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Javaid N, Lo SW, Nisar MI, Basharat A, Jaleel H, Rasool K, Sultana Q, Kabir F, Hotwani A, Breiman RF, Bentley SD, Shakoor S, Mirza S. Strain features of pneumococcal isolates in the pre- and post-PCV10 era in Pakistan. Microb Genom 2024; 10:001163. [PMID: 38270581 PMCID: PMC10868622 DOI: 10.1099/mgen.0.001163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 12/06/2023] [Indexed: 01/26/2024] Open
Abstract
Pakistan is amongst the four countries with the highest number of pneumococcal deaths. While the PCV10 vaccine was introduced in Pakistan in October 2012, data regarding the impact of the vaccine on the population dynamics of Streptococcus pneumoniae in Pakistan remain obscure. Using whole genome sequencing of 190 isolates (nasopharyngeal carriage=75, disease=113, unknown sites=2) collected between 2002 and 2020, this study presents characteristics of pneumococcal strains in Pakistan in the pre- and post-vaccine era. The isolates were characterized on the basis of serotype distribution, genetic lineages (or Global Pneumococcal Sequence Cluster, GPSC) and antibiotic resistance. A high level of diversity in serotype and genetic lineages of pneumococci was observed in Pakistan. Among 190 isolates, we identified 54 serotypes, 67 GPSCs and 116 sequence types (STs) including 23 new STs. The most prevalent GPSCs and their associated serotypes in nasopharyngeal carriage were GPSC54 (expressing serotype 9V), GPSC5 (15A and 7B, and serogroup 24), GPSC25 (15B/15C), GPSC67 (18C) and GPSC376 (6A and 6D). Similarly, among 113 disease-causing isolates, the most prevalent GPSC/serotype combinations were GPSC2 (serotype 1), GPSC10 (serotypes 14, 10A, 19A and 19F), GPSC43 (serotypes 13, 11A, 23B, 35A and 9V), GPSC67 (serotypes 18A and 18C) and GPSC642 (serotype 11A). Of the 190 isolates, the highest levels of resistance were observed against penicillin (58.9 %, n=122), erythromycin (29.5 %, n=56), clindamycin (13.2 %, n=25), co-trimoxazole (94.2 %, n=179) and tetracycline/doxycycline (53.2 %, n=101). A higher proportion of disease-causing isolates were multidrug resistant as compared to carriage isolates (54 % vs 25 %). Our data suggest limited coverage of PCV10 in nasopharyngeal (21.6 %, 16/74) as well as disease-causing (38.1 %, 16/42) isolates among children ≤5 years old; however, higher valent vaccine PCV13 would increase the coverage rates to 33.8 % in nasopharyngeal and 54.8 % in disease-causing isolates, whereas PCV24/25 would offer the highest coverage rates. Owing to the diversity of serotypes observed during the post-vaccine period, the suggested inclusion of serotype in future vaccine formulations will require investigations with larger data sets with an extended temporal window. This article contains data hosted by Microreact.
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Affiliation(s)
- Nida Javaid
- Department of Life Sciences, School of Science and Engineering, Lahore University of Management Science, Lahore, Pakistan
- Parasites and Microbes, Wellcome Sanger Institute, Hinxton, UK
| | - Stephanie W. Lo
- Parasites and Microbes, Wellcome Sanger Institute, Hinxton, UK
- Milner Centre for Evolution, Department of Life Science, University of Bath, Bath, UK
| | - Muhammad Imran Nisar
- Departments of Pathology, Pediatrics, and Medicine, Aga Khan University, Karachi, Pakistan
| | - Asma Basharat
- Department of Life Sciences, School of Science and Engineering, Lahore University of Management Science, Lahore, Pakistan
| | - Hadiqa Jaleel
- Department of Life Sciences, School of Science and Engineering, Lahore University of Management Science, Lahore, Pakistan
| | - Karam Rasool
- Department of Microbiology, Chughtai Lab/Chughtai Institute of Pathology, Lahore, Pakistan
| | - Qamar Sultana
- Department of Microbiology, Chughtai Lab/Chughtai Institute of Pathology, Lahore, Pakistan
| | - Furqan Kabir
- Infectious Diseases Research Laboratory (IDRL), Dept. of Paediatrics & Child Health, Aga Khan University, Karachi, Pakistan
| | - Aneeta Hotwani
- Departments of Pathology, Pediatrics, and Medicine, Aga Khan University, Karachi, Pakistan
| | - Robert F. Breiman
- Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | | | - Sadia Shakoor
- Departments of Pathology, Pediatrics, and Medicine, Aga Khan University, Karachi, Pakistan
| | - Shaper Mirza
- Department of Life Sciences, School of Science and Engineering, Lahore University of Management Science, Lahore, Pakistan
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Javaid N, Olwagen C, Nzenze S, Hawkins P, Gladstone R, McGee L, Breiman RF, Bentley SD, Madhi SA, Lo S. Population genomics of pneumococcal carriage in South Africa following the introduction of the 13-valent pneumococcal conjugate vaccine (PCV13) immunization. Microb Genom 2022; 8. [PMID: 35737523 PMCID: PMC9455715 DOI: 10.1099/mgen.0.000831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Streptococcus pneumoniae is a major human pathogen responsible for over 317000 deaths in children <5 years of age with the burden of the disease being highest in low- and middle-income countries including South Africa. Following the introduction of the 7-valent and 13-valent pneumococcal conjugate vaccine (PCV) in South Africa in 2009 and 2011, respectively, a decrease in both invasive pneumococcal infections and asymptomatic carriage of vaccine-type pneumococci were reported. In this study, we described the changing epidemiology of the pneumococcal carriage population in South Africa, by sequencing the genomes of 1825 isolates collected between 2009 and 2013. Using these genomic data, we reported the changes in serotypes, Global Pneumococcal Sequence Clusters (GPSCs), and antibiotic resistance before and after the introduction of PCV13. The pneumococcal carriage population in South Africa has a high level of diversity, comprising of 126 GPSCs and 49 serotypes. Of the ten most prevalent GPSCs detected, six were predominantly found in Africa (GPSC22, GPSC21, GPSC17, GPSC33, GPSC34 and GPSC52). We found a significant decrease in PCV7 serotypes (19F, 6B, 23F and 14) and an increase in non-vaccine serotypes (NVT) (16F, 34, 35B and 11A) among children <2 years of age. The increase in NVTs was driven by pneumococcal lineages GPSC33, GPSC34, GPSC5 and GPSC22. Overall, a decrease in antibiotic resistance for 11 antimicrobials was detected in the PCV13 era. Further, we reported a higher resistance prevalence among vaccine types (VTs), as compared to NVTs; however, an increase in penicillin resistance among NVT was observed between the PCV7 and PCV13 eras. The carriage isolates from South Africa predominantly belonged to pneumococcal lineages, which are endemic to Africa. While the introduction of PCV resulted in an overall reduction of resistance in pneumococcal carriage isolates, an increase in penicillin resistance among NVTs was detected in children aged between 3 and 5 years, driven by the expansion of penicillin-resistant clones associated with NVTs in the PCV13 era.
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Affiliation(s)
- Nida Javaid
- Department of Biology, Syed Babar Ali School of Science and Engineering, Lahore University of Management Sciences, Lahore, Pakistan
- Parasites and Microbes, Wellcome Sanger Institute, Hinxton, UK
- *Correspondence: Nida Javaid, ;
| | - Courtney Olwagen
- Department of Science and Technology/National Research Foundation: Vaccine Preventable Diseases, University of the Witwatersrand, Johannesburg, South Africa
- Medical Research Council: Respiratory and Meningeal Pathogens Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Susan Nzenze
- Department of Science and Technology/National Research Foundation: Vaccine Preventable Diseases, University of the Witwatersrand, Johannesburg, South Africa
- Medical Research Council: Respiratory and Meningeal Pathogens Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Paulina Hawkins
- Centers for Disease Control and Prevention, Atlanta, GA, USA
| | | | - Lesley McGee
- Centers for Disease Control and Prevention, Atlanta, GA, USA
| | | | - Stephen D. Bentley
- Parasites and Microbes, Wellcome Sanger Institute, Hinxton, UK
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Shabir A. Madhi
- Department of Science and Technology/National Research Foundation: Vaccine Preventable Diseases, University of the Witwatersrand, Johannesburg, South Africa
- Medical Research Council: Respiratory and Meningeal Pathogens Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- *Correspondence: Shabir A. Madhi,
| | - Stephanie Lo
- Parasites and Microbes, Wellcome Sanger Institute, Hinxton, UK
- *Correspondence: Stephanie Lo,
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