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Kobayashi J, Ohkusu M, Matsumoto T, Kubota N, Ishiwada N. Bacteriological and molecular characterization of temperature- and CO 2-dependent Streptococcus pneumoniae serotype 24F ST162 isolated from Japanese children. Microbiol Spectr 2023; 11:e0216523. [PMID: 37823633 PMCID: PMC10714769 DOI: 10.1128/spectrum.02165-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 09/06/2023] [Indexed: 10/13/2023] Open
Abstract
IMPORTANCE We characterized Streptococcus pneumoniae serotype 24F sequence type (ST) 162 isolated from Japanese children with invasive pneumococcal disease (IPD). Owing to its highly invasive nature, serotype 24F is expected to be isolated from clinically significant cases. Serotype 24F ST162 isolates tested in the present study did not grow at 35°C in ambient air. Therefore, antimicrobial susceptibility testing using the broth microdilution method, which is usually conducted in ambient air, cannot be performed, posing a clinical challenge. Clinical practitioners and laboratory personnel should be aware of the epidemiological, bacteriological, and molecular characteristics of serotype 24F ST162. We believe that our findings can help diagnose and treat IPD caused by serotype 24F ST162, a serotype expected to become problematic in the post-13 valent pneumococcal conjugate vaccine era.
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Affiliation(s)
- Jun Kobayashi
- Department of Laboratory Medicine, Nagano Children’s Hospital, Azumino, Japan
- Life Science Research Center, Nagano Children’s Hospital, Azumino, Japan
| | - Misako Ohkusu
- Department of Infectious Diseases, Medical Mycology Research Center, Chiba University, Chiba, Japan
| | - Takehisa Matsumoto
- Department of Laboratory Sciences, Gunma University Graduate School of Health Sciences, Maebashi, Japan
| | - Noriko Kubota
- Department of Laboratory Medicine, Nagano Children’s Hospital, Azumino, Japan
- Life Science Research Center, Nagano Children’s Hospital, Azumino, Japan
| | - Naruhiko Ishiwada
- Department of Infectious Diseases, Medical Mycology Research Center, Chiba University, Chiba, Japan
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2
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Chen YY, Chi H, Liao WC, Li SW, Yang YC, Lin HC, Chang HP, Pan YJ, Chiang RL, Hsieh YC. Genomic analysis of penicillin-binding proteins and recombination events in an emerging amoxicillin- and meropenem-resistant PMEN3 (Spain 9V-3, ST156) variant in Taiwan and comparison with global descendants of this lineage. Microbiol Spectr 2023; 11:e0184023. [PMID: 37930013 PMCID: PMC10715136 DOI: 10.1128/spectrum.01840-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 10/03/2023] [Indexed: 11/07/2023] Open
Abstract
From 2008 to 2020, the Taiwan National Notifiable Disease Surveillance System database demonstrated that the incidence of non-vaccine serotype 23A invasive pneumococcal disease (IPD) approximately doubled. In this study, 276 non-repetitive pneumococcal clinical isolates were collected from two medical centers in Taiwan between 2019 and 2021. Of these 267 pneumococci, 60 were serotype 23A. Among them, 50 (83%) of serotype 23A isolates belonged to the sequence type (ST) 166 variant of the Spain9V-3 clone. Pneumococcal 23A-ST166 isolates were collected to assess their evolutionary relationships using whole-genome sequencing. All 23A-ST166 isolates were resistant to amoxicillin and meropenem, and 96% harbored a novel combination of penicillin-binding proteins (PBPs) (1a:2b:2x):15:11:299, the newly identified PBP2x-299 in Taiwan. Transformation of the pbp1a, pbp2b, and pbp2x alleles into the β-lactam-susceptible R6 strain revealed that PBP2x-299 and PBP2b-11 increased the MIC of ceftriaxone and meropenem by 16-fold, respectively. Prediction analysis of recombination sites in PMEN3 descendants (23A-ST166 in Taiwan, 35B-ST156 in the United States, and 11A-ST838/ST6521 in Europe) showed that adaptive evolution involved repeated, selectively favored convergent recombination in the capsular polysaccharide synthesis region, PBPs, murM, and folP genome sites. In the late 13-valent pneumococcal conjugate vaccine era, PMEN3 continuously displayed an evolutionary capacity for global dissemination and persistence, increasing IPD incidence, leading to an offset in the decrease of pneumococcal conjugate vaccine serotype-related diseases, and contributing to high antibiotic resistance. A clonal shift with a highly β-lactam-resistant non-vaccine serotype 23A, from ST338 to ST166, increased in Taiwan. ST166 is a single-locus variant of the Spain9V-3 clone, which is also called the PMEN3 lineage. All 23A-ST166 isolates, in this study, were resistant to amoxicillin and meropenem, and 96% harbored a novel combination of penicillin-binding proteins (PBPs) (1a:2b:2x):15:11:299. PBP2x-299 and PBP2b-11 contributed to the increasing MIC of ceftriaxone and meropenem, respectively. Prediction analysis of recombination sites in PMEN3 descendants showed that adaptive evolution involved repeated, selectively favored convergent recombination in the capsular polysaccharide synthesis region, PBPs, murM, and folP genome sites. In the late 13-valent pneumococcal conjugate vaccine era, PMEN3 continuously displays the evolutionary capacity for dissemination, leading to an offset in the decrease of pneumococcal conjugate vaccine serotype-related diseases and contributing to high antibiotic resistance.
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Affiliation(s)
- Yi-Yin Chen
- Department of Pediatrics, Chang Gung Children’s Hospital, Chang Gung Memorial Hospital, Chang Gung University, College of Medicine, Taoyuan, Taiwan
| | - Hsin Chi
- Department of Medicine, MacKay Medicine College, New Taipei, Taiwan
- Department of Pediatrics, MacKay Children’s Hospital and MacKay Memorial Hospital, Taipei, Taiwan
- Department of Medical Research, MacKay Memorial Hospital, Taipei, Taiwan
| | - Wei-Chao Liao
- Department of Pediatrics, Chang Gung Children’s Hospital, Chang Gung Memorial Hospital, Chang Gung University, College of Medicine, Taoyuan, Taiwan
- Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
| | - Shiao-Wen Li
- Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
- Department of Life Sciences, National University of Kaohsiung, Kaohsiung, Taiwan
| | - Yu-Ching Yang
- Department of Pediatrics, Chang Gung Children’s Hospital, Chang Gung Memorial Hospital, Chang Gung University, College of Medicine, Taoyuan, Taiwan
| | - Ho-Chen Lin
- Department of Pediatrics, Chang Gung Children’s Hospital, Chang Gung Memorial Hospital, Chang Gung University, College of Medicine, Taoyuan, Taiwan
| | - Hsiao-Pei Chang
- Department of Pediatrics, Chang Gung Children’s Hospital, Chang Gung Memorial Hospital, Chang Gung University, College of Medicine, Taoyuan, Taiwan
| | - Yi-Jiun Pan
- Department of Microbiology and Immunology, School of Medicine, College of Medicine, China Medical University, Taichung, Taiwan
| | - Ruei-Lin Chiang
- Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
| | - Yu-Chia Hsieh
- Department of Pediatrics, Chang Gung Children’s Hospital, Chang Gung Memorial Hospital, Chang Gung University, College of Medicine, Taoyuan, Taiwan
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Ohkusu M, Takeshita K, Takeuchi N, Ishiwada N. Increase in prevalence of Streptococcus pneumoniae serogroup 24 in children upon introducing 13-valent pneumococcal conjugate vaccine in Japan. Access Microbiol 2023; 5:000507.v3. [PMID: 37091738 PMCID: PMC10118250 DOI: 10.1099/acmi.0.000507.v3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 02/03/2023] [Indexed: 03/18/2023] Open
Abstract
After introducing the 13-valent pneumococcal conjugate vaccine (PCV13) for children, a change in the prevalence of different
Streptococcus pneumoniae
serotypes that cause invasive pneumococcal diseases (IPDs) has been observed. The prevalence of vaccine serotypes has decreased and that of non-vaccine serotypes has increased. Currently, serogroup 24 has become one of the major non-vaccine serotypes causing IPDs in children in Japan. The aim of this study was to characterize clinical and genomic features of
S. pneumoniae
serogroup 24 strains isolated from sterile body sites in Japanese children. Serotyping, multi-locus sequence typing and genomic analysis of capsular polysaccharides of 61 strains of serogroup 24 were performed from 2015 to 2021. Among the 61 strains, 36, 23 and two belonged to serotypes 24F, 24B and 24C, respectively. The 24F sequence type (ST) 2572 and 24B ST 2572 were the major serotypes and sequence types observed from 2015 to 2019. By contrast, 24F ST 162 and 24B ST 2754 were the two major serotypes and sequence types observed after 2020. Two strains of serotype 24C were detected for the first time in Japan. Sequence analysis of the abpA gene, which plays a role in the synthesis of capsular polysaccharides in
S. pneumoniae
, was performed to distinguish different strains of serogroup 24. After the introduction of PCV13 in Japan, serogroup 24 has become one of the most prevalent non-vaccine serotypes causing IPDs in children. This serogroup has not been targeted in the next-generation pneumococcal conjugate vaccines. Therefore, monitoring of
S. pneumoniae
serogroup 24 that causes IPDs in children is essential.
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Affiliation(s)
- Misako Ohkusu
- Department of Infectious Diseases, Medical Mycology Research Center, Chiba University, Chiba, 260-8673, Japan
| | - Kenichi Takeshita
- Department of Infectious Diseases, Medical Mycology Research Center, Chiba University, Chiba, 260-8673, Japan
| | - Noriko Takeuchi
- Department of Infectious Diseases, Medical Mycology Research Center, Chiba University, Chiba, 260-8673, Japan
| | - Naruhiko Ishiwada
- Department of Infectious Diseases, Medical Mycology Research Center, Chiba University, Chiba, 260-8673, Japan
- *Correspondence: Naruhiko Ishiwada,
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Janssens E, Flamaing J, Vandermeulen C, Peetermans WE, Desmet S, De Munter P. The 20-valent pneumococcal conjugate vaccine (PCV20): expected added value. Acta Clin Belg 2023; 78:78-86. [PMID: 35171752 DOI: 10.1080/17843286.2022.2039865] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
OBJECTIVES Currently existing pneumococcal vaccines have contributed to a major reduction in pneumococcal disease. However, there remains an unmet need for vaccine coverage of serotypes not included in PCV13 to further reduce the burden of disease. The objective of this review is to assess the potential impact of implementation of the investigational 20-valent pneumococcal conjugate vaccine (PCV20) in the childhood and adult immunization programme in Belgium and Europe. METHODS A literature search was conducted to identify publications and surveillance reports concerning the effectiveness and safety of pneumococcal vaccines, epidemiological data on pneumococcal disease or serotype distribution dynamics after introduction of systematic vaccination. RESULTS Serotypes included in PCV20 currently account for the majority of pneumococcal disease in Belgium and Europe. In Belgium, PCV20-serotypes accounted for 71.4% of invasive pneumococcal disease (IPD) cases across all age groups in 2019, of which 39.2% were caused by PCV20-non-PCV13-serotypes. In Europe, these seven serotypes accounted for 37,6% of IPD cases in 2018. PCV20 has proven to be well tolerated in vaccine-naïve adults and elicits a substantial immune response against all serotypes included. CONCLUSION Due to serotype replacement following the introduction of PCV7 and PCV13, a considerable proportion of pneumococcal disease is currently caused by PCV20-serotypes. PCV20 has the potential of preventing more pneumococcal disease in children and the adult population at risk than the existing conjugate vaccines. The available evidence on safety and immunogenicity of PCV20 is promising, but further research is needed to provide data about vaccine effectiveness, immune response duration and replacement phenomenon after introduction of PCV20.
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Affiliation(s)
- Esther Janssens
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
| | - Johan Flamaing
- Department of Geriatric Medicine, University Hospitals Leuven, Leuven, Belgium.,Department of Public Health & Primary Care, KU Leuven, Leuven, Belgium
| | - Corinne Vandermeulen
- Department of Public Health & Primary Care, KU Leuven, Leuven, Belgium.,Leuven University Vaccinology Centre, Leuven, Belgium
| | - Willy E Peetermans
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium.,Department of General Internal Medicine, University Hospitals Leuven, Leuven, Belgium
| | - Stefanie Desmet
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium.,National Reference Centre for Streptococcus Pneumoniae, University Hospitals Leuven, Leuven, Belgium
| | - Paul De Munter
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium.,Department of General Internal Medicine, University Hospitals Leuven, Leuven, Belgium
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Eriksen HB, Fuursted K, Jensen A, Jensen CS, Nielsen X, Christensen JJ, Shewmaker P, Rebelo AR, Aarestrup FM, Schønning K, Slotved HC. Predicting β-lactam susceptibility from the genome of Streptococcus pneumoniae and other mitis group streptococci. Front Microbiol 2023; 14:1120023. [PMID: 36937294 PMCID: PMC10018206 DOI: 10.3389/fmicb.2023.1120023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 02/13/2023] [Indexed: 03/06/2023] Open
Abstract
Introduction For Streptococcus pneumoniae, β-lactam susceptibility can be predicted from the amino acid sequence of the penicillin-binding proteins PBP1a, PBP2b, and PBP2x. The combination of PBP-subtypes provides a PBP-profile, which correlates to a phenotypic minimal inhibitory concentration (MIC). The non-S. pneumoniae Mitis-group streptococci (MGS) have similar PBPs and exchange pbp-alleles with S. pneumoniae. We studied whether a simple BLAST analysis could be used to predict phenotypic susceptibility in Danish S. pneumoniae isolates and in internationally collected MGS. Method Isolates with available WGS and phenotypic susceptibility data were included. For each isolate, the best matching PBP-profile was identified by BLAST analysis. The corresponding MICs for penicillin and ceftriaxone was retrieved. Category agreement (CA), minor-, major-, and very major discrepancy was calculated. Genotypic-phenotypic accuracy was examined with Deming regression. Results Among 88 S. pneumoniae isolates, 55 isolates had a recognized PBP-profile, and CA was 100% for penicillin and 98.2% for ceftriaxone. In 33 S. pneumoniae isolates with a new PBP-profile, CA was 90.9% (penicillin) and 93.8% (ceftriaxone) using the nearest recognized PBP-profile. Applying the S. pneumoniae database to non-S. pneumoniae MGS revealed that none had a recognized PBP-profile. For Streptococcus pseudopneumoniae, CA was 100% for penicillin and ceftriaxone in 19 susceptible isolates. In 33 Streptococcus mitis isolates, CA was 75.8% (penicillin) and 86.2% (ceftriaxone) and in 25 Streptococcus oralis isolates CA was 8% (penicillin) and 100% (ceftriaxone). Conclusion Using a simple BLAST analysis, genotypic susceptibility prediction was accurate in Danish S. pneumoniae isolates, particularly in isolates with recognized PBP-profiles. Susceptibility was poorly predicted in other MGS using the current database.
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Affiliation(s)
- Helle Brander Eriksen
- Department of Clinical Microbiology, Herlev and Gentofte Hospital, Herlev, Denmark
- *Correspondence: Helle Brander Eriksen,
| | - Kurt Fuursted
- Department of Bacteria, Parasites, and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Anders Jensen
- Department of Clinical Microbiology, Sygehus Lillebælt, Vejle, Denmark
| | | | - Xiaohui Nielsen
- The Regional Department of Clinical Microbiology, Slagelse, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Jens Jørgen Christensen
- The Regional Department of Clinical Microbiology, Slagelse, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | | | - Ana Rita Rebelo
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Frank Møller Aarestrup
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Kristian Schønning
- Department of Clinical Microbiology, Rigshospitalet, Copenhagen, Denmark
| | - Hans-Christian Slotved
- Department of Bacteria, Parasites, and Fungi, Statens Serum Institut, Copenhagen, Denmark
- Hans-Christian Slotved,
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Mills RO, Abdullah MR, Akwetey SA, Sappor DC, Bolivar JA, Gámez G, van der Linden MPG, Hammerschmidt S. Molecular Characterization and Antibiotic Susceptibility of Non-PCV13 Pneumococcal Serotypes among Vaccinated Children in Cape Coast, Ghana. Microorganisms 2022; 10:microorganisms10102054. [PMID: 36296330 PMCID: PMC9609747 DOI: 10.3390/microorganisms10102054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 10/03/2022] [Accepted: 10/06/2022] [Indexed: 11/24/2022] Open
Abstract
Preventive strategies involving the use of pneumococcal conjugate vaccines (PCVs) are known to drastically reduce pneumococcal disease. However, PCV vaccination has been plagued with serotype replacement by non-PCV serotypes. In this study, we describe the prevalence and molecular characteristics of non-PCV13 serotypes (non-vaccine serotypes, NVTs) from pneumococcal carriage isolates obtained from children < 5 years old in Cape Coast, Ghana, after PCV introduction. The isolates were subjected to antibiotic susceptibility testing and multilocus sequence typing (MLST), and molecular techniques were used to detect the presence of virulence genes. Serotypes 11A, 13, 15B, 23B, and 34 formed the top five of the 93 NVT isolates. As such, 20 (21.5%), 49 (48.4%), and 70 (74.3%) isolates were non-susceptible to penicillin, tetracycline, and cotrimoxazole, respectively. Sixteen (17.2%) multidrug-resistant isolates were identified. However, non-susceptibility to ceftriaxone and erythromycin was low and all isolates were fully susceptible to levofloxacin, linezolid, and vancomycin. Whereas pcpA, pavB, lytA, and psrP genes were detected in nearly all serotypes, pilus islet genes were limited to serotypes 11A, 13, and 23B. MLST for predominant serotype 23B isolates revealed three known and seven novel sequence types (STs). ST172 and novel ST15111 were the most dominant and both STs were related to PMEN clone Columbia23F-26 (ST338). In conclusion, non-PCV13 serotype 23B was the most prevalent, with characteristics of rapid clonal expansion of ST172 and ST15111, which are related to international clones of the pneumococcus. Continuous monitoring of NVTs in Ghana is, therefore, essential, as they have the potential to cause invasive disease, show high antibiotic resistance, and attenuate the effects of PCV vaccination.
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Affiliation(s)
- Richael O. Mills
- Department of Molecular Genetics and Infection Biology, Interfaculty Institute for Genetics and Functional Genomics, Center for Functional Genomics of Microbes, University of Greifswald, 17489 Greifswald, Germany
- Department of Biomedical Sciences, School of Allied Health Science, University of Cape Coast, Cape Coast PMB TF0494, Ghana
| | - Mohammed R. Abdullah
- Department of Molecular Genetics and Infection Biology, Interfaculty Institute for Genetics and Functional Genomics, Center for Functional Genomics of Microbes, University of Greifswald, 17489 Greifswald, Germany
| | - Samuel A. Akwetey
- Department of Biomedical Sciences, School of Allied Health Science, University of Cape Coast, Cape Coast PMB TF0494, Ghana
- Department of Clinical Microbiology, School of Medicine, University of Development Studies, Tamale PMB TF0494, Ghana
| | - Dorcas C. Sappor
- Department of Medical Laboratory Sciences, School of Allied Health Sciences, University of Cape Coast, Cape Coast PMB TF0494, Ghana
| | - Johan A. Bolivar
- Genetics, Regeneration and Cancer (GRC), University Research Centre (SIU), University of Antioquia (UdeA), Medellín 050010, Colombia
- Basic and Applied Microbiology (MICROBA), School of Microbiology, University of Antioquia Medellin, Antioquia 050010, Colombia
| | - Gustavo Gámez
- Genetics, Regeneration and Cancer (GRC), University Research Centre (SIU), University of Antioquia (UdeA), Medellín 050010, Colombia
- Basic and Applied Microbiology (MICROBA), School of Microbiology, University of Antioquia Medellin, Antioquia 050010, Colombia
| | - Mark P. G. van der Linden
- German National Reference Center for Streptococci, Department of Medical Microbiology, University Hospital RWTH Aachen, 52074 Aachen, Germany
| | - Sven Hammerschmidt
- Department of Molecular Genetics and Infection Biology, Interfaculty Institute for Genetics and Functional Genomics, Center for Functional Genomics of Microbes, University of Greifswald, 17489 Greifswald, Germany
- Correspondence: ; Tel.: +49-(0)3834-420-5700
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7
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Lo SW, Mellor K, Cohen R, Alonso AR, Belman S, Kumar N, Hawkins PA, Gladstone RA, von Gottberg A, Veeraraghavan B, Ravikumar KL, Kandasamy R, Pollard SAJ, Saha SK, Bigogo G, Antonio M, Kwambana-Adams B, Mirza S, Shakoor S, Nisar I, Cornick JE, Lehmann D, Ford RL, Sigauque B, Turner P, Moïsi J, Obaro SK, Dagan R, Diawara I, Skoczyńska A, Wang H, Carter PE, Klugman KP, Rodgers G, Breiman RF, McGee L, Bentley SD, Almagro CM, Varon E, Corso A, Davydov A, Maguire A, Kiran A, Moiane B, Beall B, Zhao C, Aanensen D, Everett D, Faccone D, Foster-Nyarko E, Bojang E, Egorova E, Voropaeva E, Sampane-Donkor E, Sadowy E, Nagaraj G, Mucavele H, Belabbès H, Elmdaghri N, Verani J, Keenan J, Lees J, N Nair Thulasee Bhai J, Ndlangisa K, Zerouali K, Bentley L, Titov L, De Gouveia L, Alaerts M, Ip M, de Cunto Brandileone MC, Hasanuzzaman M, Paragi M, Nurse-Lucas M, du Plessis M, Ali M, Croucher N, Wolter N, Givon-Lavi N, Porat N, Köseoglu Eser Ö, Ho PL, Eberechi Akpaka P, Gagetti P, Tientcheu PE, Law P, Benisty R, Mostowy R, Malaker R, Grassi Almeida SC, Doiphode S, Madhi S, Devi Sekaran S, Clarke S, Srifuengfung S, Nzenze S, Kastrin T, Ochoa T, Hryniewicz W, Urban Y. Emergence of a multidrug-resistant and virulent Streptococcus pneumoniae lineage mediates serotype replacement after PCV13: an international whole-genome sequencing study. THE LANCET. MICROBE 2022; 3:e735-e743. [PMID: 35985351 PMCID: PMC9519462 DOI: 10.1016/s2666-5247(22)00158-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 06/01/2022] [Accepted: 06/01/2022] [Indexed: 12/24/2022]
Abstract
BACKGROUND Serotype 24F is one of the emerging pneumococcal serotypes after the introduction of pneumococcal conjugate vaccine (PCV). We aimed to identify lineages driving the increase of serotype 24F in France and place these findings into a global context. METHODS Whole-genome sequencing was performed on a collection of serotype 24F pneumococci from asymptomatic colonisation (n=229) and invasive disease (n=190) isolates among individuals younger than 18 years in France, from 2003 to 2018. To provide a global context, we included an additional collection of 24F isolates in the Global Pneumococcal Sequencing (GPS) project database for analysis. A Global Pneumococcal Sequence Cluster (GPSC) and a clonal complex (CC) were assigned to each genome. Phylogenetic, evolutionary, and spatiotemporal analysis were conducted using the same 24F collection and supplemented with a global collection of genomes belonging to the lineage of interest from the GPS project database (n=25 590). FINDINGS Serotype 24F was identified in numerous countries mainly due to the clonal spread of three lineages: GPSC10 (CC230), GPSC16 (CC156), and GPSC206 (CC7701). GPSC10 was the only multidrug-resistant lineage. GPSC10 drove the increase in 24F in France and had high invasive disease potential. The international dataset of GPSC10 (n=888) revealed that this lineage expressed 16 other serotypes, with only six included in 13-valent PCV (PCV13). All serotype 24F isolates were clustered in a single clade within the GPSC10 phylogeny and long-range transmissions were detected from Europe to other continents. Spatiotemporal analysis showed GPSC10-24F took 3-5 years to spread across France and a rapid change of serotype composition from PCV13 serotype 19A to 24F during the introduction of PCV13 was observed in neighbouring country Spain. INTERPRETATION Our work reveals that GPSC10 alone is a challenge for serotype-based vaccine strategy. More systematic investigation to identify lineages like GPSC10 will better inform and improve next-generation preventive strategies against pneumococcal diseases. FUNDING Bill & Melinda Gates Foundation, Wellcome Sanger Institute, and the US Centers for Disease Control and Prevention.
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Affiliation(s)
- Stephanie W Lo
- Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, UK,Correspondence to: Dr Stephanie W Lo, Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
| | - Kate Mellor
- Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, UK
| | - Robert Cohen
- ACTIV, Association Clinique et Thérapeutique Infantile du Val-de-Marne, Saint Maur-des-Fossés, France,GPIP, Groupe de Pathologie Infectieuse Pédiatrique, Paris, France,AFPA, Association Française de Pédiatrie Ambulatoire, Saint-Germain-en-Laye, France,Université Paris Est, IMRB-GRC GEMINI, Créteil, France,Clinical Research Center, Centre Hospitalier Intercommunal de Créteil, Créteil, France,Unité Court Séjour, Petits nourrissons, Service de Néonatalogie, Centre Hospitalier Intercommunal de Créteil, Créteil, France
| | - Alba Redin Alonso
- Department of RDI Microbiology, Institut de Recerca Sant Joan de Deu, Hospital Sant Joan de Deu, Barcelona, Spain,School of Medicine, Universitat Internacional de Catalunya, Barcelona, Spain,Spanish Network of Epidemiology and Public Health, CIBERESP, Instituto de Salud Carlos III, Madrid, Spain
| | - Sophie Belman
- Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, UK
| | - Narender Kumar
- Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, UK
| | | | - Rebecca A Gladstone
- Department of Biostatistics, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Anne von Gottberg
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, Johannesburg, South Africa
| | | | - K L Ravikumar
- Central Research Laboratory, Kempegowda Institute of Medical Sciences, Bangalore, India
| | - Rama Kandasamy
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Churchill Hospital, Oxford, UK,NIHR Oxford Biomedical Research Centre, Oxford, UK,School of Women and Children's Health, University of New South Wales, Sydney, NSW, Australia,Discipline of Paediatrics and Child Health, School of Clinical Medicine, University of New South Wales, Sydney, NSW, Australia
| | - Sir Andrew J Pollard
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Churchill Hospital, Oxford, UK,NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Samir K Saha
- Child Health Research Foundation, Dhaka, Bangladesh
| | | | - Martin Antonio
- WHO Collaborating Centre for New Vaccines Surveillance, Medical Research Council Unit The Gambia at The London School of Hygiene & Tropical Medicine, Fajara, The Gambia
| | - Brenda Kwambana-Adams
- WHO Collaborating Centre for New Vaccines Surveillance, Medical Research Council Unit The Gambia at The London School of Hygiene & Tropical Medicine, Fajara, The Gambia,NIHR Global Health Research Unit on Mucosal Pathogens, Division of Infection and Immunity, University College London, London, UK
| | - Shaper Mirza
- Microbiology and Immunology Laboratory, Department of Biology, Lahore University of Management Sciences, Lahore, Pakistan
| | - Sadia Shakoor
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Imran Nisar
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Jennifer E Cornick
- Malawi-Liverpool-Wellcome-Trust, Blantyre, Malawi,Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Deborah Lehmann
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, The University of Western Australia, Perth, WA, Australia
| | - Rebecca L Ford
- Papua New Guinea Institute of Medical Research, Goroka, Papua New Guinea
| | - Betuel Sigauque
- Centro de Investigação em Saúde da Manhiça, Maputo, Mozambique
| | - Paul Turner
- Cambodia Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - Stephen K Obaro
- Division of Pediatric Infectious Disease, University of Nebraska Medical Center Omaha, Omaha, NE, USA,International Foundation against Infectious Diseases in Nigeria, Abuja, Nigeria
| | - Ron Dagan
- Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Idrissa Diawara
- Department of Microbiology, Faculty of Medicine and Pharmacy of Casablanca, Hassan II University of Casablanca, Casablanca, Morocco,National Reference Laboratory, Mohammed VI University of Health Sciences, Casablanca, Morocco
| | - Anna Skoczyńska
- Department of Epidemiology and Clinical Microbiology, National Medicines Institute, Warsaw, Poland
| | - Hui Wang
- Peking University People ‘s Hospital, Beijing, China
| | - Philip E Carter
- Institute of Environmental Science and Research Limited, Kenepuru Science Centre, Porirua, New Zealand
| | - Keith P Klugman
- Rollins School Public Health, Emory University, Atlanta, GA, USA
| | - Gail Rodgers
- Pneumonia Program, Bill & Melinda Gates Foundation, Seattle, WA, USA
| | - Robert F Breiman
- Rollins School Public Health, Emory University, Atlanta, GA, USA,Emory Global Health Institute, Emory University, Atlanta, GA, USA
| | - Lesley McGee
- Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Stephen D Bentley
- Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, UK
| | - Carmen Muñoz Almagro
- Department of RDI Microbiology, Institut de Recerca Sant Joan de Deu, Hospital Sant Joan de Deu, Barcelona, Spain,School of Medicine, Universitat Internacional de Catalunya, Barcelona, Spain,Spanish Network of Epidemiology and Public Health, CIBERESP, Instituto de Salud Carlos III, Madrid, Spain
| | - Emmanuelle Varon
- National Reference Center for Pneumococci, Centre Hospitalier Intercommunal de Créteil, Créteil, France
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8
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Tobuse AJ, Ang CW, Yeong KY. Modern vaccine development via reverse vaccinology to combat antimicrobial resistance. Life Sci 2022; 302:120660. [PMID: 35642852 DOI: 10.1016/j.lfs.2022.120660] [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: 03/25/2022] [Revised: 05/02/2022] [Accepted: 05/19/2022] [Indexed: 10/18/2022]
Abstract
With the continuous evolution of bacteria, the global antimicrobial resistance health threat is causing millions of deaths yearly. While depending on antibiotics as a primary treatment has its merits, there are no effective alternatives thus far in the pharmaceutical market against some drug-resistant bacteria. In recent years, vaccinology has become a key topic in scientific research. Combining with the growth of technology, vaccine research is seeing a new light where the process is made faster and more efficient. Although less discussed, bacterial vaccine is a feasible strategy to combat antimicrobial resistance. Some vaccines have shown promising results with good efficacy against numerous multidrug-resistant strains of bacteria. In this review, we aim to discuss the findings from studies utilizing reverse vaccinology for vaccine development against some multidrug-resistant bacteria, as well as provide a summary of multi-year bacterial vaccine studies in clinical trials. The advantages of reverse vaccinology in the generation of new bacterial vaccines are also highlighted. Meanwhile, the limitations and future prospects of bacterial vaccine concludes this review.
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Affiliation(s)
- Asuka Joy Tobuse
- School of Science, Monash University Malaysia Campus, Jalan Lagoon Selatan, Bandar Sunway 47500, Selangor, Malaysia
| | - Chee Wei Ang
- School of Science, Monash University Malaysia Campus, Jalan Lagoon Selatan, Bandar Sunway 47500, Selangor, Malaysia
| | - Keng Yoon Yeong
- School of Science, Monash University Malaysia Campus, Jalan Lagoon Selatan, Bandar Sunway 47500, Selangor, Malaysia.
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9
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Tabatabaei SR, Shamshiri A, Azimi L, Nazari-Alam A, Karimi A, Mirjavadi SA, Tariverdi M. Co-infection with dual Streptococcus pneumoniae serotypes as a cause of pediatric bacterial meningitis in Iran: a multi-center cross-sectional study. BMC Infect Dis 2022; 22:625. [PMID: 35850636 PMCID: PMC9290261 DOI: 10.1186/s12879-022-07606-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 07/06/2022] [Indexed: 11/19/2022] Open
Abstract
Background Meningitis is considered a life-threatening infection with high mortality all over the world. Hemophilus influenzae (H. influenzae) and Streptococcus pneumoniae (S. pneumoniae) are regarded as the two most common infectious agents causing bacterial meningitis. This study aimed to identify H. influenzae and S. pneumoniae serotypes in blood and cerebrospinal fluid (CSF) of pediatric patients with meningitis, using polymerase chain reaction (PCR). Methods This multi-center cross-sectional study included 284 children with suspected meningitis referred to 4 target hospitals. Overall, 412 samples (128 blood and 284 CSF samples) were obtained from the patients from November 14, 2016 to November 15, 2017. The extracted DNA was examined using multiplex real time PCR to screen for S. pneumoniae and H. influenzae. S. pneumoniae serotyping was also done by multiplex PCR. Results Out of 284 CSF specimens, 22 were positive for ply S. pneumoniae. Of 20 DNA samples meeting the Quality Control (QC) standards for serotyping, 7 (35%), 6 (30%), 2 (10%), 2 (10%), 2 (10%), 1 (5%), 1 (5%), 1 (5%), 1 (5%) and 1 (5%) were positive for serotypes 3, 11A, 6A, 14, 7C, 23F, 23B, 19A, and 19F and 5, respectively. Overall, nine samples were positive for two serotypes, of whom 3 and 11A were the most common from Tehran province. Of note, one of these CSF samples showed a new co-infection with serotypes 7C and 14. Also, 6 samples (30%) were positive for H. influenzae detected by bexA primer. None of the blood samples were positive for S. pneumoniae or H. influenzae. Conclusion Co-infection with S. pneumoniae serotypes can occur in bacterial meningitis and it might be missed if all serotypes are not evaluated in CSF specimens.
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Affiliation(s)
- Sedigheh Rafiei Tabatabaei
- Pediatric Infections Research Center, Research Institute for Children's Health, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Ahmadreza Shamshiri
- Department of Epidemiology and Biostatistics, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Leila Azimi
- Pediatric Infections Research Center, Research Institute for Children's Health, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Ali Nazari-Alam
- Infectious Diseases Research Center, Kashan University of Medical Sciences, Kashan, Iran
| | - Abdollah Karimi
- Pediatric Infections Research Center, Research Institute for Children's Health, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | | | - Marjan Tariverdi
- Department of Pediatric Infectious Diseases, Faculty of Medicine, Children's Clinical Research Development Center, Hormozgan University of Medical Sciences, Bandar Abbas, Iran.
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10
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Yamba Yamba L, Uddén F, Fuursted K, Ahl J, Slotved HC, Riesbeck K. Extensive/Multidrug-Resistant Pneumococci Detected in Clinical Respiratory Tract Samples in Southern Sweden Are Closely Related to International Multidrug-Resistant Lineages. Front Cell Infect Microbiol 2022; 12:824449. [PMID: 35392607 PMCID: PMC8981583 DOI: 10.3389/fcimb.2022.824449] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 02/21/2022] [Indexed: 11/13/2022] Open
Abstract
Background/ObjectiveThe frequencies of non-susceptibility against common antibiotics among pneumococci vary greatly across the globe. When compared to other European countries antibiotic resistance against penicillin and macrolides has been uncommon in Sweden in recent years. Multidrug resistance (MDR) is, however, of high importance since relevant treatment options are scarce. The purpose of this study was to characterize the molecular epidemiology, presence of resistance genes and selected virulence genes of extensively drug-resistant (XDR) (n=15) and MDR (n=10) Streptococcus pneumoniae detected in clinical respiratory tract samples isolated from patients in a southern Swedish county 2016-2018. With the aim of relating them to global MDR pneumococci.MethodsWhole genome sequencing (WGS) was performed to determine molecular epidemiology, resistance genes and presence of selected virulence factors. Antimicrobial susceptibility profiles were determined using broth microdilution testing. Further analyses were performed on isolates from the study and from the European nucleotide archive belonging to global pneumococcal sequence cluster (GPSC) 1 (n=86), GPSC9 (n=55) and GPSC10 (n=57). Bacteria were analyzed regarding selected virulence determinants (pilus islet 1, pilus islet 2 and Zinc metalloproteinase C) and resistance genes.ResultsNineteen of 25 isolates were related to dominant global MDR lineages. Seventeen belonged to GPSC1, GPSC9 or GPSC10 with MDR non-PCV serotypes in GPSC9 (serotype 15A and 15C) as well as GPSC10 (serotype 7B, 15B and serogroup 24). Pilus islet-1 and pilus islet-2 were present in most sequence types belonging to GPSC1 and in two isolates within GPSC9 but were not detected in isolates belonging to GPSC10. Zinc metalloproteinase C was well conserved within all analyzed isolates belonging to GPSC9 but were not found in isolates from GPSC1 or GPSC10.ConclusionsAlthough MDR S. pneumoniae is relatively uncommon in Sweden compared to other countries, virulent non-PCV serotypes that are MDR may become an increasing problem, particularly from clusters GPSC9 and GPSC10. Since the incidence of certain serotypes (3, 15A, and 19A) found among our MDR Swedish study isolates are persistent or increasing in invasive pneumococcal disease further surveillance is warranted.
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Affiliation(s)
- Linda Yamba Yamba
- Clinical Microbiology, Department of Translational Medicine, Faculty of Medicine, Lund University, Malmö, Sweden
| | - Fabian Uddén
- Clinical Microbiology, Department of Translational Medicine, Faculty of Medicine, Lund University, Malmö, Sweden
| | - Kurt Fuursted
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Jonas Ahl
- Infectious Diseases, Department of Translational Medicine, Faculty of Medicine, Lund University, Malmö, Sweden
| | - Hans-Christian Slotved
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Kristian Riesbeck
- Clinical Microbiology, Department of Translational Medicine, Faculty of Medicine, Lund University, Malmö, Sweden
- *Correspondence: Kristian Riesbeck,
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11
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Epidemiological characteristics in serotype 24 pediatric invasive pneumococcal disease according to an 11-year population-based study in Japan. Epidemiol Infect 2022; 150:e66. [PMID: 35311634 PMCID: PMC8950979 DOI: 10.1017/s0950268822000395] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
After the introduction of the 13-valent pneumococcal conjugate vaccine (PCV13), serotype replacement has occurred in Japan, and serotype 24 has become the most common serotype in paediatric invasive pneumococcal disease (IPD). To understand the characteristics of serotype 24-IPD in Japanese children in the post-PCV13 era, we conducted a retrospective study in children aged ≤15 years from 2010 to 2020 using a database of paediatric IPD surveillance in Chiba prefecture, Japan. We identified a total of 357 IPD cases and collected clinical information on 225 cases (24: 32 cases, non-24: 193 cases). Compared with the non-serotype 24-IPD, serotype 24-IPD was independently related to be <2 years of age [odds ratio (OR) 3.91, 95% confidence interval (CI) 1.47–10.44; P = 0.0064] and bacteremia (OR 2.28, 95% CI 1.01–5.13; P = 0.0475), as a result of the multivariate regression analysis. We also conducted a bacterial analysis, and the isolates of serotype 24-IPD had tendencies of PCG-susceptible (24: 100.0%, non-24: 61.3%; P < 0.0001) and macrolide-resistance (24: 100.0%, non-24: 87.3%; P = 0.0490). Their multilocus sequence typing was mostly ST2572 and the variants, which were unique to Japan. This tendency might have been a result of the progress made in the Japanese PCV13 immunisation programme.
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12
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Zintgraff J, Gagetti P, Napoli D, Sanchez Eluchans N, Irazu L, Moscoloni M, Regueira M, Lara CS, Corso A. Invasive Streptococcus pneumoniae isolates from pediatric population in Argentina for the period 2006-2019. Temporal progression of serotypes distribution and antibiotic resistance. Vaccine 2021; 40:459-470. [PMID: 34920903 DOI: 10.1016/j.vaccine.2021.12.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 11/26/2021] [Accepted: 12/02/2021] [Indexed: 11/26/2022]
Abstract
Streptococcus pneumoniae is a major cause of severe invasive disease associated with high mortality and morbidity worldwide. A total of 2908 pneumococcal isolates were analyzed between 2006 and 2019. Gold standard pneumococcal serotyping (the Neufeld-Quellung reaction) was performed to identify the serotypes associated with infection in children < 5 years in Argentina and agar dilution method was carried out to determine their profiles to 14 antimicrobial agents. In 2012, the 13-valent pneumococcal conjugate vaccine (PCV13) was included in the National Immunization Program. In this work we have analyzed the local epidemiology of invasive pneumococcal diseases before and after the introduction of this vaccine in order to understand the epidemiological relevance and impact of PCV13. During the periods compared in the present study there was a significant increase in the proportion of non-PCV13 serotypes, serogroup 24 (246.7%) and 12F (85.7%), and a significant decrease in PCV13 serotypes, including serotypes 14 (91.2%), 5 (95.6%) and 1 (84.6%) among others. Another observation was that serotypes 3 (7.4%) and 19A (4.9%) still remain among the most frequent serotypes despite being part of the PCV13 formulation. Regarding antimicrobial resistance, in the present study we observed an increase in erythromycin resistance during the period of study mainly associated to serotype 14 in the pre-PCV13 period and to serogroup 24 in the post-PCV13 period, which also was the major NVT serotype associated with antimicrobial resistance and MDR. Serotypes 14, 24A/B/F and 19A were in the first three places among isolates resistant to all the antibiotics tested. Our data highlight the importance of continuous surveillance to assess the impact of pneumococcal vaccines and the use of antibiotics in the dynamic of pneumococcal serotypes.
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Affiliation(s)
- Jonathan Zintgraff
- Servicio de Bacteriología Clínica, Departamento de Bacteriología. Instituto Nacional de Enfermedades Infecciosas (INEI)-ANLIS "Dr. Carlos G. Malbrán", Buenos Aires, Argentina.
| | - Paula Gagetti
- Servicio Antimicrobianos, Departamento de Bacteriología. Instituto Nacional de Enfermedades Infecciosas (INEI)-ANLIS "Dr. Carlos G. Malbrán", Buenos Aires, Argentina
| | - Daniela Napoli
- Servicio de Bacteriología Clínica, Departamento de Bacteriología. Instituto Nacional de Enfermedades Infecciosas (INEI)-ANLIS "Dr. Carlos G. Malbrán", Buenos Aires, Argentina
| | - Nahuel Sanchez Eluchans
- Servicio de Bacteriología Clínica, Departamento de Bacteriología. Instituto Nacional de Enfermedades Infecciosas (INEI)-ANLIS "Dr. Carlos G. Malbrán", Buenos Aires, Argentina
| | - Lucia Irazu
- Instituto Nacional de Enfermedades Infecciosas (INEI)-ANLIS "Dr. Carlos G. Malbrán", Buenos Aires, Argentina
| | - Maria Moscoloni
- Servicio de Bacteriología Clínica, Departamento de Bacteriología. Instituto Nacional de Enfermedades Infecciosas (INEI)-ANLIS "Dr. Carlos G. Malbrán", Buenos Aires, Argentina
| | | | - Mabel Regueira
- Servicio de Bacteriología Clínica, Departamento de Bacteriología. Instituto Nacional de Enfermedades Infecciosas (INEI)-ANLIS "Dr. Carlos G. Malbrán", Buenos Aires, Argentina
| | - Claudia S Lara
- Servicio de Bacteriología Clínica, Departamento de Bacteriología. Instituto Nacional de Enfermedades Infecciosas (INEI)-ANLIS "Dr. Carlos G. Malbrán", Buenos Aires, Argentina
| | - Alejandra Corso
- Servicio Antimicrobianos, Departamento de Bacteriología. Instituto Nacional de Enfermedades Infecciosas (INEI)-ANLIS "Dr. Carlos G. Malbrán", Buenos Aires, Argentina
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13
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Cao H, Chiu KHY, Chiu SS, Jiang S, Chow KH, Ho PL. Genomic investigation of a Streptococcus pneumoniae serotype 24F strain causing meningoencephalitis in Hong Kong. Int J Med Microbiol 2021; 311:151543. [PMID: 34864352 DOI: 10.1016/j.ijmm.2021.151543] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 10/25/2021] [Accepted: 11/29/2021] [Indexed: 12/13/2022] Open
Abstract
Pneumococcal conjugate vaccines (PCVs) successfully decreased the incidence of invasive pneumococcal disease in children. However, many countries have reported serotype replacement and a rebound in diseases from non-vaccine serotypes. Here, we report the genomic investigation of a Streptococcus pneumoniae strain M215 that caused severe meningoencephalitis in an infant in 2019. The strain was assigned to serotype 24F using the bioinformatic pipeline SeroBA and pneumococcal type specific anti-sera. The strain was resistant to cotrimoxazole from mutations in both folA and folP genes. It was susceptible to penicillin and other non-β-lactam antibiotics. Phylogenetically, it belongs to Global Pneumococcal Sequence Cluster (GPSC) 6 and multi-locus sequence type 162. A total of 38 virulence genes were detected in the genome of M215. Upon comparison of the profile of virulence genes, GPSC6 but not non-GPSC6 strains of serotype 24F and related serotypes were found to possess the major virulence determinant, pilus islet-1, comprising genes encoding sortases (srtB, srtC, srtD), pilus proteins (rrgA, rrgB and rrgC) and one transcriptional regulator (rlrA), which was previously described to be characteristic feature of international clones in the pre-PCV era. In our locality, this represented the first detection of serotype 24F and GPSC6/ST162 causing serious pneumococcal disease. The emergence of the non-vaccine serotype 24F GPSC6/ST162 lineage with molecular feature of high virulence is concerning and emphasizes the need for full characterization of strains causing severe disease.
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Affiliation(s)
- Huiluo Cao
- Carol Yu Center for Infection and Department of Microbiology, University of Hong Kong, Hong Kong, China
| | | | - Susan S Chiu
- Department of Paediatrics and Adolescent Medicine, University of Hong Kong, Hong Kong, China
| | - Shuo Jiang
- Carol Yu Center for Infection and Department of Microbiology, University of Hong Kong, Hong Kong, China
| | - Kin-Hung Chow
- Carol Yu Center for Infection and Department of Microbiology, University of Hong Kong, Hong Kong, China
| | - Pak-Leung Ho
- Carol Yu Center for Infection and Department of Microbiology, University of Hong Kong, Hong Kong, China; Department of Microbiology, Queen Mary Hospital, Hong Kong, China.
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14
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Tinggaard M, Slotved HC, Fuursted K, Storgaard M, Dröse S, Johansen IS, Thorsteinsson K, Kronborg G, Lebech AM, Benfield T. Oral and anal carriage of Streptococcus pneumoniae among sexually active men with HIV who have sex with men. J Infect Dis 2021; 225:1575-1580. [PMID: 34622276 DOI: 10.1093/infdis/jiab512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 10/04/2021] [Indexed: 11/12/2022] Open
Abstract
People with HIV are at increased risk of pneumococcal disease. We investigate oral and anal carriage rates of Streptococcus pneumoniae by molecular methods among 82 men with HIV who have sex with men (MSM). A questionnaire, oral wash and anal swab samples were obtained at baseline and 12 months. Oral carriage rates were 32.9% (27/82) at baseline and 41.7% (30/72) at follow-up. Anal carriage rates were 2.4% (2/82) at baseline and 2.9% (2/70) at follow-up. Genogroup 24 was predominant. Results suggest high oral carriage rates of S. pneumoniae among MSM living with HIV. A minority were anal carriers.
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Affiliation(s)
- Michaela Tinggaard
- Department of Infectious Diseases, Copenhagen University Hospital - Amager and Hvidovre, Hvidovre, Denmark
| | - Hans-Christian Slotved
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Kurt Fuursted
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Merete Storgaard
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark
| | - Sandra Dröse
- Department of Infectious Diseases, Odense University Hospital, Odense, Denmark.,Research Unit for Infectious Diseases, Odense University Hospital, University of Southern Denmark, Denmark
| | - Isik Somuncu Johansen
- Department of Infectious Diseases, Odense University Hospital, Odense, Denmark.,Research Unit for Infectious Diseases, Odense University Hospital, University of Southern Denmark, Denmark
| | - Kristina Thorsteinsson
- Department of Infectious Diseases, Copenhagen University Hospital - Amager and Hvidovre, Hvidovre, Denmark
| | - Gitte Kronborg
- Department of Infectious Diseases, Copenhagen University Hospital - Amager and Hvidovre, Hvidovre, Denmark.,Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Anne-Mette Lebech
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Department of Infectious Diseases, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
| | - Thomas Benfield
- Department of Infectious Diseases, Copenhagen University Hospital - Amager and Hvidovre, Hvidovre, Denmark.,Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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15
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Gagetti P, Lo SW, Hawkins PA, Gladstone RA, Regueira M, Faccone D, Sireva-Argentina Group, Klugman KP, Breiman RF, McGee L, Bentley SD, Corso A. Population genetic structure, serotype distribution and antibiotic resistance of Streptococcus pneumoniae causing invasive disease in children in Argentina. Microb Genom 2021; 7. [PMID: 34586054 PMCID: PMC8715423 DOI: 10.1099/mgen.0.000636] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Invasive disease caused by Streptococcus pneumoniae (IPD) is one of the leading causes of morbidity and mortality in young children worldwide. In Argentina, PCV13 was introduced into the childhood immunization programme nationwide in 2012 and PCV7 was available from 2000, but only in the private market. Since 1993 the National IPD Surveillance Programme, consisting of 150 hospitals, has conducted nationwide pneumococcal surveillance in Argentina in children under 6 years of age, as part of the SIREVA II-OPS network. A total of 1713 pneumococcal isolates characterized by serotype (Quellung) and antimicrobial resistance (agar dilution) to ten antibiotics, belonging to three study periods: pre-PCV7 era 1998-1999 (pre-PCV), before the introduction of PCV13 2010-2011 (PCV7) and after the introduction of PCV13 2012-2013 (PCV13), were available for inclusion. Fifty-four serotypes were identified in the entire collection and serotypes 14, 5 and 1 represented 50 % of the isolates. Resistance to penicillin was 34.9 %, cefotaxime 10.6 %, meropenem 4.9 %, cotrimoxazole 45 %, erythromycin 21.5 %, tetracycline 15.4 % and chloramphenicol 0.4 %. All the isolates were susceptible to levofloxacin, rifampin and vancomycin. Of 1713 isolates, 1061 (61.9 %) were non-susceptible to at least one antibiotic and 235(13.7 %) were multidrug resistant. A subset of 413 isolates was randomly selected and whole-genome sequenced as part of Global Pneumococcal Sequencing Project (GPS). The genome data was used to investigate the population structure of S. pneumoniae defining pneumococcal lineages using Global Pneumococcal Sequence Clusters (GPSCs), sequence types (STs) and clonal complexes (CCs), prevalent serotypes and their associated pneumococcal lineages and genomic inference of antimicrobial resistance. The collection showed a great diversity of strains. Among the 413 isolates, 73 known and 36 new STs were identified belonging to 38 CCs and 25 singletons, grouped into 52 GPSCs. Important changes were observed among vaccine types when pre-PCV and PCV13 periods were compared; a significant decrease in serotypes 14, 6B and 19F and a significant increase in 7F and 3. Among non-PCV13 types, serogroup 24 increased from 0 % in pre-PCV to 3.2 % in the PCV13 period. Our analysis showed that 66.1 % (273/413) of the isolates were predicted to be non-susceptible to at least one antibiotic and 11.9 % (49/413) were multidrug resistant. We found an agreement of 100 % when comparing the serotype determined by Quellung and WGS-based serotyping and 98.4 % of agreement in antimicrobial resistance. Continued surveillance of the pneumococcal population is needed to reveal the dynamics of pneumococcal isolates in Argentina in post-PCV13. This article contains data hosted by Microreact.
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Affiliation(s)
- Paula Gagetti
- Antimicrobial Agents Division. National Reference Laboratory in Antimicrobial Resistance. INEI-ANLIS "Dr. Carlos G. Malbrán", Buenos Aires, Argentina
| | - Stephanie W Lo
- Parasites and Microbes, The Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Paulina A Hawkins
- Rollins School of Public Health, Emory University, Atlanta, GA, USA.,Centers for Disease Control and Prevention, Atlanta, USA
| | - Rebecca A Gladstone
- Parasites and Microbes, The Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Mabel Regueira
- Bacteriology Division. INEI-ANLIS "Dr. Carlos G. Malbrán", Buenos Aires, Argentina
| | - Diego Faccone
- Antimicrobial Agents Division. National Reference Laboratory in Antimicrobial Resistance. INEI-ANLIS "Dr. Carlos G. Malbrán", Buenos Aires, Argentina
| | | | - Keith P Klugman
- Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Robert F Breiman
- Rollins School of Public Health, Emory University, Atlanta, GA, USA.,Emory Global Health Institute, Atlanta, USA
| | - Lesley McGee
- Centers for Disease Control and Prevention, Atlanta, USA
| | - Stephen D Bentley
- Parasites and Microbes, The Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Alejandra Corso
- Antimicrobial Agents Division. National Reference Laboratory in Antimicrobial Resistance. INEI-ANLIS "Dr. Carlos G. Malbrán", Buenos Aires, Argentina
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16
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Incidence of Vaccine-Preventable Childhood Diseases in the European Union and in the European Free Trade Association Countries. Vaccines (Basel) 2021; 9:vaccines9070796. [PMID: 34358212 PMCID: PMC8310256 DOI: 10.3390/vaccines9070796] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 07/12/2021] [Accepted: 07/14/2021] [Indexed: 01/26/2023] Open
Abstract
Introduction: Despite the widespread availability of vaccines, the incidence of vaccine-preventable childhood diseases (VPCD) started to grow in recent years. The aim of the study was to compare the annual incidence of selected VPCDs in the EU (European Union) and EFTA (European Free Trade Association) countries in the period of the last 5 years (2014–2019 or other intervals, depending on data availability), and the country-specific vaccine schedules. Methods: VPCD incidence rates in Europe were based on “The Surveillance Atlas of Infectious Diseases” by the ECDC (European Centre for Disease Prevention and Control); vaccination schedules were based on ECDC reports. Results: The obligation to vaccinate was not universal, and it generally only applied to two preparations: the MMR (measles, mumps, rubella) vaccine and the one against polio. During the study, the situation associated with mumps did not change or improve in individual countries; the median incidence amounted to 30 cases. The median incidence associated with rubella amounted to 1 case, but in a few countries, it grew very rapidly, i.e., in Germany, Italy, and Romania; in Poland, the incidence was clearly decreasing, from 5923 to 1532 cases. The most dynamic situation concerned measles. The total median was 2.4 cases per 100,000 population; the only one country with falling incidence was Germany. The diseases associated with Streptococcus pneumoniae and Neisseria meningitidis remained at a stable level in all analyzed countries. Conclusion: Vaccine schedules differ among the countries, so does the epidemiological situation of selected diseases. Morbidity on measles was the most disturbing phenomenon: the incidence rate increased in almost 40% of all countries, regardless of the obligation to vaccinate. The increasing incidence of VPCD may be due to anti-vaccine movements, the activity of which is often caused by mistrust and spreading misinformation. In order to better prevent the increase in morbidity, standardization of vaccine schedules and documentation should be considered in the EU countries.
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Coronas E, Martinot A, Varon E, Wallet F, Dubos F. Stable Incidence of Invasive Pneumococcal Disease in Children in Northern France From 2014 Through 2018. Pediatr Infect Dis J 2021; 40:688-693. [PMID: 34097661 DOI: 10.1097/inf.0000000000003095] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
BACKGROUND The 13-valent pneumococcal conjugate vaccine (PCV13) has been recommended in France since June 2010. The aim of this study was to evaluate the trends in the incidence of invasive pneumococcal disease (IPD) resulting in hospitalization of children younger than 18 years of age, to identify the vaccination status of these patients and to analyze the serotypic evolution of the pneumococci involved in the various types of IPD. METHODS This multicenter retrospective study reviewed all admissions of children younger than 18 years of age for IPD from 2014 through 2018 in all hospitals with a pediatric or neonatal unit in northern France. Data completeness was obtained by matching 3 independent databases. The incidence of IPD resulting in hospitalization was calculated per age group. The clinical course and the vaccine and nonvaccine types were described overall and by the IPD type. RESULTS One hundred thirty cases of IPD were identified: 51 with bacteremia, 45 meningitis, 28 pneumonia or pleuropneumonia and 6 arthritis. The IPD incidence ranged from 2.4 to 3.0/100,000 in children under 18 years of age (95% confidence intervals, 1.4-3.3 and 1.9-4.1, respectively), and from 9.5 to 15.9/100,000 in children under 2 years of age, with no significant differences over time. Nonvaccine types were predominant (81%), mainly 24F, 23B and 10A. Vaccine serotype 3 was involved in 10 cases of IPD, 2 of which were in correctly vaccinated children. Two cases of IPD could have been prevented by vaccination. Neurologic sequelae affected 26% of these children (62% of those with meningitis). Six children died from IPD (5%). CONCLUSION The incidence of IPD resulting in hospitalization remained stable in northern France during the study period, with no significant increase in nonvaccine types. Further surveillance is needed to adjust the vaccination strategy if necessary.
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Affiliation(s)
- Emilie Coronas
- From the CHU Lille, Pediatric Emergency Unit and Infectious Diseases
| | - Alain Martinot
- From the CHU Lille, Pediatric Emergency Unit and Infectious Diseases
- University of Lille, ULR 2694-METRICS: Evaluation des technologies de Santé et des pratiques médicales, Lille
| | - Emmanuelle Varon
- Centre National de Référence du Pneumocoque, Centre Hospitalier Intercommunal de Créteil
| | - Frédéric Wallet
- CHU Lille, Laboratory of bacteriology, Pathology-Biology Center, Lille, France
| | - François Dubos
- From the CHU Lille, Pediatric Emergency Unit and Infectious Diseases
- University of Lille, ULR 2694-METRICS: Evaluation des technologies de Santé et des pratiques médicales, Lille
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18
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Structural, Genetic, and Serological Elucidation of Streptococcus pneumoniae Serogroup 24 Serotypes: Discovery of a New Serotype, 24C, with a Variable Capsule Structure. J Clin Microbiol 2021; 59:e0054021. [PMID: 33883183 DOI: 10.1128/jcm.00540-21] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Pneumococcal capsules are important in pneumococcal pathogenesis and vaccine development. Although conjugate vaccines have brought about a significant reduction in invasive pneumococcal disease (IPD) caused by vaccine serotypes, the relative serotype prevalence has shifted with the dramatic emergence of serotype 24F in some countries. Here, we describe 14 isolates (13 IPD and 1 non-IPD) expressing a new capsule type, 24C, which resembles 24F but has a novel serological profile. We also describe the antigenic, biochemical, and genetic basis of 24F and 24C and the related serotypes 24A and 24B. Structural studies show that 24B, 24C, and 24F have identical polysaccharide backbones [β-Ribf-(1→4)-α-Rhap-(1→3)-β-GlcpNAc-(1→4)-β-Rhap-(1→4)-β-Glcp] but with different side chains, as follows: 24F has arabinitol-phosphate and 24B has ribitol-phosphate. 24C has a mixture of 24F and 24B repeating units, with the ratio of ribitol to arabinitol being strain dependent. In contrast, the 24A capsule has a backbone without β-Ribf but with arabinitol-phosphate and phosphocholine side chains. These structures indicate that factor-sera 24d and 24e recognize arabinitol and ribitol, respectively, which explains the serology of serogroup 24, including those of 24C. The structures can be genetically described by the bispecificity of wcxG, which is capable of transferring arabinitol or ribitol when arabinitol is limiting. Arabinitol is likely not produced in 24B but is produced in reduced amounts in 24C due to various mutations in abpA or abpB genes. Our findings demonstrate how pneumococci modulate their capsule structure and immunologic properties with small genetic changes, thereby evading host immune responses. Our findings also suggest a potential for new capsule types within serogroup 24.
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19
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Hansen CB, Fuursted K, Valentiner-Branth P, Dalby T, Jørgensen CS, Slotved HC. Molecular characterization and epidemiology of Streptococcus pneumoniae serotype 8 in Denmark. BMC Infect Dis 2021; 21:421. [PMID: 33952197 PMCID: PMC8097992 DOI: 10.1186/s12879-021-06103-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 04/22/2021] [Indexed: 12/05/2022] Open
Abstract
Background Streptococcus pneumoniae serotype 8 incidence has increased in Denmark after the introduction of pneumococcal conjugated vaccines (PCV). The mechanism behind the serotype 8 replacement is not well understood. In this study, we aimed to present epidemiological data on invasive pneumococcal disease (IPD) and molecular characterization of 96 serotype 8 clinical isolates. Methods IPD data from 1999 to 2019 were used to calculate the incidence and age distribution. Whole-genome sequencing (WGS) analysis was performed on 96 isolates (6.8% of the total serotype 8 IPD isolates in the period) to characterize the isolates with respect to pneumococcal lineage traits, a range of genes with potential species discrimination, presence of colonization and virulence factors, and molecular resistance pattern. Results The serotype 8 IPD incidence increased significantly (P < 0.05) for the age groups above 15 years after the introduction of PCV13, primarily affecting the elderly (65+). All isolates were phenotypically susceptible to penicillin, erythromycin and clindamycin. Molecular characterization revealed seven different MLST profiles with ST53 as the most prevalent lineage (87.5%) among the analyzed serotype 8 isolates. The genes covering the cell-surface proteins: lytA, rspB, pspA, psaA & Xisco and the pneumococcal toxin pneumolysin = ply were present in all isolates, while genes for the membrane transporter proteins: piaA/piaB/piaC; the capsular genes: cpsA (wzg) & psrP; the metallo-binding proteins zmpB & zmpC; and the neuroamidase proteins: nanA/nanB were variably present. Surprisingly, the putative transcriptional regulator gene SP2020 was not present in all isolates (98%). Susceptibility to penicillin, erythromycin and clindamycin was molecularly confirmed. Conclusion The observed serotype 8 replacement was not significantly reflected with a change in the MLST profile or changes in antibiotic resistance- or virulence determinants. Supplementary Information The online version contains supplementary material available at 10.1186/s12879-021-06103-w.
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Affiliation(s)
- Camilla Bülow Hansen
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Artillerivej 5, DK-2300, Copenhagen S, Denmark
| | - Kurt Fuursted
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Artillerivej 5, DK-2300, Copenhagen S, Denmark
| | | | - Tine Dalby
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Artillerivej 5, DK-2300, Copenhagen S, Denmark
| | - Charlotte Sværke Jørgensen
- Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - H-C Slotved
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Artillerivej 5, DK-2300, Copenhagen S, Denmark.
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20
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Reslan L, Finianos M, Bitar I, Moumneh MB, Araj GF, Zaghlout A, Boutros C, Jisr T, Nabulsi M, Kara Yaccoub G, Hamze M, Osman M, Bou Raad E, Hrabak J, Matar GM, Dbaibo G. The Emergence of Invasive Streptococcus pneumoniae Serotype 24F in Lebanon: Complete Genome Sequencing Reveals High Virulence and Antimicrobial Resistance Characteristics. Front Microbiol 2021; 12:637813. [PMID: 33746930 PMCID: PMC7967862 DOI: 10.3389/fmicb.2021.637813] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 01/29/2021] [Indexed: 12/16/2022] Open
Abstract
Background Invasive pneumococcal disease (IPD) remains a global health problem. IPD incidence has significantly decreased by the use of pneumococcal conjugate vaccines (PCV). Nevertheless, non-PCV serotypes remain a matter of concern. Eight Streptococcus pneumoniae serotype 24F isolates, belonging to a non-PCV serotype, were detected through the Lebanese Inter-Hospital Pneumococcal Surveillance Program. The aim of the study is to characterize phenotypic and genomic features of the 24F isolates in Lebanon. Methods WGS using long reads sequencing (PacBio) was performed to produce complete circular genomes and to determine clonality, antimicrobial resistance and virulence determinants. Results The sequencing results yielded eight closed circular genomes. Three multilocus sequence typing (MLST) types were identified (ST11618, ST14184, ST15253). Both MLST and WGS analyses revealed that these isolates from Lebanon were genetically homogenous belonging to clonal complex CC230 and clustered closely with isolates originating from Canada, United States of America, United Kingdom and Iceland. Their penicillin binding protein profiles correlated with both β-lactam susceptibility patterns and MLST types. Moreover, the isolates harbored the macrolide and tetracycline resistance genes and showed a similar virulence gene profile. To our knowledge, this study represents the first report of complete phenotypic and genomic characterization of the emerging Streptococcus pneumoniae, serotype 24F, in the Middle East and North Africa region.
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Affiliation(s)
- Lina Reslan
- Center for Infectious Diseases Research (CIDR) and WHO Collaborating Center for Reference and Research on Bacterial Pathogens, American University of Beirut, Beirut, Lebanon
| | - Marc Finianos
- Department of Microbiology, Faculty of Medicine and University Hospital in Plzen, Charles University, Plzen, Czechia
| | - Ibrahim Bitar
- Department of Microbiology, Faculty of Medicine and University Hospital in Plzen, Charles University, Plzen, Czechia
| | - Mohamad Bahij Moumneh
- Center for Infectious Diseases Research (CIDR) and WHO Collaborating Center for Reference and Research on Bacterial Pathogens, American University of Beirut, Beirut, Lebanon
| | - George F Araj
- Center for Infectious Diseases Research (CIDR) and WHO Collaborating Center for Reference and Research on Bacterial Pathogens, American University of Beirut, Beirut, Lebanon.,Department of Pathology and Laboratory Medicine, American University of Beirut Medical Center, Beirut, Lebanon
| | - Alissar Zaghlout
- Center for Infectious Diseases Research (CIDR) and WHO Collaborating Center for Reference and Research on Bacterial Pathogens, American University of Beirut, Beirut, Lebanon
| | - Celina Boutros
- Center for Infectious Diseases Research (CIDR) and WHO Collaborating Center for Reference and Research on Bacterial Pathogens, American University of Beirut, Beirut, Lebanon
| | - Tamima Jisr
- Department of Laboratory and Blood, Makassed General Hospital, Beirut, Lebanon
| | | | | | - Monzer Hamze
- Department of Microbiology, Nini Hospital, Tripoli, Lebanon
| | - Marwan Osman
- El-Youssef Hospital Center, Department of Clinical Laboratory, Halba, Lebanon
| | - Elie Bou Raad
- El-Youssef Hospital Center, Department of Clinical Laboratory, Halba, Lebanon
| | - Jaroslav Hrabak
- Department of Microbiology, Faculty of Medicine and University Hospital in Plzen, Charles University, Plzen, Czechia
| | - Ghassan M Matar
- Center for Infectious Diseases Research (CIDR) and WHO Collaborating Center for Reference and Research on Bacterial Pathogens, American University of Beirut, Beirut, Lebanon.,Department of Experimental Pathology, Immunology, and Microbiology, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Ghassan Dbaibo
- Center for Infectious Diseases Research (CIDR) and WHO Collaborating Center for Reference and Research on Bacterial Pathogens, American University of Beirut, Beirut, Lebanon.,Department of Pediatrics and Adolescent Medicine, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
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21
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Liu Y, Li W, Dong Q, Chen M, Li W, Wang X, Fu J, Ye X. Non-linear relationships between children age and pneumococcal vaccine coverage: Important implications for vaccine prevention strategies. Vaccine 2021; 39:1392-1401. [PMID: 33531198 DOI: 10.1016/j.vaccine.2021.01.056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 01/04/2021] [Accepted: 01/20/2021] [Indexed: 10/22/2022]
Abstract
BACKGROUND Streptococcus pneumoniae (S. pneumoniae) is an important pathogen causing both invasive and non-invasive infections in children, with significant morbidity and mortality worldwide. This study aimed to determine the potential relationships between age and vaccine coverage and between multiple phenotype-genotype characteristics of S. pneumoniae isolated from children. METHODS All S. pneumoniae isolates were tested for antimicrobial susceptibility, virulence genes, serotypes, and sequence types. The restricted cubic spline models were used to reveal potential relationships between children age and pneumococcal vaccine coverage. RESULTS For capsular-based vaccines, we observed a high coverage rate of 13-valent pneumococcal conjugate vaccine (PCV13, 85.8%) and a significantly non-linear relationship between children age and vaccine coverage (including PCV7, PCV10, and PCV13), with marked fluctuations in children aged < 2 years. For protein-based and pilus-based vaccine candidates, we demonstrated dynamic non-linear relationships between age and vaccine coverage, maintaining a stable and high coverage rate of ply and lytA for all age groups. Moreover, there were significantly high-dimensional corresponding relationships among multiple phenotype-genotype characteristics of S. pneumoniae isolates (such as ST271 associated with serotype 19F, PI-2, and extensively drug-resistance). CONCLUSIONS Our findings suggest that the age for high PCV coverage being children aged ≥ 2 years and also provide important evidence for supporting ply and lytA as priority candidate targets for the development of new-generation protein vaccines.
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Affiliation(s)
- Yanling Liu
- School of Public Health, Guangdong Pharmaceutical University, Guangzhou, China
| | - Wenhui Li
- School of Public Health, Guangdong Pharmaceutical University, Guangzhou, China
| | - Qian Dong
- School of Public Health, Guangdong Pharmaceutical University, Guangzhou, China
| | - Minqi Chen
- School of Public Health, Guangdong Pharmaceutical University, Guangzhou, China
| | - Wenyu Li
- School of Public Health, Guangdong Pharmaceutical University, Guangzhou, China
| | - Xulin Wang
- School of Public Health, Guangdong Pharmaceutical University, Guangzhou, China
| | - Jinjian Fu
- Department of Prevention and Health Care, Liuzhou Maternity and Child Health Care Hospital, Liuzhou, China.
| | - Xiaohua Ye
- School of Public Health, Guangdong Pharmaceutical University, Guangzhou, China.
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22
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Uddén F, Filipe M, Slotved HC, Yamba-Yamba L, Fuursted K, Pintar Kuatoko P, Larsson M, Bjurgert J, Månsson V, Pelkonen T, Reimer Å, Riesbeck K. Pneumococcal carriage among children aged 4 - 12 years in Angola 4 years after the introduction of a pneumococcal conjugate vaccine. Vaccine 2020; 38:7928-7937. [PMID: 33143954 DOI: 10.1016/j.vaccine.2020.10.060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 10/16/2020] [Accepted: 10/19/2020] [Indexed: 10/23/2022]
Abstract
Children in Angola are affected by a high burden of disease caused by pneumococcal infections. The 13-valent pneumococcal conjugate vaccine (PCV13) was introduced in the childhood immunization programme in 2013 but the serotype distribution of Streptococcus pneumoniae and antimicrobial susceptibility patterns are unknown. We did a cross-sectional nasopharyngeal carriage study in Luanda and Saurimo, Angola (PCV13 3rd dose coverage 67% and 84%, respectively) during November to December 2017 comprising 940 children aged 4-12 years. The main objective was to assess vaccine serotype coverage and antimicrobial susceptibility rates for S. pneumoniae. Our secondary aim was to characterize colonizinig strains of Haemophilus influenzae and Moraxella catarrhalis. Pneumococcal colonization was found in 35% (95% CI 32-39%) of children (n = 332), with 41% of serotypes covered by PCV13. The most common serotypes were 3 (8%), 18C (6%), 23F (6%), 11A (6%), 34 (6%), 19F (5%) and 16 (5%). Carriage of H. influenzae and M. catarrhalis was detected in 13% (95% CI 11-15%) and 15% (95% CI 13-17%) of children, respectively. Non-susceptibility to penicillin was common among pneumococci (40%), particularly among PCV13-included serotypes (50% vs. 33%; p = 0.003), although the median minimal inhibitory concentration was low (0.19 µg/mL, IQR 0.13-0.25 µg/mL). Most pneumococci and H. influenzae were susceptible to amoxicillin (99% and 88%, respectively). Furthermore, resistance to trimethoprim-sulfamethoxazole was>70% among all three species. Multidrug-resistant pneumococci (non-susceptible to ≥ 3 antibiotics; 7% [n = 24]) were further studied with whole genome sequencing to investigate clonality as an underlying cause for this phenotype. No clearly dominating clone(s) were, however, detected. The results indicate that continued use of PCV13 may have positive direct and herd effects on pneumococcal infections in Angola as carriage of vaccine serotypes was common in the non-vaccinated age group. Finally, amoxicillin is assessed to be a feasible empirical treatment of respiratory tract infections in Angola.
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Affiliation(s)
- Fabian Uddén
- Clinical microbiology, Department of Translational Medicine, Faculty of Medicine, Lund university, Jan Waldenströms gata 59, SE-205 02 Malmö, Sweden.
| | - Matuba Filipe
- ORL-department, Hospital Josina Machel, Luanda, Angola; Faculty of Medicine, Agostinho Neto University, Luanda, Angola
| | - Hans-Christian Slotved
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark.
| | - Linda Yamba-Yamba
- Clinical microbiology, Department of Translational Medicine, Faculty of Medicine, Lund university, Jan Waldenströms gata 59, SE-205 02 Malmö, Sweden.
| | - Kurt Fuursted
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark.
| | - Palmira Pintar Kuatoko
- ORL-department, Hospital Josina Machel, Luanda, Angola; Faculty of Medicine, Agostinho Neto University, Luanda, Angola
| | - Måns Larsson
- Clinical microbiology, Department of Translational Medicine, Faculty of Medicine, Lund university, Jan Waldenströms gata 59, SE-205 02 Malmö, Sweden
| | - Jonas Bjurgert
- Clinical microbiology, Department of Translational Medicine, Faculty of Medicine, Lund university, Jan Waldenströms gata 59, SE-205 02 Malmö, Sweden
| | - Viktor Månsson
- Clinical microbiology, Department of Translational Medicine, Faculty of Medicine, Lund university, Jan Waldenströms gata 59, SE-205 02 Malmö, Sweden.
| | - Tuula Pelkonen
- Children's Hospital, Helsinki University Hospital, Helsinki, Finland; University of Helsinki, Helsinki, Finland
| | - Åke Reimer
- ENT-Outpatient Department, Slottsstadens Läkarhus, Malmö, Sweden
| | - Kristian Riesbeck
- Clinical microbiology, Department of Translational Medicine, Faculty of Medicine, Lund university, Jan Waldenströms gata 59, SE-205 02 Malmö, Sweden.
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23
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Colijn C, Corander J, Croucher NJ. Designing ecologically optimized pneumococcal vaccines using population genomics. Nat Microbiol 2020; 5:473-485. [PMID: 32015499 PMCID: PMC7614922 DOI: 10.1038/s41564-019-0651-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 12/03/2019] [Indexed: 12/14/2022]
Abstract
Streptococcus pneumoniae (the pneumococcus) is a common nasopharyngeal commensal that can cause invasive pneumococcal disease (IPD). Each component of current protein-polysaccharide conjugate vaccines (PCVs) generally induces immunity specific to one of the approximately 100 pneumococcal serotypes, and typically eliminates it from carriage and IPD through herd immunity. Overall carriage rates remain stable owing to replacement by non-PCV serotypes. Consequently, the net change in IPD incidence is determined by the relative invasiveness of the pre- and post-PCV-carried pneumococcal populations. In the present study, we identified PCVs expected to minimize the post-vaccine IPD burden by applying Bayesian optimization to an ecological model of serotype replacement that integrated epidemiological and genomic data. We compared optimal formulations for reducing infant-only or population-wide IPD, and identified potential benefits to including non-conserved pneumococcal carrier proteins. Vaccines were also devised to minimize IPD resistant to antibiotic treatment, despite the ecological model assuming that resistance levels in the carried population would be preserved. We found that expanding infant-administered PCV valency is likely to result in diminishing returns, and that complementary pairs of infant- and adult-administered vaccines could be a superior strategy. PCV performance was highly dependent on the circulating pneumococcal population, further highlighting the advantages of a diversity of anti-pneumococcal vaccination strategies.
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Affiliation(s)
- Caroline Colijn
- Department of Mathematics, Simon Fraser University, Burnaby, BC, Canada.
- Department of Mathematics, Imperial College London, London, UK.
| | - Jukka Corander
- Department of Biostatistics, University of Oslo, Oslo, Norway
- Helsinki Institute of Information Technology, Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland
- Parasites & Microbes, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Nicholas J Croucher
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
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24
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Del Rosal T, Caminoa MB, González-Guerrero A, Falces-Romero I, Romero-Gómez MP, Baquero-Artigao F, Sainz T, Méndez-Echevarría A, Escosa-García L, Aracil FJ, Calvo C. Outcome of Severe Bacterial Pneumonia in the Era of Pneumococcal Vaccination. Front Pediatr 2020; 8:576519. [PMID: 33384973 PMCID: PMC7769833 DOI: 10.3389/fped.2020.576519] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 11/27/2020] [Indexed: 11/13/2022] Open
Abstract
Introduction: After the introduction of pneumococcal conjugate vaccines, community-acquired pneumonia (CAP) caused by Streptococcus pneumoniae has decreased whereas Staphylococcus aureus and Streptococcus pyogenes could be increasing. These bacteria have been associated with high rates of complications. Aims: (1) To describe the characteristics of pediatric bacterial CAP requiring hospitalization. (2) To compare outcomes according to causative microorganisms. (3) To analyze changes in bacterial CAP rate and etiology over time. Patients and Methods: Retrospective single-center study of inpatients aged 1 month-16 years with culture-confirmed bacterial CAP in 2010-2018 in Madrid, Spain. Results: We included 64 cases (42 S. pneumoniae, 13 S. pyogenes and 9 S. aureus). Culture-confirmed CAP represented 1.48-2.33/1,000 all-cause pediatric hospital admissions, and its rate did not vary over time. However, there was a significant decrease in pneumococcal CAP in the last 3 years of the study (78% of CAP in 2010-2015 vs. 48% in 2016-18, p = 0.017). Median hospital stay was 10.5 days (interquartile range 5-19.5), 38 patients (59%) developed complications and 28 (44%) were admitted to the intensive care unit. Outcomes were similar among children with S. pneumoniae and S. aureus CAP, whereas S. pyogenes was associated with a higher risk for complications (OR 8 [95%CI 1.1-57.2]) and ICU admission (OR 7.1 [95%CI 1.7-29.1]) compared with pneumococcal CAP. Conclusion: In a setting with high PCV coverage, culture-confirmed bacterial CAP did not decrease over time and there was a relative increase of S. pyogenes and S. aureus. Children with CAP caused by S. pyogenes were more likely to develop complications.
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Affiliation(s)
- Teresa Del Rosal
- Department of Pediatric Infectious Diseases, Hospital Universitario La Paz and IdiPAZ Research Institute, Madrid, Spain
| | | | - Alba González-Guerrero
- Department of Pediatric Infectious Diseases, Hospital Universitario La Paz and IdiPAZ Research Institute, Madrid, Spain
| | - Iker Falces-Romero
- Department of Microbiology, Hospital Universitario La Paz, Madrid, Spain
| | | | - Fernando Baquero-Artigao
- Department of Pediatric Infectious Diseases, Hospital Universitario La Paz and IdiPAZ Research Institute, Madrid, Spain
| | - Talía Sainz
- Department of Pediatric Infectious Diseases, Hospital Universitario La Paz and IdiPAZ Research Institute, Madrid, Spain.,Red de Investigación Traslacional en Infectología Pediátrica, Madrid, Spain
| | - Ana Méndez-Echevarría
- Department of Pediatric Infectious Diseases, Hospital Universitario La Paz and IdiPAZ Research Institute, Madrid, Spain
| | - Luis Escosa-García
- Department of Pediatric Infectious Diseases, Hospital Universitario La Paz and IdiPAZ Research Institute, Madrid, Spain
| | - Francisco Javier Aracil
- Department of Pediatric Infectious Diseases, Hospital Universitario La Paz and IdiPAZ Research Institute, Madrid, Spain
| | - Cristina Calvo
- Department of Pediatric Infectious Diseases, Hospital Universitario La Paz and IdiPAZ Research Institute, Madrid, Spain.,Red de Investigación Traslacional en Infectología Pediátrica, Madrid, Spain
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25
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Prevalence of Various Vaccine Candidate Proteins in Clinical Isolates of Streptococcus pneumoniae: Characterization of the Novel Pht Fusion Proteins PhtA/B and PhtA/D. Pathogens 2019; 8:pathogens8040162. [PMID: 31554325 PMCID: PMC6963846 DOI: 10.3390/pathogens8040162] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 09/09/2019] [Accepted: 09/23/2019] [Indexed: 12/14/2022] Open
Abstract
Pneumococcal proteins unrelated to serotypes are considered to be candidates of antigens in next-generation vaccines. In the present study, the prevalence of vaccine candidate protein genes, along with serotypes and antimicrobial resistance determinants, was investigated in a total of 57 isolates obtained from a tertiary care hospital in Japan. All of the pediatric isolates and 76.6% of the adult isolates did not belong to PCV13 (a 13-valent pneumococcal conjugate vaccine) serotypes, and 70.2% of all isolates showed multidrug resistance. All of the isolates had ply, pavA, nanA, and nanB, and high prevalence was noted for the pspA and pspC genes (96.5% and 78.9%, respectively). Detection rates for the pneumococcal histidine triad protein (Pht) genes phtA, phtB, phtD, and phtE were 49.1%, 26.3%, 61.4%, and 100%, respectively. Two fusion-type genes, phtA/B and phtA/D, were identified, with a prevalence of 36.9% and 14.0%, respectively. These fusion types showed 78.1–90.0% nucleotide sequence identity with phtA, phtB, and phtD. The most prevalent pht profile was phtA + phtD + phtE (26.3%), followed by phtA/B + phtE (19.3%) and phtA/B + phtD + phtE (17.5%), while pht profiles including phtD and/or phtA/phtD were found in 71.9% of isolates. The present study revealed the presence of two fusion types of Pht and their unexpectedly high prevalence. These fusion types, as well as PhtA and PhtB, contained sequences similar to the B cell epitopes that have been previously reported for PhtD.
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