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Sharew B, Moges F, Yismaw G, Mihret A, Lobie TA, Abebe W, Fentaw S, Frye S, Vestrheim D, Tessema B, Caugant DA. Molecular epidemiology of Streptococcus pneumoniae isolates causing invasive and noninvasive infection in Ethiopia. Sci Rep 2024; 14:21409. [PMID: 39271789 PMCID: PMC11399344 DOI: 10.1038/s41598-024-72762-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Accepted: 09/10/2024] [Indexed: 09/15/2024] Open
Abstract
Streptococcus pneumoniae, a medically important opportunistic bacterial pathogen of the upper respiratory tract, is a major public health concern, causing a wide range of pneumococcal illnesses, both invasive and noninvasive. It is associated with significant global morbidity and mortality, including pneumonia, meningitis, sepsis, and acute otitis media. The major purpose of this study was to determine the molecular epidemiology of Streptococcus pneumoniae strains that cause invasive and noninvasive infections in Ethiopia. A prospective study was undertaken in two regional hospitals between January 2018 and December 2019. Whole-genome sequencing was used to analyze all isolates. Serotypes and multilocus sequence types (MLST) were derived from genomic data. The E-test was used for antimicrobial susceptibility testing. Patient samples obtained 54 Streptococcus pneumoniae isolates, 33 from invasive and 21 from noninvasive specimens. Our findings identified 32 serotypes expressed by 25 Global Pneumococcal Sequence Clusters (GPSCs) and 42 sequence types (STs), including 21 new STs. The most common sequence types among the invasive isolates were ST3500, ST5368, ST11162, ST15425, ST15555, ST15559, and ST15561 (2/33, 6% each). These sequence types were linked to serotypes 8, 7 C, 15B/C, 16 F, 10 A, 15B, and 6 A, respectively. Among the noninvasive isolates, only ST15432, associated with serotype 23 A, had numerous isolates (4/21, 19%). Serotype 14 was revealed as the most resistant strain to penicillin G, whereas isolates from serotypes 3, 8, 7 C, and 10 A were resistant to erythromycin. Notably, all serotype 6 A isolates were resistant to both erythromycin and penicillin G. Our findings revealed an abnormally significant number of novel STs, as well as extremely diversified serotypes and sequence types, implying that Ethiopia may serve as a breeding ground for novel STs. Recombination can produce novel STs that cause capsular switching. This has the potential to influence how immunization campaigns affect the burden of invasive pneumococcal illness. The findings highlight the importance of continuous genetic surveillance of the pneumococcal population as a vital step toward enhancing future vaccine design.
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Affiliation(s)
- Bekele Sharew
- Department of Medical Laboratory Sciences, College of Health Sciences, Debre Tabor University, Debre Tabor, Ethiopia.
| | - Feleke Moges
- Department of Medical Microbiology, School of Biomedical and Laboratory Sciences, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
| | | | - Adane Mihret
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia
| | - Tekle Airgecho Lobie
- Department of Microbiology, Oslo University Hospital and University of Oslo, Oslo, Norway
- Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science andTechnology (NTNU), 7491, Trondheim, Norway
| | - Wondwossen Abebe
- Department of Medical Microbiology, School of Biomedical and Laboratory Sciences, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
| | - Surafal Fentaw
- Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Stephan Frye
- Department of Microbiology, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Didrik Vestrheim
- Division for Infection Control and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Belay Tessema
- Department of Medical Microbiology, School of Biomedical and Laboratory Sciences, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
- Institute of Clinical Immunology, Faculty of Medicine, University of Leipzig, Leipzig, Germany
| | - Dominique A Caugant
- Division for Infection Control and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway
- Department of Community Medicine, University of Oslo, Oslo, Norway
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Savinova T, Brzhozovskaya E, Alyabieva N, Lazareva A, Shagin D, Mayanskiy N. Multiple-Drug Resistant Nasopharyngeal Streptococcus pneumoniae Isolated in Russia: Serotypes, Antimicrobial Susceptibility, and Molecular Characterization of the Emergent Serotype 13/ST2754 Lineage. Microb Drug Resist 2021; 28:39-47. [PMID: 34357824 DOI: 10.1089/mdr.2021.0074] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The pneumococcal population structure and drug resistance patterns are constantly changing worldwide. In this study, we described serotypes and antimicrobial susceptibility among 478 multiple-drug resistant (MDR) pediatric nasopharyngeal pneumococci recovered in 2010-2017. The majority of isolates (89.3%; n = 427) carried pneumococcal conjugate vaccine (PCV)13 serotypes, predominantly 6A/B, 14, 19A/F, and 23F. A non-PCV13 serotype capsule was detected in 44 (9.2%) MDR pneumococci, including serotypes 23A (n = 8), 13 (n = 7), 28F (n = 6), 11A (n = 5), and serogroup 35 (n = 10) isolates. The remaining seven (1.5%) MDR isolates were nontypeable. The majority of non-PCV13-serotype isolates were resistant to tetracycline, erythromycin, and clindamycin; most harbored both the ermB and mef genes. Among the 44 serotyped MDR non-PCV13 isolates, multilocus sequence typing analysis revealed 24 different sequence types (STs). ST2754 was the most abundant lineage demonstrating an unusual association with serotypes 13 (n = 7) and 9N (n = 1). The whole-genome sequencing-based analysis demonstrated that the serotype 13/ST2754 lineage was closely related to the serotype 13/ST2754 isolate recovered in Africa (Malawi) in 2013, possessed a Tn6002-like transposon carrying the erm(B) and tet(M) genes, and harbored additional virulence determinants, including arginine metabolism genes and a putative bacteriocin locus. Such a favorable genetic background may provide competitive advantages and potential for spreading and expansion of this clone among pneumococci. These data warrant further molecular monitoring of the genetic composition of the changing pneumococcal population.
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Affiliation(s)
- Tatiana Savinova
- Pirogov Russian National Research Medical University, Moscow, Russia
| | | | - Natalia Alyabieva
- National Medical Research Center for Children's Health, Moscow, Russia
| | - Anna Lazareva
- National Medical Research Center for Children's Health, Moscow, Russia
| | - Dmitry Shagin
- Pirogov Russian National Research Medical University, Moscow, Russia
| | - Nikolay Mayanskiy
- Pirogov Russian National Research Medical University, Moscow, Russia
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