1
|
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.
Collapse
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.
| |
Collapse
|
2
|
Tabatabaei SR, Shamshiri A, Azimi L, Nazari-Alam A, Karimi A, Mirjavadi SA, Tariverdi M. Co-infection with dual Streptococcus pneumoniae serotypes as a cause of pediatric bacterial meningitis in Iran: a multi-center cross-sectional study. BMC Infect Dis 2022; 22:625. [PMID: 35850636 PMCID: PMC9290261 DOI: 10.1186/s12879-022-07606-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 07/06/2022] [Indexed: 11/19/2022] Open
Abstract
Background Meningitis is considered a life-threatening infection with high mortality all over the world. Hemophilus influenzae (H. influenzae) and Streptococcus pneumoniae (S. pneumoniae) are regarded as the two most common infectious agents causing bacterial meningitis. This study aimed to identify H. influenzae and S. pneumoniae serotypes in blood and cerebrospinal fluid (CSF) of pediatric patients with meningitis, using polymerase chain reaction (PCR). Methods This multi-center cross-sectional study included 284 children with suspected meningitis referred to 4 target hospitals. Overall, 412 samples (128 blood and 284 CSF samples) were obtained from the patients from November 14, 2016 to November 15, 2017. The extracted DNA was examined using multiplex real time PCR to screen for S. pneumoniae and H. influenzae. S. pneumoniae serotyping was also done by multiplex PCR. Results Out of 284 CSF specimens, 22 were positive for ply S. pneumoniae. Of 20 DNA samples meeting the Quality Control (QC) standards for serotyping, 7 (35%), 6 (30%), 2 (10%), 2 (10%), 2 (10%), 1 (5%), 1 (5%), 1 (5%), 1 (5%) and 1 (5%) were positive for serotypes 3, 11A, 6A, 14, 7C, 23F, 23B, 19A, and 19F and 5, respectively. Overall, nine samples were positive for two serotypes, of whom 3 and 11A were the most common from Tehran province. Of note, one of these CSF samples showed a new co-infection with serotypes 7C and 14. Also, 6 samples (30%) were positive for H. influenzae detected by bexA primer. None of the blood samples were positive for S. pneumoniae or H. influenzae. Conclusion Co-infection with S. pneumoniae serotypes can occur in bacterial meningitis and it might be missed if all serotypes are not evaluated in CSF specimens.
Collapse
Affiliation(s)
- Sedigheh Rafiei Tabatabaei
- Pediatric Infections Research Center, Research Institute for Children's Health, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Ahmadreza Shamshiri
- Department of Epidemiology and Biostatistics, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Leila Azimi
- Pediatric Infections Research Center, Research Institute for Children's Health, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Ali Nazari-Alam
- Infectious Diseases Research Center, Kashan University of Medical Sciences, Kashan, Iran
| | - Abdollah Karimi
- Pediatric Infections Research Center, Research Institute for Children's Health, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | | | - Marjan Tariverdi
- Department of Pediatric Infectious Diseases, Faculty of Medicine, Children's Clinical Research Development Center, Hormozgan University of Medical Sciences, Bandar Abbas, Iran.
| |
Collapse
|
3
|
Jullien S, Richard-Greenblatt M, Casellas A, Tshering K, Ribó JL, Sharma R, Tshering T, Pradhan D, Dema K, Ngai M, Muñoz-Almagro C, Kain KC, Bassat Q. Association of Clinical Signs, Host Biomarkers and Etiology With Radiological Pneumonia in Bhutanese Children. Glob Pediatr Health 2022; 9:2333794X221078698. [PMID: 35252478 PMCID: PMC8891828 DOI: 10.1177/2333794x221078698] [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: 10/27/2021] [Accepted: 01/20/2022] [Indexed: 11/15/2022] Open
Abstract
Diagnosing pneumonia and identifying those requiring antibiotherapy remain challenging. Chest radiographs (CXR) are often used as the reference standard. We aimed to describe clinical characteristics, host-response biomarkers and etiology, and assess their relationship to CXR findings in children with pneumonia in Thimphu, Bhutan. Children between 2 and 59 months hospitalized with WHO-defined pneumonia were prospectively enrolled and classified into radiological endpoint and non-endpoint pneumonia. Blood and nasopharyngeal washing were collected for microbiological analyses and plasma levels of 11 host-response biomarkers were measured. Among 149 children with readable CXR, 39 (26.2%) presented with endpoint pneumonia. Identification of respiratory viruses was common, with no significant differences by radiological outcomes. No clinical sign was suggestive of radiological pneumonia, but children with radiological pneumonia presented higher erythrocyte sedimentation rate, C-reactive protein and procalcitonin. Markers of endothelial and immune activation had little accuracy for the reliable identification of radiological pneumonia.
Collapse
Affiliation(s)
- Sophie Jullien
- ISGlobal, Hospital Clínic – Universitat de Barcelona, Barcelona, Spain
- Jigme Dorji Wangchuck National Referral Hospital, Thimphu, Bhutan
| | - Melissa Richard-Greenblatt
- Hospital of the University of Pennsylvania, Philadelphia, PA, USA
- Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- University of Pennsylvania, Philadelphia, PA, USA
| | - Aina Casellas
- ISGlobal, Hospital Clínic – Universitat de Barcelona, Barcelona, Spain
- Universitat de Barcelona, Barcelona, Spain
| | | | - Jose Luis Ribó
- Hospital Universitari General de Catalunya, Barcelona, Spain
| | - Ragunath Sharma
- Jigme Dorji Wangchuck National Referral Hospital, Thimphu, Bhutan
| | - Tashi Tshering
- Khesar Gyalpo University of Medical Sciences of Bhutan, Thimphu, Bhutan
| | - Dinesh Pradhan
- Khesar Gyalpo University of Medical Sciences of Bhutan, Thimphu, Bhutan
| | - Kumbu Dema
- Jigme Dorji Wangchuck National Referral Hospital, Thimphu, Bhutan
| | - Michelle Ngai
- University Health Network-Toronto General Hospital, Toronto, ON, Canada
| | - Carmen Muñoz-Almagro
- Hospital Sant Joan de Déu (University of Barcelona), Barcelona, Spain
- Consorcio de Investigación Biomédica en Red de Epidemiología y Salud Pública, Madrid, Spain
- Universitat Internacional of Catalunya, Barcelona, Spain
| | - Kevin C. Kain
- University Health Network-Toronto General Hospital, Toronto, ON, Canada
- University of Toronto, Toronto, ON, Canada
| | - Quique Bassat
- ISGlobal, Hospital Clínic – Universitat de Barcelona, Barcelona, Spain
- Hospital Sant Joan de Déu (University of Barcelona), Barcelona, Spain
- Consorcio de Investigación Biomédica en Red de Epidemiología y Salud Pública, Madrid, Spain
- ICREA, Barcelona, Spain
- Centro de Investigação em Saúde de Manhiça, Maputo, Mozambique
| |
Collapse
|
4
|
Serotypes and Clonal Composition of Streptococcus pneumoniae Isolates Causing IPD in Children and Adults in Catalonia before 2013 to 2015 and after 2017 to 2019 Systematic Introduction of PCV13. Microbiol Spectr 2021; 9:e0115021. [PMID: 34878302 PMCID: PMC8653838 DOI: 10.1128/spectrum.01150-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The goal of this study was to investigate the distribution of serotypes and clonal composition of Streptococcus pneumoniae isolates causing invasive pneumococcal disease (IPD) in Catalonia, before and after systematic introduction of PCV13. Pneumococcal strains isolated from normally sterile sites obtained from patients of all ages with IPD received between 2013 and 2019 from 25 health centers of Catalonia were included. Two study periods were defined: presystematic vaccination period (2013 and 2015) and systematic vaccination period (SVP) (2017 to 2019). A total of 2,303 isolates were analyzed. In the SVP, there was a significant decrease in the incidence of IPD cases in children 5 to 17 years old (relative risk [RR] 0.61; 95% confidence interval [CI] 0.38 to 0.99), while there was a significant increase in the incidence of IPD cases in 18- to 64-year-old adults (RR 1.33; 95% CI 1.16 to 1.52) and adults over 65 years old (RR 1.23; 95% CI 1.09 to 1.38). Serotype 8 was the major emerging serotype in all age groups except in 5- to 17-year-old children. In children younger than 5 years old, the main serotypes in SVP were 24F, 15A, and 3, while in adults older than 65 years they were serotypes 3, 8, and 12F. A significant decrease in the proportions of clonal complexes CC156, CC191, and ST306 and an increase in those of CC180, CC53, and CC404 were observed. A steady decrease in the incidence of IPD caused by PCV13 serotypes indicates the importance and impact of systematic vaccination. The increase of non-PCV13 serotypes highlights the need to expand serotype coverage in future vaccines and rethink vaccination programs for older adults. IMPORTANCE We found that with the incorporation of the PCV13 vaccine, the numbers of IPD cases caused by serotypes included in this vaccine decreased in all of the age groups. Still, there was an unforeseen increase of the serotypes not included in this vaccine causing IPD, especially in the >65-year-old group. Moreover, a significant increase of serotype 3 included in the vaccine has been observed; this event has been reported by other researchers. These facts call for the incorporation of more serotypes in future vaccines and a more thorough surveillance of the dynamics of this microorganism.
Collapse
|
5
|
González-Peris S, Campins M, García-García JJ, Díaz-Conradi Á, Domínguez Á, Ciruela P, de Sevilla MF, Hernández S, Muñoz-Almagro C, Izquierdo C, Codina G, Uriona S, Esteva C, Solé-Ribalta A, Soldevila N, Planes AM, Martínez-Osorio J, Salleras L, Moraga-Llop F. Necrotizing pneumonia due to Streptococcus pneumoniae in children during the period of non-systematic use of PCV13 in Catalonia, Spain. ENFERMEDADES INFECCIOSAS Y MICROBIOLOGIA CLINICA (ENGLISH ED.) 2021; 39:486-492. [PMID: 34865709 DOI: 10.1016/j.eimce.2020.08.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 08/15/2020] [Indexed: 06/13/2023]
Abstract
BACKGROUND Some studies have observed an increased incidence of necrotizing pneumonia (NP) in recent years. This might be related to the emergence of non-vaccine S. pneumoniae serotypes after PCV7 introduction although it is suggested that evolutionary factors may have modified the virulence and the interactions of pneumococci. The aim of this study was to clinically and microbiologically define NP in the population served by the three major paediatric hospitals in Barcelona (Catalonia, Spain). METHODS A prospective observational study was conducted in patients <18 years hospitalized due to invasive pneumococcal disease (January 2012-June 2016). Data of confirmed cases of pneumococcal NP (diagnosed by culture or DNA detection and serotyped) were collected. PCV13 was not systematically administered in Catalonia during the study period, but was available in the private market so the vaccination coverage in children increased from 48.2% to 74.5%. RESULTS 35 cases of NP were identified. 77.1% of cases were associated with empyema. In the first 4 years, a trend to a decrease in NP incidence was observed (p=0.021), especially in children <5 years (p=0.006). Serotype 3 was responsible for 48.6% of NP cases. Five patients with NP due to serotype 3 were fully vaccinated for their age with PCV13. CONCLUSIONS Serotype 3 has a preeminent role in pneumococcal NP and was associated with all PCV13 vaccination failures. Although in our series the incidence does not seem to be increasing, evolution of pneumococcal NP rates should be monitored after inclusion of PCV13 in the systematic calendar.
Collapse
Affiliation(s)
| | - Magda Campins
- Hospital Universitari Vall d'Hebron, Barcelona, Spain; Grup de Recerca en Epidemiologia i Salut Pública, Vall d'Hebron Institut de Recerca, Barcelona, Spain
| | - Juan José García-García
- CIBER de Epidemiología y Salud Pública (CIBERESP), Madrid, Spain; Hospital Sant Joan de Déu, Universitat de Barcelona, Barcelona, Spain; Malalties Prevenibles amb Vacunes, Institut de Recerca Sant Joan de Déu, Esplugues de Llobregat, Spain
| | | | - Ángela Domínguez
- CIBER de Epidemiología y Salud Pública (CIBERESP), Madrid, Spain; Departament de Medicina, Universitat de Barcelona, Barcelona, Spain
| | - Pilar Ciruela
- CIBER de Epidemiología y Salud Pública (CIBERESP), Madrid, Spain; Agència de Salut Pública de Catalunya, Barcelona, Spain
| | - Mariona F de Sevilla
- CIBER de Epidemiología y Salud Pública (CIBERESP), Madrid, Spain; Hospital Sant Joan de Déu, Universitat de Barcelona, Barcelona, Spain; Malalties Prevenibles amb Vacunes, Institut de Recerca Sant Joan de Déu, Esplugues de Llobregat, Spain
| | | | - Carmen Muñoz-Almagro
- CIBER de Epidemiología y Salud Pública (CIBERESP), Madrid, Spain; Hospital Sant Joan de Déu, Universitat de Barcelona, Barcelona, Spain; Departament de Medicina, Universitat Internacional de Catalunya, Barcelona, Spain
| | - Conchita Izquierdo
- CIBER de Epidemiología y Salud Pública (CIBERESP), Madrid, Spain; Agència de Salut Pública de Catalunya, Barcelona, Spain
| | - Gemma Codina
- Hospital Universitari Vall d'Hebron, Barcelona, Spain
| | - Sonia Uriona
- Hospital Universitari Vall d'Hebron, Barcelona, Spain; Grup de Recerca en Epidemiologia i Salut Pública, Vall d'Hebron Institut de Recerca, Barcelona, Spain
| | - Cristina Esteva
- CIBER de Epidemiología y Salud Pública (CIBERESP), Madrid, Spain; Hospital Sant Joan de Déu, Universitat de Barcelona, Barcelona, Spain
| | - Anna Solé-Ribalta
- Hospital Sant Joan de Déu, Universitat de Barcelona, Barcelona, Spain
| | - Núria Soldevila
- CIBER de Epidemiología y Salud Pública (CIBERESP), Madrid, Spain; Departament de Medicina, Universitat de Barcelona, Barcelona, Spain
| | | | | | - Luis Salleras
- CIBER de Epidemiología y Salud Pública (CIBERESP), Madrid, Spain; Departament de Medicina, Universitat de Barcelona, Barcelona, Spain
| | | |
Collapse
|
6
|
Henares D, Rocafort M, Brotons P, de Sevilla MF, Mira A, Launes C, Cabrera-Rubio R, Muñoz-Almagro C. Rapid Increase of Oral Bacteria in Nasopharyngeal Microbiota After Antibiotic Treatment in Children With Invasive Pneumococcal Disease. Front Cell Infect Microbiol 2021; 11:744727. [PMID: 34712623 PMCID: PMC8546175 DOI: 10.3389/fcimb.2021.744727] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 09/10/2021] [Indexed: 01/04/2023] Open
Abstract
Introduction Antibiotics are commonly prescribed to young children for treating bacterial infections such as invasive pneumococcal disease (IPD) caused by Streptococcus pneumoniae. Despite the obvious benefits of antibiotics, little is known about their possible side effects on children’s nasopharyngeal microbiota. In other ecological niches, antibiotics have been described to perturb the balanced microbiota with short- and long-term effects on children’s health. The present study aims to evaluate and compare the nasopharyngeal microbiota of children with IPD and different degree of antibiotic exposure. Methods We investigated differences in nasopharyngeal microbiota of two groups of children <18 years with IPD: children not exposed to antibiotics before sample collection (n=27) compared to children previously exposed (n=54). Epidemiological/clinical data were collected from subjects, and microbiota was characterized by Illumina sequencing of V3-V4 amplicons of the 16S rRNA gene. Results Main epidemiological/clinical factors were similar across groups. Antibiotic-exposed patients were treated during a median of 4 days (IQR: 3–6) with at least one beta-lactam (100.0%). Higher bacterial richness and diversity were found in the group exposed to antibiotics. Different streptococcal amplicon sequence variants (ASVs) were differentially abundant across groups: antibiotic use was associated to lower relative abundances of Streptococcus ASV2 and Streptococcus ASV11 (phylogenetically close to S. pneumoniae), and higher relative abundances of Streptococcus ASV3 and Streptococcus ASV12 (phylogenetically close to viridans group streptococci). ASVs assigned to typical bacteria from the oral cavity, including Veillonella, Alloprevotella, Porphyromonas, Granulicatella, or Capnocytophaga, were associated to the antibiotic-exposed group. Common nosocomial genera such as Staphylococcus, Acinetobacter, and Pseudomonas were also enriched in the group exposed to antibiotics. Conclusion Our results point toward a reduction of S. pneumoniae abundance on the nasopharynx of children with IPD after antibiotic treatment and a short-term repopulation of this altered niche by oral and nosocomial bacteria. Future research studies will have to evaluate the clinical implications of these findings and if these populations would benefit from the probiotic/prebiotic administration or even from the improvement on oral hygiene practices frequently neglected among hospitalized children.
Collapse
Affiliation(s)
- Desiree Henares
- Institut de Recerca Sant Joan de Deu, Hospital Sant Joan de Deu, Barcelona, Spain.,CIBER of Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain
| | - Muntsa Rocafort
- Institut de Recerca Sant Joan de Deu, Hospital Sant Joan de Deu, Barcelona, Spain.,CIBER of Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain
| | - Pedro Brotons
- Institut de Recerca Sant Joan de Deu, Hospital Sant Joan de Deu, Barcelona, Spain.,CIBER of Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain.,School of Medicine, Universitat Internacional de Catalunya, Barcelona, Spain
| | - Mariona F de Sevilla
- CIBER of Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain.,Pediatric Department, Hospital Sant Joan de Deu, University of Barcelona, Barcelona, Spain
| | - Alex Mira
- CIBER of Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain.,Department of Health and Genomics, Center for Advanced Research in Public Health, Fundacion para el Fomento de la Investigacion Sanitaria y Biomedica de la Comunitat Valenciana (FISABIO), Valencia, Spain
| | - Cristian Launes
- Institut de Recerca Sant Joan de Deu, Hospital Sant Joan de Deu, Barcelona, Spain.,CIBER of Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain.,Pediatric Department, Hospital Sant Joan de Deu, University of Barcelona, Barcelona, Spain
| | - Raul Cabrera-Rubio
- Teagasc Food Research Centre (TEAGASC), Moorepark, Fermoy, Ireland.,APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Carmen Muñoz-Almagro
- Institut de Recerca Sant Joan de Deu, Hospital Sant Joan de Deu, Barcelona, Spain.,CIBER of Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain.,School of Medicine, Universitat Internacional de Catalunya, Barcelona, Spain
| |
Collapse
|
7
|
Martínez-Osorio J, García-García JJ, Moraga-Llop F, Díaz A, Hernández S, Solé-Ribalta A, González-Peris S, Izquierdo C, Esteva C, Codina G, Planes AM, Uriona S, Campins M, Ciruela P, Salleras L, Domínguez Á, Muñoz-Almagro C, de Sevilla MF. Invasive pneumococcal disease in children under 60 months before and after availability of 13-valent conjugate vaccine. An Pediatr (Barc) 2021; 96:501-510. [PMID: 34238710 DOI: 10.1016/j.anpede.2021.06.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 05/20/2021] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Invasive pneumococcal disease (IPD) is the most important bacterial infection in young children, and the introduction of pneumococcal conjugate vaccines has changed its presentation. This study compared the incidence, characteristics and serotype distribution of IPD before and after the introduction of the pneumococcal conjugate vaccine (PCV13). METHODS Prospective enrolment of patients with IPD aged less than 60 months and admitted to either of 2 tertiary care hospitals between January 2007 and December 2009 (pre-PCV13 period) and January 2012 and June-2016 (PCV13 period). RESULTS We identified 493 cases, 319 in the pre-PCV13 period and 174 in the PCV13 period. The incidence of IPD decreased from 89.7 to 34.4 casos per 100 000 habitantes ( -62%; P < .001). This decrease was observed in all forms of disease except necrotising pneumonia (increase from 0.8 to 3.7 casos/100 000 population). There was a significant reduction in all serotypes included in the PCV13 and not included in the PCV7. We did not find significant differences in length of stay, mortality or the frequency of sequelae between both periods, but in the PCV13 period, the length of stay in the paediatric intensive care unit and the duration of mechanical ventilation were longer (P = .00). The incidence of serotype 3 decreased from 10.4 to 6.9 casos per 100 000 population, although it was the serotype involved most frequently in patients with severe disease. CONCLUSIONS After the introduction of the PCV13, there has been a significant decrease in IPD cases. Serotype 3 continues to be an important cause of severe IPD.
Collapse
Affiliation(s)
| | - Juan José García-García
- Malalties Prevenibles amb Vacunes, Institut de Recerca Sant Joan de Déu, Hospital Sant Joan de Déu, Universitat de Barcelona, Barcelona, Spain; Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
| | | | | | - Sergi Hernández
- Agència de Salut Pública de Catalunya, Generalitat de Catalunya, Barcelona, Spain
| | - Anna Solé-Ribalta
- Hospital Sant Joan de Déu, Universitat de Barcelona, Barcelona, Spain
| | | | - Conchita Izquierdo
- Agència de Salut Pública de Catalunya, Generalitat de Catalunya, Barcelona, Spain
| | - Cristina Esteva
- Malalties Prevenibles amb Vacunes, Institut de Recerca Sant Joan de Déu, Hospital Sant Joan de Déu, Universitat de Barcelona, Barcelona, Spain; Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
| | - Gemma Codina
- Hospital Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Ana María Planes
- Hospital Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Sonia Uriona
- Hospital Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Magda Campins
- Hospital Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Pilar Ciruela
- Agència de Salut Pública de Catalunya, Generalitat de Catalunya, Barcelona, Spain
| | - Luis Salleras
- Departament de Medicina, Universitat de Barcelona, Barcelona, Spain
| | - Ángela Domínguez
- Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain; Departament de Medicina, Universitat de Barcelona, Barcelona, Spain
| | - Carmen Muñoz-Almagro
- Malalties Prevenibles amb Vacunes, Institut de Recerca Sant Joan de Déu, Hospital Sant Joan de Déu, Universitat de Barcelona, Barcelona, Spain; Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain; Departament de Medicina, Universitat Internacional de Catalunya, Barcelona, Spain
| | - Mariona F de Sevilla
- Malalties Prevenibles amb Vacunes, Institut de Recerca Sant Joan de Déu, Hospital Sant Joan de Déu, Universitat de Barcelona, Barcelona, Spain; Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
| |
Collapse
|
8
|
Martínez-Osorio J, García-García JJ, Moraga-Llop F, Díaz A, Hernández S, Solé-Ribalta A, González-Peris S, Izquierdo C, Esteva C, Codina G, Planes AM, Uriona S, Campins M, Ciruela P, Salleras L, Domínguez Á, Muñoz-Almagro C, de Sevilla MF. [Invasive pneumococcal disease in children under 60 months before and after availability of 13-valent conjugate vaccine]. An Pediatr (Barc) 2021; 96:S1695-4033(21)00206-X. [PMID: 34217675 DOI: 10.1016/j.anpedi.2021.05.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 05/11/2021] [Accepted: 05/20/2021] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Invasive pneumococcal disease (IPD) is the most important bacterial infection in young children, and the introduction of pneumococcal conjugate vaccines has changed its presentation. This study compared the incidence, characteristics and serotype distribution of IPD before and after the introduction of the pneumococcal conjugate vaccine (PCV13). METHODS Prospective enrolment of patients with IPD aged less than 60 months and admitted to either of 2 tertiary care hospitals between January 2007 and December 2009 (pre-PCV13 period) and January 2012 and June-2016 (PCV13 period). RESULTS We identified 493 cases, 319 in the pre-PCV13 period and 174 in the PCV13 period. The incidence of IPD decreased from 89.7 to 34.4 cases per 100,000 population (-62%; P<.001). This decrease was observed in all forms of disease except necrotising pneumonia (increase from 0.8 to 3.7 cases/100,000 population). There was a significant reduction in all serotypes included in the PCV13 and not included in the PCV7. We did not find significant differences in length of stay, mortality or the frequency of sequelae between both periods, but in the PCV13 period, the length of stay in the paediatric intensive care unit and the duration of mechanical ventilation were longer (P=.00). The incidence of serotype 3 decreased from 10.4 to 6.9 cases per 100,000 population, although it was the serotype involved most frequently in patients with severe disease. CONCLUSIONS After the introduction of the PCV13, there has been a significant decrease in IPD cases. Serotype 3 continues to be an important cause of severe IPD.
Collapse
Affiliation(s)
| | - Juan José García-García
- Malalties Prevenibles amb Vacunes, Institut de Recerca Sant Joan de Déu, Hospital Sant Joan de Déu, Universitat de Barcelona, Barcelona, España; Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP), Barcelona, España
| | | | | | - Sergi Hernández
- Agència de Salut Pública de Catalunya, Generalitat de Catalunya, Barcelona, España
| | | | | | - Conchita Izquierdo
- Agència de Salut Pública de Catalunya, Generalitat de Catalunya, Barcelona, España
| | - Cristina Esteva
- Malalties Prevenibles amb Vacunes, Institut de Recerca Sant Joan de Déu, Hospital Sant Joan de Déu, Universitat de Barcelona, Barcelona, España; Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP), Barcelona, España
| | - Gemma Codina
- Hospital Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona, España
| | - Ana María Planes
- Hospital Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona, España
| | - Sonia Uriona
- Hospital Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona, España
| | - Magda Campins
- Hospital Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona, España
| | - Pilar Ciruela
- Agència de Salut Pública de Catalunya, Generalitat de Catalunya, Barcelona, España
| | - Luis Salleras
- Departament de Medicina, Universitat de Barcelona, Barcelona, España
| | - Ángela Domínguez
- Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP), Barcelona, España; Departament de Medicina, Universitat de Barcelona, Barcelona, España
| | - Carmen Muñoz-Almagro
- Malalties Prevenibles amb Vacunes, Institut de Recerca Sant Joan de Déu, Hospital Sant Joan de Déu, Universitat de Barcelona, Barcelona, España; Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP), Barcelona, España; Departament de Medicina, Universitat Internacional de Catalunya, Barcelona, España
| | - Mariona F de Sevilla
- Malalties Prevenibles amb Vacunes, Institut de Recerca Sant Joan de Déu, Hospital Sant Joan de Déu, Universitat de Barcelona, Barcelona, España; Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP), Barcelona, España
| |
Collapse
|
9
|
Makenga G, Mtove G, Yin JK, Mziray A, Bwana VM, Kisinza W, Mjema J, Amos B, Antony L, Shingadia D, Oftadeh S, Booy R. Immunogenicity and Efficacy of Pneumococcal Conjugate Vaccine (Prevenar13 ®) in Preventing Acquisition of Carriage of Pneumococcal Vaccine Serotypes in Tanzanian Children With HIV/AIDS. Front Immunol 2021; 12:673392. [PMID: 34220819 PMCID: PMC8248180 DOI: 10.3389/fimmu.2021.673392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Accepted: 05/31/2021] [Indexed: 11/13/2022] Open
Abstract
In every year, up to one million children die due to pneumococcal disease. Children infected with Human Immunodeficiency Virus (HIV) are mostly affected, as they appear to have higher rates of pneumococcal carriage and invasive disease. Successful immunity is dependent on mounting a sufficient immune response to the vaccine. We conducted a double blinded crossover randomised controlled trial to determine the serum antibody response (≥4-fold and geometric mean concentration) to pneumococcal vaccine (PCV13) serotypes at 3 months after second vaccination. We also determined the number and proportion of children carrying new (not present at baseline) vaccine serotypes of S. pneumoniae isolated from nasopharynx at 6 months post initial vaccination in recipients of Prevenar13® compared with those given Haemophilus influenzae-type b (Hib) vaccine (control). The study was conducted at St Augustine's also known as Teule Hospital in Muheza, Tanga Tanzania. 225 HIV infected children aged 1-14 years were enrolled from Jan 2013 to Nov 2013 and randomised to Prevenar13® or Hib vaccines each given at baseline and 2-3 months later. Nasopharyngeal and serum samples were collected at baseline and 4-6 months later. Serotyping was done by Quellung Reaction using Staten antisera. Serum antibodies were ELISA quantified. The study revealed a non-significant reduction in the acquisition of new vaccine serotypes of S. pneumoniae in the recipients of PCV13 by nearly a third compared to those who received Hib vaccine. The vaccine efficacy was 30.5% (95% confidence interval [CI] -6.4-54.6%, P = 0.100)]. The antibody response was not enough to induce a 4-fold rise in GMC in 7 of the 13 vaccine serotypes. When combining the effects of preventing new acquisition and clearing existing vaccine type carriage, the overall efficacy was 31.5% (95% CI 1.5-52.4%, P = 0.045). In the PCV13 group, the proportion of participants carrying vaccine serotype was significantly lower after 2 doses of PCV13 (30%; 32/107), compared with the baseline proportion (48%; 51/107). The introduction of PCV13 targeting HIV-positive children in a setting similar to Tanzania is likely to be associated with appreciable decrease in the acquisition and carriage of pneumococci, which is an important marker of the likely effect of the vaccine on pneumococcal disease. Clinical Trial Registration https://www.anzctr.org.au/Trial/Registration/TrialReview.aspx?id=335579, identifier ACTRN12610000999033.
Collapse
Affiliation(s)
- Geofrey Makenga
- National Institute for Medical Research (NIMR), Amani Research Center, Muheza, Tanzania
| | - George Mtove
- National Institute for Medical Research (NIMR), Amani Research Center, Muheza, Tanzania
| | - J. Kevin Yin
- Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
- National Centre for Immunisation Research and Surveillance, University of Sydney, Sydney, NSW, Australia
| | - Abubakary Mziray
- National Institute for Medical Research (NIMR), Amani Research Center, Muheza, Tanzania
| | - Veneranda M. Bwana
- National Institute for Medical Research (NIMR), Amani Research Center, Muheza, Tanzania
| | - William Kisinza
- National Institute for Medical Research (NIMR), Amani Research Center, Muheza, Tanzania
| | - Julius Mjema
- St Augustine’s, Hospitali Teule, Private Bag, Tanga, Tanzania
| | - Ben Amos
- St Augustine’s, Hospitali Teule, Private Bag, Tanga, Tanzania
| | - Laura Antony
- Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
| | - Delane Shingadia
- Great Ormond Street Hospital for Children NHS Trust, London, United Kingdom
| | - Shahin Oftadeh
- NSW and ACT Pneumococcal Reference Laboratory, Centre for Infectious Diseases and Microbiology, Institute of Clinical Pathology and Medical Research, Westmead Hospital, Westmead, NSW, Australia
| | - Robert Booy
- Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
- National Centre for Immunisation Research and Surveillance, University of Sydney, Sydney, NSW, Australia
| |
Collapse
|
10
|
Félix S, Henares D, Muñoz-Almagro C, Sá-Leão R. Carriage of multiple Streptococcus pneumoniae capsular types is frequent among children with invasive pneumococcal disease. Eur J Clin Microbiol Infect Dis 2021; 40:2397-2401. [PMID: 33797644 PMCID: PMC8017099 DOI: 10.1007/s10096-021-04231-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 03/17/2021] [Indexed: 12/01/2022]
Abstract
Streptococcus pneumoniae (pneumococcus) is a human pathogen that colonizes the nasopharynx. We investigated serotype distribution in paired invasive and nasopharyngeal samples obtained from 57 children during invasive pneumococcal disease. Of 39 nasopharyngeal samples positive for pneumococci, 46.2% contained a serotype different from the one causing disease. This study reports a high frequency of pneumococcal multiple serotype carriage in children with invasive pneumococcal disease. Whether multiple serotype carriage is important for the onset and progress to pneumococcal infection warrants further investigation.
Collapse
Affiliation(s)
- Sofia Félix
- Laboratory of Molecular Microbiology of Human Pathogens, Instituto de Tecnologia Química e Biológica António Xavier/Universidade Nova de Lisboa (ITQB/NOVA), Oeiras, Portugal
| | - Desirée Henares
- Molecular Microbiology Department, Instituto de Recerca Pediatrica/University Hospital Sant Joan de Déu, Barcelona, Spain
| | - Carmen Muñoz-Almagro
- Molecular Microbiology Department, Instituto de Recerca Pediatrica/University Hospital Sant Joan de Déu, Barcelona, Spain.,CIBER de Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain.,Department of Medicine, Universitat Internacional de Catalunya, Barcelona, Spain
| | - Raquel Sá-Leão
- Laboratory of Molecular Microbiology of Human Pathogens, Instituto de Tecnologia Química e Biológica António Xavier/Universidade Nova de Lisboa (ITQB/NOVA), Oeiras, Portugal.
| |
Collapse
|
11
|
Bocharova DV, Alekseev YI, Kurochkin VE. Effect of Electric Field Voltage on the Efficiency of Separation of Single-Stranded DNA Fragments by Capillary Gel Electrophoresis in Polymers Based on Linear Poly(N,N-Dimethylacrylamide). JOURNAL OF ANALYTICAL CHEMISTRY 2020. [DOI: 10.1134/s1061934820100032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
12
|
Jullien S, Sharma R, Lhamu Mynak M, Henares D, Muñoz-Almagro C, Bassat Q. Pneumococcal nasopharyngeal carriage among Bhutanese children hospitalized with clinical pneumonia: serotypes and viral co-infection. BMC Infect Dis 2020; 20:940. [PMID: 33297987 PMCID: PMC7725031 DOI: 10.1186/s12879-020-05674-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 11/30/2020] [Indexed: 10/26/2022] Open
Abstract
BACKGROUND Pneumococcal nasopharyngeal colonization (PNC) generally precedes pneumococcal disease. The purpose of this study was to determine the prevalence of PNC and to identify the pneumococcal serotypes circulating among Bhutanese children under five years of age admitted with clinical pneumonia, before the introduction of pneumococcal conjugate vaccine (PCV13) in the country. We also aimed to contribute to the understanding of the interplay between PNC and viral co-infection among this population. METHODS This was a prospective study conducted at the Jigme Dorji Wangchuck National Referral Hospital in Bhutan over 12 consecutive months. Children aged 2 to 59 months admitted with WHO-defined clinical pneumonia were eligible for recruitment. We collected blood for bacterial culture and molecular identification of S. pneumoniae, and nasopharyngeal washing for screening of respiratory viruses, and for the detection and capsular typing of S. pneumoniae by real-time polymerase chain reaction (RT-PCR). RESULTS Overall, 189 children were recruited, and PNC was tested in 121 of them (64.0%). PNC was found in 76/121 children (62.8%) and S. pneumoniae was identified in blood (both by culture and RT-PCR) in a single child. Respiratory viruses were detected in a similar proportion among children with (62/70; 88.6%) and without PNC (36/40; 90.0%; p = 1.000), but rhinovirus detection was less common among children with PNC (20/70; 28.6% versus 19/40; 47.5%; p = 0.046). Capsular typing identified 30 different serotypes. Thirty-nine children (51.3%) were colonised with two to five different serotypes. A third of the children presented with serotypes considered highly invasive. Over half of the children (44/76; 57.9%) were carrying at least one serotype included in PCV13. CONCLUSIONS This study provides baseline information on the status of PNC among Bhutanese children admitted with clinical pneumonia prior to the introduction of PCV13, which is valuable to monitor its potential impact. PCV13 could theoretically have averted up to 58% of the pneumococcal infections among the children in this study, suggesting a future role for the vaccine to significantly reduce the burden associated with S. pneumoniae in Bhutan.
Collapse
Affiliation(s)
- Sophie Jullien
- Barcelona Institute for Global Health (ISGlobal), Hospital Clinic, Universitat de Barcelona, Barcelona, Spain. .,Jigme Dorji Wangchuck National Referral Hospital, Thimphu, Bhutan.
| | - Ragunath Sharma
- Jigme Dorji Wangchuck National Referral Hospital, Thimphu, Bhutan
| | - Mimi Lhamu Mynak
- Jigme Dorji Wangchuck National Referral Hospital, Thimphu, Bhutan
| | - Desiree Henares
- Instituto de Recerca Pediatrica, Hospital Sant Joan de Deu (University of Barcelona), Barcelona, Spain.,CIBER of Epidemiology and Public Health CIBERESP, Madrid, Spain
| | - Carmen Muñoz-Almagro
- Instituto de Recerca Pediatrica, Hospital Sant Joan de Deu (University of Barcelona), Barcelona, Spain.,CIBER of Epidemiology and Public Health CIBERESP, Madrid, Spain.,Department of Medicine, Universitat Internacional of Catalunya, Barcelona, Spain
| | - Quique Bassat
- Barcelona Institute for Global Health (ISGlobal), Hospital Clinic, Universitat de Barcelona, Barcelona, Spain.,CIBER of Epidemiology and Public Health CIBERESP, Madrid, Spain.,Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain.,Pediatric Infectious Diseases Unit, Pediatrics Department, Hospital Sant Joan de Déu (University of Barcelona), Barcelona, Spain.,Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique
| |
Collapse
|
13
|
Garcia-Garcia S, Perez-Arguello A, Henares D, Timoneda N, Muñoz-Almagro C. Rapid identification, capsular typing and molecular characterization of Streptococcus pneumoniae by using whole genome nanopore sequencing. BMC Microbiol 2020; 20:347. [PMID: 33187472 PMCID: PMC7666501 DOI: 10.1186/s12866-020-02032-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Accepted: 11/03/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Whole genome sequencing has emerged as a useful tool for identification and molecular characterization of pathogens. MinION (Oxford Nanopore) is a real-time third generation sequencer whose portability, affordability and speed in data production make of it an attractive device for whole genome sequencing. The objective of this study is to evaluate MinION sequencer for pathogen identification and molecular characterization of Streptococcus pneumoniae isolated at a children's Hospital. Whole genome sequencing of 32 Streptococcus pneumoniae invasive isolates, previously characterized by standard methods (Quellung reaction, Multiplex PCR and Sanger-MLST), were performed. DNA was extracted using ZymoBIOMICS DNA Microprep kit. Quantification and purity of DNA was assessed by Qubit and Nanodrop, respectively. Library preparation was performed using the Rapid Barcoding Kit. Real-time workflow EPI2ME platform "What's it in my pot" was used for species identification. Fast5 sequences were converted into FASTQ by Albacore software. Reads were assembled using CANU software. PathogenWatch, genomic epidemiology and pubmlst online tools were used for capsular typing and/or whole genome-MLST profile. RESULTS Rapid identification of Streptococcus pneumoniae was achieved by "What's in my pot". Capsular typing was correctly assigned with PathogenWatch in all 32 isolates at serogroup level and 24 at serotype level. Whole genome-MLST results obtained by genomic epidemiology and pubmlst were consistent with double locus variant clonal complex obtained by Sanger-MLST in 31 isolates. CONCLUSION MinION sequencer provides a rapid, cost-effective and promising pathway for performing WGS by a pocked-sized device for epidemiological purposes but improving its sequencing accuracy will make it more appealing to be used in clinical microbiology laboratories.
Collapse
Affiliation(s)
- S Garcia-Garcia
- Institut de Recerca Sant Joan de Deu, Hospital Sant Joan de Deu, Barcelona, Spain.
| | - A Perez-Arguello
- Institut de Recerca Sant Joan de Deu, Hospital Sant Joan de Deu, Barcelona, Spain
| | - D Henares
- Institut de Recerca Sant Joan de Deu, Hospital Sant Joan de Deu, Barcelona, Spain
- CIBER de Epidemiologia y Salud Publica (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain
| | - N Timoneda
- Institut de Recerca Sant Joan de Deu, Hospital Sant Joan de Deu, Barcelona, Spain
- CIBER de Epidemiologia y Salud Publica (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain
| | - C Muñoz-Almagro
- Institut de Recerca Sant Joan de Deu, Hospital Sant Joan de Deu, Barcelona, Spain
- CIBER de Epidemiologia y Salud Publica (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain
- Departament de Medicina, Universitat Internacional de Catalunya, Barcelona, Spain
| |
Collapse
|
14
|
Pneumococcal serotypes in children, clinical presentation and antimicrobial susceptibility in the PCV13 era. Epidemiol Infect 2020; 148:e279. [PMID: 33148361 PMCID: PMC7770381 DOI: 10.1017/s0950268820002708] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The aim was to analyse invasive pneumococcal disease (IPD) serotypes in children aged ⩽17 years according to clinical presentation and antimicrobial susceptibility. We conducted a prospective study (January 2012–June 2016). IPD cases were diagnosed by culture and/or real-time polymerase chain reaction (PCR). Demographic, microbiological and clinical data were analysed. Associations were assessed using the odds ratio (OR) and 95% confidence intervals (CI). Of the 253 cases, 34.4% were aged <2 years, 38.7% 2–4 years and 26.9% 5–17 years. Over 64% were 13-valent pneumococcal conjugate vaccine (PCV13) serotypes. 48% of the cases were diagnosed only by real-time PCR. Serotypes 3 and 1 were associated with complicated pneumonia (P < 0.05) and non-PCV13 serotypes with meningitis (OR 7.32, 95% CI 2.33–22.99) and occult bacteraemia (OR 3.6, 95% CI 1.56–8.76). Serotype 19A was more frequent in children aged <2 years and serotypes 3 and 1 in children aged 2–4 years and 5–17 years, respectively. 36.1% of cases were not susceptible to penicillin and 16.4% were also non-susceptible to cefotaxime. Serotypes 14, 24F and 23B were associated with non-susceptibility to penicillin (P < 0.05) and serotypes 11, 14 and 19A to cefotaxime (P < 0.05). Serotype 19A showed resistance to penicillin (P = 0.002). In conclusion, PCV13 serotypes were most frequent in children aged ⩽17 years, mainly serotypes 3, 1 and 19A. Non-PCV13 serotypes were associated with meningitis and occult bacteraemia and PCV13 serotypes with pneumonia. Non-susceptibility to antibiotics of non-PCV13 serotypes should be monitored.
Collapse
|
15
|
González-Peris S, Campins M, García-García JJ, Díaz-Conradi Á, Domínguez Á, Ciruela P, de Sevilla MF, Hernández S, Muñoz-Almagro C, Izquierdo C, Codina G, Uriona S, Esteva C, Solé-Ribalta A, Soldevila N, Planes AM, Martínez-Osorio J, Salleras L, Moraga-Llop F. Necrotizing pneumonia due to Streptococcus pneumoniae in children during the period of non-systematic use of PCV13 in Catalonia, Spain. Enferm Infecc Microbiol Clin 2020; 39:S0213-005X(20)30291-3. [PMID: 33131931 DOI: 10.1016/j.eimc.2020.08.022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 08/11/2020] [Accepted: 08/15/2020] [Indexed: 11/17/2022]
Abstract
BACKGROUND Some studies have observed an increased incidence of necrotizing pneumonia (NP) in recent years. This might be related to the emergence of non-vaccine S. pneumoniae serotypes after PCV7 introduction although it is suggested that evolutionary factors may have modified the virulence and the interactions of pneumococci. The aim of this study was to clinically and microbiologically define NP in the population served by the three major paediatric hospitals in Barcelona (Catalonia, Spain). METHODS A prospective observational study was conducted in patients <18 years hospitalized due to invasive pneumococcal disease (January 2012-June 2016). Data of confirmed cases of pneumococcal NP (diagnosed by culture or DNA detection and serotyped) were collected. PCV13 was not systematically administered in Catalonia during the study period, but was available in the private market so the vaccination coverage in children increased from 48.2% to 74.5%. RESULTS 35 cases of NP were identified. 77.1% of cases were associated with empyema. In the first 4 years, a trend to a decrease in NP incidence was observed (p=0.021), especially in children <5 years (p=0.006). Serotype 3 was responsible for 48.6% of NP cases. Five patients with NP due to serotype 3 were fully vaccinated for their age with PCV13. CONCLUSIONS Serotype 3 has a preeminent role in pneumococcal NP and was associated with all PCV13 vaccination failures. Although in our series the incidence does not seem to be increasing, evolution of pneumococcal NP rates should be monitored after inclusion of PCV13 in the systematic calendar.
Collapse
Affiliation(s)
| | - Magda Campins
- Hospital Universitari Vall d'Hebron, Barcelona, Spain; Grup de Recerca en Epidemiologia i Salut Pública, Vall d'Hebron Institut de Recerca, Barcelona, Spain
| | - Juan José García-García
- CIBER de Epidemiología y Salud Pública (CIBERESP), Madrid, Spain; Hospital Sant Joan de Déu, Universitat de Barcelona, Barcelona, Spain; Malalties Prevenibles amb Vacunes, Institut de Recerca Sant Joan de Déu, Esplugues de Llobregat, Spain
| | | | - Ángela Domínguez
- CIBER de Epidemiología y Salud Pública (CIBERESP), Madrid, Spain; Departament de Medicina, Universitat de Barcelona, Barcelona, Spain
| | - Pilar Ciruela
- CIBER de Epidemiología y Salud Pública (CIBERESP), Madrid, Spain; Agència de Salut Pública de Catalunya, Barcelona, Spain
| | - Mariona F de Sevilla
- CIBER de Epidemiología y Salud Pública (CIBERESP), Madrid, Spain; Hospital Sant Joan de Déu, Universitat de Barcelona, Barcelona, Spain; Malalties Prevenibles amb Vacunes, Institut de Recerca Sant Joan de Déu, Esplugues de Llobregat, Spain
| | | | - Carmen Muñoz-Almagro
- CIBER de Epidemiología y Salud Pública (CIBERESP), Madrid, Spain; Hospital Sant Joan de Déu, Universitat de Barcelona, Barcelona, Spain; Departament de Medicina, Universitat Internacional de Catalunya, Barcelona, Spain
| | - Conchita Izquierdo
- CIBER de Epidemiología y Salud Pública (CIBERESP), Madrid, Spain; Agència de Salut Pública de Catalunya, Barcelona, Spain
| | - Gemma Codina
- Hospital Universitari Vall d'Hebron, Barcelona, Spain
| | - Sonia Uriona
- Hospital Universitari Vall d'Hebron, Barcelona, Spain; Grup de Recerca en Epidemiologia i Salut Pública, Vall d'Hebron Institut de Recerca, Barcelona, Spain
| | - Cristina Esteva
- CIBER de Epidemiología y Salud Pública (CIBERESP), Madrid, Spain; Hospital Sant Joan de Déu, Universitat de Barcelona, Barcelona, Spain
| | - Anna Solé-Ribalta
- Hospital Sant Joan de Déu, Universitat de Barcelona, Barcelona, Spain
| | - Núria Soldevila
- CIBER de Epidemiología y Salud Pública (CIBERESP), Madrid, Spain; Departament de Medicina, Universitat de Barcelona, Barcelona, Spain
| | | | | | - Luis Salleras
- CIBER de Epidemiología y Salud Pública (CIBERESP), Madrid, Spain; Departament de Medicina, Universitat de Barcelona, Barcelona, Spain
| | | |
Collapse
|
16
|
de Paz HD, Brotons P, Esteva C, Muñoz-Almagro C. Validation of a Loop-Mediated Isothermal Amplification Assay for Rapid Diagnosis of Invasive Pneumococcal Disease. Front Cell Infect Microbiol 2020; 10:115. [PMID: 32266166 PMCID: PMC7105778 DOI: 10.3389/fcimb.2020.00115] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 03/02/2020] [Indexed: 12/29/2022] Open
Abstract
Current molecular PCR-based techniques used for detecting Streptococcus pneumoniae, the causative pathogen of invasive pneumococcal disease (IPD), are accurate but have a run time of several hours. We aimed to develop and validate a novel real-time loop mediated amplification (LAMP) assay for rapid detection of pneumococcus in normally sterile samples with accuracy comparable to a gold standard real-time PCR. Conserved regions of lytA were used for the design of the LAMP test. Analytical validation included assessment of linearity, limit of detection (LOD), intra-assay and inter-assay precision and analytical specificity, which was evaluated by using reference strain S. pneumoniae R6 and a quality control panel. Clinical performance was assessed on all samples collected from children with suspicion of IPD attended in Hospital Sant Joan de Deu (Barcelona, Spain) during the period April-September 2015. Fresh samples were analyzed after DNA extraction. The following values of analytical parameters were determined: linearity within the range 108-104 copies/mL; limit of detection, 5·103 copies/mL; intra- and inter-assay precision measured by mean coefficient of variance, 3.61 and 6.59%; analytical specificity, 9/9 pathogens similar to S. pneumoniae and 14/14 strains of different S. pneumoniae serotypes correctly identified as negative and positive results, respectively. Diagnostic sensitivity and specificity values were 100.0 and 99.3%. Median time of DNA amplification was 15 min. The new LAMP assay showed to have similar accuracy as PCR while being 5-fold faster and could become a useful diagnostic tool for early diagnosis of IPD.
Collapse
Affiliation(s)
- Héctor David de Paz
- Department of Molecular Microbiology, Institut de Recerca Pediatrica, Hospital Sant Joan de Déu, Barcelona, Spain
| | - Pedro Brotons
- Department of Molecular Microbiology, Institut de Recerca Pediatrica, Hospital Sant Joan de Déu, Barcelona, Spain.,CIBER of Epidemiology and Public Health, CIBERESP, Madrid, Spain.,Department of Medicine, Universitat Internacional de Catalunya, Barcelona, Spain
| | - Cristina Esteva
- Department of Molecular Microbiology, Institut de Recerca Pediatrica, Hospital Sant Joan de Déu, Barcelona, Spain.,CIBER of Epidemiology and Public Health, CIBERESP, Madrid, Spain
| | - Carmen Muñoz-Almagro
- Department of Molecular Microbiology, Institut de Recerca Pediatrica, Hospital Sant Joan de Déu, Barcelona, Spain.,CIBER of Epidemiology and Public Health, CIBERESP, Madrid, Spain.,Department of Medicine, Universitat Internacional de Catalunya, Barcelona, Spain
| |
Collapse
|
17
|
Aper D, Frömbling J, Bağcıoğlu M, Ehling-Schulz M, Hennig-Pauka I. Comparison of metabolic adaptation and biofilm formation of Actinobacillus pleuropneumoniae field isolates from the upper and lower respiratory tract of swine with respiratory disease. Vet Microbiol 2019; 240:108532. [PMID: 31902502 DOI: 10.1016/j.vetmic.2019.108532] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 11/25/2019] [Accepted: 11/26/2019] [Indexed: 12/27/2022]
Abstract
Most outbreaks of disease due to infection with Actinobacillus (A.) pleuropneumoniae are caused by pigs already pre-colonised in tonsillar tissue, where the pathogen is protected from exposure to antibiotic substances administered for treatment. As it has been shown recently under experimental conditions, A. pleuropneumoniae displays host tissue-specific metabolic adaptation. In this study, pairs of A. pleuropneumoniae field isolates were recovered from lung as well as from tonsillar and nasal tissue from 20 pigs suffering from acute clinical signs of pleuropneumonia and showing characteristic pathological lung alterations. Metabolic adaptation to the porcine lower and upper respiratory tract of 32 A. pleuropneumoniae serotype 2 field isolates was examined using Fourier transform infrared (FTIR) spectroscopy as a high resolution metabolic fingerprinting method. All strains showed metabolic adaptations to organ tissue reflected by hierarchical cluster analysis of FTIR spectra similar to those previously observed under experimental conditions. Notably, differences in antimicrobial resistance patterns and minimal inhibitory concentrations of isolates from different tissues in the same animal, but not in biofilm production capability in a microtiter plate assay were found. Overall, biofilm formation was observed for 71 % of the isolates, confirming that A. pleuropneumoniae field isolates are generally able to form biofilms, although rather in a serotype-specific than in an organ-specific manner. A. pleuropneumoniae serotype 6 isolates formed significantly more biofilm than the other serotypes. Furthermore, biofilm production was negatively correlated to the lung lesion scores and tonsillar isolates tended to be more susceptible to antimicrobial substances with high bioavailability than lung isolates.
Collapse
Affiliation(s)
- Doris Aper
- Field Station for Epidemiology, University of Veterinary Medicine Hannover, Foundation, D-49456 Bakum, Germany
| | - Janna Frömbling
- Institute of Microbiology, Department of Pathobiology, University of Veterinary Medicine Vienna, Veterinaerplatz 1, A-1210 Vienna, Austria
| | - Murat Bağcıoğlu
- Institute of Microbiology, Department of Pathobiology, University of Veterinary Medicine Vienna, Veterinaerplatz 1, A-1210 Vienna, Austria
| | - Monika Ehling-Schulz
- Institute of Microbiology, Department of Pathobiology, University of Veterinary Medicine Vienna, Veterinaerplatz 1, A-1210 Vienna, Austria
| | - Isabel Hennig-Pauka
- Field Station for Epidemiology, University of Veterinary Medicine Hannover, Foundation, D-49456 Bakum, Germany.
| |
Collapse
|
18
|
Invasive Pneumococcal Disease and Influenza Activity in a Pediatric Population: Impact of PCV13 Vaccination in Pandemic and Nonpandemic Influenza Periods. J Clin Microbiol 2019; 57:JCM.00363-19. [PMID: 31189583 DOI: 10.1128/jcm.00363-19] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 06/02/2019] [Indexed: 11/20/2022] Open
Abstract
The objective of this study was to analyze the incidence, clinical presentation, and severity of invasive pneumococcal disease (IPD)-causing serotypes and the impact of the 13-valent pneumococcal conjugate vaccination during epidemic and nonepidemic influenza periods in Catalonia, Spain. This was a prospective study in persons aged <18 years diagnosed with IPD between 2012 and 2015 in three Catalan pediatric hospitals. IPD was defined as clinical infection together with isolation of Streptococcus pneumoniae by culture and/or detection by reverse transcription-PCR in a normally sterile sample. Incidence rate ratios (IRRs) and the fraction of IPD prevented associated with 13-valent pneumococcal conjugate vaccine (PCV13) were calculated. The bivariate analysis used the χ2 test and the multivariate analysis nonconditional logistic regression. A total of 229 cases of IPD were recorded. The incidence was higher during influenza epidemic periods (IRR, 2.7; 95% confidence interval [CI], 2.05 to 3.55; P < 0.001), especially for pneumonia (IRR, 3.25; 95% CI, 2.36 to 4.47; P < 0.001), with no differences in the distribution of pneumococcal serotypes. Complications during admission and sequel at discharge were greater during epidemic periods (adjusted odds ratio [aOR], 2.00; 95% CI, 1.06 to 3.77; P = 0.03) than at nonepidemic periods (aOR, 3.38; 95% CI, 1.37 to 8.29; P = 0.01). The prevented fraction for the population (PFp) of IPD in children aged 7 to 59 months was 48% to 49.4%. The PFp was higher in influenza epidemic than nonepidemic periods and increased when ≥2 doses of PCV13 or ≥1 after 24 months were administered. Influenza virus circulation increases the incidence of IPD in persons aged <18 years. In influenza epidemic periods, IPD cases were more severe. Increased PCV13 coverage might increase the fraction of IPD prevented in epidemic and nonepidemic periods.
Collapse
|
19
|
Díaz-Conradi A, Hernández S, García-García JJ, Muñoz-Almagro C, Moraga-Llop F, Ciruela P, Izquierdo C, Campins M, de Sevilla MF, González-Peris S, Uriona S, Martínez-Osorio J, Solé-Ribalta A, Codina G, Esteva C, Planes AM, Soldevila N, Salleras L, Domínguez A. Complicated pneumococcal pneumonia with pleural effusion or empyema in the 13-valent pneumococcal conjugate vaccine era. Pediatr Pulmonol 2019; 54:517-524. [PMID: 30784235 DOI: 10.1002/ppul.24279] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 01/09/2019] [Indexed: 11/06/2022]
Abstract
AIM The aim was to analyze the epidemiological, microbiological and clinical characteristics of patients with complicated pneumococcal pneumonia with pleural effusion (PE) or empyema. METHOD Prospective study in three Catalan hospitals in persons aged <18 years diagnosed with complicated pneumonia with PE or empyema with isolation of Streptococcus pneumoniae in blood or pleural fluid by culture or real-time PCR between January 2012 and June 2016. Patients were divided into <2 years and 2-17 years age groups. Epidemiological, microbiological, and clinical data of patients were compared annually in both groups. PCV13 vaccination coverage increased from 48.2% in 2012 to 74.5% in 2015. RESULTS We included 143 patients. The incidence of pneumococcal pneumonia was 6.83 cases × 10-5 persons/year in cases with PE or empyema and 2.09 cases × 10-5 person-years in cases without (rate ratio [RR]: 3.27; 2.25-4.86; P < 0.001). Empyema was more frequent than PE (79.7% vs 20.3%, P < 0.005). Of 143 cases studied, 93 (65.0%, P < 0.001) were diagnosed by real-time-PCR, 43 (30.1%) by culture and RT-PCR and 7 (4.9%) by culture only. PCV13 serotypes were more frequent in complicated than in uncomplicated pneumonia (116/142, 81.7% vs 27/45, 60.0%; P = 0.003), especially serotype 1 (41/142, 28.9% vs 6/45, 13.3%, P : 0.036). From 2012 to 2015 there was a significant reduction in serotype 1 (16/43, 37.2% vs 3/27, 11.1%, P = 0.026), and a trend to an increase in non-PCV13 serotypes (6/43, 14% vs 9/27, 33.3%, P = 0.054). CONCLUSIONS A directly proportional relationship was observed between the reduction in pneumonia complicated with PE or empyema and a significant reduction in PCV13 serotypes, especially serotype 1, coinciding with increased PCV13 coverage.
Collapse
Affiliation(s)
| | - Sergi Hernández
- Agència de Salut Publica de Catalunya, Generalitat de Catalunya, Barcelona, Spain
| | - Juan José García-García
- CIBER de Epidemiologia y Salud Pública (CIBERESP), Madrid, Spain.,Malalties Prevenibles amb vacunes, Institut de Recerca Sant Joan de Déu, Esplugues, Barcelona, Spain.,Hospital Sant Joan de Déu Barcelona, Universitat de Barcelona, Barcelona, Spain
| | - Carmen Muñoz-Almagro
- CIBER de Epidemiologia y Salud Pública (CIBERESP), Madrid, Spain.,Malalties Prevenibles amb vacunes, Institut de Recerca Sant Joan de Déu, Esplugues, Barcelona, Spain.,Hospital Sant Joan de Déu Barcelona, Universitat de Barcelona, Barcelona, Spain.,Departament de Medicina, Universitat Internacional de Catalunya, Barcelona, Spain
| | | | - Pilar Ciruela
- Agència de Salut Publica de Catalunya, Generalitat de Catalunya, Barcelona, Spain.,CIBER de Epidemiologia y Salud Pública (CIBERESP), Madrid, Spain
| | - Conchita Izquierdo
- Agència de Salut Publica de Catalunya, Generalitat de Catalunya, Barcelona, Spain
| | - Magda Campins
- Hospital Universitari Vall d'Hebron, Barcelona, Spain.,Grup de Recerca en Epidemiologia i Salut Pública, Vall d'Hebron Institut de Recerca, Barcelona, Spain
| | - Mariona F de Sevilla
- CIBER de Epidemiologia y Salud Pública (CIBERESP), Madrid, Spain.,Malalties Prevenibles amb vacunes, Institut de Recerca Sant Joan de Déu, Esplugues, Barcelona, Spain.,Hospital Sant Joan de Déu Barcelona, Universitat de Barcelona, Barcelona, Spain
| | | | - Sonia Uriona
- Hospital Universitari Vall d'Hebron, Barcelona, Spain.,Grup de Recerca en Epidemiologia i Salut Pública, Vall d'Hebron Institut de Recerca, Barcelona, Spain
| | | | - Anna Solé-Ribalta
- Hospital Sant Joan de Déu Barcelona, Universitat de Barcelona, Barcelona, Spain
| | - Gemma Codina
- Hospital Universitari Vall d'Hebron, Barcelona, Spain
| | - Cristina Esteva
- CIBER de Epidemiologia y Salud Pública (CIBERESP), Madrid, Spain.,Malalties Prevenibles amb vacunes, Institut de Recerca Sant Joan de Déu, Esplugues, Barcelona, Spain.,Hospital Sant Joan de Déu Barcelona, Universitat de Barcelona, Barcelona, Spain
| | | | - Nuria Soldevila
- CIBER de Epidemiologia y Salud Pública (CIBERESP), Madrid, Spain.,Departament de Medicina, Universitat de Barcelona, Barcelona, Spain
| | - Luis Salleras
- CIBER de Epidemiologia y Salud Pública (CIBERESP), Madrid, Spain.,Departament de Medicina, Universitat de Barcelona, Barcelona, Spain
| | - Angela Domínguez
- CIBER de Epidemiologia y Salud Pública (CIBERESP), Madrid, Spain.,Departament de Medicina, Universitat de Barcelona, Barcelona, Spain
| |
Collapse
|
20
|
Midouni B, Mehiri E, Ghariani A, Draoui H, Essalah L, Bouzouita I, Raoult D, Slim-Saidi L, Fournier P. Genetic diversity of Streptococcus pneumoniae in Tunisia. Int J Antimicrob Agents 2019; 53:63-69. [DOI: 10.1016/j.ijantimicag.2018.09.023] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Revised: 09/26/2018] [Accepted: 09/29/2018] [Indexed: 12/16/2022]
|
21
|
Schembri J, Gillis HD, Lang ALS, Warhuus M, Martin I, Demczuk W, ElSherif M, McNeil SA, LeBlanc JJ. Multi-target plasmid controls for conventional and real-time PCR-based serotyping of Streptococcus pneumoniae. Plasmid 2018; 98:45-51. [PMID: 30217467 DOI: 10.1016/j.plasmid.2018.09.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 09/10/2018] [Accepted: 09/10/2018] [Indexed: 11/28/2022]
Abstract
BACKGROUND Serotyping of Streptococcus pneumoniae is an integral part of disease surveillance, with over 92 serotypes characterized to date using traditional serotyping. To identify the most predominant disease causing serotypes, molecular serotyping methods are now increasingly being used, like conventional and real-time multiplex PCR (cmPCR and rmPCR, respectively). Given that cmPCR consists of eight reactions spanning 41 targets, and rmPCR consists of seven triplex reactions, standardizing positive controls for these assays is challenging. As such, a 43-target plasmid for cmPCR (pSpn-CM1) and a 23 target plasmid for rmPCR (pSpn-RM1) were designed and validated. METHODS Plasmid pSpn-RM1 was designed and synthesized as chimeric DNA sequences to include all PCR target primer binding sites sequences for cmPCR. Plasmid pSpn-RM1 consisted of all primer and probe sequences required for rmPCR. Additional targets (lytA and cpsA) were included in both plasmids for quantification, following their propagation and purification from Escherichia coli. RESULTS When tested using the cmPCR reactions, all targets could be reproducibly be detected using pSpn-CM1 as template, with good amplicon visibility at a concentration of 1.4 (± 0.3) × 105 copies/ml was used. For the rmPCR reactions, all targets were reproducibly amplified with a concentration of 1.1 (± 0.2) × 104 copies/ml of pSpn-RM1, and the PCR efficiency for each target was equivalent to DNA extracted from representative S. pneumoniae serotypes. CONCLUSIONS These quantifiable multi-target plasmids simplify the preparation of controls for PCR-based serotyping of S. pneumoniae, and methods herein could be extended to other highly multiplexed PCR assays.
Collapse
Affiliation(s)
- Jack Schembri
- Canadian Center for Vaccinology (CCfV) Dalhousie University, IWK Health Centre, and Nova Scotia Health Authority (NSHA), Halifax, Nova Scotia, Canada
| | - Hayley D Gillis
- Canadian Center for Vaccinology (CCfV) Dalhousie University, IWK Health Centre, and Nova Scotia Health Authority (NSHA), Halifax, Nova Scotia, Canada
| | - Amanda L S Lang
- Canadian Center for Vaccinology (CCfV) Dalhousie University, IWK Health Centre, and Nova Scotia Health Authority (NSHA), Halifax, Nova Scotia, Canada
| | - Michelle Warhuus
- Canadian Center for Vaccinology (CCfV) Dalhousie University, IWK Health Centre, and Nova Scotia Health Authority (NSHA), Halifax, Nova Scotia, Canada
| | - Irene Martin
- Streptococci and STI Unit, National Microbiology Laboratory (NML), Public Health Agency of Canada (PHAC), Winnipeg, Manitoba, Canada
| | - Walter Demczuk
- Streptococci and STI Unit, National Microbiology Laboratory (NML), Public Health Agency of Canada (PHAC), Winnipeg, Manitoba, Canada
| | - May ElSherif
- Canadian Center for Vaccinology (CCfV) Dalhousie University, IWK Health Centre, and Nova Scotia Health Authority (NSHA), Halifax, Nova Scotia, Canada
| | - Shelly A McNeil
- Canadian Center for Vaccinology (CCfV) Dalhousie University, IWK Health Centre, and Nova Scotia Health Authority (NSHA), Halifax, Nova Scotia, Canada
| | - Jason J LeBlanc
- Canadian Center for Vaccinology (CCfV) Dalhousie University, IWK Health Centre, and Nova Scotia Health Authority (NSHA), Halifax, Nova Scotia, Canada.
| |
Collapse
|
22
|
Epping L, van Tonder AJ, Gladstone RA, The Global Pneumococcal Sequencing Consortium, Bentley SD, Page AJ, Keane JA. SeroBA: rapid high-throughput serotyping of Streptococcus pneumoniae from whole genome sequence data. Microb Genom 2018; 4. [PMID: 29870330 PMCID: PMC6113868 DOI: 10.1099/mgen.0.000186] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Streptococcus pneumoniae is responsible for 240 000–460 000 deaths in children under 5 years of age each year. Accurate identification of pneumococcal serotypes is important for tracking the distribution and evolution of serotypes following the introduction of effective vaccines. Recent efforts have been made to infer serotypes directly from genomic data but current software approaches are limited and do not scale well. Here, we introduce a novel method, SeroBA, which uses a k-mer approach. We compare SeroBA against real and simulated data and present results on the concordance and computational performance against a validation dataset, the robustness and scalability when analysing a large dataset, and the impact of varying the depth of coverage on sequence-based serotyping. SeroBA can predict serotypes, by identifying the cps locus, directly from raw whole genome sequencing read data with 98 % concordance using a k-mer-based method, can process 10 000 samples in just over 1 day using a standard server and can call serotypes at a coverage as low as 15–21×. SeroBA is implemented in Python3 and is freely available under an open source GPLv3 licence from: https://github.com/sanger-pathogens/seroba
Collapse
Affiliation(s)
- Lennard Epping
- 2Microbial Genomics, Robert Koch Institute, Berlin, Germany.,1Pathogen Informatics, Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Andries J van Tonder
- 3Infection Genomics, Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Rebecca A Gladstone
- 3Infection Genomics, Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | | | - Stephen D Bentley
- 3Infection Genomics, Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Andrew J Page
- 1Pathogen Informatics, Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK.,4Quadram Institute, Norwich Research Park, Norwich, UK
| | - Jacqueline A Keane
- 1Pathogen Informatics, Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| |
Collapse
|
23
|
Ganaie F, Nagaraj G, Govindan V, Basha R, Hussain M, Ashraf N, Ahmed S, Ravi Kumar K. Impact of Hajj on the S. pneumoniae carriage among Indian pilgrims during 2016- a longitudinal molecular surveillance study. Travel Med Infect Dis 2018; 23:64-71. [DOI: 10.1016/j.tmaid.2018.04.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Revised: 03/21/2018] [Accepted: 04/02/2018] [Indexed: 12/27/2022]
|
24
|
Brotons P, Bassat Q, Lanaspa M, Henares D, Perez-Arguello A, Madrid L, Balcells R, Acacio S, Andres-Franch M, Marcos MA, Valero-Rello A, Muñoz-Almagro C. Nasopharyngeal bacterial load as a marker for rapid and easy diagnosis of invasive pneumococcal disease in children from Mozambique. PLoS One 2017; 12:e0184762. [PMID: 28910402 PMCID: PMC5599037 DOI: 10.1371/journal.pone.0184762] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Accepted: 08/30/2017] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Current diagnostic methods for detection of Streptococcus pneumoniae in children with suspected invasive pneumococcal disease have limitations of accuracy, timeliness, and patient convenience. This study aimed to determine the performance of pneumococcal load quantified with a real-time polymerase-chain reaction in nasopharyngeal samples to diagnose invasive pneumococcal disease in children. METHODS Matched case-control study of patients <5 years of age with invasive pneumococcal disease admitted to the Manhiça District Hospital (Mozambique) and asymptomatic controls recruited in different periods between 2006 and 2014. Cases were confirmed by a positive bacterial culture for S. pneumoniae in blood or cerebrospinal fluid. Nasopharyngeal aspirates were collected from cases and controls and pneumococcal density was quantified by lytA real-time polymerase-chain reaction. RESULTS Thirty cases (median age 12.8 months) and sixty controls (median age 11.7 months) were enrolled and 70% of them were male. Nasopharyngeal pneumococcal carriage was high in both groups: 28/30 (93.3%) for cases vs. 53/60 (88.3%) for controls (p = 0.71). Mean nasopharyngeal pneumococcal load was identified as a marker for invasive pneumococcal disease (7.0 log10 copies/mL in cases vs. 5.8 log10 copies/mL in controls, p<0.001) and showed good discriminatory power (AUC-ROC: 82.1%, 95% CI 72.5%-91.8%). A colonization density of 6.5 log10 copies/mL was determined as the optimal cut-off value to distinguish cases from controls (sensitivity 75.0%, specificity 73.6%). CONCLUSION Use of non-invasive nasopharyngeal aspirates coupled with rapid and accurate quantification of pneumococcal load by real-time polymerase chain reaction has the potential to become a useful surrogate marker for early diagnosis of invasive pneumococcal disease in children.
Collapse
Affiliation(s)
- Pedro Brotons
- Molecular Microbiology Department, Institut de Recerca Sant Joan de Déu, University Hospital Sant Joan de Déu, Barcelona, Spain
- CIBER de Epidemiología y Salud Pública CIBERESP, Instituto de Salud Carlos III, Madrid, Spain
| | - Quique Bassat
- ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic - Universitat de Barcelona, Barcelona, Spain
- Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique
- ICREA, Pg. Lluís Companys 23, Barcelona, Spain
- Pediatric Infectious Diseases Unit, Pediatrics Department, Hospital Sant Joan de Deu (University of Barcelona), Barcelona, Spain
- Universidad Europea de Madrid, Madrid, Spain
| | - Miguel Lanaspa
- ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic - Universitat de Barcelona, Barcelona, Spain
- ICREA, Pg. Lluís Companys 23, Barcelona, Spain
| | - Desiree Henares
- Molecular Microbiology Department, Institut de Recerca Sant Joan de Déu, University Hospital Sant Joan de Déu, Barcelona, Spain
| | - Amaresh Perez-Arguello
- Molecular Microbiology Department, Institut de Recerca Sant Joan de Déu, University Hospital Sant Joan de Déu, Barcelona, Spain
| | - Lola Madrid
- ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic - Universitat de Barcelona, Barcelona, Spain
- ICREA, Pg. Lluís Companys 23, Barcelona, Spain
| | | | | | - Maria Andres-Franch
- Molecular Microbiology Department, Institut de Recerca Sant Joan de Déu, University Hospital Sant Joan de Déu, Barcelona, Spain
- CIBER de Epidemiología y Salud Pública CIBERESP, Instituto de Salud Carlos III, Madrid, Spain
| | - Maria Angeles Marcos
- ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic - Universitat de Barcelona, Barcelona, Spain
| | - Ana Valero-Rello
- Molecular Microbiology Department, Institut de Recerca Sant Joan de Déu, University Hospital Sant Joan de Déu, Barcelona, Spain
- CIBER de Epidemiología y Salud Pública CIBERESP, Instituto de Salud Carlos III, Madrid, Spain
| | - Carmen Muñoz-Almagro
- Molecular Microbiology Department, Institut de Recerca Sant Joan de Déu, University Hospital Sant Joan de Déu, Barcelona, Spain
- CIBER de Epidemiología y Salud Pública CIBERESP, Instituto de Salud Carlos III, Madrid, Spain
- School of Medicine, Universitat Internacional de Catalunya, Barcelona, Spain
- * E-mail:
| |
Collapse
|
25
|
Marimón JM, Morales M, Gamen S, Manrique A, Ercibengoa M, Cilla G. A reverse-hybridization test for the identification of 76 pneumococcal serotypes, 42 individually and 34 in pairs. J Microbiol Methods 2017; 143:13-16. [PMID: 28818600 DOI: 10.1016/j.mimet.2017.08.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Revised: 08/01/2017] [Accepted: 08/12/2017] [Indexed: 10/19/2022]
Abstract
The S. PneumoStrip test is a recently developed reverse hybridization strip-based commercial assay that allows for the identification of 76 pneumococcal serotypes, 42 individually and 34 in pairs, according to their specific gene sequences. The test was validated with reference strains of 92 different pneumococcal serotypes and with a selection of 75 clinical isolates representing 55 serotypes, showing 100% sensitivity and specificity. The test was also applied to 64 pneumococcal invasive isolates (23 different serotypes) consecutively collected between June 2016 and March 2017, with 60 (93.8%) being serotyped. Four isolates belonging to serotypes 13, 29, and 35B (2 isolates), which are not included in the test, did not produce a hybridization signal with serotype specific probes. The identification of most serotypes causing invasive pneumococcal disease together with the simplicity of performance and results interpretation, and the use of routine laboratory equipment make this test very suitable for most clinical and research laboratories.
Collapse
Affiliation(s)
- José M Marimón
- Microbiology Department, Hospital Universitario Donostia-Instituto de Investigación Sanitaria Biodonostia, San Sebastián, Spain; Biomedical Research Center Network for Respiratory Diseases (CIBERES), Madrid, Spain.
| | - María Morales
- Biomedical Research Center Network for Respiratory Diseases (CIBERES), Madrid, Spain
| | | | | | - María Ercibengoa
- Biomedical Research Center Network for Respiratory Diseases (CIBERES), Madrid, Spain
| | - Gustavo Cilla
- Microbiology Department, Hospital Universitario Donostia-Instituto de Investigación Sanitaria Biodonostia, San Sebastián, Spain; Biomedical Research Center Network for Respiratory Diseases (CIBERES), Madrid, Spain
| |
Collapse
|
26
|
Effectiveness of the 13-valent pneumococcal conjugate vaccine in preventing invasive pneumococcal disease in children aged 7-59 months. A matched case-control study. PLoS One 2017; 12:e0183191. [PMID: 28806737 PMCID: PMC5555701 DOI: 10.1371/journal.pone.0183191] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 07/31/2017] [Indexed: 11/19/2022] Open
Abstract
Background The 13-valent pneumococcal conjugate vaccine (PCV13) was licensed based on the results of immunogenicity studies and correlates of protection derived from randomized clinical trials of the 7-valent conjugate pneumococcal vaccine. We assessed the vaccination effectiveness (VE) of the PCV13 in preventing invasive pneumococcal disease (IPD) in children aged 7–59 months in a population with suboptimal vaccination coverage of 55%. Methods The study was carried out in children with IPD admitted to three hospitals in Barcelona (Spain) and controls matched by hospital, age, sex, date of hospitalization and underlying disease. Information on the vaccination status was obtained from written medical records. Conditional logistic regression was made to estimate the adjusted VE and 95% confidence intervals (CI). Results 169 cases and 645 controls were included. The overall VE of ≥1 doses of PCV13 in preventing IPD due to vaccine serotypes was 75.8% (95% CI, 54.1–87.2) and 90% (95% CI, 63.9–97.2) when ≥2 doses before 12 months, two doses on or after 12 months or one dose on or after 24 months, were administered. The VE of ≥1 doses was 89% (95% CI, 42.7–97.9) against serotype 1 and 86.0% (95% CI, 51.2–99.7) against serotype 19A. Serotype 3 showed a non-statistically significant effectiveness (25.9%; 95% CI, -65.3 to 66.8). Conclusions The effectiveness of ≥1 doses of PCV13 in preventing IPD caused by all PCV13 serotypes in children aged 7–59 months was good and, except for serotype 3, the effectiveness of ≥1 doses against the most frequent PCV13 serotypes causing IPD was high when considered individually.
Collapse
|
27
|
Bautista-Rodriguez C, Launes C, Jordan I, Andres M, Arias MT, Lozano F, Garcia-Garcia JJ, Muñoz-Almagro C. Mannose-binding lectin-deficient genotypes as a risk factor of pneumococcal meningitis in infants. PLoS One 2017; 12:e0178377. [PMID: 28562692 PMCID: PMC5451051 DOI: 10.1371/journal.pone.0178377] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2017] [Accepted: 05/11/2017] [Indexed: 12/24/2022] Open
Abstract
Objectives The objective of this study was to evaluate to evaluate the role of mannose-binding-lectin deficient genotypes in pneumococcal meningitis (PM) in children. Methods We performed a 16-year retrospective study (January 2001 to March 2016) including patients ≤ 18 years with PM. Variables including attack rate of pneumococcal serotype (high or low invasive capacity) and MBL2 genotypes associated with low serum MBL levels were recorded. Results Forty-eight patients were included in the study. Median age was 18.5 months and 17/48 episodes (35.4%) occurred in children ≤ 12 months old. Serotypes with high-invasive disease potential were identified in 15/48 episodes (31.2%). MBL2 deficient genotypes accounted for 18.8% (9/48). Children ≤ 12 months old had a 7-fold risk (95% CI: 1.6–29.9; p < 0.01) of having a MBL2 deficient genotype in comparison to those > 12 months old. A sub-analysis of patients by age group revealed significant proportions of carriers of MBL2 deficient genotypes among those ≤ 12 months old with PM caused by opportunistic serotypes (54.5%), admitted to the PICU (Pediatric Intensive Care Unit) (46.7%) and of White ethnicity (35.7%). These proportions were significantly higher than in older children (all p<0.05). Conclusions Our results suggest that differences in MBL2 genotype in children ≤12 months old affects susceptibility to PM, and it may have an important role in the episodes caused by non-high invasive disease potential serotypes.
Collapse
Affiliation(s)
| | - Cristian Launes
- Pediatrics Department, University Hospital Sant Joan de Deu, Barcelona, Spain
- CIBER de Epidemiologia y Salud Publica (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain
| | - Iolanda Jordan
- CIBER de Epidemiologia y Salud Publica (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain
- Pediatric Intensive Care Department, University Hospital Sant Joan de Deu, Barcelona, Spain
- School of Medicine, University of Barcelona, Barcelona, Spain
| | - Maria Andres
- CIBER de Epidemiologia y Salud Publica (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain
- Molecular Microbiology Department, University Hospital Sant Joan de Deu, Barcelona, Spain
| | - Maria Teresa Arias
- Department of Immunology, Centre de Diagnostic Biomedic, Hospital Clinic of Barcelona, Barcelona, Spain
| | - Francisco Lozano
- School of Medicine, University of Barcelona, Barcelona, Spain
- Department of Immunology, Centre de Diagnostic Biomedic, Hospital Clinic of Barcelona, Barcelona, Spain
- Immunoreceptors of the Innate and Adaptive Systems, Institut Investigacions Biomediques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Juan Jose Garcia-Garcia
- Pediatrics Department, University Hospital Sant Joan de Deu, Barcelona, Spain
- CIBER de Epidemiologia y Salud Publica (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain
- School of Medicine, University of Barcelona, Barcelona, Spain
| | - Carmen Muñoz-Almagro
- CIBER de Epidemiologia y Salud Publica (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain
- Molecular Microbiology Department, University Hospital Sant Joan de Deu, Barcelona, Spain
- School of Medicine, Universitat Internacional de Catalunya, Barcelona, Spain
- * E-mail:
| |
Collapse
|
28
|
Lian DS, Zhao SJ. Capillary electrophoresis based on nucleic acid detection for diagnosing human infectious disease. Clin Chem Lab Med 2017; 54:707-38. [PMID: 26352354 DOI: 10.1515/cclm-2015-0096] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Accepted: 06/17/2015] [Indexed: 01/22/2023]
Abstract
Rapid transmission, high morbidity, and mortality are the features of human infectious diseases caused by microorganisms, such as bacteria, fungi, and viruses. These diseases may lead within a short period of time to great personal and property losses, especially in regions where sanitation is poor. Thus, rapid diagnoses are vital for the prevention and therapeutic intervention of human infectious diseases. Several conventional methods are often used to diagnose infectious diseases, e.g. methods based on cultures or morphology, or biochemical tests based on metabonomics. Although traditional methods are considered gold standards and are used most frequently, they are laborious, time consuming, and tedious and cannot meet the demand for rapid diagnoses. Disease diagnosis using capillary electrophoresis methods has the advantages of high efficiency, high throughput, and high speed, and coupled with the different nucleic acid detection strategies overcomes the drawbacks of traditional identification methods, precluding many types of false positive and negative results. Therefore, this review focuses on the application of capillary electrophoresis based on nucleic detection to the diagnosis of human infectious diseases, and offers an introduction to the limitations, advantages, and future developments of this approach.
Collapse
|
29
|
Single-Step Multiplex PCR Assay for Determining 92 Pneumococcal Serotypes. J Clin Microbiol 2016; 54:2197-200. [PMID: 27280423 DOI: 10.1128/jcm.01156-16] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Accepted: 06/03/2016] [Indexed: 12/31/2022] Open
Abstract
For pneumococcal disease surveillance, simple and cost-effective methods capable of determining all serotypes are needed. Combining a single-tube multiplex PCR with fluorescently labeled primers followed by amplicon analysis using automated fluorescent capillary electrophoresis, each serotype of 92 reference isolates and 297 recently collected clinical isolates was successfully determined.
Collapse
|
30
|
PCR-Based Serotyping of Streptococcus pneumoniae from Culture-Negative Specimens: Novel Primers for Detection of Serotypes within Serogroup 18. J Clin Microbiol 2016; 54:2178-81. [PMID: 27252464 PMCID: PMC4963509 DOI: 10.1128/jcm.00419-16] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2016] [Accepted: 05/24/2016] [Indexed: 11/20/2022] Open
Abstract
Six multiplex-compatible PCR primers were designed to distinguish Streptococcus pneumoniae serotypes within serogroup 18 from culturable/nonculturable pneumococcal specimens, with no cross-reactivity with other serotypes and respiratory organisms. These primers will aid in the generation of better data on vaccine/nonvaccine serotypes in invasive and carriage pneumococcal surveillance and contribute to future vaccine formulation and impact studies.
Collapse
|
31
|
Jin P, Wu L, Oftadeh S, Kudinha T, Kong F, Zeng Q. Using a practical molecular capsular serotype prediction strategy to investigate Streptococcus pneumoniae serotype distribution and antimicrobial resistance in Chinese local hospitalized children. BMC Pediatr 2016; 16:53. [PMID: 27118458 PMCID: PMC4847217 DOI: 10.1186/s12887-016-0589-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/20/2015] [Accepted: 04/16/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND China is one of ten countries with the highest prevalence rate of pneumococcal infections. However, there is limited serotype surveillance data for Streptococcus pneumoniae, especially from the community or rural regions, partly due to limited serotyping capacity because Quellung serotyping is only available in few centers in China. The aim of this study was to develop a simple, practical and economic pneumococcal serotype prediction strategy suitable for future serotype surveillance in China. METHODS In this study, 193 S. pneumoniae isolates were collected from hospitalized children, 96.9 % of whom were < 5 years old. The cpsB sequetyping, complemented by selective and modified USA CDC sequential multiplex-PCR, was performed on all the isolates, and serotypes 6A-6D specific PCRs were done on all serogroup 6 isolates. Based on systematic analysis of available GenBank cpsB sequences, we established a more comprehensive cpsB sequence database than originally published for cpsB sequetyping. Antibiotic susceptibility of all isolates was determined using the disk diffusion or E-test assays. RESULTS We built up a comprehensive S. pneumoniae serotype cpsB sequetyping database for all the 95 described serotypes first, and then developed a simple strategy for serotype prediction based on the improved cpsB sequetyping and selective multiplex-PCR. Using the developed serotype prediction strategy, 191 of 193 isolates were successfully "serotyped", and only two isolates were "non-serotypeable". Sixteen serotypes were identified among the 191 "serotypeable" isolates. The serotype distribution of the isolates from high to low was: 19 F (34.7 %), 23 F (17.1 %), 19A (11.9 %), 14 (7.3 %), 15B/15C (6.7 %), 6B (6.7 %), 6A (6.2 %), 9 V/9A (1.6 %); serotypes 6C, 3, 15 F/15A, 23A and 20 (each 1.1 %); serotypes 10B, 28 F/28A and 34 (each 0.5 %). The prevalence of parenteral penicillin resistance was 1.0 % in the non-meningitis isolates and 88.6 % in meningitis isolates. The total rate of multidrug resistance was 86.8 %. CONCLUSIONS The integrated cpsB sequetyping supplemented with selective mPCR and serotypes 6A-6D specific PCRs "cocktail" strategy is practical, simple and cost-effective for use in pneumococcal infection serotype surveillance in China. For hospitalized children with non-meningitis penicillin-susceptible pneumococcal infections, clinicians still can use narrow-spectrum and cheaper penicillin, using the parenteral route, rather than using broader-spectrum and more expensive antimicrobials.
Collapse
Affiliation(s)
- Ping Jin
- Pediatric Center, Zhujiang Hospital, Southern Medical University, Guangzhou, 510282, P. R. China.,Paediatric Intensive Care Unit, Bao'an Maternity & Child Health Hospital affiliated with Jinan University, Shenzhen, P. R. China
| | - Lijuan Wu
- Department of Clinical Laboratory, Bao'an Maternity & Child Health Hospital affiliated with Jinan University, Shenzhen, P. R. China
| | - Shahin Oftadeh
- Centre for Infectious Diseases and Microbiology Laboratory Services, ICPMR - Pathology West, University of Sydney, Westmead Hospital, Darcy Road, Westmead, NSW, Australia
| | - Timothy Kudinha
- Centre for Infectious Diseases and Microbiology Laboratory Services, ICPMR - Pathology West, University of Sydney, Westmead Hospital, Darcy Road, Westmead, NSW, Australia.,Charles Sturt University, Leeds Parade, Orange, NSW, Australia
| | - Fanrong Kong
- Centre for Infectious Diseases and Microbiology Laboratory Services, ICPMR - Pathology West, University of Sydney, Westmead Hospital, Darcy Road, Westmead, NSW, Australia
| | - Qiyi Zeng
- Pediatric Center, Zhujiang Hospital, Southern Medical University, Guangzhou, 510282, P. R. China.
| |
Collapse
|
32
|
Molecular surveillance of nasopharyngeal carriage of Streptococcus pneumoniae in children vaccinated with conjugated polysaccharide pneumococcal vaccines. Sci Rep 2016; 6:23809. [PMID: 27046258 PMCID: PMC4820691 DOI: 10.1038/srep23809] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Accepted: 03/15/2016] [Indexed: 11/16/2022] Open
Abstract
Following the introduction of pneumococcal conjugate vaccines (PCVs) for infants, surveillance studies on Streptococcus pneumoniae carriage have proven valuable for monitoring vaccine effects. Here, we compared molecular versus conventional diagnostic methods in prospective cross-sectional surveillances in vaccinated infants in the Netherlands. Nasopharyngeal samples (n = 1169) from 11- and 24-month-old children, collected during autumn/winter 2010/2011 and 2012/2013, were tested by conventional culture for S. pneumoniae. DNA extracted from all culture-plate growth was tested by qPCR for pneumococcal-specific genes (lytA/piaB) and selected serotypes (including PCV13-serotypes). qPCR significantly increased the number of carriers detected compared to culture (69% vs. 57%, p < 0.0001). qPCR assays targeting vaccine-serotypes 4 and 5 proved non-specific (results excluded). For serotypes reliably targeted by qPCR, the number of serotype-carriage events detected by qPCR (n = 709) was 1.68× higher compared to culture (n = 422). There was a strong correlation (rho = 0.980; p < 0.0001) between the number of serotypes detected using qPCR and by culture. This study demonstrates the high potential of molecular methods in pneumococcal surveillances, particularly for enhanced serotype detection. We found no evidence of a hidden circulation of vaccine-targeted serotypes, despite vaccine-serotypes still significantly contributing to invasive pneumococcal disease in unvaccinated individuals, supporting the presence of a substantial S. pneumoniae reservoir outside vaccinated children.
Collapse
|
33
|
Messaoudi M, Milenkov M, Albrich WC, van der Linden MPG, Bénet T, Chou M, Sylla M, Barreto Costa P, Richard N, Klugman KP, Endtz HP, Paranhos-Baccalà G, Telles JN. The Relevance of a Novel Quantitative Assay to Detect up to 40 Major Streptococcus pneumoniae Serotypes Directly in Clinical Nasopharyngeal and Blood Specimens. PLoS One 2016; 11:e0151428. [PMID: 26986831 PMCID: PMC4795784 DOI: 10.1371/journal.pone.0151428] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Accepted: 02/28/2016] [Indexed: 12/25/2022] Open
Abstract
For epidemiological and surveillance purposes, it is relevant to monitor the distribution and dynamics of Streptococcus pneumoniae serotypes. Conventional serotyping methods do not provide rapid or quantitative information on serotype loads. Quantitative serotyping may enable prediction of the invasiveness of a specific serotype compared to other serotypes carried. Here, we describe a novel, rapid multiplex real-time PCR assay for identification and quantification of the 40 most prevalent pneumococcal serotypes and the assay impacts in pneumonia specimens from emerging and developing countries. Eleven multiplex PCR to detect 40 serotypes or serogroups were optimized. Quantification was enabled by reference to standard dilutions of known bacterial load. Performance of the assay was evaluated to specifically type and quantify S. pneumoniae in nasopharyngeal and blood samples from adult and pediatric patients hospitalized with pneumonia (n = 664) from five different countries. Serogroup 6 was widely represented in nasopharyngeal specimens from all five cohorts. The most frequent serotypes in the French, South African, and Brazilian cohorts were 1 and 7A/F, 3 and 19F, and 14, respectively. When both samples were available, the serotype in blood was always present as carriage with other serotypes in the nasopharynx. Moreover, the ability of a serotype to invade the bloodstream may be linked to its nasopharyngeal load. The mean nasopharyngeal concentration of the serotypes that moved to the blood was 3 log-fold higher than the ones only found in the nasopharynx. This novel, rapid, quantitative assay may potentially predict some of the S. pneumoniae serotypes invasiveness and assessment of pneumococcal serotype distribution.
Collapse
Affiliation(s)
- Melina Messaoudi
- Emerging Pathogens Laboratory, Fondation Mérieux - Centre International de Recherche en Infectiologie (CIRI), Lyon, France
| | - Milen Milenkov
- Emerging Pathogens Laboratory, Fondation Mérieux - Centre International de Recherche en Infectiologie (CIRI), Lyon, France
| | - Werner C. Albrich
- Department of Infectious Diseases and Hospital Epidemiology, Kantonsspital St. Gallen, St. Gallen, Switzerland
- Medical Research Council Respiratory and Meningeal Pathogens Research Unit, University of the Witwatersrand, Johannesburg, South Africa
| | - Mark P. G. van der Linden
- National Reference Center for Streptococci, Institute of Medical Microbiology, University Hospital RWTH Aachen, Aachen, Germany
| | - Thomas Bénet
- Service d'Hygiène, Epidémiologie et Prévention, Hôpital Edouard Herriot - Hospices Civils de Lyon, France
| | - Monidarin Chou
- Faculty of Pharmacy, University of Health Sciences, Phnom Penh, Cambodia
| | | | - Patricia Barreto Costa
- Laboratório de vírus respiratórios e do sarampo, Instituto Oswaldo Cruz/Fiocruz, Rio de Janeiro, Brazil
| | - Nathalie Richard
- Service de Réanimation Pédiatrique Médico-Chirurgicale, HFME, Groupement Hospitalier Est, Bron, France
| | - Keith P. Klugman
- Medical Research Council Respiratory and Meningeal Pathogens Research Unit, University of the Witwatersrand, Johannesburg, South Africa
- Hubert Department of Global Health and Division of Infectious Diseases, Emory University, Atlanta, Georgia, United States of America
| | - Hubert P. Endtz
- Emerging Pathogens Laboratory, Fondation Mérieux - Centre International de Recherche en Infectiologie (CIRI), Lyon, France
- Departement of Medical Microbiology & Infectious Diseases Erasmus MC, Rotterdam, The Netherlands
| | - Gláucia Paranhos-Baccalà
- Emerging Pathogens Laboratory, Fondation Mérieux - Centre International de Recherche en Infectiologie (CIRI), Lyon, France
| | - Jean-Noël Telles
- Emerging Pathogens Laboratory, Fondation Mérieux - Centre International de Recherche en Infectiologie (CIRI), Lyon, France
| |
Collapse
|
34
|
del Amo E, Esteva C, Hernandez-Bou S, Galles C, Navarro M, Sauca G, Diaz A, Gassiot P, Marti C, Larrosa N, Ciruela P, Jane M, Sá-Leão R, Muñoz-Almagro C. Serotypes and Clonal Diversity of Streptococcus pneumoniae Causing Invasive Disease in the Era of PCV13 in Catalonia, Spain. PLoS One 2016; 11:e0151125. [PMID: 26953887 PMCID: PMC4783110 DOI: 10.1371/journal.pone.0151125] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Accepted: 02/24/2016] [Indexed: 11/28/2022] Open
Abstract
The aim of this study was to study the serotypes and clonal diversity of pneumococci causing invasive pneumococcal disease in Catalonia, Spain, in the era of 13-valent pneumococcal conjugate vaccine (PCV13). In our region, this vaccine is only available in the private market and it is estimated a PCV13 vaccine coverage around 55% in children. A total of 1551 pneumococcal invasive isolates received between 2010 and 2013 in the Molecular Microbiology Department at Hospital Sant Joan de Déu, Barcelona, were included. Fifty-two serotypes and 249 clonal types-defined by MLST-were identified. The most common serotypes were serotype 1 (n = 182; 11.7%), 3 (n = 145; 9.3%), 19A (n = 137; 8.8%) and 7F (n = 122; 7.9%). Serotype 14 was the third most frequent serotype in children < 2 years (15 of 159 isolates). PCV7 serotypes maintained their proportion along the period of study, 16.6% in 2010 to 13.4% in 2013, whereas there was a significant proportional decrease in PCV13 serotypes, 65.3% in 2010 to 48.9% in 2013 (p<0.01). This decrease was mainly attributable to serotypes 19A and 7F. Serotype 12F achieved the third position in 2013 (n = 22, 6.4%). The most frequent clonal types found were ST306 (n = 154, 9.9%), ST191 (n = 111, 7.2%), ST989 (n = 85, 5.5%) and ST180 (n = 80, 5.2%). Despite their decrease, PCV13 serotypes continue to be a major cause of disease in Spain. These results emphasize the need for complete PCV13 vaccination.
Collapse
Affiliation(s)
- Eva del Amo
- Department of Molecular Microbiology, Hospital Sant Joan de Deu, Esplugues de Llobregat, Spain
| | - Cristina Esteva
- Department of Molecular Microbiology, Hospital Sant Joan de Deu, Esplugues de Llobregat, Spain
| | - Susanna Hernandez-Bou
- Department of Paediatrics, Hospital Sant Joan de Deu and University of Barcelona, Esplugues de Llobregat, Spain
| | - Carmen Galles
- Department of Microbiology, Hospital Sant Jaume, Calella, Spain
| | | | - Goretti Sauca
- Department of Microbiology, Hospital de Mataró, Mataró, Spain
| | - Alvaro Diaz
- Department of Microbiology, Hospital de Nens, Barcelona, Spain
| | - Paula Gassiot
- Department of Microbiology, Hospital de Figueres, Figueres, Spain
| | - Carmina Marti
- Department of Microbiology, Hospital General de Granollers, Granollers, Spain
| | - Nieves Larrosa
- Department of Microbiology, Hospital Vall d’Hebron, Barcelona, Spain
| | - Pilar Ciruela
- Public Health Agency, Government of Catalonia, Barcelona, Spain
| | - Mireia Jane
- Public Health Agency, Government of Catalonia, Barcelona, Spain
| | - Raquel Sá-Leão
- Laboratory of Molecular Microbiology of Human Pathogens, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Carmen Muñoz-Almagro
- Department of Molecular Microbiology, Hospital Sant Joan de Deu, Esplugues de Llobregat, Spain
| | | |
Collapse
|
35
|
Dube FS, van Mens SP, Robberts L, Wolter N, Nicol P, Mafofo J, Africa S, Zar HJ, Nicol MP. Comparison of a Real-Time Multiplex PCR and Sequetyping Assay for Pneumococcal Serotyping. PLoS One 2015; 10:e0137349. [PMID: 26335454 PMCID: PMC4559314 DOI: 10.1371/journal.pone.0137349] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Accepted: 08/14/2015] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Pneumococcal serotype identification is essential to monitor pneumococcal vaccine effectiveness and serotype replacement. Serotyping by conventional serological methods are costly, labour-intensive, and require significant technical expertise. We compared two different molecular methods to serotype pneumococci isolated from the nasopharynx of South African infants participating in a birth cohort study, the Drakenstein Child Health Study, in an area with high 13-valent pneumococcal conjugate vaccine (PCV13) coverage. METHODS A real-time multiplex PCR (rmPCR) assay detecting 21 different serotypes/-groups and a sequetyping assay, based on the sequence of the wzh gene within the pneumococcal capsular locus, were compared. Forty pneumococcal control isolates, with serotypes determined by the Quellung reaction, were tested. In addition, 135 pneumococcal isolates obtained from the nasopharynx of healthy children were tested by both serotyping assays and confirmed by Quellung testing. Discordant results were further investigated by whole genome sequencing of four isolates. RESULTS Of the 40 control isolates tested, 25 had a serotype covered by the rmPCR assay. These were all correctly serotyped/-grouped. Sequetyping PCR failed in 7/40 (18%) isolates. For the remaining isolates, sequetyping assigned the correct serotype/-group to 29/33 (88%) control isolates. Of the 132/135 (98%) nasopharyngeal pneumococcal isolates that could be typed, 69/132 (52%) and 112/132 (85%) were assigned the correct serotype/-group by rmPCR and sequetyping respectively. The serotypes of 63/132 (48%) isolates were not included in the rmPCR panel. All except three isolates (serotype 25A and 38) were theoretically amplified and differentiated into the correct serotype/-group with some strains giving ambigous results (serotype 13/20, 17F/33C, and 11A/D/1818F). Of the pneumococcal serotypes detected in this study, 69/91 (76%) were not included in the current PCV13. The most frequently identified serotypes were 11A, 13, 15B/15C, 16F and 10A. CONCLUSION The rmPCR assay performed well for the 21 serotypes/-groups included in the assay. However, in our study setting, a large proportion of serotypes were not detected by rmPCR. The sequetyping assay performed well, but did misassign specific serotypes. It may be useful for regions where vaccine serotypes are less common, however confirmatory testing is advisable.
Collapse
Affiliation(s)
- Felix S. Dube
- Division of Medical Microbiology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Suzan P. van Mens
- Division of Medical Microbiology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Department of Medical Microbiology and Immunology, St Antonius Hospital, Nieuwegein, the Netherlands
| | - Lourens Robberts
- Division of Medical Microbiology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Nicole Wolter
- Centre for Respiratory Diseases and Meningitis (CRDM), National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witswatersrand, Johannesburg, South Africa
| | - Paul Nicol
- The State Agricultural Biotechnology Centre, Murdoch University, Murdoch, Australia
| | - Joseph Mafofo
- Centre for Proteomic and Genomic Research (CPGR), Cape Town, South Africa
| | - Samantha Africa
- Division of Medical Microbiology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Heather J. Zar
- Department of Paediatrics and Child Health, Red Cross War Memorial Children’s Hospital, Cape Town, South Africa
- MRC Unit on Child and Adolesscent Health, University of Cape Town, Cape Town, South Africa
| | - Mark P. Nicol
- Division of Medical Microbiology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- National Health Laboratory Service, Groote Schuur Hospital, Cape Town, South Africa
| |
Collapse
|
36
|
Wu L, Yin X, Zheng L, Zou J, Jin P, Hu Y, Kudinha T, Kong F, Chen X, Wang Q. Practical Prediction of Ten Common Streptococcus pneumoniae Serotypes/Serogroups in One PCR Reaction by Multiplex Ligation-Dependent Probe Amplification and Melting Curve (MLPA-MC) Assay in Shenzhen, China. PLoS One 2015; 10:e0130664. [PMID: 26151828 PMCID: PMC4495002 DOI: 10.1371/journal.pone.0130664] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Accepted: 05/22/2015] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Streptococcus pneumoniae has more than 95 distinct serotypes described to date. However, only certain serotypes are more likely to cause pneumococcal diseases. Thus serotype surveillance is important for vaccine formula design as well as in post-vaccine serotype shift monitor. The goal of this study was to develop a practical screening assay for ten Shenzhen China common pneumococcal serotypes/serogroups in one molecular reaction. METHODS A molecular assay, based on multiplex ligation-dependent probe amplification (MLPA) and melting curve (MC) analysis, was developed in an integrated approach (MLPA-MC) for the detection of ten capsular serotypes/serogroups 4, 6 (6A/6B/6C/6D), 9V/9A, 14, 15F/15A, 15B/15C, 18 (18F/18A/18B/18C), 19F, 19A and 23F. We designed serotype/serogroup-specific MLPA probes and fluorescent detection probes to discriminate the different serotypes/serogroups in one molecular reaction. The three steps of MLPA-MC assay are continuous reactions in one well detected by LightCycler 480. A total of 210 S. pneumoniae isolates from our local Maternity and Child Health Hospital were randomly chosen to evaluate the assay against published multiplex PCR assays. RESULTS Our results showed that 198 (94.3%) of S. pneumoniae isolates were type-able by our assays and the results were in complete concordance with the published multiplex PCRs. Using the MLPA-MC assay, 96 S. pneumoniae isolates could be typed within 3 hours with limited hands-on time. This serotype/serogroup-screening assay can be easily modified or extended by modification of the serotype/serogroup-specific MLPA probes combinations according to the needs of different laboratories. CONCLUSIONS We recommend use of this assay as a starting point for screening serotype/serogroup frequencies. There is a need for this assay to be combined with other molecular typing assays, like published serotype specific PCRs, or even the Quellung reaction for serotype confirmation.
Collapse
Affiliation(s)
- Lijuan Wu
- Laboratory Medical Centre, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong Province, China
- Clinical Laboratory, Bao’an Maternity and Child Health Hospital, Shenzhen, Guangdong Province, China
| | - Xiaomao Yin
- Clinical Laboratory, The Fifth Affiliated Hospital of Southern Medical University, Guangzhou, Guangdong Province, China
| | - Lei Zheng
- Laboratory Medical Centre, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong Province, China
| | - Jianhua Zou
- Clinical Laboratory, Bao’an Maternity and Child Health Hospital, Shenzhen, Guangdong Province, China
| | - Ping Jin
- Clinical Laboratory, Bao’an Maternity and Child Health Hospital, Shenzhen, Guangdong Province, China
| | - Yanwei Hu
- Laboratory Medical Centre, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong Province, China
| | - Timothy Kudinha
- Charles Sturt University, Leeds Parade, Orange, New South Wales, Australia
| | - Fanrong Kong
- Centre for Infectious Diseases and Microbiology, Institute of Clinical Pathology and Medical Research–Pathology West, Westmead Hospital, New South Wales, Australia
| | - Xu Chen
- Clinical Laboratory, Bao’an Maternity and Child Health Hospital, Shenzhen, Guangdong Province, China
| | - Qian Wang
- Laboratory Medical Centre, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong Province, China
- * E-mail:
| |
Collapse
|
37
|
Jauneikaite E, Tocheva AS, Jefferies JMC, Gladstone RA, Faust SN, Christodoulides M, Hibberd ML, Clarke SC. Current methods for capsular typing of Streptococcus pneumoniae. J Microbiol Methods 2015; 113:41-9. [PMID: 25819558 DOI: 10.1016/j.mimet.2015.03.006] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Revised: 02/21/2015] [Accepted: 03/08/2015] [Indexed: 10/23/2022]
Abstract
Streptococcus pneumoniae is a major respiratory tract pathogen causing pneumococcal disease mainly in children aged less than five years and in the elderly. Ninety-eight different capsular types (serotypes) of pneumococci have been reported, but pneumococcal conjugate vaccines (PCV) include polysaccharide antigens against only 7, 10 or 13 serotypes. It is therefore important to track the emergence of serotypes due to the clonal expansion of non-vaccine serotypes. Increased numbers of carried and disease-causing pneumococci are now being analysed as part of the post-PCV implementation surveillance studies and hence rapid, accurate and cost-effective typing methods are important. Here we describe serotyping methods published prior to 10th November 2014 for pneumococcal capsule typing. Sixteen methods were identified; six were based on serological tests using immunological properties of the capsular epitopes, eight were semi-automated molecular tests, and one describes the identification of capsular type directly from whole genome data, which also allows for further intra and inter-genome analyses. There was no single method that could be recommended for all pneumococcal capsular typing applications. Although the Quellung reaction is still considered to be the gold-standard, laboratories should take into account the number of pneumococcal isolates and the type of samples to be used for testing, the time frame for the results and the resources available in order to select the most appropriate method. Most likely, a combination of phenotypic and genotypic methods would be optimal to monitor and evaluate the impact of pneumococcal conjugate vaccines and to provide information for future vaccine formulations.
Collapse
Affiliation(s)
- Elita Jauneikaite
- Faculty of Medicine and Institute for Life Sciences, University of Southampton, Southampton SO16 6YD, UK; Infectious Diseases, Genome Institute of Singapore, 138672, Singapore
| | - Anna S Tocheva
- Faculty of Medicine and Institute for Life Sciences, University of Southampton, Southampton SO16 6YD, UK
| | - Johanna M C Jefferies
- Faculty of Medicine and Institute for Life Sciences, University of Southampton, Southampton SO16 6YD, UK; NIHR Southampton Respiratory Biomedical Research Unit, University Hospital Southampton NHS Foundation Trust, Southampton SO16 6YD, UK
| | - Rebecca A Gladstone
- Faculty of Medicine and Institute for Life Sciences, University of Southampton, Southampton SO16 6YD, UK
| | - Saul N Faust
- Faculty of Medicine and Institute for Life Sciences, University of Southampton, Southampton SO16 6YD, UK; NIHR Southampton Respiratory Biomedical Research Unit, University Hospital Southampton NHS Foundation Trust, Southampton SO16 6YD, UK; NIHR Wellcome Trust Clinical Research Facility, University Hospital Southampton NHS Foundation Trust, Southampton SO16 6YD, UK
| | - Myron Christodoulides
- Faculty of Medicine and Institute for Life Sciences, University of Southampton, Southampton SO16 6YD, UK
| | - Martin L Hibberd
- Infectious Diseases, Genome Institute of Singapore, 138672, Singapore; London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
| | - Stuart C Clarke
- Faculty of Medicine and Institute for Life Sciences, University of Southampton, Southampton SO16 6YD, UK; NIHR Southampton Respiratory Biomedical Research Unit, University Hospital Southampton NHS Foundation Trust, Southampton SO16 6YD, UK.
| |
Collapse
|
38
|
del Amo E, Selva L, de Sevilla MF, Ciruela P, Brotons P, Triviño M, Hernandez S, Garcia-Garcia JJ, Dominguez Á, Muñoz-Almagro C. Estimation of the invasive disease potential of Streptococcus pneumoniae in children by the use of direct capsular typing in clinical specimens. Eur J Clin Microbiol Infect Dis 2014; 34:705-11. [PMID: 25413925 DOI: 10.1007/s10096-014-2280-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Accepted: 11/05/2014] [Indexed: 11/24/2022]
Abstract
Traditionally, invasiveness indexes have been based on culture methods. We aimed to establish a new classification of the invasive disease potential of pneumococcal serotypes causing invasive pediatric disease in the era of conjugate vaccines in Catalonia, Spain, by adding capsular typing of Streptococcus pneumoniae in direct sample. Two samples of children attended at the University Hospital Sant Joan de Déu (Barcelona, Spain) between 2007 and 2011 were compared: a first sample of 358 children with invasive pneumococcal disease and a second sample of 402 pneumococcal nasopharyngeal carriers selected from 714 healthy children admitted for minor surgical procedures. The most common invasive serotypes were 1 (20.1 %, n = 72), 19A (13.9 %, n = 50), 3 (12.3 %, n = 44), and 7FA (7.5 %, n = 27), whereas the most common serotypes in carriage were 19A (8.7 %, n = 38), 10FC33C (7.8 %, n = 34), 6C (6.9 %, n = 30), and 19FBC (5.5 %, n = 24). We detected a rate of cocolonization of 26.4 % (n = 89) among the 336 samples serotyped in the carriers population. Serotypes 1, 3, and 7FA were significantly associated with high invasiveness. Serotypes 6C, 10FC33C, 23A, 35B, 19FBC, 21, 11AD, 15BC, 23B, 34, and 6A were significantly associated with low invasiveness. Our results proved that the use of molecular techniques in direct sample for both the detection and the capsular identification of Streptococcus pneumoniae is very useful to obtain a more accurate calculation of the invasiveness of the different pneumococcal serotypes.
Collapse
Affiliation(s)
- E del Amo
- Department of Molecular Microbiology, University Hospital Sant Joan de Déu, P° Sant Joan de Déu, n° 2, 08950, Esplugues, Barcelona, Spain
| | | | | | | | | | | | | | | | | | | |
Collapse
|
39
|
MuÑoz-Almagro C, Bautista C, Arias M, Boixeda R, del Amo E, Borrás C, Armiger N, Garcia L, Sauca G, Selva L, de Sevilla M, Ciruela P, Yebenes J, Pallares R, Lozano F. High prevalence of genetically-determined mannose binding lectin deficiency in young children with invasive pneumococcal disease. Clin Microbiol Infect 2014; 20:O745-52. [DOI: 10.1111/1469-0691.12615] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Revised: 02/18/2014] [Accepted: 03/02/2014] [Indexed: 12/27/2022]
|
40
|
Satzke C, Turner P, Virolainen-Julkunen A, Adrian PV, Antonio M, Hare KM, Henao-Restrepo AM, Leach AJ, Klugman KP, Porter BD, Sá-Leão R, Scott JA, Nohynek H, O'Brien KL. Standard method for detecting upper respiratory carriage of Streptococcus pneumoniae: updated recommendations from the World Health Organization Pneumococcal Carriage Working Group. Vaccine 2014; 32:165-79. [PMID: 24331112 DOI: 10.1016/j.vaccine.2013.08.062] [Citation(s) in RCA: 328] [Impact Index Per Article: 32.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2013] [Revised: 07/25/2013] [Accepted: 08/23/2013] [Indexed: 11/29/2022]
Abstract
In 2003 the World Health Organization (WHO) convened a working group and published a set of standard methods for studies measuring nasopharyngeal carriage of Streptococcus pneumoniae (the pneumococcus). The working group recently reconvened under the auspices of the WHO and updated the consensus standard methods. These methods describe the collection, transport and storage of nasopharyngeal samples, as well as provide recommendations for the identification and serotyping of pneumococci using culture and non-culture based approaches. We outline the consensus position of the working group, the evidence supporting this position, areas worthy of future research, and the epidemiological role of carriage studies. Adherence to these methods will reduce variability in the conduct of pneumococcal carriage studies undertaken in the context of pneumococcal vaccine trials, implementation studies, and epidemiology studies more generally so variability in methodology does not confound the interpretation of study findings.
Collapse
Affiliation(s)
- Catherine Satzke
- Pneumococcal Research, Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, VIC, Australia; Centre for International Child Health, Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, VIC, Australia; Department of Microbiology and Immunology, The University of Melbourne, Parkville, VIC, Australia.
| | - Paul Turner
- Microbiology Department, Angkor Hospital for Children, Siem Reap, Kingdom of Cambodia; Centre for Tropical Medicine, University of Oxford, Oxford, United Kingdom
| | - Anni Virolainen-Julkunen
- Department of Infectious Disease Surveillance and Control, National Institute for Health and Welfare, Helsinki, Finland
| | - Peter V Adrian
- MRC/Wits Respiratory and Meningeal Pathogens Research Unit, University of the Witwatersrand, Johannesburg, South Africa
| | | | - Kim M Hare
- Child Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia
| | | | - Amanda J Leach
- Child Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia
| | - Keith P Klugman
- Rollins School of Public Health, Emory University, Atlanta, GA, USA; Respiratory and Meningeal Pathogens Research Unit, University of Witwatersrand, Johannesburg, South Africa
| | - Barbara D Porter
- Pneumococcal Research, Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, VIC, Australia
| | - Raquel Sá-Leão
- Laboratory of Molecular Microbiology of Human Pathogens, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
| | - J Anthony Scott
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya; London School of Hygiene & Tropical Medicine, London, UK
| | - Hanna Nohynek
- Vaccine Programme Unit, National Institute for Health and Welfare, Helsinki, Finland
| | - Katherine L O'Brien
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | | |
Collapse
|
41
|
del Amo E, Brotons P, Monsonis M, Trivióo M, Ióigo M, Selva L, Sa-Leão R, Muóoz-Almagro C. High invasiveness of pneumococcal serotypes included in the new generation of conjugate vaccines. Clin Microbiol Infect 2014; 20:684-9. [DOI: 10.1111/1469-0691.12422] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2013] [Revised: 09/19/2013] [Accepted: 10/01/2013] [Indexed: 11/28/2022]
|
42
|
Direct identification of Streptococcus pneumoniae capsular types in pleural fluids by using multiplex PCR combined with automated fluorescence-based capillary electrophoresis. J Clin Microbiol 2014; 52:2736-7. [PMID: 24740085 DOI: 10.1128/jcm.00906-14] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
|
43
|
Liyanapathirana V, Ang I, Tsang D, Fung K, Ng TK, Zhou H, Ip M. Application of a target enrichment-based next-generation sequencing protocol for identification and sequence-based prediction of pneumococcal serotypes. BMC Microbiol 2014; 14:60. [PMID: 24612771 PMCID: PMC3984734 DOI: 10.1186/1471-2180-14-60] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2013] [Accepted: 02/28/2014] [Indexed: 03/24/2023] Open
Abstract
BACKGROUND The use of whole-genome sequencing in microbiology at a diagnostic level, although feasible, is still limited by the expenses associated and by the complex bioinformatics pipelines in data analyses. We describe the use of target enrichment-based next-generation sequencing for pneumococcal identification and serotyping as applied to the polysaccharide 23 valent vaccine serotypes as an affordable alternative to whole genome sequencing. RESULTS Correct identification of Streptococcus pneumoniae and prediction of common vaccine serotypes: 12 to serotype level and the rest to serogroup levels were achieved for all serotypes with >500 reads mapped against serotypes sequences. A proportion-based criterion also enabled the identification of two serotypes present in the same sample, thus indicating the possibility of using this method in detecting co-colonizing serotypes. The results obtained were comparable to or an improvement on the currently existing molecular serotyping methods for S. pneumoniae in relation to the polysaccharide vaccine serotypes. CONCLUSION We propose that this method has the potential to become an affordable and adaptable alternative to whole-genome sequencing for pneumococcal identification and serotyping.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Margaret Ip
- Department of Microbiology, The Chinese University of Hong Kong, The Prince of Wales Hospital, Hong Kong, China.
| |
Collapse
|
44
|
Raymond F, Boucher N, Allary R, Robitaille L, Lefebvre B, Tremblay C, Corbeil J, Gervaix A. Serotyping of Streptococcus pneumoniae based on capsular genes polymorphisms. PLoS One 2013; 8:e76197. [PMID: 24086706 PMCID: PMC3782451 DOI: 10.1371/journal.pone.0076197] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Accepted: 08/20/2013] [Indexed: 11/18/2022] Open
Abstract
Streptococcus pneumoniae serotype epidemiology is essential since serotype replacement is a concern when introducing new polysaccharide-conjugate vaccines. A novel PCR-based automated microarray assay was developed to assist in the tracking of the serotypes. Autolysin, pneumolysin and eight genes located in the capsular operon were amplified using multiplex PCR. This step was followed by a tagged fluorescent primer extension step targeting serotype-specific polymorphisms. The tagged primers were then hybridized to a microarray. Results were exported to an expert system to identify capsular serotypes. The assay was validated on 166 cultured S. pneumoniae samples from 63 different serotypes as determined by the Quellung method. We show that typing only 12 polymorphisms located in the capsular operon allows the identification at the serotype level of 22 serotypes and the assignation of 24 other serotypes to a subgroup of serotypes. Overall, 126 samples (75.9%) were correctly serotyped, 14 were assigned to a member of the same serogroup, 8 rare serotypes were erroneously serotyped, and 18 gave negative serotyping results. Most of the discrepancies involved rare serotypes or serotypes that are difficult to discriminate using a DNA-based approach, for example 6A and 6B. The assay was also tested on clinical specimens including 43 cerebrospinal fluid samples from patients with meningitis and 59 nasopharyngeal aspirates from bacterial pneumonia patients. Overall, 89% of specimens positive for pneumolysin were serotyped, demonstrating that this method does not require culture to serotype clinical specimens. The assay showed no cross-reactivity for 24 relevant bacterial species found in these types of samples. The limit of detection for serotyping and S. pneumoniae detection was 100 genome equivalent per reaction. This automated assay is amenable to clinical testing and does not require any culturing of the samples. The assay will be useful for the evaluation of serotype prevalence changes after new conjugate vaccines introduction.
Collapse
Affiliation(s)
- Frédéric Raymond
- Centre de Recherche en Infectiologie and Département de Microbiologie et Immunologie, Faculté de Médecine, Université Laval, Québec, Québec, Canada
- * E-mail:
| | - Nancy Boucher
- Centre de Recherche en Infectiologie and Département de Microbiologie et Immunologie, Faculté de Médecine, Université Laval, Québec, Québec, Canada
| | - Robin Allary
- Centre de Recherche en Infectiologie and Département de Microbiologie et Immunologie, Faculté de Médecine, Université Laval, Québec, Québec, Canada
| | - Lynda Robitaille
- Centre de Recherche en Infectiologie and Département de Microbiologie et Immunologie, Faculté de Médecine, Université Laval, Québec, Québec, Canada
| | - Brigitte Lefebvre
- Laboratoire de Santé Publique du Québec, Institut National de Santé Publique, Ste-Anne-de-Bellevue, Québec, Canada
| | - Cécile Tremblay
- Laboratoire de Santé Publique du Québec, Institut National de Santé Publique, Ste-Anne-de-Bellevue, Québec, Canada
| | - Jacques Corbeil
- Centre de Recherche en Infectiologie and Département de Microbiologie et Immunologie, Faculté de Médecine, Université Laval, Québec, Québec, Canada
| | - Alain Gervaix
- Department of Pediatrics, University Hospitals of Geneva, Geneva, Switzerland
| |
Collapse
|