Mucavele, Helio, Belabbès, Houria, Diawara, Idrissa, Moïsi, Jennifer, Verani, Jennifer, Keenan, Jeremy, Nair Thulasee Bhai, Jyothish N, Ndlangisa, Kedibone M, Zerouali, Khalid, Ravikumar, K L, Titov, Leonid, De Gouveia, Linda, Alaerts, Maaike, Ip, Margaret, de Cunto Brandileone, Maria Cristina, Hasanuzzaman, Md, Paragi, Metka, Nurse-Lucas, Michele, Ali, Mushal, Elmdaghri, Naima, Croucher, Nicholas, Wolter, Nicole, Porat, Nurit, Eser, Özgen Köseoglu, Akpaka, Patrick E, Turner, Paul, Gagetti, Paula, Tientcheu, Peggy-Estelle, Carter, Philip E, Mostowy, Rafal, Kandasamy, Rama, Ford, Rebecca, Henderson, Rebecca, Malaker, Roly, Shakoor, Sadia, Grassi Almeida, Samanta Cristine, Saha, Samir K, Doiphode, Sanjay, Madhi, Shabir A, Devi Sekaran, Shamala, Srifuengfung, Somporn, Obaro, Stephen, Clarke, Stuart C, Nzenze, Susan A, Kastrin, Tamara, Ochoa, Theresa J, Balaji, Veeraraghavan, Hryniewicz, Waleria, Urban, Yulia, Lo, Stephanie W, Gladstone, Rebecca A, van Tonder, Andries J, Lees, John A, du Plessis, Mignon, Benisty, Rachel, Givon-Lavi, Noga, Hawkins, Paulina A, Cornick, Jennifer E, Kwambana-Adams, Brenda, Law, Pierra Y, Ho, Pak Leung, Antonio, Martin, Everett, Dean B, Dagan, Ron, von Gottberg, Anne, Klugman, Keith P, McGee, Lesley, Breiman, Robert F, and Bentley, Stephen D

Published
2019
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2. Nine differentially expressed genes from a post mortem study and their association with suicidal status in a sample of suicide completers, attempters and controls

Author

Balestri, Martina, Crisafulli, Concetta, Donato, Luigi, Giegling, Ina, Calati, Raffaella, Antypa, Niki, Schneider, Barbara, Marusic, Dragan, Tarozzi, Maria Eugenia, Marusic, Dorjan, Paragi, Metka, Hartmann, Annette M., Konte, Bettina, Marsano, Agnese, Serretti, Alessandro, and Rujescu, Dan

Published
2017
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3. The epidemiology of invasive meningococcal disease in EU/EEA countries, 2004–2014

Author

Kanitz, Elisabeth, Richter, Lukas, Mattheus, Wesley, Bleyenheuft, Corinne, Georgieva, Teodora, Simeonovski, Ivan, Vučina, Vesna Višekruna, Filipović, Sanja Kurečić, Koliou, Maria, Bagatzouni, Despo Pieridou, Krizova, Pavla, Sebestova, Helena, Hoffmann, Steen, Valentiner-Branth, Palle, Kerbo, Natalia, Peetso, Rita, Kuusi, Markku, Toropainen, Maija, Parent, Isabelle, Taha, Muhamed-Kheir, Vogel, Ulrich, Hellenbrand, Wiebke, Georgakopoulou, Theano, Tzanakaki, Georgina, Krisztalovics, Katalin, Tirczka, Tamás, Gudnason, Thorolfur, Hardardottir, Hjordis, O'Lorcain, Piaras, Bennett, Desiree, D'Ancona, Fortunato, Stefanelli, Paola, Savrasova, Larissa, Vasilevska, Darja, Kuprevičienė, Nerija, Liausedienė, Rasa, Demuth, Irène, Scheiden, Gérard, Melillo, Jackie Maistre, Caruana, Paul, van der Ende, Arie, Mollema, Liesbeth, Caugant, Dominique, Blystad, Hans, Skoczyńska, Anna, Zota, Lavinia, Pana, Marina, Grgič Vitek, Marta, Paragi, Metka, Cano, Rosa, Abad, Raquel, Lepp, Tiia, Campbell, Helen, Whittaker, Robert, Dias, Joana Gomes, Ramliden, Miriam, Ködmön, Csaba, Economopoulou, Assimoula, Beer, Netta, and Pastore Celentano, Lucia

Published
2017
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4. Nasopharyngeal carriage of Streptococcus pneumoniae and serotypes indentified among nursing home residents in comparison to the elderly and patients younger than 65 years living in domestic environment

Author

Kolšek-šušteršič Maja, Beg Krasnič Andreja, Mioč Verica, Paragi Metka, and Rifel Janez

Subjects
s. pneumoniae, nasopharyngeal carriage, serotype identification, retirement home residents, vaccination, pnevmokok, nosilstvo v nosnem žrelu, identifikacija serotipov, oskrbovanci doma starejših občanov, cepljenje, Public aspects of medicine, RA1-1270
Abstract

In Slovenia, there is little data available on pneumococcal vaccination rates and no data on asymptomatic NPCR and serotypes in the population of nursing home residents in comparison to the elderly living in domestic environment, therefore the goal was to gain these data.

Published
2017
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5. Centralized and decentralized wastewater-based epidemiology to infer COVID-19 transmission – A brief review

Author

Gonçalves, José, primary, Torres-Franco, Andrés, additional, Rodriguéz, Elisa, additional, Diaz, Israel, additional, Koritnik, Tom, additional, Silva, Priscilla Gomes da, additional, Mesquita, João R., additional, Trkov, Marija, additional, Paragi, Metka, additional, Muñoz, Raúl, additional, and García-Encina, Pedro A., additional

Published
2022
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6. Emergence of a multidrug-resistant and virulent Streptococcus pneumoniae lineage mediates serotype replacement after PCV13: an international whole-genome sequencing study

Author

Lo, Stephanie W, primary, Mellor, Kate, additional, Cohen, Robert, additional, Alonso, Alba Redin, additional, Belman, Sophie, additional, Kumar, Narender, additional, Hawkins, Paulina A, additional, Gladstone, Rebecca A, additional, von Gottberg, Anne, additional, Veeraraghavan, Balaji, additional, Ravikumar, K L, additional, Kandasamy, Rama, additional, Pollard, Sir Andrew J, additional, Saha, Samir K, additional, Bigogo, Godfrey, additional, Antonio, Martin, additional, Kwambana-Adams, Brenda, additional, Mirza, Shaper, additional, Shakoor, Sadia, additional, Nisar, Imran, additional, Cornick, Jennifer E, additional, Lehmann, Deborah, additional, Ford, Rebecca L, additional, Sigauque, Betuel, additional, Turner, Paul, additional, Moïsi, Jennifer, additional, Obaro, Stephen K, additional, Dagan, Ron, additional, Diawara, Idrissa, additional, Skoczyńska, Anna, additional, Wang, Hui, additional, Carter, Philip E, additional, Klugman, Keith P, additional, Rodgers, Gail, additional, Breiman, Robert F, additional, McGee, Lesley, additional, Bentley, Stephen D, additional, Muñoz-Almagro, Carmen, additional, Varon, Emmanuelle, additional, Brooks, Abdullah, additional, Corso, Alejandra, additional, Davydov, Alexander, additional, Maguire, Alison, additional, Kiran, Anmol, additional, Moiane, Benild, additional, Beall, Bernard, additional, Zhao, Chunjiang, additional, Aanensen, David, additional, Everett, Dean, additional, Faccone, Diego, additional, Foster-Nyarko, Ebenezer, additional, Bojang, Ebrima, additional, Egorova, Ekaterina, additional, Voropaeva, Elena, additional, Sampane-Donkor, Eric, additional, Sadowy, Ewa, additional, Nagaraj, Geetha, additional, Mucavele, Helio, additional, Belabbès, Houria, additional, Elmdaghri, Naima, additional, Verani, Jennifer, additional, Keenan, Jeremy, additional, Lees, John, additional, N Nair Thulasee Bhai, Jyothish, additional, Ndlangisa, Kedibone, additional, Zerouali, Khalid, additional, Bentley, Leon, additional, Titov, Leonid, additional, De Gouveia, Linda, additional, Alaerts, Maaike, additional, Ip, Margaret, additional, de Cunto Brandileone, Maria Cristina, additional, Hasanuzzaman, Md, additional, Paragi, Metka, additional, Nurse-Lucas, Michele, additional, du Plessis, Mignon, additional, Ali, Mushal, additional, Croucher, Nicholas, additional, Wolter, Nicole, additional, Givon-Lavi, Noga, additional, Porat, Nurit, additional, Köseoglu Eser, Özgen, additional, Ho, Pak-Leung, additional, Eberechi Akpaka, Patrick, additional, Gagetti, Paula, additional, Tientcheu, Peggy-Estelle, additional, Law, Pierra, additional, Benisty, Rachel, additional, Mostowy, Rafal, additional, Malaker, Roly, additional, Grassi Almeida, Samanta Cristine, additional, Doiphode, Sanjay, additional, Madhi, Shabir, additional, Devi Sekaran, Shamala, additional, Clarke, Stuart, additional, Srifuengfung, Somporn, additional, Nzenze, Susan, additional, Kastrin, Tamara, additional, Ochoa, Theresa, additional, Hryniewicz, Waleria, additional, and Urban, Yulia, additional

Published
2022
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8. Centralized and decentralized wastewater-based epidemiology to infer COVID-19 transmission - A brief review

Author

Carita Gonçalves, José Manuel, Torres Franco, Andrés Felipe, Rodríguez, Elisa, Díaz Villalobos, Israel, Koritnik, Tom, Gomes da Silva, Priscilla, Mesquita, João, Trkov, Marija, Paragi, Metka, Muñoz Torre, Raúl, and García Encina, Pedro Antonio

Subjects
Aguas residuales, COVID-19 (Disease), Infectious Diseases, 3202 Epidemiología, Public Health, Environmental and Occupational Health, Wastewater, COVID-19 (Enfermedad)
Abstract

Producción Científica, Wastewater-based epidemiology has shown to be a promising and innovative approach to measure a wide variety of illicit drugs that are consumed in the communities. In the same way as for illicit drugs, wastewater-based epidemiology is a promising approach to understand the prevalence of viruses in a community-level. The ongoing coronavirus disease 2019 (COVID-19) pandemic created an unprecedented burden on public health and diagnostic laboratories all over the world because of the need for massive laboratory testing. Many studies have shown the applicability of a centralized wastewater-based epidemiology (WBE) approach, where samples are collected at WWTPs. A more recent concept is a decentralized approach for WBE where samples are collected at different points of the sewer system and at polluted water bodies. The second being particularly important in countries where there are insufficient connections from houses to municipal sewage pipelines and thus untreated wastewater is discharged directly in environmental waters. A decentralized approach can be used to focus the value of diagnostic tests in what we call targeted-WBE, by monitoring wastewater in parts of the population where an outbreak is likely to happen, such as student dorms, retirement homes and hospitals. A combination of centralized and decentralized WBE should be considered for an affordable, sustainable, and successful WBE implementation in high-, middle- and low-income countries., Junta de Castilla y León - Fondo Europeo de Desarrollo Regional (projects CLU 2017-09, UIC315 and VA266P20)

Published
2022

9. International links between Streptococcus pneumoniae vaccine serotype 4 sequence type (ST) 801 in Northern European shipyard outbreaks of invasive pneumococcal disease

Author

Gladstone, R.A., primary, Siira, L., additional, Brynildsrud, O.B., additional, Vestrheim, D.F., additional, Turner, P., additional, Clarke, S.C., additional, Srifuengfung, S., additional, Ford, R., additional, Lehmann, D., additional, Egorova, E., additional, Voropaeva, E., additional, Haraldsson, G., additional, Kristinsson, K.G., additional, McGee, L., additional, Breiman, R.F., additional, Bentley, S.D., additional, Sheppard, C.L., additional, Fry, N.K., additional, Corander, J., additional, Toropainen, M, additional, Steens, A., additional, Akpaka, Patrick E, additional, Ampofo, Krow, additional, Antonio, Martin, additional, Balaji, Veeraraghavan, additional, Beall, Bernard W., additional, Belabbès, Houria, additional, Benisty, Rachel, additional, Bigogo, Godfrey, additional, Brooks, Abdullah W, additional, Carter, Philip E., additional, Cornick, Jennifer E., additional, Corso, Alejandra, additional, Cristina de Cunto Brandileone, Maria, additional, Cristine Grassi Almeida, Samanta, additional, Croucher, Nicholas J., additional, Dagan, Ron, additional, Davydov, Alexander, additional, Diawara, Idrissa, additional, Doiphode, Sanjay, additional, du Plessis, Mignon, additional, Elmdaghri, Naima, additional, Köseoglu Eser, Özgen, additional, Everett, Dean B., additional, Faccone, Diego, additional, Gagetti, Paula, additional, Givon-Lavi, Noga, additional, Hasanuzzaman, Md, additional, Hawkins, Paulina A., additional, Hryniewicz, Waleria, additional, Hulten, Kristina G., additional, Ip, Margaret, additional, Kapusta, Aurelie, additional, Kandasamy, Rama, additional, Kastrin, Tamara, additional, Keenan, Jeremy, additional, Klugman, Keith P., additional, Kwambana-Adams, Brenda, additional, Law, Pierra Y., additional, Lees, John A, additional, Leung Ho, Pak, additional, Li, Yuan, additional, Lo, Stephanie W., additional, Ochoa, Theresa J., additional, Madhi, Shabir A., additional, Metcalf, Benjamin J, additional, Moïsi, Jennifer, additional, Mucavele Fundação Manhiça, Helio, additional, Ndlangisa, Kedibone M., additional, Nurse-Lucas, Michele, additional, Nzenze, Susan A., additional, Obaro, Stephen K, additional, Paragi, Metka, additional, Pollard, Andrew J, additional, Ravikumar, KL., additional, Sadowy, Ewa, additional, Saha, Samir K., additional, Sampane-Donkor, Eric, additional, Devi Sekaran, Shamala, additional, Shakoor, Sadia, additional, Shrestha, Shrijana, additional, Sigauque, Betuel, additional, Skoczynska, Anna, additional, Soo ko, Kwan, additional, Tientcheu, Peggy-Estelle, additional, Titov, Leonid, additional, Urban, Yulia, additional, Verani, Jennifer, additional, van Tonder, Andries J., additional, von Gottberg, Anne, additional, and Wolter, Nicole, additional

Published
2022
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12. Assessment of weather and atmospheric pollution as a co-factor in the spread of SARS-CoV-2

Author

Gonçalves, José, Koritnik, Tom, and Paragi, Metka

Subjects
Coronavirus, PM, SARS-CoV-2, Air Pollution, Air quality, SARS-CoV-2, COVID-19, COVID-19, Humans, Original Article, Weather, Pandemics
Abstract

Background and aim: COVID-19 is a persistent and ongoing global pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Non-anthropogenic factors, such as weather conditions and air quality are possible predictors of respiratory diseases, such as COVID-19. Weather conditions may also be a direct cause of biological interactions between SARS-CoV-2 and humans and vary widely between regions. The course of an epidemic is determined by several factors, including demographic and environmental parameters, many of which have an unknown correlation with COVID-19. The goal of this study is to access the influence of ground surface particulate matter and weather parameters on the dissemination of COVID-19 in Ljubljana, Slovenia. Methods: Data on average, minimum and maximum daily temperature, relative humidity; precipitation; sun duration in hours; and daily particle matter (PM10 and PM2.5) was obtained from the Slovenian Environmental Agency. The dataset on the number of daily COVID-19 cases in Ljubljana was obtained from the National Institute of Public Health. Data was divided into three groups: entire dataset; partial lifting of measures (from 1st of June to 30th of September); and less stringent containment measures (from 1st of July to 30th of September). Spearman rank correlation was used to investigate the association between new daily COVID-19 cases and weather data. Results: The weather data and the daily new COVID -19 cases did not show any significant correlation during the entire period under investigation, except for PM 10 (0.30). With the beginning of the less stringent containment measures, five of the six weather parameters correlated significantly with the daily cases of COVID-19. Relative humidity showed the highest correlation coefficient (0.48). Conclusions: The correlations observed are highly dependent on the local policies that were in force during the period under study. The interaction between weather conditions and human behaviour may also be an important factor in understanding the relationship between weather and the spread of COVID -19. (www.actabiomedica.it)

Published
2021

13. Changes in Invasive Pneumococcal Disease Caused by Serotype 1 Following Introduction of PCV10 and PCV13: Findings from the PSERENADE Project

Author

Bennett, Julia C, Hetrich, Marissa K, Quesada, Maria Garcia, Sinkevitch, Jenna N, Knoll, Maria Deloria, Feikin, Daniel R, Zeger, Scott L, Kagucia, Eunice W, Cohen, Adam L, Ampofo, Krow, Brandileone, Maria-Cristina C, Bruden, Dana, Camilli, Romina, Castilla, Jesús, Chan, Guanhao, Cook, Heather, Cornick, Jennifer E, Dagan, Ron, Dalby, Tine, Danis, Kostas, Miguel, Sara de, Wals, Philippe De, Desmet, Stefanie, Georgakopoulou, Theano, Gilkison, Charlotte, Grgic-Vitek, Marta, Hammitt, Laura L, Hilty, Markus, Ho, Pak-Leung, Jayasinghe, Sanjay, Kellner, James D, Kleynhans, Jackie, Knol, Mirjam J, Kozakova, Jana, Kristinsson, Karl G, Ladhani, Shamez N, MacDonald, Laura, Mackenzie, Grant A, Mad'arová, Lucia, McGeer, Allison, Mereckiene, Jolita, Morfeldt, Eva, Mungun, Tuya, Muñoz-Almagro, Carmen, Nuorti, J Pekka, Paragi, Metka, Pilishvili, Tamara, Puentes, Rodrigo, Saha, Samir K, Khan, Aalisha Sahu, Savrasova, Larisa, Scott, J Anthony, Skoczyńska, Anna, Suga, Shigeru, Linden, Mark van der, Verani, Jennifer R, Gottberg, Anne von, Winje, Brita A, Yildirim, Inci, Zerouali, Khalid, Hayford, Kyla, and The Pserenade Team

Subjects
serotypes, pneumococcal conjugate vaccines, vaccine impact, invasive pneumococcal disease
Abstract

Streptococcus pneumoniae serotype 1 (ST1) was an important cause of invasive pneumococcal disease (IPD) globally before the introduction of pneumococcal conjugate vaccines (PCVs) containing ST1 antigen. The Pneumococcal Serotype Replacement and Distribution Estimation (PSERENADE) project gathered ST1 IPD surveillance data from sites globally and aimed to estimate PCV10/13 impact on ST1 IPD incidence. We estimated ST1 IPD incidence rate ratios (IRRs) comparing the pre-PCV10/13 period to each post-PCV10/13 year by site using a Bayesian multi-level, mixed-effects Poisson regression and all-site IRRs using a linear mixed-effects regression (N = 45 sites). Following PCV10/13 introduction, the incidence rate (IR) of ST1 IPD declined among all ages. After six years of PCV10/13 use, the all-site IRR was 0.05 (95% credibility interval 0.04-0.06) for all ages, 0.05 (0.04-0.05) for

Published
2021

16. A Laboratory-Based Surveillance Study of Invasive Neisseria meningitidis, Streptococcus pneumoniae, and Haemophilus influenzae Diseases in a Serbian Pediatric Population—Implications for Vaccination

Author

Delic, Snezana, primary, Mijac, Vera, additional, Gajic, Ina, additional, Kekic, Dusan, additional, Ranin, Lazar, additional, Jegorovic, Boris, additional, Culic, Davor, additional, Cirkovic, Valentina, additional, Siljic, Marina, additional, Stanojevic, Maja, additional, Paragi, Metka, additional, Markovic, Milos, additional, and Opavski, Natasa, additional

Published
2021
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18. Automated digital reporting of clinical laboratory information to national public health surveillance systems, results of a EU/EEA survey, 2018

Author

Leitmeyer, Katrin, Espinosa, Laura, Broberg, Eeva K., Struelens, Marc J., Allerberger, Franz, Dupont, Yves, Van Gucht, Steven, Quoilin, Sophie, Christova, Iva, Hunjak, Blaženka, Karagiannis, Christos, Křížová, Pavla, Částková, Jitka, Nielsen, Eva Møller, Kähler, Jonas, Peetso, Rita, Salmenlinna, Saara, Möttönen, Teemu, Coignard, Bruno, Diercke, Michaela, Vatopoulos, Alkiviadis, Tóth, Ákos, Kristinsson, Karl Gustaf, McNamara, Eleanor, Pantosi, Annalisa, Mavcutko, Violeta, Griškevičius, Algirdas, Mossong, Joël, Barbara, Christopher, Kortbeek, Titia, Caugant, Dominique A, Dahle, Ulf R, Vold, Line, Skoczyńska, Anna, Machado, Jorge, Ionescu, Gabriel, Madarova, Lucia, Avdičová, Mária, Paragi, Metka, Vazquez, Julio Moreno, Wisell, Karin Tegmark, and Zambon, Maria

Subjects
medicine.medical_specialty, Epidemiology, Surveillance Methods, communicable diseases, automated data reporting, early-warning, Antimicrobial Stewardship, Public health surveillance, Virology, medicine, media_common.cataloged_instance, Electronic Health Records, Humans, antimicrobial resistance, European Union, European union, Data reporting, Disease Notification, media_common, Communicable disease, Surveillance, business.industry, electronic laboratory reporting, Information Dissemination, Public health, Public Health, Environmental and Occupational Health, Information technology, Clinical Laboratory Services, medicine.disease, public health surveillance, digital surveillance, Europe, Management information systems, Epidemiological Monitoring, clinical microbiology testing, Business, Medical emergency, Public Health
Abstract

Background Timely reporting of microbiology test results is essential for infection management. Automated, machine-to-machine (M2M) reporting of diagnostic and antimicrobial resistance (AMR) data from laboratory information management systems (LIMS) to public health agencies improves timeliness and completeness of communicable disease surveillance. Aim We surveyed microbiology data reporting practices for national surveillance of EU-notifiable diseases in European Union/European Economic Area (EU/EEA) countries in 2018. Methods European Centre for Disease Prevention and Control (ECDC) National Microbiology and Surveillance Focal Points completed a questionnaire on the modalities and scope of clinical microbiology laboratory data reporting. Results Complete data were provided for all 30 EU/EEA countries. Clinical laboratories used a LIMS in 28 countries. LIMS data on EU-notifiable diseases and AMR were M2M-reported to the national level in 14 and nine countries, respectively. In the 14 countries, associated demographic data reported allowed the de-duplication of patient reports. In 13 countries, M2M-reported data were used for cluster detection at the national level. M2M laboratory data reporting had been validated against conventional surveillance methods in six countries, and replaced those in five. Barriers to M2M reporting included lack of information technology support and financial incentives. Conclusion M2M-reported laboratory data were used for national public health surveillance and alert purposes in nearly half of the EU/EEA countries in 2018. Reported data on infectious diseases and AMR varied in extent and disease coverage across countries and laboratories. Improving automated laboratory-based surveillance will depend on financial and regulatory incentives, and harmonisation of health information and communication systems.

Published
2020

24. Pneumococcal lineages associated with serotype replacement and antibiotic resistance in childhood invasive pneumococcal disease in the post-PCV13 era: an international whole-genome sequencing study

Author

Lo, Stephanie W, primary, Gladstone, Rebecca A, additional, van Tonder, Andries J, additional, Lees, John A, additional, du Plessis, Mignon, additional, Benisty, Rachel, additional, Givon-Lavi, Noga, additional, Hawkins, Paulina A, additional, Cornick, Jennifer E, additional, Kwambana-Adams, Brenda, additional, Law, Pierra Y, additional, Ho, Pak Leung, additional, Antonio, Martin, additional, Everett, Dean B, additional, Dagan, Ron, additional, von Gottberg, Anne, additional, Klugman, Keith P, additional, McGee, Lesley, additional, Breiman, Robert F, additional, Bentley, Stephen D, additional, Brooks, Abdullah W, additional, Corso, Alejandra, additional, Davydov, Alexander, additional, Maguire, Alison, additional, Pollard, Andrew, additional, Kiran, Anmol, additional, Skoczynska, Anna, additional, Moiane, Benild, additional, Beall, Bernard, additional, Sigauque, Betuel, additional, Aanensen, David, additional, Lehmann, Deborah, additional, Faccone, Diego, additional, Foster-Nyarko, Ebenezer, additional, Bojang, Ebrima, additional, Egorova, Ekaterina, additional, Voropaeva, Elena, additional, Sampane-Donkor, Eric, additional, Sadowy, Ewa, additional, Bigogo, Godfrey, additional, Mucavele, Helio, additional, Belabbès, Houria, additional, Diawara, Idrissa, additional, Moïsi, Jennifer, additional, Verani, Jennifer, additional, Keenan, Jeremy, additional, Nair Thulasee Bhai, Jyothish N, additional, Ndlangisa, Kedibone M, additional, Zerouali, Khalid, additional, Ravikumar, K L, additional, Titov, Leonid, additional, De Gouveia, Linda, additional, Alaerts, Maaike, additional, Ip, Margaret, additional, de Cunto Brandileone, Maria Cristina, additional, Hasanuzzaman, Md, additional, Paragi, Metka, additional, Nurse-Lucas, Michele, additional, Ali, Mushal, additional, Elmdaghri, Naima, additional, Croucher, Nicholas, additional, Wolter, Nicole, additional, Porat, Nurit, additional, Eser, Özgen Köseoglu, additional, Akpaka, Patrick E, additional, Turner, Paul, additional, Gagetti, Paula, additional, Tientcheu, Peggy-Estelle, additional, Carter, Philip E, additional, Mostowy, Rafal, additional, Kandasamy, Rama, additional, Ford, Rebecca, additional, Henderson, Rebecca, additional, Malaker, Roly, additional, Shakoor, Sadia, additional, Grassi Almeida, Samanta Cristine, additional, Saha, Samir K, additional, Doiphode, Sanjay, additional, Madhi, Shabir A, additional, Devi Sekaran, Shamala, additional, Srifuengfung, Somporn, additional, Obaro, Stephen, additional, Clarke, Stuart C, additional, Nzenze, Susan A, additional, Kastrin, Tamara, additional, Ochoa, Theresa J, additional, Balaji, Veeraraghavan, additional, Hryniewicz, Waleria, additional, and Urban, Yulia, additional

Published
2019
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26. Nasopharyngeal carriage of Streptococcus pneumoniae and serotypes indentified among nursing home residents in comparison to the elderly and patients younger than 65 years living in domestic environment: Nosilstvo pnevmokoka v nosnem žrelu in identifikacija serotipov med oskrbovanci doma starejših občanov v primerjavi s starostniki in mlajšimi od 65 let, ki živijo v domačem okolju

Author

Beg Krasnič, Andreja, Kolšek-Šušteršič, Maja, Mioč, Verica, Paragi, Metka, and Rifel, Janez

Published
2017

27. A mosaic tetracycline resistance gene tet(S/M) detected in an MDR pneumococcal CC230 lineage that underwent capsular switching in South Africa.

Author

Lo, Stephanie W, Gladstone, Rebecca A, Tonder, Andries J van, Plessis, Mignon Du, Cornick, Jennifer E, Hawkins, Paulina A, Madhi, Shabir A, Nzenze, Susan A, Kandasamy, Rama, Ravikumar, K L, Elmdaghri, Naima, Kwambana-Adams, Brenda, Almeida, Samanta Cristine Grassi, Skoczynska, Anna, Egorova, Ekaterina, Titov, Leonid, Saha, Samir K, Paragi, Metka, Everett, Dean B, and Antonio, Martin

Subjects
TETRACYCLINES, DRUG resistance in bacteria, PNEUMOCOCCAL vaccines, GENES, STREPTOCOCCUS pneumoniae, PENICILLIN, RESEARCH, SEQUENCE analysis, RESEARCH methodology, MEDICAL cooperation, EVALUATION research, STREPTOCOCCUS, SEROTYPES, COMPARATIVE studies, RESEARCH funding, DRUG resistance in microorganisms, ANTIBIOTICS, PHARMACODYNAMICS
Abstract

Objectives: We reported tet(S/M) in Streptococcus pneumoniae and investigated its temporal spread in relation to nationwide clinical interventions.Methods: We whole-genome sequenced 12 254 pneumococcal isolates from 29 countries on an Illumina HiSeq sequencer. Serotype, multilocus ST and antibiotic resistance were inferred from genomes. An SNP tree was built using Gubbins. Temporal spread was reconstructed using a birth-death model.Results: We identified tet(S/M) in 131 pneumococcal isolates and none carried other known tet genes. Tetracycline susceptibility testing results were available for 121 tet(S/M)-positive isolates and all were resistant. A majority (74%) of tet(S/M)-positive isolates were from South Africa and caused invasive diseases among young children (59% HIV positive, where HIV status was available). All but two tet(S/M)-positive isolates belonged to clonal complex (CC) 230. A global phylogeny of CC230 (n=389) revealed that tet(S/M)-positive isolates formed a sublineage predicted to exhibit resistance to penicillin, co-trimoxazole, erythromycin and tetracycline. The birth-death model detected an unrecognized outbreak of this sublineage in South Africa between 2000 and 2004 with expected secondary infections (effective reproductive number, R) of ∼2.5. R declined to ∼1.0 in 2005 and <1.0 in 2012. The declining epidemic could be related to improved access to ART in 2004 and introduction of pneumococcal conjugate vaccine (PCV) in 2009. Capsular switching from vaccine serotype 14 to non-vaccine serotype 23A was observed within the sublineage.Conclusions: The prevalence of tet(S/M) in pneumococci was low and its dissemination was due to an unrecognized outbreak of CC230 in South Africa. Capsular switching in this MDR sublineage highlighted its potential to continue to cause disease in the post-PCV13 era. [ABSTRACT FROM AUTHOR]

Published
2020
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28. Establishment of the European meningococcal strain collection genome library (EMSC-GL) for the 2011 to 2012 epidemiological year

Author

Bratcher, Holly B, primary, Brehony, Carina, additional, Heuberger, Sigrid, additional, Pieridou-Bagatzouni, Despo, additional, Křížová, Pavla, additional, Hoffmann, Steen, additional, Toropainen, Maija, additional, Taha, Muhamed-Kheir, additional, Claus, Heike, additional, Tzanakaki, Georgina, additional, Erdôsi, Tímea, additional, Galajeva, Jelena, additional, van der Ende, Arie, additional, Skoczyńska, Anna, additional, Pana, Marina, additional, Vaculíková, Alena, additional, Paragi, Metka, additional, Maiden, Martin CJ, additional, and Caugant, Dominique A, additional

Published
2018
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29. The epidemiology of invasive meningococcal disease in EU/EEA countries, 2004–2014

Author

Whittaker, Robert, primary, Dias, Joana Gomes, additional, Ramliden, Miriam, additional, Ködmön, Csaba, additional, Economopoulou, Assimoula, additional, Beer, Netta, additional, Pastore Celentano, Lucia, additional, Kanitz, Elisabeth, additional, Richter, Lukas, additional, Mattheus, Wesley, additional, Bleyenheuft, Corinne, additional, Georgieva, Teodora, additional, Simeonovski, Ivan, additional, Vučina, Vesna Višekruna, additional, Filipović, Sanja Kurečić, additional, Koliou, Maria, additional, Bagatzouni, Despo Pieridou, additional, Krizova, Pavla, additional, Sebestova, Helena, additional, Hoffmann, Steen, additional, Valentiner-Branth, Palle, additional, Kerbo, Natalia, additional, Peetso, Rita, additional, Kuusi, Markku, additional, Toropainen, Maija, additional, Parent, Isabelle, additional, Taha, Muhamed-Kheir, additional, Vogel, Ulrich, additional, Hellenbrand, Wiebke, additional, Georgakopoulou, Theano, additional, Tzanakaki, Georgina, additional, Krisztalovics, Katalin, additional, Tirczka, Tamás, additional, Gudnason, Thorolfur, additional, Hardardottir, Hjordis, additional, O'Lorcain, Piaras, additional, Bennett, Desiree, additional, D'Ancona, Fortunato, additional, Stefanelli, Paola, additional, Savrasova, Larissa, additional, Vasilevska, Darja, additional, Kuprevičienė, Nerija, additional, Liausedienė, Rasa, additional, Demuth, Irène, additional, Scheiden, Gérard, additional, Melillo, Jackie Maistre, additional, Caruana, Paul, additional, van der Ende, Arie, additional, Mollema, Liesbeth, additional, Caugant, Dominique, additional, Blystad, Hans, additional, Skoczyńska, Anna, additional, Zota, Lavinia, additional, Pana, Marina, additional, Grgič Vitek, Marta, additional, Paragi, Metka, additional, Cano, Rosa, additional, Abad, Raquel, additional, Lepp, Tiia, additional, and Campbell, Helen, additional

Published
2017
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30. Meningococcal serogroup Y disease in Europe: Continuation of high importance in some European regions in 2013

Author

Broeker, Michael Emonet, Stephane Fazio, Cecilia Jacobsson, Susanne Koliou, Maria Kuusi, Markku Pace, David Paragi, Metka Pysik, Alexander Simoes, Maria Joao Skoczynska, Anna and Stefanelli, Paola Toropainen, Maija Taha, Muhamed-Kheir and Tzanakaki, Georgina

Abstract

Neisseria meningitidis or meningococcus is divided into 12 distinct serogroups of which A, B, C, W, X, and Y are medically most important and cause health problems in different parts of the world. The epidemiology of N. meningitidis is unpredictable over time and across geographic regions. Globally, serogoup A has been prevalent in the African meningitis belt whereas serogroup B and C have predominated in Europe. In a paper published earlier in this journal(1), an increase in serogroup Y invasive meningococcal disease (IMD) in some European countries was reported based on the epidemiological data for 2010, 2011 and 2012. Here, we report additional data from 30 European countries indicating that high or increased serogroup Y disease levels have continued in 2013 in certain regions of Europe. In the Western and Central Europe, there were no major changes in the proportion of serogroup Y IMD cases in 2013 compared to 2012. In the Scandinavian countries, proportion of serogroup Y disease remained high, ranging from 26% to 51% in 2013. This was in contrast to Baltic, Eastern and most Southern European countries, where the proportion of serogroup Y IMD was low similarly to previous years. For the last 2 decades, the mean age of patients affected by serogroup Y was 41 y for 7 countries from which data was available and 50% of cases were in patients aged 45 to 88 y. The age distribution of serogroup Y was bimodal and did not change significantly despite the increase of the total number and the proportion of serogroup Y IMD in some European regions.

Published
2015

31. Lack of correlation between reduced outpatient consumption of macrolides and macrolide resistance of invasive Streptococcus pneumoniaeisolates in Slovenia during 1997–2017

Author

Kastrin, Tamara, Paragi, Metka, Erčulj, Vanja, Žohar Čretnik, Tjaša, Bajec, Tom, and Čižman, Milan

Abstract

•In Slovenia macrolide consumption decreased by 42.4% in the period 1997 to 2017.•The macrolide resistance of invasive pneumococci increased from 5.8% to 12.8%.•Spread of a clone explains the increased macrolide resistance among invasive pneumococci.•Reduced consumption of antibiotics is not enough to reverse microbial resistance.

Published
2019
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35. Meningococcal serogroup Y disease in Europe: Continuation of high importance in some European regions in 2013

Author

Bröker, Michael, primary, Emonet, Stéphane, additional, Fazio, Cecilia, additional, Jacobsson, Susanne, additional, Koliou, Maria, additional, Kuusi, Markku, additional, Pace, David, additional, Paragi, Metka, additional, Pysik, Alexander, additional, Simões, Maria João, additional, Skoczynska, Anna, additional, Stefanelli, Paola, additional, Toropainen, Maija, additional, Taha, Muhamed-Kheir, additional, and Tzanakaki, Georgina, additional

Published
2015
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36. Target gene sequencing to characterize the penicillin G susceptibility of Neisseria meningitidis

Author

Taha, Muhamed-Kheir Vazquez, Julio A. Hong, Eva Bennett, Desiree E. Bertrand, Sophie Bukovski, Suzana Cafferkey, Mary T. Carion, Frangoise Christensen, Jens Jorgen Diggle, Mathew and Edwards, Giles Enriquez, Rocio Fazio, Cecilia Frosch, Matthias Heuberger, Sigrid Hoffmann, Steen Jolley, Keith A. and Kadlubowski, Marcin Kechrid, Amel Kesanopoulos, Konstantinos and Kriz, Paula Larnbertsen, Lotte Levenet, Ileanna Musilek, Martin Paragi, Metka Saguer, Aouatef Skoczynska, Anna and Stefanelli, Paola Thulin, Sara Tzanakaki, Georgina Unemo, Magnus Vogel, Ulrich Zarantonelli, Maria Leticia

Abstract

Clinical isolates of Neisseria meningitidis with reduced susceptibility to penicillin G (intermediate isolates, Pen(I)) harbor alterations in the penA gene encoding the penicillin binding protein 2 (PBP2). A 402-bp DNA fragment in the 3’ half of penA was sequenced from a collection of 1,670 meningococcal clinical isolates from 22 countries that spanned 60 years. Phenotyping, genotyping, and the determination of MICs of penicillin G were also performed. A total of 139 different pen,4 alleles were detected with 38 alleles that were highly related, clustered together in maximum-likelihood analysis and corresponded to the penicillin G-susceptible isolates. The remaining 101 penA alleles were highly diverse, corresponded to different genotypes or phenotypes, and accounted for 38% of isolates, but no clonal expansion was detected. Analysis of the altered alleles that were represented by at least five isolates showed high correlation with the Pen(I) phenotype. The deduced amino acid sequence of the corresponding PBP2 comprised five amino acid residues that were always altered. This correlation was not complete for rare alleles, suggesting that other mechanisms may also be involved in conferring reduced susceptibility to penicillin. Evidence of mosaic structures through events of interspecies recombination was also detected in altered alleles. A new website was created based on the data from this work (http://neisseria.org/nm/typing/penA). These data argue for the use of penA sequencing to identify isolates with reduced susceptibility to penicillin G and as a tool to improve typing of meningococcal isolates, as well as to analyze DNA exchange among Neisseria species.

Published
2007

38. Target Gene Sequencing To Characterize the Penicillin G Susceptibility of Neisseria meningitidis

Author

Taha, Muhamed-Kheir, primary, Vázquez, Julio A., additional, Hong, Eva, additional, Bennett, Desiree E., additional, Bertrand, Sophie, additional, Bukovski, Suzana, additional, Cafferkey, Mary T., additional, Carion, Françoise, additional, Christensen, Jens Jørgen, additional, Diggle, Mathew, additional, Edwards, Giles, additional, Enríquez, Rocío, additional, Fazio, Cecilia, additional, Frosch, Matthias, additional, Heuberger, Sigrid, additional, Hoffmann, Steen, additional, Jolley, Keith A., additional, Kadlubowski, Marcin, additional, Kechrid, Amel, additional, Kesanopoulos, Konstantinos, additional, Kriz, Paula, additional, Lambertsen, Lotte, additional, Levenet, Ileanna, additional, Musilek, Martin, additional, Paragi, Metka, additional, Saguer, Aouatef, additional, Skoczynska, Anna, additional, Stefanelli, Paola, additional, Thulin, Sara, additional, Tzanakaki, Georgina, additional, Unemo, Magnus, additional, Vogel, Ulrich, additional, and Zarantonelli, Maria Leticia, additional

Published
2007
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43. Regional variation in antibiotic use in children in Slovenia.

Author

Čižman, Milan, Vrečar, Vida, Starašinič, Nina, Limbek, Vesna, Bajec, Tom, Čad, Silva Pečar, Rokavec, Tatjana, and Paragi, Metka

Subjects
*ANTIBIOTICS, *DRUG utilization, *PENICILLIN, *BRONCHITIS in children, *URINARY tract infections, *OTITIS media in children, *THERAPEUTICS, EFFECT of drugs on streptococcus pneumoniae
Abstract

Differences in antibiotic consumption are not seen only in different countries but also within countries. We retrospectively (2000-2012) analyzed the consumption of antibiotics in children in 9 regions in Slovenia and tried to find out the determinants of regional variation in the year 2006 and 2009. For each year we saw a 1.5 fold (range 1.2-1.8) difference between the regions with the lowest and the highest total antibiotic consumption. The interregional use of different antibiotic classes varied up to 8.5-fold. No correlation between antibiotic consumption and socioeconomic determinants was found. Very high and high correlation was found between antibiotic consumption and incidence of common acute respiratory tract infections like upper respiratory tract infections, sore throat, acute laryngitis/tracheitis and acute bronchitis. In 2006 there was a correlation between antibiotic use, urinary tract infections and acute otitis media. High overall consumption of antibiotics especially penicillins was associated with higher resistance of S. pneumoniae to penicillin. Regional variation in antibiotic use and its pattern are seen also in a small country as Slovenia and indicate the need for improvement. [ABSTRACT FROM AUTHOR]

Published
2014
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44. Nine differentially expressed genes from a post mortem study and their association with suicidal status in a sample of suicide completers, attempters and controls

Author

Bettina Konte, Martina Balestri, Raffaella Calati, Barbara Schneider, Agnese Marsano, Dorjan Marušič, Niki Antypa, Concetta Crisafulli, Ina Giegling, Dan Rujescu, Alessandro Serretti, Dragan Marušič, Maria Eugenia Tarozzi, Metka Paragi, Annette M. Hartmann, Luigi Donato, Balestri, M, Crisafulli, C, Donato, L, Giegling, I, Calati, R, Antypa, N, Schneider, B, Marusic, D, Tarozzi, M, Paragi, M, Hartmann, A, Konte, B, Marsano, A, Serretti, A, Rujescu, D, Balestri, Martina, Crisafulli, Concetta, Donato, Luigi, Giegling, Ina, Calati, Raffaella, Antypa, Niki, Schneider, Barbara, Marusic, Dragan, Tarozzi, Maria Eugenia, Marusic, Dorjan, Paragi, Metka, Hartmann, Annette M., Konte, Bettina, Marsano, Agnese, Serretti, Alessandro, and Rujescu, Dan

Subjects
Adult, Male, 0301 basic medicine, Oncology, medicine.medical_specialty, Candidate gene, Genotype, media_common.quotation_subject, Post-mortem, Suicide, Attempted, PDGFRB, Anger, Polymorphism, Single Nucleotide, Suicidal Ideation, Candidate genes, 03 medical and health sciences, 0302 clinical medicine, Arts and Humanities (miscellaneous), Surveys and Questionnaires, Internal medicine, medicine, Humans, Receptor-Like Protein Tyrosine Phosphatases, Class 7, Allele, Candidate genes, Personality, Post-mortem, Suicide, Arts and Humanities (miscellaneous), Psychiatry and Mental Health, Biological Psychiatry, Biological Psychiatry, Aged, media_common, Extracellular Matrix Proteins, Haplotype, Middle Aged, Psychiatry and Mental health, Suicide, 030104 developmental biology, Endophenotype, Etiology, Female, Autopsy, Psychology, Self-Injurious Behavior, 030217 neurology & neurosurgery, Clinical psychology, Personality
Abstract

Several lines of evidence indicate that suicidal behaviour is partly heritable, with multiple genes implicated in its aetiology. We focused on nine genes (S100A13, EFEMP1, PCDHB5, PDGFRB, CDCA7L, SCN2B, PTPRR, MLC1 and ZFP36) which we previously detected as differentially expressed in the cortex of suicide victims compared to controls. We investigated 84 variants within these genes in 495 suicidal subjects (299 completers and 196 attempters) and 1513 controls (109 post-mortem and 1404 healthy). We evaluated associations with: 1) suicidal phenotype; 2) possible endophenotypes for suicidal behaviour. Overall positive results did not survive the correction threshold. However, we found a nominally different distribution of EFEMP1 genotypes, alleles and haplotypes between suicidal subjects and controls, results that were partially replicated when we separately considered the subgroup of suicide completers and post-mortem controls. A weaker association emerged also for PTPRR. Both EFEMP1 and PTPRR genes were also related to possible endophenotypes for suicidal behaviour such as anger, depression-anxiety and fatigue. Because of the large number of analyses performed and the low significance values further replication are mandatory. Nevertheless, neurotrophic gene variants, in particular EFEMP1 and PTPRR, may have a role in the pathogenesis of suicidal behaviour.

Published
2017

45. A Streptococcus pneumoniae lineage usually associated with pneumococcal conjugate vaccine (PCV) serotypes is the most common cause of serotype 35B invasive disease in South Africa, following routine use of PCV.

Author

Ndlangisa KM, du Plessis M, Lo S, de Gouveia L, Chaguza C, Antonio M, Kwambana-Adams B, Cornick J, Everett DB, Dagan R, Hawkins PA, Beall B, Corso A, Grassi Almeida SC, Ochoa TJ, Obaro S, Shakoor S, Donkor ES, Gladstone RA, Ho PL, Paragi M, Doiphode S, Srifuengfung S, Ford R, Moïsi J, Saha SK, Bigogo G, Sigauque B, Eser ÖK, Elmdaghri N, Titov L, Turner P, Kumar KLR, Kandasamy R, Egorova E, Ip M, Breiman RF, Klugman KP, McGee L, Bentley SD, von Gottberg A, and The Global Pneumococcal Sequencing Consortium

Subjects
Humans, Pneumococcal Vaccines, Serogroup, South Africa epidemiology, Vaccines, Conjugate, Pneumococcal Infections epidemiology, Pneumococcal Infections prevention & control, Streptococcus pneumoniae genetics
Abstract

Pneumococcal serotype 35B is an important non-conjugate vaccine (non-PCV) serotype. Its continued emergence, post-PCV7 in the USA, was associated with expansion of a pre-existing 35B clone (clonal complex [CC] 558) along with post-PCV13 emergence of a non-35B clone previously associated with PCV serotypes (CC156). This study describes lineages circulating among 35B isolates in South Africa before and after PCV introduction. We also compared 35B isolates belonging to a predominant 35B lineage in South Africa (GPSC5), with isolates belonging to the same lineage in other parts of the world. Serotype 35B isolates that caused invasive pneumococcal disease in South Africa in 2005-2014 were characterized by whole-genome sequencing (WGS). Multi-locus sequence types and global pneumococcal sequence clusters (GPSCs) were derived from WGS data of 63 35B isolates obtained in 2005-2014. A total of 262 isolates that belong to GPSC5 (115 isolates from South Africa and 147 from other countries) that were sequenced as part of the global pneumococcal sequencing (GPS) project were included for comparison. Serotype 35B isolates from South Africa were differentiated into seven GPSCs and GPSC5 was most common (49 %, 31/63). While 35B was the most common serotype among GPSC5/CC172 isolates in South Africa during the PCV13 period (66 %, 29/44), 23F was the most common serotype during both the pre-PCV (80 %, 37/46) and PCV7 period (32 %, 8/25). Serotype 35B represented 15 % (40/262) of GPSC5 isolates within the global GPS database and 75 % (31/40) were from South Africa. The predominance of the GPSC5 lineage within non-vaccine serotype 35B, is possibly unique to South Africa and warrants further molecular surveillance of pneumococci.

Published
2022
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46. Assessment of weather and atmospheric pollution as a co-factor in the spread of SARS-CoV-2.

Author

Gonçalves J, Koritnik T, and Paragi M

Subjects
Humans, Pandemics, SARS-CoV-2, Weather, Air Pollution adverse effects, Air Pollution analysis, COVID-19
Abstract

Background and Aim: COVID-19 is a persistent and ongoing global pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Non-anthropogenic factors, such as weather conditions and air quality are possible predictors of respiratory diseases, such as COVID-19. Weather conditions may also be a direct cause of biological interactions between SARS-CoV-2 and humans and vary widely between regions. The course of an epidemic is determined by several factors, including demographic and environmental parameters, many of which have an unknown correlation with COVID-19. The goal of this study is to access the influence of ground surface particulate matter and weather parameters on the dissemination of COVID-19 in Ljubljana, Slovenia., Methods: Spearman rank correlation was used to investigate the association between new daily COVID-19 cases and weather data., Results: The current study has found correlations between weather variables and PM particles with new cases of COVID-19., Conclusions: The correlations observed are highly dependent on the local policies that were in force during the period under study. The interaction between weather conditions and human behaviour may also be an important factor in understanding the relationship between weather and the spread of COVID -19.

Published
2021
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47. Global Landscape Review of Serotype-Specific Invasive Pneumococcal Disease Surveillance among Countries Using PCV10/13: The Pneumococcal Serotype Replacement and Distribution Estimation (PSERENADE) Project.

Author

Deloria Knoll M, Bennett JC, Garcia Quesada M, Kagucia EW, Peterson ME, Feikin DR, Cohen AL, Hetrich MK, Yang Y, Sinkevitch JN, Ampofo K, Aukes L, Bacci S, Bigogo G, Brandileone MC, Bruce MG, Camilli R, Castilla J, Chan G, Chanto Chacón G, Ciruela P, Cook H, Corcoran M, Dagan R, Danis K, de Miguel S, De Wals P, Desmet S, Galloway Y, Georgakopoulou T, Hammitt LL, Hilty M, Ho PL, Jayasinghe S, Kellner JD, Kleynhans J, Knol MJ, Kozakova J, Kristinsson KG, Ladhani SN, Lara CS, León ME, Lepp T, Mackenzie GA, Mad'arová L, McGeer A, Mungun T, Mwenda JM, Nuorti JP, Nzoyikorera N, Oishi K, De Oliveira LH, Paragi M, Pilishvili T, Puentes R, Rafai E, Saha SK, Savrasova L, Savulescu C, Scott JA, Scott KJ, Serhan F, Setchanova LP, Sinkovec Zorko N, Skoczyńska A, Swarthout TD, Valentiner-Branth P, van der Linden M, Vestrheim DF, von Gottberg A, Yildirim I, and Hayford K

Abstract

Serotype-specific surveillance for invasive pneumococcal disease (IPD) is essential for assessing the impact of 10- and 13-valent pneumococcal conjugate vaccines (PCV10/13). The Pneumococcal Serotype Replacement and Distribution Estimation (PSERENADE) project aimed to evaluate the global evidence to estimate the impact of PCV10/13 by age, product, schedule, and syndrome. Here we systematically characterize and summarize the global landscape of routine serotype-specific IPD surveillance in PCV10/13-using countries and describe the subset that are included in PSERENADE. Of 138 countries using PCV10/13 as of 2018, we identified 109 with IPD surveillance systems, 76 of which met PSERENADE data collection eligibility criteria. PSERENADE received data from most (n = 63, 82.9%), yielding 240,639 post-PCV10/13 introduction IPD cases. Pediatric and adult surveillance was represented from all geographic regions but was limited from lower income and high-burden countries. In PSERENADE, 18 sites evaluated PCV10, 42 PCV13, and 17 both; 17 sites used a 3 + 0 schedule, 38 used 2 + 1, 13 used 3 + 1, and 9 used mixed schedules. With such a sizeable and generally representative dataset, PSERENADE will be able to conduct robust analyses to estimate PCV impact and inform policy at national and global levels regarding adult immunization, schedule, and product choice, including for higher valency PCVs on the horizon.

Published
2021
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48. Changes in Invasive Pneumococcal Disease Caused by Streptococcus pneumoniae Serotype 1 Following Introduction of PCV10 and PCV13: Findings from the PSERENADE Project.

Author

Bennett JC, Hetrich MK, Garcia Quesada M, Sinkevitch JN, Deloria Knoll M, Feikin DR, Zeger SL, Kagucia EW, Cohen AL, Ampofo K, Brandileone MC, Bruden D, Camilli R, Castilla J, Chan G, Cook H, Cornick JE, Dagan R, Dalby T, Danis K, de Miguel S, De Wals P, Desmet S, Georgakopoulou T, Gilkison C, Grgic-Vitek M, Hammitt LL, Hilty M, Ho PL, Jayasinghe S, Kellner JD, Kleynhans J, Knol MJ, Kozakova J, Kristinsson KG, Ladhani SN, MacDonald L, Mackenzie GA, Mad'arová L, McGeer A, Mereckiene J, Morfeldt E, Mungun T, Muñoz-Almagro C, Nuorti JP, Paragi M, Pilishvili T, Puentes R, Saha SK, Sahu Khan A, Savrasova L, Scott JA, Skoczyńska A, Suga S, van der Linden M, Verani JR, von Gottberg A, Winje BA, Yildirim I, Zerouali K, and Hayford K

Abstract

Streptococcus pneumoniae serotype 1 (ST1) was an important cause of invasive pneumococcal disease (IPD) globally before the introduction of pneumococcal conjugate vaccines (PCVs) containing ST1 antigen. The Pneumococcal Serotype Replacement and Distribution Estimation (PSERENADE) project gathered ST1 IPD surveillance data from sites globally and aimed to estimate PCV10/13 impact on ST1 IPD incidence. We estimated ST1 IPD incidence rate ratios (IRRs) comparing the pre-PCV10/13 period to each post-PCV10/13 year by site using a Bayesian multi-level, mixed-effects Poisson regression and all-site IRRs using a linear mixed-effects regression (N = 45 sites). Following PCV10/13 introduction, the incidence rate (IR) of ST1 IPD declined among all ages. After six years of PCV10/13 use, the all-site IRR was 0.05 (95% credibility interval 0.04-0.06) for all ages, 0.05 (0.04-0.05) for <5 years of age, 0.08 (0.06-0.09) for 5-17 years, 0.06 (0.05-0.08) for 18-49 years, 0.06 (0.05-0.07) for 50-64 years, and 0.05 (0.04-0.06) for ≥65 years. PCV10/13 use in infant immunization programs was followed by a 95% reduction in ST1 IPD in all ages after approximately 6 years. Limited data availability from the highest ST1 disease burden countries using a 3+0 schedule constrains generalizability and data from these settings are needed.

Published
2021
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