Search

Your search keyword '"Cornick, Jennifer E."' showing total 49 results
Start Over Author "Cornick, Jennifer E."
49 results on '"Cornick, Jennifer E."'

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

Author

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

Published
2022
Full Text
View/download PDF

2. Shigella Detection and Molecular Serotyping With a Customized TaqMan Array Card in the Enterics for Global Health (EFGH): Shigella Surveillance Study

Author

Liu, Jie, primary, Garcia Bardales, Paul F, additional, Islam, Kamrul, additional, Jarju, Sheikh, additional, Juma, Jane, additional, Mhango, Chimwemwe, additional, Naumanga, Queen, additional, Qureshi, Sonia, additional, Sonye, Catherine, additional, Ahmed, Naveed, additional, Aziz, Fatima, additional, Bhuiyan, Md Taufiqur Rahman, additional, Charles, Mary, additional, Cunliffe, Nigel A, additional, Abdou, Mahamadou, additional, Galagan, Sean R, additional, Gitteh, Ensa, additional, Guindo, Ibrehima, additional, Jahangir Hossain, M, additional, Jabang, Abdoulie M J, additional, Jere, Khuzwayo C, additional, Kawonga, Flywell, additional, Keita, Mariama, additional, Keita, Noumou Yakhouba, additional, Kotloff, Karen L, additional, Shapiama Lopez, Wagner V, additional, Munga, Stephen, additional, Paredes Olortegui, Maribel, additional, Omore, Richard, additional, Pavlinac, Patricia B, additional, Qadri, Firdausi, additional, Qamar, Farah Naz, additional, Azadul Alam Raz, S M, additional, Riziki, Laura, additional, Schiaffino, Francesca, additional, Stroup, Suzanne, additional, Traore, Sarata Nassoun, additional, Pinedo Vasquez, Tackeshy, additional, Yousafzai, Mohammad Tahir, additional, Antonio, Martin, additional, Cornick, Jennifer E, additional, Kabir, Furqan, additional, Khanam, Farhana, additional, Kosek, Margaret N, additional, Ochieng, John Benjamin, additional, Platts-Mills, James A, additional, Tennant, Sharon M, additional, and Houpt, Eric R, additional

Published
2024
Full Text
View/download PDF

3. 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
Full Text
View/download PDF

4. International genomic definition of pneumococcal lineages, to contextualise disease, antibiotic resistance and vaccine impact

Author

Gladstone, Rebecca A., Lo, Stephanie W., Lees, John A., Croucher, Nicholas J., van Tonder, Andries J., Corander, Jukka, Page, Andrew J., Marttinen, Pekka, Bentley, Leon J., Ochoa, Theresa J., Ho, Pak Leung, du Plessis, Mignon, Cornick, Jennifer E., Kwambana-Adams, Brenda, Benisty, Rachel, Nzenze, Susan A., Madhi, Shabir A., Hawkins, Paulina A., Everett, Dean B., Antonio, Martin, Dagan, Ron, Klugman, Keith P., von Gottberg, Anne, McGee, Lesley, Breiman, Robert F., and Bentley, Stephen D.

Published
2019
Full Text
View/download PDF

6. The global distribution and diversity of protein vaccine candidate antigens in the highly virulent Streptococcus pnuemoniae serotype 1

Author

Cornick, Jennifer E., Tastan Bishop, Özlem, Yalcin, Feyruz, Kiran, Anmol M., Kumwenda, Benjamin, Chaguza, Chrispin, Govindpershad, Shanil, Ousmane, Sani, Senghore, Madikay, du Plessis, Mignon, Pluschke, Gerd, Ebruke, Chinelo, McGee, Lesley, Sigaùque, Beutel, Collard, Jean-Marc, Bentley, Stephen D., Kadioglu, Aras, Antonio, Martin, von Gottberg, Anne, French, Neil, Klugman, Keith P., Heyderman, Robert S., Alderson, Mark, and Everett, Dean B.

Published
2017
Full Text
View/download PDF

7. Bacterial genome-wide association study of hyper-virulent pneumococcal serotype 1 identifies genetic variation associated with neurotropism

Author

Chaguza, Chrispin, Yang, Marie, Cornick, Jennifer E., du Plessis, Mignon, Gladstone, Rebecca A., Kwambana-Adams, Brenda A., Lo, Stephanie W., Ebruke, Chinelo, Tonkin-Hill, Gerry, Peno, Chikondi, Senghore, Madikay, Obaro, Stephen K., Ousmane, Sani, Pluschke, Gerd, Collard, Jean-Marc, Sigaùque, Betuel, French, Neil, Klugman, Keith P., Heyderman, Robert S., McGee, Lesley, Antonio, Martin, Breiman, Robert F., von Gottberg, Anne, Everett, Dean B., Kadioglu, Aras, and Bentley, Stephen D.

Published
2020
Full Text
View/download PDF

10. 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
Full Text
View/download PDF

11. 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
Full Text
View/download PDF

12. Emergence of a multidrug resistant and virulent Streptococcus pneumoniae lineage mediates serotype replacement after PCV13

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, KL, additional, Kandasamy, Rama, additional, Pollard, 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, Moisi, Jennifer, additional, Obaro, Stephen K, additional, Dagan, Ron, additional, Elmdaghri, Naima, additional, Skoczynska, 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, Almagro, Carmen Munoz, additional, and Varon, Emmanuelle, additional

Published
2021
Full Text
View/download PDF

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

15. Lower Density and Shorter Duration of Nasopharyngeal Carriage by Pneumococcal Serotype 1 (ST217) May Explain Its Increased Invasiveness over Other Serotypes

Author

Bricio-Moreno, Laura, primary, Chaguza, Chrispin, additional, Yahya, Reham, additional, Shears, Rebecca K., additional, Cornick, Jennifer E., additional, Hokamp, Karsten, additional, Yang, Marie, additional, Neill, Daniel R., additional, French, Neil, additional, Hinton, Jay C. D., additional, Everett, Dean B., additional, and Kadioglu, Aras, additional

Published
2020
Full Text
View/download PDF

16. Comparative Genomics of Disease and Carriage Serotype 1 Pneumococci.

Author

Chaguza, Chrispin, Ebruke, Chinelo, Senghore, Madikay, Lo, Stephanie W., Tientcheu, Peggy-Estelle, Gladstone, Rebecca A., Tonkin-Hill, Gerry, Cornick, Jennifer E., Yang, Marie, Worwui, Archibald, McGee, Lesley, Breiman, Robert F., Klugman, Keith P., Kadioglu, Aras, Everett, Dean B., Mackenzie, Grant, Croucher, Nicholas J., Roca, Anna, Kwambana-Adams, Brenda A., and Antonio, Martin

Subjects
STREPTOCOCCUS pneumoniae, COMPARATIVE genomics, GENOME-wide association studies, GENETIC variation, PHENOTYPIC plasticity, NASOPHARYNX diseases
Abstract

The isolation of Streptococcus pneumoniae serotypes in systemic tissues of patients with invasive disease versus the nasopharynx of healthy individuals with asymptomatic carriage varies widely. Some serotypes are hyper-invasive, particularly serotype 1, but the underlying genetics remain poorly understood due to the rarity of carriage isolates, reducing the power of comparison with invasive isolates. Here, we use a well-controlled genome-wide association study to search for genetic variation associated with invasiveness of serotype 1 pneumococci from a serotype 1 endemic setting in Africa. We found no consensus evidence that certain genomic variation is overrepresented among isolates from patients with invasive disease than asymptomatic carriage. Overall, the genomic variation explained negligible phenotypic variability, suggesting a minimal effect on the disease status. Furthermore, changes in lineage distribution were seen with lineages replacing each other over time, highlighting the importance of continued pathogen surveillance. Our findings suggest that the hyper-invasiveness is an intrinsic property of the serotype 1 strains, not specific for a "disease-associated" subpopulation disproportionately harboring unique genomic variation. [ABSTRACT FROM AUTHOR]

Published
2022
Full Text
View/download PDF

17. Invasive Streptococcus pneumoniae in Children, Malawi, 2004-2006

Author

Cornick, Jennifer E., Everett, Dean B., Broughton, Caroline, Denis, Brigitte B., Banda, Daniel L., Carrol, Enitan D., and Parry, Christopher M.

Subjects
Nucleic acids -- Separation, Drug resistance in microorganisms -- Genetic aspects, Pneumonia, Pneumococcal -- Genetic aspects -- Drug therapy, Pneumonia in children -- Genetic aspects -- Drug therapy, Health
Abstract

Streptococcus pneumoniae causes a spectrum of disease, ranging from relatively mild otitis media to life-threatening pneumonia, meningitis, and septicemia. Recent estimates suggest that pneumococcal disease is responsible for 1 million [...]

Published
2011
Full Text
View/download PDF

18. 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
Full Text
View/download PDF

19. Early Signals of Vaccine-driven Perturbation Seen in Pneumococcal Carriage Population Genomic Data

Author

Chaguza, Chrispin, primary, Heinsbroek, Ellen, additional, Gladstone, Rebecca A, additional, Tafatatha, Terence, additional, Alaerts, Maaike, additional, Peno, Chikondi, additional, Cornick, Jennifer E, additional, Musicha, Patrick, additional, Bar-Zeev, Naor, additional, Kamng’ona, Arox, additional, Kadioglu, Aras, additional, McGee, Lesley, additional, Hanage, William P, additional, Breiman, Robert F, additional, Heyderman, Robert S, additional, French, Neil, additional, Everett, Dean B, additional, and Bentley, Stephen D, additional

Published
2019
Full Text
View/download PDF

20. International Genomic Definition of Pneumococcal Lineages, to Contextualise Disease, Antibiotic Resistance and Vaccine Impact

Author

Gladstone, Rebecca, primary, Lo, Stephanie W., additional, Lees, John A., additional, Croucher, Nicholas J., additional, van Tonder, Andries J., additional, Corander, Jukka, additional, Page, Andrew J., additional, Marttinen, Pekka, additional, Bentley, Leon J., additional, Ochoa, Theresa J., additional, Ho, Pak Leung, additional, du Plessis, Mignon, additional, Cornick, Jennifer E., additional, Kwambana-Adams, Brenda, additional, Benisty, Rachel, additional, Nzenze, Susan A., additional, Madhi, Shabir A., additional, Hawkins, Paulina A., additional, Everett, Dean B., additional, Antonio, Martin, additional, Dagan, Ron, additional, Klugman, Keith P., additional, von Gottberg, Anne, additional, McGee, Lesley, additional, Breiman, Robert F., additional, Bentley, Stephen D., additional, and Consortium, The Global Pneumococcal Sequencing, additional

Published
2019
Full Text
View/download PDF

21. Early Signals of Vaccine-driven Perturbation Seen in Pneumococcal Carriage Population Genomic Data.

Author

Chaguza, Chrispin, Heinsbroek, Ellen, Gladstone, Rebecca A, Tafatatha, Terence, Alaerts, Maaike, Peno, Chikondi, Cornick, Jennifer E, Musicha, Patrick, Bar-Zeev, Naor, Kamng'ona, Arox, Kadioglu, Aras, McGee, Lesley, Hanage, William P, Breiman, Robert F, Heyderman, Robert S, French, Neil, Everett, Dean B, and Bentley, Stephen D

Subjects
DRUG resistance in microorganisms, GENES, GENOMES, PNEUMOCOCCAL vaccines, SEROLOGY, STREPTOCOCCUS, SURVEYS, POPULATION health, SEQUENCE analysis
Abstract

Background Pneumococcal conjugate vaccines (PCVs) have reduced pneumococcal diseases globally. Pneumococcal genomic surveys elucidate PCV effects on population structure but are rarely conducted in low-income settings despite the high disease burden. Methods We undertook whole-genome sequencing (WGS) of 660 pneumococcal isolates collected through surveys from healthy carriers 2 years from 13-valent PCV (PCV13) introduction and 1 year after rollout in northern Malawi. We investigated changes in population structure, within-lineage serotype dynamics, serotype diversity, and frequency of antibiotic resistance (ABR) and accessory genes. Results In children <5 years of age, frequency and diversity of vaccine serotypes (VTs) decreased significantly post-PCV, but no significant changes occurred in persons ≥5 years of age. Clearance of VT serotypes was consistent across different genetic backgrounds (lineages). There was an increase of nonvaccine serotypes (NVTs)—namely 7C, 15B/C, and 23A—in children <5 years of age, but 28F increased in both age groups. While carriage rates have been recently shown to remain stable post-PCV due to replacement serotypes, there was no change in diversity of NVTs. Additionally, frequency of intermediate-penicillin-resistant lineages decreased post-PCV. Although frequency of ABR genes remained stable, other accessory genes, especially those associated with mobile genetic element and bacteriocins, showed changes in frequency post-PCV. Conclusions We demonstrate evidence of significant population restructuring post-PCV driven by decreasing frequency of vaccine serotypes and increasing frequency of few NVTs mainly in children under 5. Continued surveillance with WGS remains crucial to fully understand dynamics of the residual VTs and replacement NVT serotypes post-PCV. [ABSTRACT FROM AUTHOR]

Published
2020
Full Text
View/download PDF

22. 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
Full Text
View/download PDF

23. Early signals of vaccine driven perturbation seen in pneumococcal carriage population genomic data

Author

Chaguza, Chrispin, primary, Heinsbroek, Ellen, additional, Gladstone, Rebecca A., additional, Tafatatha, Terence, additional, Alaerts, Maaike, additional, Peno, Chikondi, additional, Cornick, Jennifer E., additional, Musicha, Patrick, additional, Bar-Zeev, Naor, additional, Kamng’ona, Arox, additional, Kadioglu, Aras, additional, Mcgee, Lesley, additional, Hanage, William P., additional, Breiman, Robert F., additional, Heyderman, Robert S., additional, French, Neil, additional, Everett, Dean B., additional, and Bentley, Stephen D., additional

Published
2018
Full Text
View/download PDF

24. Erratum for Cornick et al., “Epidemiological and Molecular Characterization of an Invasive Group A Streptococcus emm 32.2 Outbreak”

Author

Cornick, Jennifer E., primary, Kiran, Anmol M., additional, Vivancos, Roberto, additional, Van Aartsen, Jon, additional, Clarke, Jenny, additional, Bevan, Edward, additional, Alsahag, Mansoor, additional, Alaearts, Maaike, additional, Bricio Moreno, Laura, additional, Jenkinson, Howard F., additional, Nobbs, Angela H., additional, Anson, James, additional, Kadioglu, Aras, additional, French, Neil, additional, and Everett, Dean B., additional

Published
2018
Full Text
View/download PDF

25. Global Distribution of Invasive Serotype 35D Streptococcus pneumoniae Isolates following Introduction of 13-Valent Pneumococcal Conjugate Vaccine

Author

Lo, Stephanie W., primary, Gladstone, Rebecca A., additional, van Tonder, Andries J., additional, Hawkins, Paulina A., additional, Kwambana-Adams, Brenda, additional, Cornick, Jennifer E., additional, Madhi, Shabir A., additional, Nzenze, Susan A., additional, du Plessis, Mignon, additional, Kandasamy, Rama, additional, Carter, Philip E., additional, Eser, Özgen Köseoglu, additional, Ho, Pak Leung, additional, Elmdaghri, Naima, additional, Shakoor, Sadia, additional, Clarke, Stuart C., additional, Antonio, Martin, additional, Everett, Dean B., additional, von Gottberg, Anne, additional, Klugman, Keith P., additional, McGee, Lesley, additional, Breiman, Robert F., additional, and Bentley, Stephen D., additional

Published
2018
Full Text
View/download PDF

26. Recombination in <named-content content-type='genus-species'>Streptococcus pneumoniae</named-content> Lineages Increase with Carriage Duration and Size of the Polysaccharide Capsule

Author

Chaguza, Chrispin, Andam, Cheryl P, Harris, Simon R, Cornick, Jennifer E, Yang, Marie, Bricio-Moreno, Laura, Kamng'ona, Arox W, Parkhill, Julian, French, Neil, Heyderman, Robert S, Kadioglu, Aras, Everett, Dean B, Bentley, Stephen D, and Hanage, William P

Subjects
Journal Article, Microbiology, QR1-502
Abstract

Streptococcus pneumoniae causes a high burden of invasive pneumococcal disease (IPD) globally, especially in children from resource-poor settings. Like many bacteria, the pneumococcus can import DNA from other strains or even species by transformation and homologous recombination, which has allowed the pneumococcus to evade clinical interventions such as antibiotics and pneumococcal conjugate vaccines (PCVs). Pneumococci are enclosed in a complex polysaccharide capsule that determines the serotype; the capsule varies in size and is associated with properties including carriage prevalence and virulence. We determined and quantified the association between capsule and recombination events using genomic data from a diverse collection of serotypes sampled in Malawi. We determined both the amount of variation introduced by recombination relative to mutation (the relative rate) and how many individual recombination events occur per isolate (the frequency). Using univariate analyses, we found an association between both recombination measures and multiple factors associated with the capsule, including duration and prevalence of carriage. Because many capsular factors are correlated, we used multivariate analysis to correct for collinearity. Capsule size and carriage duration remained positively associated with recombination, although with a reduced P value, and this effect may be mediated through some unassayed additional property associated with larger capsules. This work describes an important impact of serotype on recombination that has been previously overlooked. While the details of how this effect is achieved remain to be determined, it may have important consequences for the serotype-specific response to vaccines and other interventions.IMPORTANCE: The capsule determines >90 different pneumococcal serotypes, which vary in capsule size, virulence, duration, and prevalence of carriage. Current serotype-specific vaccines elicit anticapsule antibodies. Pneumococcus can take up exogenous DNA by transformation and insert it into its chromosome by homologous recombination. This mechanism has disseminated drug resistance and generated vaccine escape variants. It is hence crucial to pneumococcal evolutionary response to interventions, but there has been no systematic study quantifying whether serotypes vary in recombination and whether this is associated with serotype-specific properties such as capsule size or carriage duration. Larger capsules could physically inhibit DNA uptake, or given the longer carriage duration for larger capsules, this may promote recombination. We find that recombination varies among capsules and is associated with capsule size, carriage duration, and carriage prevalence and negatively associated with invasiveness. The consequence of this work is that serotypes with different capsules may respond differently to selective pressures like vaccines.

Published
2016
Full Text
View/download PDF

27. Population genetic structure, antibiotic resistance, capsule switching and evolution of invasive pneumococci before conjugate vaccination in Malawi

Author

Chaguza, Chrispin, primary, Cornick, Jennifer E., additional, Andam, Cheryl P., additional, Gladstone, Rebecca A., additional, Alaerts, Maaike, additional, Musicha, Patrick, additional, Peno, Chikondi, additional, Bar-Zeev, Naor, additional, Kamng'ona, Arox W., additional, Kiran, Anmol M., additional, Msefula, Chisomo L., additional, McGee, Lesley, additional, Breiman, Robert F., additional, Kadioglu, Aras, additional, French, Neil, additional, Heyderman, Robert S., additional, Hanage, William P., additional, Bentley, Stephen D., additional, and Everett, Dean B., additional

Published
2017
Full Text
View/download PDF

28. Epidemiological and Molecular Characterization of an Invasive Group A Streptococcus emm 32.2 Outbreak

Author

Cornick, Jennifer E., primary, Kiran, Anmol M., additional, Vivancos, Roberto, additional, Van Aartsen, Jon, additional, Clarke, Jenny, additional, Bevan, Edward, additional, Alsahag, Mansoor, additional, Alaearts, Maaike, additional, Bricio Moreno, Laura, additional, Jenkinson, Howard F., additional, Nobbs, Angela H., additional, Anson, James, additional, Kadioglu, Aras, additional, French, Neil, additional, and Everett, Dean B., additional

Published
2017
Full Text
View/download PDF

29. Understanding pneumococcal serotype 1 biology through population genomic analysis

Author

University of Helsinki, Department of Mathematics and Statistics, Chaguza, Chrispin, Cornick, Jennifer E., Harris, Simon R., Andam, Cheryl P., Bricio-Moreno, Laura, Yang, Marie, Yalcin, Feyruz, Ousmane, Sani, Govindpersad, Shanil, Senghore, Madikay, Ebruke, Chinelo, Du Plessis, Mignon, Kiran, Anmol M., Pluschke, Gerd, Sigauque, Betuel, McGee, Lesley, Klugman, Keith P., Turner, Paul, Corander, Jukka, Parkhill, Julian, Collard, Jean-Marc, Antonio, Martin, von Gottberg, Anne, Heyderman, Robert S., French, Neil, Kadioglu, Aras, Hanage, William P., Everett, Dean B., Bentley, Stephen D., PAGe Consortium, University of Helsinki, Department of Mathematics and Statistics, Chaguza, Chrispin, Cornick, Jennifer E., Harris, Simon R., Andam, Cheryl P., Bricio-Moreno, Laura, Yang, Marie, Yalcin, Feyruz, Ousmane, Sani, Govindpersad, Shanil, Senghore, Madikay, Ebruke, Chinelo, Du Plessis, Mignon, Kiran, Anmol M., Pluschke, Gerd, Sigauque, Betuel, McGee, Lesley, Klugman, Keith P., Turner, Paul, Corander, Jukka, Parkhill, Julian, Collard, Jean-Marc, Antonio, Martin, von Gottberg, Anne, Heyderman, Robert S., French, Neil, Kadioglu, Aras, Hanage, William P., Everett, Dean B., Bentley, Stephen D., and PAGe Consortium

Abstract

Background: Pneumococcus kills over one million children annually and over 90 % of these deaths occur in low-income countries especially in Sub-Saharan Africa (SSA) where HIV exacerbates the disease burden. In SSA, serotype 1 pneumococci particularly the endemic ST217 clone, causes majority of the pneumococcal disease burden. To understand the evolution of the virulent ST217 clone, we analysed ST217 whole genomes from isolates sampled from African and Asian countries. Methods: We analysed 226 whole genome sequences from the ST217 lineage sampled from 9 African and 4 Asian countries. We constructed a whole genome alignment and used it for phylogenetic and coalescent analyses. We also screened the genomes to determine presence of antibiotic resistance conferring genes. Results: Population structure analysis grouped the ST217 isolates into five sequence clusters (SCs), which were highly associated with different geographical regions and showed limited intracontinental and intercontinental spread. The SCs showed lower than expected genomic sequence, which suggested strong purifying selection and small population sizes caused by bottlenecks. Recombination rates varied between the SCs but were lower than in other successful clones such as PMEN1. African isolates showed higher prevalence of antibiotic resistance genes than Asian isolates. Interestingly, certain West African isolates harbored a defective chloramphenicol and tetracycline resistance-conferring element (Tn5253) with a deletion in the loci encoding the chloramphenicol resistance gene (cat(pC194)), which caused lower chloramphenicol than tetracycline resistance. Furthermore, certain genes that promote colonisation were absent in the isolates, which may contribute to serotype 1's rarity in carriage and consequently its lower recombination rates. Conclusions: The high phylogeographic diversity of the ST217 clone shows that this clone has been in circulation globally for a long time, which allowed its diversificati

Published
2016

30. Understanding pneumococcal serotype 1 biology through population genomic analysis

Author

Chaguza, Chrispin, Cornick, Jennifer E, Harris, Simon R, Andam, Cheryl P, Bricio-Moreno, Laura, Yang, Marie, Yalcin, Feyruz, Ousmane, Sani, Govindpersad, Shanil, Senghore, Madikay, Ebruke, Chinelo, Du Plessis, Mignon, Kiran, Anmol M, Pluschke, Gerd, Sigauque, Betuel, McGee, Lesley, Klugman, Keith P, Turner, Paul, Corander, Jukka, Parkhill, Julian, Collard, Jean-Marc, Antonio, Martin, von Gottberg, Anne, Heyderman, Robert S, French, Neil, Kadioglu, Aras, Hanage, William P, Everett, Dean B, Bentley, Stephen D, Chaguza, Chrispin, Cornick, Jennifer E, Harris, Simon R, Andam, Cheryl P, Bricio-Moreno, Laura, Yang, Marie, Yalcin, Feyruz, Ousmane, Sani, Govindpersad, Shanil, Senghore, Madikay, Ebruke, Chinelo, Du Plessis, Mignon, Kiran, Anmol M, Pluschke, Gerd, Sigauque, Betuel, McGee, Lesley, Klugman, Keith P, Turner, Paul, Corander, Jukka, Parkhill, Julian, Collard, Jean-Marc, Antonio, Martin, von Gottberg, Anne, Heyderman, Robert S, French, Neil, Kadioglu, Aras, Hanage, William P, Everett, Dean B, and Bentley, Stephen D

Abstract

Background Pneumococcus kills over one million children annually and over 90 % of these deaths occur in low-income countries especially in Sub-Saharan Africa (SSA) where HIV exacerbates the disease burden. In SSA, serotype 1 pneumococci particularly the endemic ST217 clone, causes majority of the pneumococcal disease burden. To understand the evolution of the virulent ST217 clone, we analysed ST217 whole genomes from isolates sampled from African and Asian countries. Methods We analysed 226 whole genome sequences from the ST217 lineage sampled from 9 African and 4 Asian countries. We constructed a whole genome alignment and used it for phylogenetic and coalescent analyses. We also screened the genomes to determine presence of antibiotic resistance conferring genes. Results Population structure analysis grouped the ST217 isolates into five sequence clusters (SCs), which were highly associated with different geographical regions and showed limited intracontinental and intercontinental spread. The SCs showed lower than expected genomic sequence, which suggested strong purifying selection and small population sizes caused by bottlenecks. Recombination rates varied between the SCs but were lower than in other successful clones such as PMEN1. African isolates showed higher prevalence of antibiotic resistance genes than Asian isolates. Interestingly, certain West African isolates harbored a defective chloramphenicol and tetracycline resistance-conferring element (Tn5253) with a deletion in the loci encoding the chloramphenicol resistance gene (cat pC194), which caused lower chloramphenicol than tetracycline resistance. Furthermore, certain genes that promote colonisation were absent in the isolates, which may contribute to serotype 1’s rarity in carriage and consequently its lower recombination rates. Conclusions The high phylogeographic diversity of the ST217 clone shows that this clone has been in circulation globally for a long time, which allowed its diversifi

Published
2016

31. Recombination in Streptococcus pneumoniae Lineages Increase with Carriage Duration and Size of the Polysaccharide Capsule

Author

Chaguza, Chrispin, primary, Andam, Cheryl P., additional, Harris, Simon R., additional, Cornick, Jennifer E., additional, Yang, Marie, additional, Bricio-Moreno, Laura, additional, Kamng’ona, Arox W., additional, Parkhill, Julian, additional, French, Neil, additional, Heyderman, Robert S., additional, Kadioglu, Aras, additional, Everett, Dean B., additional, Bentley, Stephen D., additional, and Hanage, William P., additional

Published
2016
Full Text
View/download PDF

32. Phylogenetic Analysis of Invasive Serotype 1 Pneumococcus in South Africa, 1989 to 2013

Author

du Plessis, Mignon, primary, Allam, Mushal, additional, Tempia, Stefano, additional, Wolter, Nicole, additional, de Gouveia, Linda, additional, von Mollendorf, Claire, additional, Jolley, Keith A., additional, Mbelle, Nontombi, additional, Wadula, Jeannette, additional, Cornick, Jennifer E., additional, Everett, Dean B., additional, McGee, Lesley, additional, Breiman, Robert F., additional, Gladstone, Rebecca A., additional, Bentley, Stephen D., additional, Klugman, Keith P., additional, and von Gottberg, Anne, additional

Published
2016
Full Text
View/download PDF

33. Genomic identification of a novel co-trimoxazole resistance genotype and its prevalence amongst Streptococcus pneumoniae in Malawi

Author

Cornick, Jennifer E, Harris, Simon R, Parry, Christopher M, Moore, Michael J, Jassi, Chikondi, Kamng'ona, Arox, Kulohoma, Benard, Heyderman, Robert S, Bentley, Stephen D, and Everett, Dean B

Abstract

OBJECTIVES: This study aimed to define the molecular basis of co-trimoxazole resistance in Malawian pneumococci under the dual selective pressure of widespread co-trimoxazole and sulfadoxine/pyrimethamine use. METHODS: We measured the trimethoprim and sulfamethoxazole MICs and analysed folA and folP nucleotide and translated amino acid sequences for 143 pneumococci isolated from carriage and invasive disease in Malawi (2002-08). RESULTS: Pneumococci were highly resistant to both trimethoprim and sulfamethoxazole (96%, 137/143). Sulfamethoxazole-resistant isolates showed a 3 or 6 bp insertion in the sulphonamide-binding site of folP. The trimethoprim-resistant isolates fell into three genotypic groups based on dihydrofolate reductase (encoded by folA) mutations: Ile-100-Leu (10%), the Ile-100-Leu substitution together with a residue 92 substitution (56%) and those with a novel uncharacterized resistance genotype (34%). The nucleotide sequence divergence and dN/dS of folA and folP remained stable from 2004 onwards. CONCLUSIONS: S. pneumoniae exhibit almost universal co-trimoxazole resistance in vitro and in silico that we believe is driven by extensive co-trimoxazole and sulfadoxine/pyrimethamine use. More than one-third of pneumococci employ a novel mechanism of co-trimoxazole resistance. Resistance has now reached a point of stabilizing evolution. The use of co-trimoxazole to prevent pneumococcal infection in HIV/AIDS patients in sub-Saharan Africa should be re-evaluated.

Published
2013

34. Erratum for Kulohoma et al., Comparative Genomic Analysis of Meningitis- and Bacteremia-Causing Pneumococci Identifies a Common Core Genome

Author

Kulohoma, Benard W., primary, Cornick, Jennifer E., additional, Chaguza, Chrispin, additional, Yalcin, Feyruz, additional, Harris, Simon R., additional, Gray, Katherine J., additional, Kiran, Anmol M., additional, Molyneux, Elizabeth, additional, French, Neil, additional, Parkhill, Julian, additional, Faragher, Brian E., additional, Everett, Dean B., additional, Bentley, Stephen D., additional, and Heyderman, Robert S., additional

Published
2015
Full Text
View/download PDF

35. Comparative Genomic Analysis of Meningitis- and Bacteremia-Causing Pneumococci Identifies a Common Core Genome

Author

Kulohoma, Benard W., primary, Cornick, Jennifer E., additional, Chaguza, Chrispin, additional, Yalcin, Feyruz, additional, Harris, Simon R., additional, Gray, Katherine J., additional, Kiran, Anmol M., additional, Molyneux, Elizabeth, additional, French, Neil, additional, Parkhill, Julian, additional, Faragher, Brian E., additional, Everett, Dean B., additional, Bentley, Stephen D., additional, and Heyderman, Robert S., additional

Published
2015
Full Text
View/download PDF

36. High multiple carriage and emergence of Streptococcus pneumoniae vaccine serotype variants in Malawian children

Author

Kamng’ona, Arox W., primary, Hinds, Jason, additional, Bar-Zeev, Naor, additional, Gould, Katherine A., additional, Chaguza, Chrispin, additional, Msefula, Chisomo, additional, Cornick, Jennifer E., additional, Kulohoma, Benard W., additional, Gray, Katherine, additional, Bentley, Stephen D., additional, French, Neil, additional, Heyderman, Robert S., additional, and Everett, Dean B., additional

Published
2015
Full Text
View/download PDF

37. Epidemiological and Molecular Characterization of an Invasive Group A Streptococcus emm32.2 Outbreak

Author

Cornick, Jennifer E., Kiran, Anmol M., Vivancos, Roberto, Van Aartsen, Jon, Clarke, Jenny, Bevan, Edward, Alsahag, Mansoor, Alaearts, Maaike, Bricio Moreno, Laura, Jenkinson, Howard F., Nobbs, Angela H., Anson, James, Kadioglu, Aras, French, Neil, and Everett, Dean B.

Abstract

ABSTRACTAn emm32.2 invasive group A streptococcus (iGAS) outbreak occurred in Liverpool from January 2010 to September 2012. This genotype had not previously been identified in Liverpool, but was responsible for 32% (14/44) of all iGAS cases reported during this time period. We performed a case-case comparison of emm32.2 iGAS cases with non-emm32.2 control iGAS cases identified in the Liverpool population over the same time period to assess patient risk factors for emm32.2 iGAS infection. The emm32.2 iGAS cases were confined to the adult population. We show that homelessness, intravenous drug use, and alcohol abuse predisposed patients to emm32.2 iGAS disease; however, no obvious epidemiological linkage between the patients with emm32.2 iGAS could be identified. Comparative whole-genome sequencing analysis of emm32.2 iGAS and non-emm32.2 control isolates was also performed to identify pathogen factors which might have driven the outbreak. We identified 19 genes, five of which had previously been implicated in virulence, which were present in all of the emm32.2 iGAS isolates but not present in any of the non-emm32.2 control isolates. We report that a novel emm32.2 genotype emerged in Liverpool in 2010 and identified a specific subset of genes, which could have allowed this novel emm32.2 genotype to persist in a disadvantaged population in the region over a 3-year period.

Published
2017
Full Text
View/download PDF

39. High multiple carriage and emergence of Streptococcus pneumoniae vaccine serotype variants in Malawian children.

Author

Kamng'ona, Arox W., Hinds, Jason, Bar-Zeev, Naor, Gould, Katherine A., Chaguza, Chrispin, Msefula, Chisomo, Cornick, Jennifer E., Kulohoma, Benard W., Gray, Katherine, Bentley, Stephen D., French, Neil, Heyderman, Robert S., and Everett, Dean B.

Subjects
STREPTOCOCCAL diseases, STREPTOCOCCUS pneumoniae, DISEASE prevalence, HIV-positive children, SEROTYPES, BACTERIAL loci, PNEUMOCOCCAL vaccines
Abstract

Background: Carriage of either single or multiple pneumococcal serotypes (multiple carriage) is a prerequisite for developing invasive pneumococcal disease. However, despite the reported high rates of pneumococcal carriage in Malawi, no data on carriage of multiple serotypes has been reported previously. Our study provides the first description of the prevalence of multiple pneumococcal carriage in Malawi. Methods: The study was conducted in Blantyre and Karonga districts in Malawi, from 2008 to 2012. We recruited 116 children aged 0-13 years. These children were either HIV-infected (N = 44) or uninfected (N = 72). Nasopharyngeal samples were collected using sterile swabs. Pneumococcal serotypes in the samples were identified by microarray. Strains that could not be typed by microarray were sequenced to characterise possible genetic alterations within the capsular polysaccharide (CPS) locus. Results: The microarray identified 179 pneumococcal strains (from 116 subjects), encompassing 43 distinct serotypes and non-typeable (NT) strains. Forty per cent (46/116) of children carried multiple serotypes. Carriage of vaccine type (VT) strains was higher (p = 0.028) in younger (0-2 years) children (71 %, 40/56) compared to older (3-13 years) children (50 %, 30/60). Genetic variations within the CPS locus of known serotypes were observed in 19 % (34/179) of the strains identified. The variants included 13-valent pneumococcal conjugate vaccine (PCV13) serotypes 6B and 19A, and the polysaccharide vaccine serotype 20. Serotype 6B variants were the most frequently isolated (47 %, 16/34). Unlike the wild type, the CPS locus of the 6B variants contained an insertion of the licD-family phosphotransferase gene. The CPS locus of 19A- and 20-variants contained an inversion in the sugar-biosynthesis (rmlD) gene and a 717 bp deletion within the transferase (whaF) gene, respectively. Conclusions: The high multiple carriage in Malawian children provides opportunities for genetic exchange through horizontal gene transfer. This may potentially lead to CPS locus variants and vaccine escape. Variants reported here occurred naturally, however, PCV13 introduction could exacerbate the CPS genetic variations. Further studies are therefore recommended to assess the invasive potential of these variants and establish whether PCV13 would offer cross-protection. We have shown that younger children (0-2 years) are a reservoir of VT serotypes, which makes them an ideal target for vaccination. [ABSTRACT FROM AUTHOR]

Published
2015
Full Text
View/download PDF

40. Changes in Invasive Pneumococcal Disease Caused by Streptococcus pneumoniae Serotype 1 following Introduction of PCV10 and PCV13: Findings from the PSERENADE Project.

Author

Bennett, Julia C., Hetrich, Marissa K., Garcia Quesada, Maria, Sinkevitch, Jenna N., Deloria Knoll, Maria, 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, and Danis, Kostas

Subjects
STREPTOCOCCUS pneumoniae, PNEUMOCOCCAL vaccines, POISSON regression, INFANTS
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. [ABSTRACT FROM AUTHOR]

Published
2021
Full Text
View/download PDF

41. Bacterial genome-wide association study of hyper-virulent pneumococcal serotype 1 identifies genetic variation associated with neurotropism

Author

Chaguza, Chrispin, Yang, Marie, Cornick, Jennifer E, Du Plessis, Mignon, Gladstone, Rebecca A, Kwambana-Adams, Brenda A, Lo, Stephanie W, Ebruke, Chinelo, Tonkin-Hill, Gerry, Peno, Chikondi, Senghore, Madikay, Obaro, Stephen K, Ousmane, Sani, Pluschke, Gerd, Collard, Jean-Marc, Sigaùque, Betuel, French, Neil, Klugman, Keith P, Heyderman, Robert S, McGee, Lesley, Antonio, Martin, Breiman, Robert F, Von Gottberg, Anne, Everett, Dean B, Kadioglu, Aras, and Bentley, Stephen D

Subjects
Central Nervous System, Adolescent, Meningitis, Pneumococcal, Genetic Variation, Infant, Sequence Analysis, DNA, Polymorphism, Single Nucleotide, 3. Good health, Viral Tropism, Streptococcus pneumoniae, Child, Preschool, Humans, Child, Phylogeny, Genome-Wide Association Study
Abstract

Funder: Bill and Melinda Gates Foundation (Bill & Melinda Gates Foundation), Hyper-virulent Streptococcus pneumoniae serotype 1 strains are endemic in Sub-Saharan Africa and frequently cause lethal meningitis outbreaks. It remains unknown whether genetic variation in serotype 1 strains modulates tropism into cerebrospinal fluid to cause central nervous system (CNS) infections, particularly meningitis. Here, we address this question through a large-scale linear mixed model genome-wide association study of 909 African pneumococcal serotype 1 isolates collected from CNS and non-CNS human samples. By controlling for host age, geography, and strain population structure, we identify genome-wide statistically significant genotype-phenotype associations in surface-exposed choline-binding (P = 5.00 × 10-08) and helicase proteins (P = 1.32 × 10-06) important for invasion, immune evasion and pneumococcal tropism to CNS. The small effect sizes and negligible heritability indicated that causation of CNS infection requires multiple genetic and other factors reflecting a complex and polygenic aetiology. Our findings suggest that certain pathogen genetic variation modulate pneumococcal survival and tropism to CNS tissue, and therefore, virulence for meningitis.

42. Understanding pneumococcal serotype 1 biology through population genomic analysis

Author

Chaguza, Chrispin, Cornick, Jennifer E., Harris, Simon R., Andam, Cheryl P., Bricio-Moreno, Laura, Yang, Marie, Yalcin, Feyruz, Ousmane, Sani, Govindpersad, Shanil, Senghore, Madikay, Ebruke, Chinelo, Du Plessis, Mignon, Kiran, Anmol M., Pluschke, Gerd, Sigauque, Betuel, McGee, Lesley, Klugman, Keith P., Turner, Paul, Corander, Jukka, Parkhill, Julian, Collard, Jean-Marc, Antonio, Martin, von Gottberg, Anne, Heyderman, Robert S., French, Neil, Kadioglu, Aras, Hanage, William P., Everett, Dean B., Bentley, Stephen D., and PAGe Consortium

Subjects
2. Zero hunger, 3. Good health

43. Understanding pneumococcal serotype 1 biology through population genomic analysis

Author

Chaguza, Chrispin, Cornick, Jennifer E, Harris, Simon R, Andam, Cheryl P, Bricio-Moreno, Laura, Yang, Marie, Yalcin, Feyruz, Ousmane, Sani, Govindpersad, Shanil, Senghore, Madikay, Ebruke, Chinelo, Du Plessis, Mignon, Kiran, Anmol M, Pluschke, Gerd, Sigauque, Betuel, McGee, Lesley, Klugman, Keith P, Turner, Paul, Corander, Jukka, Parkhill, Julian, Collard, Jean-Marc, Antonio, Martin, Von Gottberg, Anne, Heyderman, Robert S, French, Neil, Kadioglu, Aras, Hanage, William P, Everett, Dean B, Bentley, Stephen D, and PAGe Consortium

Subjects
2. Zero hunger, Recombination, Genetic, Asia, Antibiotic resistance, Evolution, Tetracycline Resistance, ST217, Genetic Variation, Serogroup, Pneumococcal Infections, 3. Good health, Phylogeography, Pneumococcal serotype 1, Streptococcus pneumoniae, Nasopharynx, Africa, Drug Resistance, Bacterial, Humans, Selection, Genetic, Phylogeny
Abstract

BACKGROUND: Pneumococcus kills over one million children annually and over 90 % of these deaths occur in low-income countries especially in Sub-Saharan Africa (SSA) where HIV exacerbates the disease burden. In SSA, serotype 1 pneumococci particularly the endemic ST217 clone, causes majority of the pneumococcal disease burden. To understand the evolution of the virulent ST217 clone, we analysed ST217 whole genomes from isolates sampled from African and Asian countries. METHODS: We analysed 226 whole genome sequences from the ST217 lineage sampled from 9 African and 4 Asian countries. We constructed a whole genome alignment and used it for phylogenetic and coalescent analyses. We also screened the genomes to determine presence of antibiotic resistance conferring genes. RESULTS: Population structure analysis grouped the ST217 isolates into five sequence clusters (SCs), which were highly associated with different geographical regions and showed limited intracontinental and intercontinental spread. The SCs showed lower than expected genomic sequence, which suggested strong purifying selection and small population sizes caused by bottlenecks. Recombination rates varied between the SCs but were lower than in other successful clones such as PMEN1. African isolates showed higher prevalence of antibiotic resistance genes than Asian isolates. Interestingly, certain West African isolates harbored a defective chloramphenicol and tetracycline resistance-conferring element (Tn5253) with a deletion in the loci encoding the chloramphenicol resistance gene (cat pC194), which caused lower chloramphenicol than tetracycline resistance. Furthermore, certain genes that promote colonisation were absent in the isolates, which may contribute to serotype 1's rarity in carriage and consequently its lower recombination rates. CONCLUSIONS: The high phylogeographic diversity of the ST217 clone shows that this clone has been in circulation globally for a long time, which allowed its diversification and adaptation in different geographical regions. Such geographic adaptation reflects local variations in selection pressures in different locales. Further studies will be required to fully understand the biological mechanisms which makes the ST217 clone highly invasive but unable to successfully colonise the human nasopharynx for long durations which results in lower recombination rates.

44. The global distribution and diversity of protein vaccine candidate antigens in the highly virulent Streptococcus pnuemoniae serotype 1

Author

Cornick, Jennifer E., Tastan Bishop, Özlem, Yalcin, Feyruz, Kiran, Anmol M., Kumwenda, Benjamin, Chaguza, Chrispin, Govindpershad, Shanil, Ousmane, Sani, Senghore, Madikay, du Plessis, Mignon, Pluschke, Gerd, Ebruke, Chinelo, McGee, Lesley, Sigaùque, Beutel, Collard, Jean-Marc, Bentley, Stephen D., Kadioglu, Aras, Antonio, Martin, von Gottberg, Anne, French, Neil, Klugman, Keith P., Heyderman, Robert S., Alderson, Mark, Everett, Dean B., and PAGe consortium

Subjects
3. Good health

46. Global Distribution of Invasive Serotype 35D Streptococcus pneumoniaeIsolates following Introduction of 13-Valent Pneumococcal Conjugate Vaccine

Author

Lo, Stephanie W., Gladstone, Rebecca A., van Tonder, Andries J., Hawkins, Paulina A., Kwambana-Adams, Brenda, Cornick, Jennifer E., Madhi, Shabir A., Nzenze, Susan A., du Plessis, Mignon, Kandasamy, Rama, Carter, Philip E., Eser, Özgen Köseoglu, Ho, Pak Leung, Elmdaghri, Naima, Shakoor, Sadia, Clarke, Stuart C., Antonio, Martin, Everett, Dean B., von Gottberg, Anne, Klugman, Keith P., McGee, Lesley, Breiman, Robert F., and Bentley, Stephen D.

Abstract

ABSTRACTA newly recognized pneumococcal serotype, 35D, which differs from the 35B polysaccharide in structure and serology by not binding to factor serum 35a, was recently reported. The genetic basis for this distinctive serology is due to the presence of an inactivating mutation in wciG, which encodes an O-acetyltransferase responsible for O-acetylation of a galactofuranose. Here, we assessed the genomic data of a worldwide pneumococcal collection to identify serotype 35D isolates and understand their geographical distribution, genetic background, and invasiveness potential. Of 21,980 pneumococcal isolates, 444 were originally typed as serotype 35B by PneumoCaT. Analysis of the wciGgene revealed 23 isolates from carriage (n= 4) and disease (n= 19) with partial or complete loss-of-function mutations, including mutations resulting in premature stop codons (n= 22) and an in-frame mutation (n= 1). These were selected for further analysis. The putative 35D isolates were geographically widespread, and 65.2% (15/23) of them was recovered after the introduction of pneumococcal conjugate vaccine 13 (PCV13). Compared with serotype 35B isolates, putative serotype 35D isolates have higher invasive disease potentials based on odds ratios (OR) (11.58; 95% confidence interval[CI], 1.42 to 94.19 versus 0.61; 95% CI, 0.40 to 0.92) and a higher prevalence of macrolide resistance mediated by mefA(26.1% versus 7.6%; P= 0.009). Using the Quellung reaction, 50% (10/20) of viable isolates were identified as serotype 35D, 25% (5/20) as serotype 35B, and 25% (5/20) as a mixture of 35B/35D. The discrepancy between phenotype and genotype requires further investigation. These findings illustrated a global distribution of an invasive serotype, 35D, among young children post-PCV13 introduction and underlined the invasive potential conferred by the loss of O-acetylation in the pneumococcal capsule.

Published
2018
Full Text
View/download PDF

47. Recombination in Streptococcus pneumoniaeLineages Increase with Carriage Duration and Size of the Polysaccharide Capsule

Author

Chaguza, Chrispin, Andam, Cheryl P., Harris, Simon R., Cornick, Jennifer E., Yang, Marie, Bricio-Moreno, Laura, Kamng’ona, Arox W., Parkhill, Julian, French, Neil, Heyderman, Robert S., Kadioglu, Aras, Everett, Dean B., Bentley, Stephen D., and Hanage, William P.

Abstract

ABSTRACTStreptococcus pneumoniaecauses a high burden of invasive pneumococcal disease (IPD) globally, especially in children from resource-poor settings. Like many bacteria, the pneumococcus can import DNA from other strains or even species by transformation and homologous recombination, which has allowed the pneumococcus to evade clinical interventions such as antibiotics and pneumococcal conjugate vaccines (PCVs). Pneumococci are enclosed in a complex polysaccharide capsule that determines the serotype; the capsule varies in size and is associated with properties including carriage prevalence and virulence. We determined and quantified the association between capsule and recombination events using genomic data from a diverse collection of serotypes sampled in Malawi. We determined both the amount of variation introduced by recombination relative to mutation (the relative rate) and how many individual recombination events occur per isolate (the frequency). Using univariate analyses, we found an association between both recombination measures and multiple factors associated with the capsule, including duration and prevalence of carriage. Because many capsular factors are correlated, we used multivariate analysis to correct for collinearity. Capsule size and carriage duration remained positively associated with recombination, although with a reduced Pvalue, and this effect may be mediated through some unassayed additional property associated with larger capsules. This work describes an important impact of serotype on recombination that has been previously overlooked. While the details of how this effect is achieved remain to be determined, it may have important consequences for the serotype-specific response to vaccines and other interventions.IMPORTANCEThe capsule determines >90 different pneumococcal serotypes, which vary in capsule size, virulence, duration, and prevalence of carriage. Current serotype-specific vaccines elicit anticapsule antibodies. Pneumococcus can take up exogenous DNA by transformation and insert it into its chromosome by homologous recombination. This mechanism has disseminated drug resistance and generated vaccine escape variants. It is hence crucial to pneumococcal evolutionary response to interventions, but there has been no systematic study quantifying whether serotypes vary in recombination and whether this is associated with serotype-specific properties such as capsule size or carriage duration. Larger capsules could physically inhibit DNA uptake, or given the longer carriage duration for larger capsules, this may promote recombination. We find that recombination varies among capsules and is associated with capsule size, carriage duration, and carriage prevalence and negatively associated with invasiveness. The consequence of this work is that serotypes with different capsules may respond differently to selective pressures like vaccines.

Published
2016
Full Text
View/download PDF

48. Visualizing variation within Global Pneumococcal Sequence Clusters (GPSCs) and country population snapshots to contextualize pneumococcal isolates.

Author

Gladstone RA, Lo SW, Goater R, Yeats C, Taylor B, Hadfield J, Lees JA, Croucher NJ, van Tonder AJ, Bentley LJ, Quah FX, Blaschke AJ, Pershing NL, Byington CL, Balaji V, Hryniewicz W, Sigauque B, Ravikumar KL, Almeida SCG, Ochoa TJ, Ho PL, du Plessis M, Ndlangisa KM, Cornick JE, Kwambana-Adams B, Benisty R, Nzenze SA, Madhi SA, Hawkins PA, Pollard AJ, Everett DB, Antonio M, Dagan R, Klugman KP, von Gottberg A, Metcalf BJ, Li Y, Beall BW, McGee L, Breiman RF, Aanensen DM, Bentley SD, and The Global Pneumococcal Sequencing Consortium

Subjects
Databases, Genetic, Drug Resistance, Bacterial, Evolution, Molecular, High-Throughput Nucleotide Sequencing, Phylogeny, Phylogeography, Poland, Serogroup, South Africa, Streptococcus pneumoniae genetics, Streptococcus pneumoniae isolation & purification, Utah, DNA Transposable Elements, Polysaccharides, Bacterial genetics, Sequence Analysis, DNA methods, Streptococcus pneumoniae classification
Abstract

Knowledge of pneumococcal lineages, their geographic distribution and antibiotic resistance patterns, can give insights into global pneumococcal disease. We provide interactive bioinformatic outputs to explore such topics, aiming to increase dissemination of genomic insights to the wider community, without the need for specialist training. We prepared 12 country-specific phylogenetic snapshots, and international phylogenetic snapshots of 73 common Global Pneumococcal Sequence Clusters (GPSCs) previously defined using PopPUNK, and present them in Microreact. Gene presence and absence defined using Roary, and recombination profiles derived from Gubbins are presented in Phandango for each GPSC. Temporal phylogenetic signal was assessed for each GPSC using BactDating. We provide examples of how such resources can be used. In our example use of a country-specific phylogenetic snapshot we determined that serotype 14 was observed in nine unrelated genetic backgrounds in South Africa. The international phylogenetic snapshot of GPSC9, in which most serotype 14 isolates from South Africa were observed, highlights that there were three independent sub-clusters represented by South African serotype 14 isolates. We estimated from the GPSC9-dated tree that the sub-clusters were each established in South Africa during the 1980s. We show how recombination plots allowed the identification of a 20 kb recombination spanning the capsular polysaccharide locus within GPSC97. This was consistent with a switch from serotype 6A to 19A estimated to have occured in the 1990s from the GPSC97-dated tree. Plots of gene presence/absence of resistance genes ( tet , erm , cat ) across the GPSC23 phylogeny were consistent with acquisition of a composite transposon. We estimated from the GPSC23-dated tree that the acquisition occurred between 1953 and 1975. Finally, we demonstrate the assignment of GPSC31 to 17 externally generated pneumococcal serotype 1 assemblies from Utah via Pathogenwatch. Most of the Utah isolates clustered within GPSC31 in a USA-specific clade with the most recent common ancestor estimated between 1958 and 1981. The resources we have provided can be used to explore to data, test hypothesis and generate new hypotheses. The accessible assignment of GPSCs allows others to contextualize their own collections beyond the data presented here.

Published
2020
Full Text
View/download PDF

49. Region-specific diversification of the highly virulent serotype 1 Streptococcus pneumoniae .

Author

Cornick JE, Chaguza C, Harris SR, Yalcin F, Senghore M, Kiran AM, Govindpershad S, Ousmane S, Plessis MD, Pluschke G, Ebruke C, McGee L, Sigaùque B, Collard JM, Antonio M, von Gottberg A, French N, Klugman KP, Heyderman RS, Bentley SD, Everett DB, and For The PAGe Consortium

Abstract

Serotype 1 Streptococcus pneumoniae is a leading cause of invasive pneumococcal disease (IPD) worldwide, with the highest burden in developing countries. We report the whole-genome sequencing analysis of 448 serotype 1 isolates from 27 countries worldwide (including 11 in Africa). The global serotype 1 population shows a strong phylogeographic structure at the continental level, and within Africa there is further region-specific structure. Our results demonstrate that region-specific diversification within Africa has been driven by limited cross-region transfer events, genetic recombination and antimicrobial selective pressure. Clonal replacement of the dominant serotype 1 clones circulating within regions is uncommon; however, here we report on the accessory gene content that has contributed to a rare clonal replacement event of ST3081 with ST618 as the dominant cause of IPD in the Gambia.

Published
2015
Full Text
View/download PDF

Catalog

Books, media, physical & digital resources
See catalog results