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Lan Y, Liu L, Hu D, Ge L, Xiang X, Peng M, Fu Y, Wang Y, Li S, Chen Y, Jiang Y, Tu Y, Vidal JE, Yu Y, Chen Z, Wu X. Limited protection of pneumococcal vaccines against emergent Streptococcus pneumoniae serotype 14/ST876 strains. Infection 2024; 52:801-811. [PMID: 37919621 PMCID: PMC11143005 DOI: 10.1007/s15010-023-02110-y] [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: 08/07/2023] [Accepted: 10/08/2023] [Indexed: 11/04/2023]
Abstract
PURPOSE Streptococcus pneumoniae (Spn) is a major cause of child death. We investigated the epidemiology of S. pneumoniae in a pediatric fever clinic and explored the genomics basis of the limited vaccine response of serotype 14 strains worldwide. METHODS Febrile disease and pneumonia were diagnosed following criteria from the WHO at the end of 2019 at a tertiary children's hospital. Spn was isolated by culture from nasopharyngeal (NP) swabs. The density was determined by lytA-base qPCR. Isolates were serotyped by Quellung and underwent antimicrobial susceptibility testing. Whole-genome sequencing was employed for molecular serotyping, MLST, antibiotic gene determination, SNP calling, recombination prediction, and phylogenetic analysis. RESULTS The presence of pneumococcus in the nasopharynx (87.5%, 7/8, p = 0.0227) and a high carriage (100%, 7/7, p = 0.0123) were significantly associated with pneumonia development. Living with siblings (73.7%, 14/19, p = 0.0125) and non-vaccination (56.0%, 28/50, p = 0.0377) contributed significantly to the Spn carriage. Serotype 14 was the most prevalent strain (16.67%, 5/30). The genome analysis of 1497 serotype 14 strains indicated S14/ST876 strains were only prevalent in China, presented limited vaccine responses with higher recombination activities within its cps locus, and unique variation patterns in the genes wzg and lrp. CONCLUSION With the lifting of the one-child policy, it will be crucial for families with multiple children to get PCV vaccinations in China. Due to the highly variant cps locus and distinctive variation patterns in capsule shedding and binding proteins genes, the prevalent S14/ST876 strains have shown poor response to current vaccines. It is necessary to continue monitoring the molecular epidemiology of this vaccine escape clone.
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Affiliation(s)
- Yinle Lan
- Department of Pulmonology, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang, China
| | - Lin Liu
- Laboratory Medicine Center, Department of Clinical Laboratory, Zhejiang Provincial People;s Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Dongping Hu
- Department of Infectious Disease, Affiliated Dongyang Hospital of Wenzhou Medical University, Dongyang, Zhejiang, China
| | - Lihong Ge
- Department of Clinical Laboratory, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang, China
| | - Xi Xiang
- Department of Clinical Laboratory, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, Zhejiang, China
| | - Minfei Peng
- Department of Clinical Laboratory, Taizhou Hospital of Zhejiang Province affiliated to Wenzhou Medical University, Taizhou, Zhejiang, China
| | - Ying Fu
- Department of Clinical Laboratory, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province, Hangzhou, Zhejiang, China
| | - Yanfei Wang
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, Zhejiang, China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Shuxian Li
- Department of Pulmonology, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang, China
| | - Yan Chen
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, Zhejiang, China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Yan Jiang
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, Zhejiang, China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Yuexing Tu
- Department of Critical Care Medicine, Tongde Hospital of Zhejiang Province, Hangzhou, Zhejiang, China
| | - Jorge E Vidal
- Department of Cell and Molecular Biology, Center for Immunology and Microbial Research, University of Mississippi Medical Center, Jackson, MS, USA
| | - Yunsong Yu
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, Zhejiang, China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Zhimin Chen
- Department of Pulmonology, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang, China.
| | - Xueqing Wu
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, Zhejiang, China.
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.
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Scasny A, Alibayov B, Khan F, Rao SJ, Murin L, Jop Vidal AG, Smith P, Li W, Edwards K, Warncke K, Vidal JE. Oxidation of hemoproteins by Streptococcus pneumoniae collapses the cell cytoskeleton and disrupts mitochondrial respiration leading to the cytotoxicity of human lung cells. Microbiol Spectr 2024; 12:e0291223. [PMID: 38084982 PMCID: PMC10783075 DOI: 10.1128/spectrum.02912-23] [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: 07/24/2023] [Accepted: 11/06/2023] [Indexed: 12/21/2023] Open
Abstract
IMPORTANCE Streptococcus pneumoniae (Spn) colonizes the lungs, killing millions every year. During its metabolism, Spn produces abundant amounts of hydrogen peroxide. When produced in the lung parenchyma, Spn-hydrogen peroxide (H2O2) causes the death of lung cells, and details of the mechanism are studied here. We found that Spn-H2O2 targets intracellular proteins, resulting in the contraction of the cell cytoskeleton and disruption of mitochondrial function, ultimately contributing to cell death. Intracellular proteins targeted by Spn-H2O2 included cytochrome c and, surprisingly, a protein of the cell cytoskeleton, beta-tubulin. To study the details of oxidative reactions, we used, as a surrogate model, the oxidation of another hemoprotein, hemoglobin. Using the surrogate model, we specifically identified a highly reactive radical whose creation was catalyzed by Spn-H2O2. In sum, we demonstrated that the oxidation of intracellular targets by Spn-H2O2 plays an important role in the cytotoxicity caused by Spn, thus providing new targets for interventions.
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Affiliation(s)
- Anna Scasny
- Department of Cell and Molecular Biology, School of Medicine, University of Mississippi Medical Center, Jackson, Mississippi, USA
- Center for Immunology and Microbial Research, School of Medicine, University of Mississippi Medical Center, Jackson, Mississippi, USA
| | - Babek Alibayov
- Department of Cell and Molecular Biology, School of Medicine, University of Mississippi Medical Center, Jackson, Mississippi, USA
- Center for Immunology and Microbial Research, School of Medicine, University of Mississippi Medical Center, Jackson, Mississippi, USA
| | - Faidad Khan
- Department of Cell and Molecular Biology, School of Medicine, University of Mississippi Medical Center, Jackson, Mississippi, USA
- Center for Immunology and Microbial Research, School of Medicine, University of Mississippi Medical Center, Jackson, Mississippi, USA
| | - Shambavi J. Rao
- Department of Otolaryngology-Head and Neck Surgery, The Ohio State School of Medicine, The Ohio State Wexner Medical Center, Columbus, Ohio, USA
| | - Landon Murin
- Department of Cell and Molecular Biology, School of Medicine, University of Mississippi Medical Center, Jackson, Mississippi, USA
- Center for Immunology and Microbial Research, School of Medicine, University of Mississippi Medical Center, Jackson, Mississippi, USA
| | - Ana G. Jop Vidal
- Department of Cell and Molecular Biology, School of Medicine, University of Mississippi Medical Center, Jackson, Mississippi, USA
- Center for Immunology and Microbial Research, School of Medicine, University of Mississippi Medical Center, Jackson, Mississippi, USA
| | - Perriann Smith
- Mississippi INBRE Research Scholar, University of Southern Mississippi, Jackson, Mississippi, USA
| | - Wei Li
- Department of Physics, Emory University, Atlanta, Georgia, USA
| | - Kristin Edwards
- Department of Cell and Molecular Biology, School of Medicine, University of Mississippi Medical Center, Jackson, Mississippi, USA
| | - Kurt Warncke
- Department of Physics, Emory University, Atlanta, Georgia, USA
| | - Jorge E. Vidal
- Department of Cell and Molecular Biology, School of Medicine, University of Mississippi Medical Center, Jackson, Mississippi, USA
- Center for Immunology and Microbial Research, School of Medicine, University of Mississippi Medical Center, Jackson, Mississippi, USA
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Wu X, Alibayov B, Xiang X, Lattar SM, Sakai F, Medders AA, Antezana B, Keller L, Vidal AGJ, Tzeng YL, Robinson DA, Stephens D, Yu Y, Vidal JE. Ultrastructural, metabolic and genetic determinants of the acquisition of macrolide resistance by Streptococcus pneumoniae. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.27.573471. [PMID: 38234816 PMCID: PMC10793443 DOI: 10.1101/2023.12.27.573471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
Aim Streptococcus pneumoniae (Spn) acquires genes for macrolide resistance, MEGA or ermB, in the human host. These genes are carried either in the chromosome, or on integrative conjugative elements (ICEs). Here, we investigated molecular determinants of the acquisition of macrolide resistance. Methods and Results Whole genome analysis was conducted for 128 macrolide-resistant pneumococcal isolates to identify the presence of MEGA (44.5%, 57/128) or ermB (100%), and recombination events in Tn916-related elements or in the locus comCDE encoding competence genes. Confocal and electron microscopy studies demonstrated that, during the acquisition of macrolide resistance, pneumococcal strains formed clusters of varying size, with the largest aggregates having a median size of ~1600 μm2. Remarkably, these pneumococcal aggregates comprise both encapsulated and nonencapsulated pneumococci, exhibited physical interaction, and spanned extracellular and intracellular compartments. We assessed the recombination frequency (rF) for the acquisition of macrolide resistance by a recipient D39 strain, from pneumococcal strains carrying MEGA (~5.4 kb) in the chromone, or in large ICEs (>23 kb). Notably, the rF for the acquisition of MEGA, whether in the chromosome or carried on an ICE was similar. However, the rF adjusted to the acquisition of the full-length ICE (~52 kb), compared to that of the capsule locus (~23 kb) that is acquired by transformation, was three orders of magnitude higher. Finally, metabolomics studies revealed a link between the acquisition of ICE and the metabolic pathways involving nicotinic acid and sucrose. Conclusions Extracellular and intracellular pneumococcal clusters facilitate the acquisition of full-length ICE at a rF higher than that of typical transformation events, involving distinct metabolic changes that present potential targets for interventions.
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Affiliation(s)
- Xueqing Wu
- Department of Infectious Diseases, Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou 310052, China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou 310052, China
| | - Babek Alibayov
- Department of Microbiology and Immunology, University of Mississippi Medical Center, Jackson MS 39056, United States
| | - Xi Xiang
- Department of Clinical Laboratory, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua 321000, China
| | - Santiago M. Lattar
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta GA 30322, United States
| | - Fuminori Sakai
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta GA 30322, United States
| | - Austin A. Medders
- Department of Microbiology and Immunology, University of Mississippi Medical Center, Jackson MS 39056, United States
| | - Brenda Antezana
- Department of Medicine, School of Medicine, Emory University, Atlanta GA 30322, United States
| | - Lance Keller
- Department of Microbiology and Immunology, University of Mississippi Medical Center, Jackson MS 39056, United States
| | - Ana G. J. Vidal
- Department of Microbiology and Immunology, University of Mississippi Medical Center, Jackson MS 39056, United States
| | - Yih-Ling Tzeng
- Department of Medicine, School of Medicine, Emory University, Atlanta GA 30322, United States
| | - D. Ashley Robinson
- Department of Microbiology and Immunology, University of Mississippi Medical Center, Jackson MS 39056, United States
| | - David Stephens
- Department of Medicine, School of Medicine, Emory University, Atlanta GA 30322, United States
| | - Yunsong Yu
- Department of Infectious Diseases, Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou 310052, China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou 310052, China
| | - Jorge E. Vidal
- Department of Microbiology and Immunology, University of Mississippi Medical Center, Jackson MS 39056, United States
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Scasny A, Alibayov B, Khan F, Rao SJ, Murin L, Jop Vidal AG, Smith P, Wei L, Edwards K, Warncke K, Vidal JE. Oxidation of hemoproteins by Streptococcus pneumoniae collapses the cell cytoskeleton and disrupts mitochondrial respiration leading to cytotoxicity of human lung cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.07.544089. [PMID: 37333138 PMCID: PMC10274756 DOI: 10.1101/2023.06.07.544089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Streptococcus pneumoniae (Spn) causes pneumonia that kills millions through acute toxicity and invasion of the lung parenchyma. During aerobic respiration, Spn releases hydrogen peroxide (Spn-H 2 O 2 ), as a by-product of enzymes SpxB and LctO, and causes cell death with signs of both apoptosis and pyroptosis by oxidizing unknown cell targets. Hemoproteins are molecules essential for life and prone to oxidation by H 2 O 2 . We recently demonstrated that during infection-mimicking conditions, Spn-H 2 O 2 oxidizes the hemoprotein hemoglobin (Hb), releasing toxic heme. In this study, we investigated details of the molecular mechanism(s) by which the oxidation of hemoproteins by Spn-H 2 O 2 causes human lung cell death. Spn strains, but not H 2 O 2 -deficient SpnΔ spxB Δ lctO strains caused time-dependent cell cytotoxicity characterized by the rearrangement of the actin, the loss of the microtubule cytoskeleton and nuclear contraction. Disruption of the cell cytoskeleton correlated with the presence of invasive pneumococci and an increase of intracellular reactive oxygen species. In cell culture, the oxidation of Hb or cytochrome c (Cyt c ) caused DNA degradation and mitochondrial dysfunction from inhibition of complex I-driven respiration, which was cytotoxic to human alveolar cells. Oxidation of hemoproteins resulted in the creation of a radical, which was identified as a protein derived side chain tyrosyl radical by using electron paramagnetic resonance (EPR). Thus, we demonstrate that Spn invades lung cells, releasing H 2 O 2 that oxidizes hemoproteins, including Cyt c , catalyzing the formation of a tyrosyl side chain radical on Hb and causing mitochondrial disruption, that ultimately leads to the collapse of the cell cytoskeleton.
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Downs SL, Madhi SA, van der Merwe L, Nunes MC, Olwagen CP. Optimization of a high-throughput nanofluidic real-time PCR to detect and quantify of 15 bacterial species and 92 Streptococcus pneumoniae serotypes. Sci Rep 2023; 13:4588. [PMID: 36944704 PMCID: PMC10030628 DOI: 10.1038/s41598-023-31820-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 03/17/2023] [Indexed: 03/23/2023] Open
Abstract
Sensitive tools for detecting concurrent colonizing pneumococcal serotypes are needed for detailed evaluation of the direct and indirect impact of routine pneumococcal conjugate vaccine (PCV) immunization. A high-throughput quantitative nanofluidic real-time PCR (Standard BioTools 'Fluidigm') reaction-set was developed to detect and quantify 92 pneumococcal serotypes in archived clinical samples. Nasopharyngeal swabs collected in 2009-2011 from South African children ≤ 5 years-old, previously serotyped with standard culture-based methods were used for comparison. The reaction-set within the 'Fluidigm' effectively amplified all targets with high efficiency (90-110%), reproducibility (R2 ≥ 0.98), and at low limit-of-detection (< 102 CFU/ml). A blind analysis of 1 973 nasopharyngeal swab samples showed diagnostic sensitivity > 80% and specificity > 95% compared with the referent standard, culture based Quellung method. The qPCR method was able to serotype pneumococcal types with good discrimination compared with Quellung (ROC-AUC: > 0.73). The high-throughput nanofluidic real-time PCR method simultaneously detects 57 individual serotypes, and 35 serotypes within 16 serogroups in 96 samples (including controls), within a single qPCR run. This method can be used to evaluate the impact of current PCV formulations on vaccine-serotype and non-vaccine-serotype colonization, including detection of multiple concurrently colonizing serotypes. Our qPCR method can allow for monitoring of serotype-specific bacterial load, as well as emergence or ongoing transmission of minor or co-colonizing serotypes that may have invasive disease potential.
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Affiliation(s)
- Sarah L Downs
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
- Department of Science and Technology/National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
| | - Shabir A Madhi
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Department of Science and Technology/National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Lara van der Merwe
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Department of Science and Technology/National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Marta C Nunes
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Department of Science and Technology/National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Courtney P Olwagen
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
- Department of Science and Technology/National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
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Antezana BS, Lohsen S, Wu X, Vidal JE, Tzeng YL, Stephens DS. Dissemination of Tn 916-Related Integrative and Conjugative Elements in Streptococcus pneumoniae Occurs by Transformation and Homologous Recombination in Nasopharyngeal Biofilms. Microbiol Spectr 2023; 11:e0375922. [PMID: 36912669 PMCID: PMC10101023 DOI: 10.1128/spectrum.03759-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 02/02/2023] [Indexed: 03/14/2023] Open
Abstract
Multidrug resistance in Streptococcus pneumoniae (or pneumococcus) continues to be a global challenge. An important class of antibiotic resistance determinants disseminating in S. pneumoniae are >20-kb Tn916-related integrative and conjugative elements (ICEs), such as Tn2009, Tn6002, and Tn2010. Although conjugation has been implicated as the transfer mechanism for ICEs in several bacteria, including S. pneumoniae, the molecular basis for widespread dissemination of pneumococcal Tn916-related ICEs remains to be fully elucidated. We found that Tn2009 acquisition was not detectable via in vitro transformation nor conjugative mating with donor GA16833, yielding a transfer frequency of <10-7. GA16833 Tn2009 conjugative gene expression was not significantly induced, and ICE circular intermediate formation was not detected in biofilms. Consistently, Tn2009 transfer efficiency in biofilms was not affected by deletion of the ICE conjugative gene ftsK. However, GA16833 Tn2009 transfer occurred efficiently at a recombination frequency (rF) of 10-4 in dual-strain biofilms formed in a human nasopharyngeal cell bioreactor. DNase I addition and deletions of the early competence gene comE or transformation apparatus genes comEA and comEC in the D39 recipient strain prevented Tn2009 acquisition (rF of <10-7). Genome sequencing and single nucleotide polymorphism analyses of independent recombinants of recipient genotype identified ~33- to ~55-kb donor DNAs containing intact Tn2009, supporting homologous recombination. Additional pneumococcal donor and recipient combinations were demonstrated to efficiently transfer Tn916-related ICEs at a rF of 10-4 in the biofilms. Tn916-related ICEs horizontally disseminate at high frequency in human nasopharyngeal S. pneumoniae biofilms by transformation and homologous recombination of >30-kb DNA fragments into the pneumococcal genome. IMPORTANCE The World Health Organization has designated Streptococcus pneumoniae as a priority pathogen for research and development of new drug treatments due to extensive multidrug resistance. Multiple strains of S. pneumoniae colonize and form mixed biofilms in the human nasopharynx, which could enable exchange of antibiotic resistance determinants. Tn916-related integrative and conjugative elements (ICEs) are largely responsible for the widespread presence of macrolide and tetracycline resistance in S. pneumoniae. Utilizing a system that simulates colonization of donor and recipient S. pneumoniae strains in the human nasopharynx, efficient transfer of Tn916-related ICEs occurred in human nasopharyngeal biofilms, in contrast to in vitro conditions of planktonic cells with exogenous DNA. This high-frequency Tn916-related ICE transfer between S. pneumoniae strains in biofilms was due to transformation and homologous recombination, not conjugation. Understanding the molecular mechanism for dissemination of Tn916-related ICEs can facilitate the design of new strategies to combat antibiotic resistance.
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Affiliation(s)
- Brenda S. Antezana
- Microbiology and Molecular Genetics Program, Graduate Division of Biological and Biomedical Sciences, Emory University Laney Graduate School, Atlanta, Georgia, USA
| | - Sarah Lohsen
- Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Xueqing Wu
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University College of Medicine, Hangzhou, China
| | - Jorge E. Vidal
- Department of Cell and Molecular Biology, University of Mississippi Medical Center, Jackson, Mississippi, USA
| | - Yih-Ling Tzeng
- Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, Atlanta, Georgia, USA
| | - David S. Stephens
- Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, Atlanta, Georgia, USA
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Ekinci E, Van Heirstraeten L, Willen L, Desmet S, Wouters I, Vermeulen H, Lammens C, Goossens H, Van Damme P, Verhaegen J, Beutels P, Theeten H, Malhotra-Kumar S. Serotype 19A and 6C Account for One-Third of Pneumococcal Carriage Among Belgian Day-Care Children Four Years After a Shift to a Lower-Valent PCV. J Pediatric Infect Dis Soc 2022; 12:36-42. [PMID: 36377804 PMCID: PMC9909365 DOI: 10.1093/jpids/piac117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 11/14/2022] [Indexed: 11/16/2022]
Abstract
BACKGROUND Pneumococcal conjugate vaccines (PCVs) effectively reduce infection and asymptomatic carriage of Streptococcus pneumoniae vaccine serotypes. In 2016, Belgium replaced its infant PCV13 program by a 4-year period of PCV10. Concomitantly, S. pneumoniae serotype carriage was monitored together with the carriage of other nasopharyngeal pathogens in children attending day-care centers. METHODS From 2016 to 2019, a total of 3459 nasopharyngeal swabs were obtained from children aged 6-30 months. Culture and qPCR were used for the identification of S. pneumoniae, Haemophilus influenzae, Moraxella catarrhalis, and Staphylococcus aureus and for serotyping and antimicrobial susceptibility assessment of S. pneumoniae strains. RESULTS S. pneumoniae colonization was frequent and stable over the study years. H. influenzae and M. catarrhalis were more frequently carried (P < .001) than S. pneumoniae, by, respectively, 92.3% and 91.0% of children. Prevalence of all PCV13 serotypes together increased significantly over time from 5.8% to 19.6% (P < .001) and was attributable to the increasing prevalence of serotype 19A. Coincidently, non-vaccine serotype 6C increased (P < .001) and the overall pneumococcal non-susceptibility to tetracycline and erythromycin. Non-susceptibility to cotrimoxazole decreased (P < .001). CONCLUSIONS The switch to a PCV program no longer covering serotypes 19A, 6A, and 3 was associated with a sustained increase of serotypes 19A and 6C in healthy children, similarly as in invasive pneumococcal disease. This resulted in a re-introduction of the 13-valent conjugate vaccine during the summer of 2019.
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Affiliation(s)
- Esra Ekinci
- Corresponding Author: Esra Ekinci, Centre for the Evaluation of Vaccination, Vaccine and Infectious Disease Institute, University of Antwerp, Campus Drie Eiken, Universiteitsplein 1, 2610 Wilrijk, Belgium. E-mail:
| | | | - Laura Willen
- Centre for the Evaluation of Vaccination, Vaccine and Infectious Disease Institute, University of Antwerp, Wilrijk, Antwerp, Belgium
| | - Stefanie Desmet
- Reference Centre for Pneumococci, University Hospitals Leuven, Leuven, Belgium
| | - Ine Wouters
- Centre for the Evaluation of Vaccination, Vaccine and Infectious Disease Institute, University of Antwerp, Wilrijk, Antwerp, Belgium
| | | | - Christine Lammens
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Wilrijk, Antwerp, Belgium
| | - Herman Goossens
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Wilrijk, Antwerp, Belgium
| | - Pierre Van Damme
- Centre for the Evaluation of Vaccination, Vaccine and Infectious Disease Institute, University of Antwerp, Wilrijk, Antwerp, Belgium
| | - Jan Verhaegen
- Reference Centre for Pneumococci, University Hospitals Leuven, Leuven, Belgium
| | - Philippe Beutels
- Centre for Health Economics Research and Modelling Infectious Diseases, University of Antwerp, Wilrijk, Antwerp, Belgium
| | - Heidi Theeten
- Centre for the Evaluation of Vaccination, Vaccine and Infectious Disease Institute, University of Antwerp, Wilrijk, Antwerp, Belgium
| | - Surbhi Malhotra-Kumar
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Wilrijk, Antwerp, Belgium
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Pneumococcal carriage in unvaccinated children at the time of vaccine implementation into the national immunization program in Poland. Sci Rep 2022; 12:5858. [PMID: 35393439 PMCID: PMC8991213 DOI: 10.1038/s41598-022-09488-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 03/14/2022] [Indexed: 11/08/2022] Open
Abstract
We investigated pneumococcal carriage among unvaccinated children under five years of age at a time when the conjugate polysaccharide vaccine (PCV) was introduced in Poland into the national immunization program (NIP). Paired nasopharyngeal swab (NPS) and saliva samples collected between 2016 and 2020 from n = 394 children were tested with conventional culture and using qPCR. The carriage rate detected by culture was 25.4% (97 of 394), by qPCR 39.1% (155 of 394), and 40.1% (158 of 394) overall. The risk of carriage was significantly elevated among day care center attendees, and during autumn/winter months. Among isolates cultured, the most common serotypes were: 23A, 6B, 15BC, 10A, 11A. The coverage of PCV10 and PCV13 was 23.2% (23 of 99) and 26.3% (26 of 99), respectively. Application of qPCR lead to detection of 168 serotype carriage events, with serogroups 15, 6, 9 and serotype 23A most commonly detected. Although the highest number of carriers was identified by testing NPS with qPCR, saliva significantly contributed to the overall number of detected carriers. Co-carriage of multiple serotypes was detected in 25.3% (40 of 158) of carriers. The results of this study represent a baseline for the future surveillance of effects of pneumococcal vaccines in NIP in Poland.
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Downs SL, Madhi SA, Van der Merwe L, Nunes MC, Olwagen CP. High-throughput nanofluidic real-time PCR to discriminate Pneumococcal Conjugate Vaccine (PCV)-associated serogroups 6, 18, and 22 to serotypes using modified oligonucleotides. Sci Rep 2021; 11:23728. [PMID: 34887480 PMCID: PMC8660885 DOI: 10.1038/s41598-021-03127-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 11/18/2021] [Indexed: 12/03/2022] Open
Abstract
Current real-time high-throughput Polymerase Chain Reaction (qPCR) methods do not distinguish serotypes 6A from 6B, 18C from 18A/B and 22F from 22A. We established a nanofluidic real-time PCR (Fluidigm) for serotyping that included Dual-Priming-Oligonucleotides (DPO), a Locked-Nucleic-Acid (LNA) probe and TaqMan assay-sets for high-throughput serotyping. The designed assay-sets target capsular gene wciP in serogroup 6, wciX and wxcM in serogroup 18, and wcwA in serogroup 22. An algorithm combining results from published assay-sets (6A/B/C/D; 6C/D; 18A/B/C; 22A/F) and designed assay-sets for 6A/C; 18B/C/F; 18C/F, 18F and 22F was validated through blind analysis of 1973 archived clinical samples collected from South African children ≤ 5-years-old (2009–2011), previously serotyped with the culture-based Quellung method. All assay-sets were efficient (92–101%), had low variation between replicates (R2 > 0.98), and were able to detect targets at a limit of detection (LOD) of < 100 Colony-Forming-Units (CFU)/mL of sample. There was high concordance (Kappa = 0.73–0.92); sensitivity (85–100%) and specificity (96–100%) for Fluidigm compared with Quellung for serotyping 6A; 6B; 6C; 18C and 22F. Fluidigm distinguishes vaccine-serotypes 6A, 6B, 18C, next-generation PCV-serotype 22F and non-vaccine-serotypes 6C, 6D, 18A, 18B, 18F and 22A. Discriminating single serotypes is important for assessing serotype replacement and the impact of PCVs on vaccine- and non-vaccine serotypes.
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Affiliation(s)
- S L Downs
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa. .,Department of Science and Technology/National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
| | - S A Madhi
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Department of Science and Technology/National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - L Van der Merwe
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Department of Science and Technology/National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - M C Nunes
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Department of Science and Technology/National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - C P Olwagen
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa. .,Department of Science and Technology/National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
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10
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Prophylactic Inhibition of Colonization by Streptococcus pneumoniae with the Secondary Bile Acid Metabolite Deoxycholic Acid. Infect Immun 2021; 89:e0046321. [PMID: 34543118 DOI: 10.1128/iai.00463-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Streptococcus pneumoniae colonizes the nasopharynx of children and the elderly but also kills millions worldwide yearly. The secondary bile acid metabolite deoxycholic acid (DoC) affects the viability of human pathogens but also plays multiple roles in host physiology. We assessed in vitro the antimicrobial activity of DoC and investigated its potential to eradicate S. pneumoniae colonization using a model of human nasopharyngeal colonization and an in vivo mouse model of colonization. At a physiological concentration, DoC (0.5 mg/ml; 1.27 mM) killed all tested S. pneumoniae strains (n = 48) 2 h postinoculation. The model of nasopharyngeal colonization showed that DoC eradicated colonization by S. pneumoniae strains as soon as 10 min postexposure. The mechanism of action did not involve activation of autolysis, since the autolysis-defective double mutants ΔlytAΔlytC and ΔspxBΔlctO were as susceptible to DoC as was the wild type (WT). Oral streptococcal species (n = 20), however, were not susceptible to DoC (0.5 mg/ml). Unlike trimethoprim, whose spontaneous resistance frequency (srF) for TIGR4 or EF3030 was ≥1 × 10-9, no spontaneous resistance was observed with DoC (srF, ≥1 × 10-12). Finally, the efficacy of DoC to eradicate S. pneumoniae colonization was assessed in vivo using a topical route via intranasal (i.n.) administration and as a prophylactic treatment. Mice challenged with S. pneumoniae EF3030 carried a median of 4.05 × 105 CFU/ml 4 days postinoculation compared to 6.67 × 104 CFU/ml for mice treated with DoC. Mice in the prophylactic group had an ∼99% reduction of the pneumococcal density (median, 2.61 × 103 CFU/ml). Thus, DoC, an endogenous human bile salt, has therapeutic potential against S. pneumoniae.
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11
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Ouattara M, Tamboura M, Kambiré D, Lê KA, Van Phan T, Velusamy S, Nguyen HA, Trang DVT, Lessa FC, Iijima M, Nguyen DT, Schwartz SB, McGee L, Traoré RO, Beall B. Triplex Direct Quantitative Polymerase Chain Reaction for the Identification of Streptococcus pneumoniae Serotypes. J Infect Dis 2021; 224:S204-S208. [PMID: 34469558 DOI: 10.1093/infdis/jiab056] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The quantitative polymerase chain reaction (qPCR) method presented in this study allows the identification of pneumococcal capsular serotypes in cerebrospinal fluid without first performing DNA extraction. This testing approach, which saves time and resources, demonstrated similar sensitivity and a high level of agreement between cycle threshold values when it was compared side-by-side with the standard qPCR method with extracted DNA.
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Affiliation(s)
- Mahamoudou Ouattara
- Division of Bacterial Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Mamadou Tamboura
- Centre Hospitalier Universitaire Pédiatrique Charles de Gaulle, Ouagadougou, Burkina Faso
| | - Dinanibè Kambiré
- Centre Hospitalier Universitaire Pédiatrique Charles de Gaulle, Ouagadougou, Burkina Faso
| | - Kim Anh Lê
- National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | - Thanh Van Phan
- Pasteur Institute of Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Srinivasan Velusamy
- Division of Bacterial Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Hien Anh Nguyen
- National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | - Dai Vo Thi Trang
- Pasteur Institute of Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Fernanda C Lessa
- Division of Bacterial Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Makiko Iijima
- World Health Organization Representative Office for Vietnam, Expanded Programme on Immunization, Hanoi, Vietnam
| | | | - Stephanie B Schwartz
- Division of Bacterial Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Lesley McGee
- Division of Bacterial Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | | | - Bernard Beall
- Division of Bacterial Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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12
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Kann S, Sao S, Phoeung C, By Y, Bryant J, Komurian-Pradel F, Saphonn V, Chou M, Turner P. MALDI-TOF mass spectrometry for sub-typing of Streptococcus pneumoniae. BMC Microbiol 2020; 20:367. [PMID: 33261551 PMCID: PMC7709296 DOI: 10.1186/s12866-020-02052-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 11/24/2020] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Serotyping of Streptococcus pneumoniae is important for monitoring of vaccine impact. Unfortunately, conventional and molecular serotyping is expensive and technically demanding. This study aimed to determine the ability of matrix-assisted laser desorption-ionisation time-of-flight (MALDI-TOF) mass spectrometry to discriminate between pneumococcal serotypes and genotypes (defined by global pneumococcal sequence cluster, GPSC). In this study, MALDI-TOF mass spectra were generated for a diverse panel of whole genome sequenced pneumococcal isolates using the bioMerieux VITEK MS in clinical diagnostic (IVD) mode. Discriminatory mass peaks were identified and hierarchical clustering was performed to visually assess discriminatory ability. Random forest and classification and regression tree (CART) algorithms were used to formally determine how well serotypes and genotypes were identified by MALDI-TOF mass spectrum. RESULTS One hundred and ninety-nine pneumococci, comprising 16 serotypes and non-typeable isolates from 46 GPSC, were analysed. In the primary experiment, hierarchical clustering revealed poor congruence between MALDI-TOF mass spectrum and serotype. The correct serotype was identified from MALDI-TOF mass spectrum in just 14.6% (random forest) or 35.4% (CART) of 130 isolates. Restricting the dataset to the nine dominant GPSC (61 isolates / 13 serotypes), discriminatory ability improved slightly: the correct serotype was identified in 21.3% (random forest) and 41.0% (CART). Finally, analysis of 69 isolates of three dominant serotype-genotype pairs (6B-GPSC1, 19F-GPSC23, 23F-GPSC624) resulted in the correct serotype identification in 81.1% (random forest) and 94.2% (CART) of isolates. CONCLUSIONS This work suggests that MALDI-TOF is not a useful technique for determination of pneumococcal serotype. MALDI-TOF mass spectra appear more associated with isolate genotype, which may still have utility for future pneumococcal surveillance activities.
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Affiliation(s)
- Sivkheng Kann
- Rodolphe Mérieux Laboratory, University of Health Sciences, Phnom Penh, Cambodia
| | - Sena Sao
- Cambodia Oxford Medical Research Unit, Angkor Hospital for Children, PO Box 50, Siem Reap, Cambodia
| | - Chanleakhena Phoeung
- Rodolphe Mérieux Laboratory, University of Health Sciences, Phnom Penh, Cambodia
| | - Youlet By
- Rodolphe Mérieux Laboratory, University of Health Sciences, Phnom Penh, Cambodia
- Fondation Mérieux, Phnom Penh, Cambodia
| | - Juliet Bryant
- Fondation Mérieux and Centre International de Recherche en Infectiologie (CIRI), INSERM, Lyon, France
| | - Florence Komurian-Pradel
- Fondation Mérieux and Centre International de Recherche en Infectiologie (CIRI), INSERM, Lyon, France
| | | | - Monidarin Chou
- Rodolphe Mérieux Laboratory, University of Health Sciences, Phnom Penh, Cambodia
| | - Paul Turner
- Cambodia Oxford Medical Research Unit, Angkor Hospital for Children, PO Box 50, Siem Reap, Cambodia.
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK.
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Wouters I, Desmet S, Van Heirstraeten L, Herzog SA, Beutels P, Verhaegen J, Goossens H, Van Damme P, Malhotra-Kumar S, Theeten H. How nasopharyngeal pneumococcal carriage evolved during and after a PCV13-to-PCV10 vaccination programme switch in Belgium, 2016 to 2018. ACTA ACUST UNITED AC 2020; 25. [PMID: 32046817 PMCID: PMC7014673 DOI: 10.2807/1560-7917.es.2020.25.5.1900303] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Background The current carriage study was set up to reinforce surveillance during/after the PCV13-to-PCVC10 switch in Belgium. Aim This observational study monitored carriage of Streptococcus pneumoniae (Sp) serotypes, particularly those no longer covered (3, 6A, 19A), as well as Haemophilus influenzae (Hi), because PCV10 contains the non-typeable Hi protein D. Methods A total of 2,615 nasopharyngeal swabs from children (6–30 months old) attending day care were collected in three periods over 2016–2018. Children’s demographic and clinical characteristics and vaccination status were obtained through a questionnaire. Sp and Hi were identified by culture and PCR. Pneumococcal strains were tested for antimicrobial (non-)susceptibility by disc diffusion and serotyped by Quellung-reaction (Quellung-reaction and PCR for serotypes 3, 6A, 19A). Results The carriage prevalence of Sp (> 75%) remained stable over the successive periods but that of Hi increased (87.4%, 664 Hi-carriers/760 in 2016 vs 93.9%, 895/953 in 2017–2018). The proportion of non-PCV13 vaccine serotypes decreased (94.6%, 438 isolates/463 in 2016 vs 89.7%, 599/668 in 2017–2018) while that of PCV13-non-PCV10 vaccine serotypes (3 + 6A + 19A) increased (0.9%, 4 isolates/463 in 2016 vs 7.8%, 52/668 in 2017–2018), with serotype 19A most frequently identified (87.9%, 58/66 isolates). Non-susceptibility of pneumococci against any of the tested antibiotics was stable over the study period (> 44%). Conclusions During and after the PCV13-to-PCV10 vaccine switch, the proportion of non-PCV13 serotypes decreased, mainly due to a serotype 19A carriage prevalence increase. These results complement invasive pneumococcal disease surveillance data, providing further basis for pneumococcal vaccination programme policy making.
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Affiliation(s)
- Ine Wouters
- Centre for the Evaluation of Vaccination, Vaccine and Infectious Disease Institute, University of Antwerp, Wilrijk, Belgium
| | - Stefanie Desmet
- Reference Centre for Pneumococci, University Hospitals Leuven, Leuven, Belgium
| | - Liesbet Van Heirstraeten
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Wilrijk, Belgium
| | - Sereina A Herzog
- Centre for Health Economics Research and Modelling Infectious Diseases, University of Antwerp, Wilrijk, Belgium
| | - Philippe Beutels
- Centre for Health Economics Research and Modelling Infectious Diseases, University of Antwerp, Wilrijk, Belgium
| | - Jan Verhaegen
- Reference Centre for Pneumococci, University Hospitals Leuven, Leuven, Belgium
| | - Herman Goossens
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Wilrijk, Belgium
| | - Pierre Van Damme
- Centre for the Evaluation of Vaccination, Vaccine and Infectious Disease Institute, University of Antwerp, Wilrijk, Belgium
| | - Surbhi Malhotra-Kumar
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Wilrijk, Belgium
| | - Heidi Theeten
- Centre for the Evaluation of Vaccination, Vaccine and Infectious Disease Institute, University of Antwerp, Wilrijk, Belgium
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- The members of the NPcarriage Study Group are listed at the end of the article
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14
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Pneumococcal colonization among healthy and hospitalized vaccine-naive Sri Lankan children. Vaccine 2020; 38:7308-7315. [PMID: 32981783 DOI: 10.1016/j.vaccine.2020.09.040] [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: 06/05/2020] [Revised: 08/05/2020] [Accepted: 09/14/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND Streptococcus pneumoniae continues to cause mortality and morbidity despite availability of effective vaccines. Pneumococcal colonization is considered a pre-requisite for disease. Identifying the serotypes circulating in a given locale is important for surveillance purposes as well as for assessing the need for vaccination. Aim of the present study was to identify nasopharyngeal pneumococcal colonization rates in healthy children and children with respiratory tract infections in central Sri Lanka. METHOD A total of 450 nasopharyngeal swabs (NPS) of children aged between 2 months and 2 years were collected from two groups; healthy children and children hospitalized with respiratory symptoms. NPS samples were processed using conventional laboratory techniques to isolate S. pneumoniae. Antibiotic susceptibility patterns of pneumococcal isolates were identified using CLSI disc diffusion method and minimum inhibitory concentration (MIC) was determined by micro-broth dilution method. RESULTS Pneumococcal colonization rate among healthy children was 31.8% (143/450) it was 39.8% (179/450) in children hospitalized with respiratory symptoms. MIC for penicillin and cefotaxime ranged between 0.015 to 4 µg/ml and <0.015 to 16 µg/ml respectively. All isolates were susceptible to levofloxacin, vancomycin, linezolid and rifampicin. Erythromycin and tetracycline non-susceptibility rates were >50% in both groups. The predominant serotypes identified were 19F (n = 66, 20.5%), 6B (n = 43, 13.4%), 6A (n = 30, 9.3%), 23F (n = 28, 8.7%) and 14 (n = 20, 6.2%). Among healthy children, presence of school going children at home and the number of household members were significantly associated with pneumococcal colonization while in hospitalized children, pneumococcal colonization was significantly associated with presence of school going children at home. CONCLUSION Pneumococcal colonization rates were considerably higher in both study cohorts and the commonest serotypes were 19F, 6B, 6A, 23F and 14. Antibiotic resistance rates were also relatively higher among the pneumococcal isolates.
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15
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Expanded sequential quadriplex real-time polymerase chain reaction (PCR) for identifying pneumococcal serotypes, penicillin susceptibility, and resistance markers. Diagn Microbiol Infect Dis 2020; 97:115037. [PMID: 32265073 DOI: 10.1016/j.diagmicrobio.2020.115037] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 03/09/2020] [Accepted: 03/09/2020] [Indexed: 01/23/2023]
Abstract
We expanded our current Centers for Disease Control and Prevention triplexed real-time polymerase chain reaction scheme identifying 11 individual serotypes and 10 serogroups to a quadriplex format identifying 34 individual serotypes and 13 small serogroups, 4 antibiotic resistance determinants, pilus targets, and penicillin susceptibility. Newly developed assays are specific for serotypes/serogroups, are sensitive (10 copies/reaction), and further discriminate larger serogroups into individual serotypes or smaller serogroups.
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16
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A Mechanism of Unidirectional Transformation, Leading to Antibiotic Resistance, Occurs within Nasopharyngeal Pneumococcal Biofilm Consortia. mBio 2018; 9:mBio.00561-18. [PMID: 29764945 PMCID: PMC5954218 DOI: 10.1128/mbio.00561-18] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Streptococcus pneumoniae acquires genes for resistance to antibiotics such as streptomycin (Str) or trimethoprim (Tmp) by recombination via transformation of DNA released by other pneumococci and closely related species. Using naturally transformable pneumococci, including strain D39 serotype 2 (S2) and TIGR4 (S4), we studied whether pneumococcal nasopharyngeal transformation was symmetrical, asymmetrical, or unidirectional. Incubation of S2Tet and S4Str in a bioreactor simulating the human nasopharynx led to the generation of SpnTet/Str recombinants. Double-resistant pneumococci emerged soon after 4 h postinoculation at a recombination frequency (rF) of 2.5 × 10−4 while peaking after 8 h at a rF of 1.1 × 10−3. Acquisition of antibiotic resistance genes by transformation was confirmed by treatment with DNase I. A high-throughput serotyping method demonstrated that all double-resistant pneumococci belonged to one serotype lineage (S2Tet/Str) and therefore that unidirectional transformation had occurred. Neither heterolysis nor availability of DNA for transformation was a factor for unidirectional transformation given that the density of each strain and extracellular DNA (eDNA) released from both strains were similar. Unidirectional transformation occurred regardless of the antibiotic-resistant gene carried by donors or acquired by recipients and regardless of whether competence-stimulating peptide-receptor cross talk was allowed. Moreover, unidirectional transformation occurred when two donor strains (e.g., S4Str and S19FTmp) were incubated together, leading to S19FStr/Tmp but at a rF 3 orders of magnitude lower (4.9 × 10−6). We finally demonstrated that the mechanism leading to unidirectional transformation was due to inhibition of transformation of the donor by the recipient. Pneumococcal transformation in the human nasopharynx may lead to the acquisition of antibiotic resistance genes or genes encoding new capsular variants. Antibiotics and vaccines are currently putting pressure on a number of strains, leading to an increase in antibiotic resistance and serotype replacement. These pneumococcal strains are also acquiring virulence traits from vaccine types via transformation. In this study, we recapitulated multiple-strain colonization with strains carrying a resistance marker and selected for those acquiring resistance to two or three antibiotics, such as would occur in the human nasopharynx. Strains acquiring dual and triple resistance originated from one progenitor, demonstrating that transformation was unidirectional. Unidirectional transformation was the result of inhibition of transformation of donor strains. Unidirectional transformation has implications for the understanding of acquisition patterns of resistance determinants or capsule-switching events.
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17
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Sakai F, Sonaty G, Watson D, Klugman KP, Vidal JE. Development and characterization of a synthetic DNA, NUversa, to be used as a standard in quantitative polymerase chain reactions for molecular pneumococcal serotyping. FEMS Microbiol Lett 2018; 364:4082726. [PMID: 28903467 PMCID: PMC5812490 DOI: 10.1093/femsle/fnx173] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Accepted: 08/04/2017] [Indexed: 01/18/2023] Open
Abstract
Identification of Streptococcus pneumoniae and its more than 90 serotypes is routinely conducted by culture and Quellung reactions. Quantitative polymerase chain reactions (qPCRs) have been developed for molecular detection, including a pan-pneumococcus lytA assay, and assays targeting 79 serotypes. Reactions require genomic DNA from every target to prepare standards, which can be time consuming. In this study, we have developed a synthetic DNA molecule as a surrogate for genomic DNA and present new single-plex qPCR reactions to increase molecular detection to 94 pneumococcal serotypes. Specificity of these new reactions was confirmed with a limit of detection between 2 and 20 genome equivalents/reaction. A synthetic DNA (NUversa, ∼8.2 kb) was then engineered to contain all available qPCR targets for serotyping and lytA. NUversa was cloned into pUC57-Amp-modified to generate pNUversa (∼10.2 kb). Standards prepared from pNUversa and NUversa were compared against standards made out of genomic DNA. Linearity [NUversa (R2 > 0.982); pNUversa (R2 > 0.991)] and efficiency of qPCR reactions were similar to those utilizing chromosomal DNA (R2 > 0.981). Quantification with plasmid pNUversa was affected, however, whereas quantification with synthetic NUversa was comparable to that of genomic DNA. Therefore, NUversa may be utilized as DNA standard in single-plex assays of the currently known 94 pneumococcal serotypes.
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Affiliation(s)
- Fuminori Sakai
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, 1518 Clifton Rd NE Room 6007, Atlanta, GA 30322, USA
| | - Griffin Sonaty
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, 1518 Clifton Rd NE Room 6007, Atlanta, GA 30322, USA
| | - David Watson
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, 1518 Clifton Rd NE Room 6007, Atlanta, GA 30322, USA
| | - Keith P Klugman
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, 1518 Clifton Rd NE Room 6007, Atlanta, GA 30322, USA.,Bill and Melinda Gates Foundation, 500 Fifth Avenue North, Seattle, WA 98109, USA
| | - Jorge E Vidal
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, 1518 Clifton Rd NE Room 6007, Atlanta, GA 30322, USA
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18
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Nelson KN, Grijalva CG, Chochua S, Hawkins PA, Gil AI, Lanata CF, Griffin MR, Edwards KM, Klugman KP, Vidal JE. Dynamics of Colonization of Streptococcus pneumoniae Strains in Healthy Peruvian Children. Open Forum Infect Dis 2018; 5:ofy039. [PMID: 29588913 PMCID: PMC5842394 DOI: 10.1093/ofid/ofy039] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 02/14/2018] [Indexed: 12/21/2022] Open
Abstract
Background Although asymptomatic carriage of Streptococcus pneumoniae (Spn) is common, acquisition of the bacteria is the first step in disease pathogenesis. We examined the effect of introduction of the 7-valent pneumococcal vaccine on Spn carriage patterns in a cohort of Peruvian children. Methods We used data from a prospective cohort study that collected monthly nasopharyngeal samples from children under 3 years of age. Spn isolates were serotyped using Quellung reactions, and bacterial density was determined by quantitative polymerase chain reaction. Changes in Spn carriage patterns, including the rate of carriage and number and density of serotypes carried over time, were evaluated before (2009) and after widespread vaccination with PCV7 (2011). Using all pneumococcal detections from each child and year, we identified serotypes that were present both at first and last detection as “persisters” and serotypes that replaced a different earlier type and were detected last as “recolonizers.” Results Ninety-two percent (467/506) of children in 2009 and 89% (451/509) in 2011 carried Spn at least once. In 2009 and 2011, rates of carriage were 9.03 and 9.04 Spn detections per person-year, respectively. In 2009, 23F, a serotype included in PCV7, was the only type identified as a persister and 6A, 15B, and 19A were identified as recolonizer serotypes. In 2011, 6B and 7C were persister serotypes and 13 was a frequent recolonizer serotype. Conclusions Overall Spn carriage among children under 3 in Peru was similar before and after introduction of PCV7; however, serotype-specific rates and longitudinal carriage patterns have shifted.
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Affiliation(s)
- Kristin N Nelson
- Department of Epidemiology, Emory University Rollins School of Public Health, Atlanta, Georgia
| | - Carlos G Grijalva
- Vanderbilt University School of Medicine, Vanderbilt University, Nashville, Tennessee
| | - Sopio Chochua
- Department of Epidemiology, Emory University Rollins School of Public Health, Atlanta, Georgia
| | - Paulina A Hawkins
- Department of Epidemiology, Emory University Rollins School of Public Health, Atlanta, Georgia
| | - Ana I Gil
- Instituto de Investigación Nutricional, Lima, Perú
| | | | - Marie R Griffin
- Vanderbilt University School of Medicine, Vanderbilt University, Nashville, Tennessee
| | - Kathryn M Edwards
- Vanderbilt University School of Medicine, Vanderbilt University, Nashville, Tennessee
| | - Keith P Klugman
- Department of Epidemiology, Emory University Rollins School of Public Health, Atlanta, Georgia.,Bill and Melinda Gates Foundation, Seattle, Washington
| | - Jorge E Vidal
- Department of Global Health, Emory University Rollins School of Public Health, Atlanta, Georgia
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19
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Tat Trung N, Van Tong H, Lien TT, Van Son T, Thanh Huyen TT, Quyen DT, Hoan PQ, Meyer CG, Song LH. Clinical utility of an optimised multiplex real-time PCR assay for the identification of pathogens causing sepsis in Vietnamese patients. Int J Infect Dis 2017; 67:122-128. [PMID: 29253706 DOI: 10.1016/j.ijid.2017.12.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2017] [Revised: 12/07/2017] [Accepted: 12/09/2017] [Indexed: 11/30/2022] Open
Abstract
INTRODUCTION For the identification of bacterial pathogens, blood culture is still the gold standard diagnostic method. However, several disadvantages apply to blood cultures, such as time and rather large volumes of blood sample required. We have previously established an optimised multiplex real-time PCR method in order to diagnose bloodstream infections. MATERIAL AND METHODS In the present study, we evaluated the diagnostic performance of this optimised multiplex RT-PCR in blood samples collected from 110 septicaemia patients enrolled at the 108 Military Central Hospital, Hanoi, Vietnam. RESULTS Positive results were obtained by blood culture, the Light Cylcler-based SeptiFast® assay and our multiplex RT-PCR in 35 (32%), 31 (28%), and 31 (28%) samples, respectively. Combined use of the three methods confirmed 50 (45.5%) positive cases of bloodstream infection, a rate significantly higher compared to the exclusive use of one of the three methods (P=0.052, 0.012 and 0.012, respectively). The sensitivity, specificity and area under the curve (AUC) of our assay were higher compared to that of the SeptiFast® assay (77.4%, 86.1% and 0.8 vs. 67.7%, 82.3% and 0.73, respectively). Combined use of blood culture and multiplex RT-PCR assay showed a superior diagnostic performance, as the sensitivity, specificity, and AUC reached 83.3%, 100%, and 0.95, respectively. The concordance between blood culture and the multiplex RT-PCR assay was highest for Klebsiella pneumonia (100%), followed by Streptococcus spp. (77.8%), Escherichia coli (66.7%), Staphylococcus spp. (50%) and Salmonella spp. (50%). In addition, the use of the newly established multiplex RT-PCR assay increased the spectrum of identifiable agents (Acintobacter baumannii, 1/32; Proteus mirabilis, 1/32). CONCLUSION The combination of culture and the multiplex RT-PCR assay provided an excellent diagnostic accomplishment and significantly supported the identification of causative pathogens in clinical samples obtained from septic patients.
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Affiliation(s)
- Ngo Tat Trung
- Department of Molecular Biology, 108 Military Central Hospital, No 1, Tran Hung Dao Street, Hai Ba Trung Dist, Hanoi, Vietnam; Vietnamese - German Centre for Medical Research (VG-CARE), Hanoi, Vietnam.
| | - Hoang Van Tong
- Vietnamese - German Centre for Medical Research (VG-CARE), Hanoi, Vietnam; Biomedical and Pharmaceutical Applied Research Center, Vietnam Military Medical University, Hanoi, Vietnam.
| | - Tran Thi Lien
- Faculty of Infectious diseases, Hai Phong Medical University, 72A Nguyen Binh Khiem, Ngo Quyen District, Hai Phong, Vietnam.
| | - Trinh Van Son
- Vietnamese - German Centre for Medical Research (VG-CARE), Hanoi, Vietnam; Institute of Clinical Infectious Diseases, 108 Military Central Hospital, No 1, Tran Hung Dao Street, Hai Ba Trung Dist, Hanoi, Vietnam.
| | - Tran Thi Thanh Huyen
- Department of Molecular Biology, 108 Military Central Hospital, No 1, Tran Hung Dao Street, Hai Ba Trung Dist, Hanoi, Vietnam.
| | - Dao Thanh Quyen
- Department of Molecular Biology, 108 Military Central Hospital, No 1, Tran Hung Dao Street, Hai Ba Trung Dist, Hanoi, Vietnam.
| | - Phan Quoc Hoan
- Department of Molecular Biology, 108 Military Central Hospital, No 1, Tran Hung Dao Street, Hai Ba Trung Dist, Hanoi, Vietnam.
| | - Christian G Meyer
- Vietnamese - German Centre for Medical Research (VG-CARE), Hanoi, Vietnam; Institute of Tropical Medicine, Eberhard Karls University Tübingen, Wilhelmstr. 27, 72074, Tübingen, Germany; Faculty of Medicine, Duy Tan University, Da Nang, Vietnam.
| | - Le Huu Song
- Vietnamese - German Centre for Medical Research (VG-CARE), Hanoi, Vietnam; Institute of Clinical Infectious Diseases, 108 Military Central Hospital, No 1, Tran Hung Dao Street, Hai Ba Trung Dist, Hanoi, Vietnam.
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Competitive Dominance within Biofilm Consortia Regulates the Relative Distribution of Pneumococcal Nasopharyngeal Density. Appl Environ Microbiol 2017; 83:AEM.00953-17. [PMID: 28576759 DOI: 10.1128/aem.00953-17] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 05/25/2017] [Indexed: 12/15/2022] Open
Abstract
Streptococcus pneumoniae is a main cause of child mortality worldwide, but strains also asymptomatically colonize the upper airways of most children and form biofilms. Recent studies have demonstrated that ∼50% of colonized children carry at least two different serotypes (i.e., strains) in the nasopharynx; however, studies of how strains coexist are limited. In this work, we investigated the physiological, genetic, and ecological requirements for the relative distribution of densities, and spatial localization, of pneumococcal strains within biofilm consortia. Biofilm consortia were prepared with vaccine type strains (i.e., serotype 6B [S6B], S19F, or S23F) and strain TIGR4 (S4). Experiments first revealed that the relative densities of S6B and S23F were similar in biofilm consortia. The density of S19F strains, however, was reduced to ∼10% in biofilm consortia, including either S6B, S23F, or TIGR4, in comparison to S19F monostrain biofilms. Reduction of S19F density within biofilm consortia was also observed in a simulated nasopharyngeal environment. Reduction of relative density was not related to growth rates, since the Malthusian parameter demonstrated similar rates of change of density for most strains. To investigate whether quorum sensing (QS) regulates relative densities in biofilm consortia, two different mutants were prepared: a TIGR4ΔluxS mutant and a TIGR4ΔcomC mutant. The density of S19F strains, however, was similarly reduced when consortia included TIGR4, TIGR4ΔluxS, or TIGR4ΔcomC Moreover, production of a different competence-stimulating peptide (CSP), CSP1 or CSP2, was not a factor that affected dominance. Finally, a mathematical model, confocal experiments, and experiments using Transwell devices demonstrated physical contact-mediated control of pneumococcal density within biofilm consortia.IMPORTANCEStreptococcus pneumoniae kills nearly half a million children every year, but it also produces nasopharyngeal biofilm consortia in a proportion of asymptomatic children, and these biofilms often contain two strains (i.e., serotypes). In our study, we investigated how strains coexist within pneumococcal consortia produced by vaccine serotypes S4, S6B, S19F, and S23F. Whereas S6B and S23F shared the biofilm consortium, our studies demonstrated reduction of the relative density of S19F strains, to ∼10% of what it would otherwise be if alone, in consortial biofilms formed with S4, S6B, or S23F. This dominance was not related to increased fitness when competing for nutrients, nor was it regulated by quorum-sensing LuxS/AI-2 or Com systems. It was demonstrated, however, to be enhanced by physical contact rather than by a product(s) secreted into the supernatant, as would naturally occur in the semidry nasopharyngeal environment. Competitive interactions within pneumococcal biofilm consortia regulate nasopharyngeal density, a risk factor for pneumococcal disease.
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Manna S, Ortika BD, Dunne EM, Holt KE, Kama M, Russell FM, Hinds J, Satzke C. A novel genetic variant of Streptococcus pneumoniae serotype 11A discovered in Fiji. Clin Microbiol Infect 2017; 24:428.e1-428.e7. [PMID: 28736074 PMCID: PMC5869949 DOI: 10.1016/j.cmi.2017.06.031] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Revised: 06/13/2017] [Accepted: 06/30/2017] [Indexed: 11/26/2022]
Abstract
Objectives As part of annual cross-sectional Streptococcus pneumoniae carriage surveys in Fiji (2012–2015), we detected pneumococci in over 100 nasopharyngeal swabs that serotyped as ‘11F-like’ by microarray. We examined the genetic basis of this divergence in the 11F-like capsular polysaccharide (cps) locus compared to the reference 11F cps sequence. The impact of this diversity on capsule phenotype, and serotype results using genetic and serologic methods were determined. Methods Genomic DNA from representative 11F-like S. pneumoniae isolates obtained from the nasopharynx of Fijian children was extracted and subject to whole genome sequencing. Genetic and phylogenetic analyses were used to identify genetic changes in the cps locus. Capsular phenotypes were evaluated using the Quellung reaction and latex agglutination. Results Compared to published 11F sequences, the wcwC and wcrL genes of the 11F-like cps locus are phylogenetically divergent, and the gct gene contains a single nucleotide insertion within a homopolymeric region. These changes within the DNA sequence of the 11F-like cps locus have modified the antigenic properties of the capsule, such that 11F-like isolates serotype as 11A by Quellung reaction and latex agglutination. Conclusions This study demonstrates the ability of molecular serotyping by microarray to identify genetic variants of S. pneumoniae and highlights the potential for discrepant results between phenotypic and genotypic serotyping methods. We propose that 11F-like isolates are not a new serotype but rather are a novel genetic variant of serotype 11A. These findings have implications for invasive pneumococcal disease surveillance as well as studies investigating vaccine impact.
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Affiliation(s)
- S Manna
- Pneumococcal Research, Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, Victoria, Australia.
| | - B D Ortika
- Pneumococcal Research, Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, Victoria, Australia
| | - E M Dunne
- Pneumococcal Research, Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, Victoria, Australia
| | - K E Holt
- Centre for Systems Genomics, The University of Melbourne, Parkville, Victoria, Australia; Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria, Australia
| | - M Kama
- Ministry of Health and Medical Services, Suva, Fiji
| | - F M Russell
- Department of Paediatrics, The University of Melbourne, Parkville, Victoria, Australia; Centre for International Child Health, Murdoch Childrens Research Institute, Melbourne, Australia
| | - J Hinds
- Institute for Infection and Immunity, St. George's, University of London, United Kingdom; BUGS Bioscience, London Bioscience Innovation Centre, London, United Kingdom
| | - C Satzke
- Pneumococcal Research, Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, Victoria, Australia; Department of Paediatrics, The University of Melbourne, Parkville, Victoria, Australia; Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, Victoria, Australia
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From Immunologically Archaic to Neoteric Glycovaccines. Vaccines (Basel) 2017; 5:vaccines5010004. [PMID: 28134792 PMCID: PMC5371740 DOI: 10.3390/vaccines5010004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Revised: 11/14/2016] [Accepted: 01/22/2017] [Indexed: 12/13/2022] Open
Abstract
Polysaccharides (PS) are present in the outermost surface of bacteria and readily come in contact with immune cells. They interact with specific antibodies, which in turn confer protection from infections. Vaccines with PS from pneumococci, meningococci, Haemophilus influenzae type b, and Salmonella typhi may be protective, although with the important constraint of failing to generate permanent immunological memory. This limitation has in part been circumvented by conjugating glycovaccines to proteins that stimulate T helper cells and facilitate the establishment of immunological memory. Currently, protection evoked by conjugated PS vaccines lasts for a few years. The same approach failed with PS from staphylococci, Streptococcus agalactiae, and Klebsiella. All those germs cause severe infections in humans and often develop resistance to antibiotic therapy. Thereby, prevention is of increasing importance to better control outbreaks. As only 23 of more than 90 pneumococcal serotypes and 4 of 13 clinically relevant Neisseria meningitidis serogroups are covered by available vaccines there is still tremendous clinical need for PS vaccines. This review focuses on glycovaccines and the immunological mechanisms for their success or failure. We discuss recent advances that may facilitate generation of high affinity anti-PS antibodies and confer specific immunity and long-lasting protection.
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Chochua S, D'Acremont V, Hanke C, Alfa D, Shak J, Kilowoko M, Kyungu E, Kaiser L, Genton B, Klugman KP, Vidal JE. Increased Nasopharyngeal Density and Concurrent Carriage of Streptococcus pneumoniae, Haemophilus influenzae, and Moraxella catarrhalis Are Associated with Pneumonia in Febrile Children. PLoS One 2016; 11:e0167725. [PMID: 27907156 PMCID: PMC5132320 DOI: 10.1371/journal.pone.0167725] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Accepted: 11/19/2016] [Indexed: 12/17/2022] Open
Abstract
Background We assessed nasopharyngeal (NP) carriage of five pathogens in febrile children with and without acute respiratory infection (ARI) of the upper (URTI) or lower tract, attending health facilities in Tanzania. Methods NP swabs collected from children (N = 960) aged 2 months to 10 years, and with a temperature ≥38°C, were utilized to quantify bacterial density of S. pneumoniae (Sp), H. influenzae (Hi), M. catarrhalis (Mc), S. aureus (Sa), and N. meningitidis (Nm). We determined associations between presence of individual species, densities, or concurrent carriage of all species combination with respiratory diseases including clinical pneumonia, pneumonia with normal chest radiography (CXR) and endpoint pneumonia. Results Individual carriage, and NP density, of Sp, Hi, or Mc, but not Sa, or Nm, was significantly associated with febrile ARI and clinical pneumonia when compared to febrile non-ARI episodes. Density was also significantly increased in severe pneumonia when compared to mild URTI (Sp, p<0.002; Hi p<0.001; Mc, p = 0.014). Accordingly, concurrent carriage of Sp+, Hi+, and Mc+, in the absence of Sa- and Nm-, was significantly more prevalent in children with ARI (p = 0.03), or clinical pneumonia (p<0.001) than non-ARI, and in children with clinical pneumonia (p = 0.0007) than URTI. Furthermore, Sp+, Hi+, and Mc+ differentiated children with pneumonia with normal CXR, or endpoint pneumonia, from those with URTI, and non-ARI cases. Conclusions Concurrent NP carriage of Sp, Hi, and Mc was a predictor of clinical pneumonia and identified children with pneumonia with normal CXR and endpoint pneumonia from those with febrile URTI, or non-ARI episodes.
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Affiliation(s)
- Sopio Chochua
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, Georgia, United States of America
| | - Valérie D'Acremont
- Swiss Tropical and Public Health Institute and University of Basel, Basel, Switzerland
- Department of Ambulatory Care and Community Medicine, University of Lausanne, Lausanne, Switzerland
| | - Christiane Hanke
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, Georgia, United States of America
| | - David Alfa
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, Georgia, United States of America
| | - Joshua Shak
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, Georgia, United States of America
| | - Mary Kilowoko
- Amana Hospital, Dar es Salaam, United Republic of Tanzania
| | - Esther Kyungu
- St. Francis Hospital, Ifakara, United Republic of Tanzania
| | - Laurent Kaiser
- Laboratory of Virology, Division of Infectious Diseases and Division of Laboratory Medicine, University Hospital of Geneva, and Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Blaise Genton
- Swiss Tropical and Public Health Institute and University of Basel, Basel, Switzerland
- Department of Ambulatory Care and Community Medicine, University of Lausanne, Lausanne, Switzerland
- Infectious Diseases Service, University Hospital, Lausanne, Switzerland
| | - Keith P. Klugman
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, Georgia, United States of America
| | - Jorge E. Vidal
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, Georgia, United States of America
- * E-mail:
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Development of a TaqMan Array Card for Pneumococcal Serotyping on Isolates and Nasopharyngeal Samples. J Clin Microbiol 2016; 54:1842-1850. [PMID: 27170020 PMCID: PMC4922116 DOI: 10.1128/jcm.00613-16] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Accepted: 04/30/2016] [Indexed: 12/31/2022] Open
Abstract
Streptococcus pneumoniae is both a commensal and a major pathogen that causes invasive disease in people of all ages. The introduction of serotype-specific pneumococcal vaccines has reduced the burden of disease but has also led to replacement with new strains; thus, serotyping remains important for vaccine-related disease surveillance. Conventional serotyping methods are laborious and expensive. We developed an easy-to-perform genotypic TaqMan array card (TAC) to identify S. pneumoniae strains, including lytA-based sequences, and 53 sequence-specific PCRs to identify 74 serotypes/serogroups covering all current vaccine types as well as prevalent nonvaccine types. The TAC method was evaluated on 146 clinical S. pneumoniae isolates and 13 nonpneumococcal species that naturally inhabit the upper respiratory tract and yielded 97% (142/146) sensitivity and 100% (13/13) specificity versus results of standard Quellung serotyping. The calculated limit of detection was 20 to 200 fg (∼8 to 84 genome equivalents) per reaction. On 23 blinded nasopharyngeal specimens that were pneumococcus culture positive, the TAC pan-pneumococcus lytA assay was positive in 21 (91% sensitivity versus culture). On TAC lytA-positive specimens, a serotype result was obtained on 86%, and the result was 95% accurate versus the subsequent culture's Quellung result. TAC also detected mixed serotypes in two specimens where Quellung detected only the predominant serotype. This TAC method yields fast and comprehensive serotyping compared to the standard method and may be useful on direct specimens.
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Bacterial Density, Serotype Distribution and Antibiotic Resistance of Pneumococcal Strains from the Nasopharynx of Peruvian Children Before and After Pneumococcal Conjugate Vaccine 7. Pediatr Infect Dis J 2016; 35:432-9. [PMID: 26974749 PMCID: PMC4820239 DOI: 10.1097/inf.0000000000001030] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
BACKGROUND Pneumococcal conjugate vaccines (PCV) have decreased nasopharyngeal carriage of vaccine types but little data exist from rural areas. We investigated bacterial density, serotype distribution and antibiotic resistance of pneumococcal strains within the nasopharynx of young children in the Peruvian Andes, 2 years after PCV7 was introduced. METHODS Pneumococcal strains were isolated from a subset of 125 children from our Peruvian cohort, who entered the study in 2009 and had pneumococcus detected in the nasopharynx in both 2009 and during follow-up in 2011. Strains were Quellung serotyped and tested for susceptibility to antibiotics. Bacterial density was determined by quantitative polymerase chain reaction. RESULTS The prevalence of PCV7 strains decreased from 48% in 2009 to 28.8% in 2011, whereas non-PCV7 types increased from 52% to 71.2% (P = 0.002). There was a 3.5-fold increase in carriage of serotype 6C in 2011 (P = 0.026). Vaccination with PCV7 did not affect pneumococcal density in children colonized by a PCV7 type but did increase density in those colonized with a non-PCV7 type. Antibiotic resistance did not change after vaccine introduction; strains were nonsusceptible to tetracycline (97.2%), trimethoprim-sulfamethoxazole (56.4%), penicillin (34%), erythromycin (22.4%), chloramphenicol (18.8%) and clindamycin (12.4%). CONCLUSIONS Serotype replacement was observed post-PCV7 vaccination with a concomitant, not previously recognized, increased nasopharyngeal density.
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Satzke C, Dunne EM, Porter BD, Klugman KP, Mulholland EK. The PneuCarriage Project: A Multi-Centre Comparative Study to Identify the Best Serotyping Methods for Examining Pneumococcal Carriage in Vaccine Evaluation Studies. PLoS Med 2015; 12:e1001903; discussion e1001903. [PMID: 26575033 PMCID: PMC4648509 DOI: 10.1371/journal.pmed.1001903] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 10/09/2015] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND The pneumococcus is a diverse pathogen whose primary niche is the nasopharynx. Over 90 different serotypes exist, and nasopharyngeal carriage of multiple serotypes is common. Understanding pneumococcal carriage is essential for evaluating the impact of pneumococcal vaccines. Traditional serotyping methods are cumbersome and insufficient for detecting multiple serotype carriage, and there are few data comparing the new methods that have been developed over the past decade. We established the PneuCarriage project, a large, international multi-centre study dedicated to the identification of the best pneumococcal serotyping methods for carriage studies. METHODS AND FINDINGS Reference sample sets were distributed to 15 research groups for blinded testing. Twenty pneumococcal serotyping methods were used to test 81 laboratory-prepared (spiked) samples. The five top-performing methods were used to test 260 nasopharyngeal (field) samples collected from children in six high-burden countries. Sensitivity and positive predictive value (PPV) were determined for the test methods and the reference method (traditional serotyping of >100 colonies from each sample). For the alternate serotyping methods, the overall sensitivity ranged from 1% to 99% (reference method 98%), and PPV from 8% to 100% (reference method 100%), when testing the spiked samples. Fifteen methods had ≥70% sensitivity to detect the dominant (major) serotype, whilst only eight methods had ≥70% sensitivity to detect minor serotypes. For the field samples, the overall sensitivity ranged from 74.2% to 95.8% (reference method 93.8%), and PPV from 82.2% to 96.4% (reference method 99.6%). The microarray had the highest sensitivity (95.8%) and high PPV (93.7%). The major limitation of this study is that not all of the available alternative serotyping methods were included. CONCLUSIONS Most methods were able to detect the dominant serotype in a sample, but many performed poorly in detecting the minor serotype populations. Microarray with a culture amplification step was the top-performing method. Results from this comprehensive evaluation will inform future vaccine evaluation and impact studies, particularly in low-income settings, where pneumococcal disease burden remains high.
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Affiliation(s)
- Catherine Satzke
- Pneumococcal Research Group, Murdoch Childrens Research Institute, Royal Children’s Hospital, Parkville, Victoria, Australia
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
- * E-mail:
| | - Eileen M. Dunne
- Pneumococcal Research Group, Murdoch Childrens Research Institute, Royal Children’s Hospital, Parkville, Victoria, Australia
| | - Barbara D. Porter
- Pneumococcal Research Group, Murdoch Childrens Research Institute, Royal Children’s Hospital, Parkville, Victoria, Australia
| | - Keith P. Klugman
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, Georgia, United States of America
| | - E. Kim Mulholland
- Pneumococcal Research Group, Murdoch Childrens Research Institute, Royal Children’s Hospital, Parkville, Victoria, Australia
- Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, United Kingdom
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Abstract
Competitive interactions between Streptococcus pneumoniae strains during host colonization could influence the serotype distribution in nasopharyngeal carriage and pneumococcal disease. We evaluated the competitive fitness of strains of serotypes 6B, 14, 19A, 19F, 23F, and 35B in a mouse model of multiserotype carriage. Isogenic variants were constructed using clinical strains as the capsule gene donors. Animals were intranasally inoculated with a mixture of up to six pneumococcal strains of different serotypes, with separate experiments involving either clinical isolates or isogenic capsule-switch variants of clinical strain TIGR4. Upper-respiratory-tract samples were repeatedly collected from animals in order to monitor changes in the serotype ratios using quantitative PCR. A reproducible hierarchy of capsular types developed in the airways of mice inoculated with multiple strains. Serotype ranks in this hierarchy were similar among pneumococcal strains of different genetic backgrounds in different strains of mice and were not altered when tested under a range of host conditions. This rank correlated with the measure of the metabolic cost of capsule synthesis and in vitro measure of pneumococcal cell surface charge, both parameters considered to be predictors of serotype-specific fitness in carriage. This study demonstrates the presence of a robust competitive hierarchy of pneumococcal serotypes in vivo that is driven mainly, but not exclusively, by the capsule itself. Streptococcus pneumoniae (pneumococcus) is the leading cause of death due to respiratory bacterial infections but also a commensal frequently carried in upper airways. Available vaccines induce immune responses against polysaccharides coating pneumococcal cells, but with over 90 different capsular types (serotypes) identified, they can only target strains of the selected few serotypes most prevalent in disease. Vaccines not only protect vaccinated individuals against disease but also protect by reducing carriage of vaccine-targeted strains to induce herd effects across whole populations. Unfortunately, reduction in the circulation of vaccine-type strains is offset by increase in carriage and disease from nonvaccine strains, indicating the importance of competitive interactions between pneumococci in shaping the population structure of this pathogen. Here, we showed that the competitive ability of pneumococcal strains to colonize the host strongly depends on the type of capsular polysaccharide expressed by pneumococci and only to a lesser degree on strain or host genetic backgrounds or on variation in host immune responses.
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