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Li T, Huang J, Yang S, Chen J, Yao Z, Zhong M, Zhong X, Ye X. Pan-Genome-Wide Association Study of Serotype 19A Pneumococci Identifies Disease-Associated Genes. Microbiol Spectr 2023; 11:e0407322. [PMID: 37358412 PMCID: PMC10433855 DOI: 10.1128/spectrum.04073-22] [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: 10/06/2022] [Accepted: 06/04/2023] [Indexed: 06/27/2023] Open
Abstract
Despite the widespread implementation of pneumococcal vaccines, hypervirulent Streptococcus pneumoniae serotype 19A is endemic worldwide. It is still unclear whether specific genetic elements contribute to complex pathogenicity of serotype 19A isolates. We performed a large-scale pan-genome-wide association study (pan-GWAS) of 1,292 serotype 19A isolates sampled from patients with invasive disease and asymptomatic carriers. To address the underlying disease-associated genotypes, a comprehensive analysis using three methods (Scoary, a linear mixed model, and random forest) was performed to compare disease and carriage isolates to identify genes consistently associated with disease phenotype. By using three pan-GWAS methods, we found consensus on statistically significant associations between genotypes and disease phenotypes (disease or carriage), with a subset of 30 consistently significant disease-associated genes. The results of functional annotation revealed that these disease-associated genes had diverse predicted functions, including those that participated in mobile genetic elements, antibiotic resistance, virulence, and cellular metabolism. Our findings suggest the multifactorial pathogenicity nature of this hypervirulent serotype and provide important evidence for the design of novel protein-based vaccines to prevent and control pneumococcal disease. IMPORTANCE It is important to understand the genetic and pathogenic characteristics of S. pneumoniae serotype 19A, which may provide important information for the prevention and treatment of pneumococcal disease. This global large-sample pan-GWAS study has identified a subset of 30 consistently significant disease-associated genes that are involved in mobile genetic elements, antibiotic resistance, virulence, and cellular metabolism. These findings suggest the multifactorial pathogenicity nature of hypervirulent S. pneumoniae serotype 19A isolates and provide implications for the design of novel protein-based vaccines.
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Affiliation(s)
- Ting Li
- School of Public Health, Guangdong Pharmaceutical University, Guangzhou, China
| | - Jiayin Huang
- School of Public Health, Guangdong Pharmaceutical University, Guangzhou, China
| | - Shimin Yang
- School of Public Health, Guangdong Pharmaceutical University, Guangzhou, China
| | - Jianyu Chen
- School of Public Health, Guangdong Pharmaceutical University, Guangzhou, China
| | - Zhenjiang Yao
- School of Public Health, Guangdong Pharmaceutical University, Guangzhou, China
| | - Minghao Zhong
- Department of Prevention and Health Care, The Sixth People’s Hospital of Dongguan City, Guangdong, China
| | - Xinguang Zhong
- Department of Prevention and Health Care, The Sixth People’s Hospital of Dongguan City, Guangdong, China
| | - Xiaohua Ye
- School of Public Health, Guangdong Pharmaceutical University, Guangzhou, China
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Gonzales BE, Mercado EH, Pinedo-Bardales M, Hinostroza N, Campos F, Chaparro E, Del Águila O, Castillo ME, Saenz A, Reyes I, Ochoa TJ. Increase of Macrolide-Resistance in Streptococcus pneumoniae Strains After the Introduction of the 13-Valent Pneumococcal Conjugate Vaccine in Lima, Peru. Front Cell Infect Microbiol 2022; 12:866186. [PMID: 35615398 PMCID: PMC9125093 DOI: 10.3389/fcimb.2022.866186] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 04/04/2022] [Indexed: 12/27/2022] Open
Abstract
Streptococcus pneumoniae upper respiratory infections and pneumonia are often treated with macrolides, but recently macrolide resistance is becoming an increasingly important problem. The 13-valent pneumococcal conjugate vaccine (PCV13) was introduced in the National Immunization Program of Peru in 2015. This study aimed to evaluate the temporal evolution of macrolide resistance in S. pneumoniae isolates collected in five cross-sectional studies conducted before and after this vaccine introduction, from 2006 to 2019 in Lima, Peru. A total of 521 and 242 S. pneumoniae isolates recovered from nasopharyngeal swabs from healthy carrier children < 2 years old (2 carriage studies) and samples from normally sterile body areas from pediatric patients with invasive pneumococcal disease (IPD) (3 IPD studies), respectively, were included in this study. Phenotypic macrolide resistance was detected using the Kirby-Bauer method and/or MIC test. We found a significant increase in macrolide resistance over time, from 33.5% to 50.0% in carriage studies, and from 24.8% to 37.5% and 70.8% in IPD studies. Macrolide resistance genes [erm(B) and mef(A/E)] were screened using PCR. In carriage studies, we detected a significant decrease in the frequency of mef(A/E) genes among macrolide-resistant S. pneumoniae strains (from 66.7% to 50.0%) after introduction of PCV13. The most common mechanism of macrolide-resistant among IPD strains was the presence of erm(B) (96.0%, 95.2% and 85.1% in the 3 IPD studies respectively). Macrolide resistance was more common in serotype 19A strains (80% and 90% among carriage and IPD strains, respectively) vs. non-serotype 19A (35.5% and 34.4% among carriage and IPD strains, respectively). In conclusion, S. pneumoniae macrolide resistance rates are very high among Peruvian children. Future studies are needed in order to evaluate macrolide resistance trends among pneumococcal strains, especially now after the COVID-19 pandemic, since azithromycin was vastly used as empiric treatment of COVID-19 in Peru.
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Affiliation(s)
- Brayan E. Gonzales
- Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Erik H. Mercado
- Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Maria Pinedo-Bardales
- Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Noemi Hinostroza
- Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Francisco Campos
- Departamento de Pediatría, Hospital Nacional Docente Madre-Niño San Bartolomé, Lima, Peru
| | - Eduardo Chaparro
- Departamento de Pediatría, Hospital Nacional Cayetano Heredia, Lima, Peru
- Facultad de Medicina, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Olguita Del Águila
- Servicio de Pediatría de Especialidades Clínicas, Hospital Nacional Edgardo Rebagliati Martins, Lima, Peru
| | - María E. Castillo
- Facultad de Medicina, Universidad Peruana Cayetano Heredia, Lima, Peru
- Oficina de Epidemiología, Instituto Nacional de Salud del Niño, Lima, Peru
| | - Andrés Saenz
- Departamento de Pediatría, Hospital Nacional Daniel Alcides Carrión, Lima, Peru
| | - Isabel Reyes
- Servicio de Hospitalización, Hospital de Emergencias Pediátricas, Lima, Peru
| | - Theresa J. Ochoa
- Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru
- Facultad de Medicina, Universidad Peruana Cayetano Heredia, Lima, Peru
- *Correspondence: Theresa J. Ochoa,
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