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Azarsa M, Mosadegh M, Habibi Ghahfarokhi S, Pourmand MR. Serotype Distribution and Multi Locus Sequence Type (MLST) of Erythromycin-Resistant Streptococcus Pneumoniae Isolates in Tehran, Iran. Rep Biochem Mol Biol 2023; 12:259-268. [PMID: 38317819 PMCID: PMC10838590 DOI: 10.61186/rbmb.12.2.259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Accepted: 07/04/2023] [Indexed: 02/07/2024]
Abstract
Background The number of erythromycin-resistant Streptococcus pneumoniae has significantly increased around the world. The present study aimed to determine the serotype distribution and molecular epidemiology of the erythromycin-resistant Streptococcus pneumoniae (ERSP) isolated from patients with invasive disease. Methods A total of 44 Streptococcus pneumoniae isolates were tested for susceptibility to several antimicrobial agents. Additionally, the polymerase chain reaction (PCR) was applied to evaluate ERSP isolates in terms of the presence of erythromycin resistance genes (e.g., ermB and mefA). The isolates were serotyped using the sequential multiplex-PCR method, and molecular epidemiology was assessed through the multilocus sequence typing (MLST) analysis. Results The results represented multidrug resistance (MDR) in approximately half of the pneumococcal isolates. Among 22 ERSP isolates, 20 (90.9%) and 12 (56%) ones contained ermB and mefA, respectively. Further, 14 (31.8%), 3 (22.7%), and 19A (18.1%) were the common serotypes among the isolates. No significant correlation was observed between serotypes and erythromycin resistance genes. Furthermore, the MLST results revealed 18 different sequence types (STs), the top ones of which were ST3130 (3 isolates) and ST166 (3 isolates). Population genetic analysis disclosed that CC63 (32%), CC156 (18%), and CC320 (18%) were identified as the predominant clonal complexes. Conclusions The ERSP isolates exhibited high genetic diversity. The large frequency of MDR isolates suggests the emergence of high resistant strains, as well as the need to implement vaccination in the immunization schedule of Iran. These accumulating evidences indicate that 13-valent pneumococcal conjugate vaccines provided higher serotype coverage in the ERSP isolates.
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Affiliation(s)
- Mohammad Azarsa
- Department of Microbiology, Khoy University of Medical Sciences, Khoy, Iran.
| | - Mehrdad Mosadegh
- Department of Pathobiology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran.
| | - Soheila Habibi Ghahfarokhi
- Department of Pathobiology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran.
| | - Mohammad Reza Pourmand
- Department of Pathobiology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran.
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Kielbik K, Grywalska E, Glowniak A, Mielnik-Niedzielska G, Korona-Glowniak I. The Molecular Epidemiology of Pneumococcal Strains Isolated from the Nasopharynx of Preschool Children 3 Years after the Introduction of the PCV Vaccination Program in Poland. Int J Mol Sci 2023; 24:ijms24097883. [PMID: 37175589 PMCID: PMC10178342 DOI: 10.3390/ijms24097883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 04/19/2023] [Accepted: 04/25/2023] [Indexed: 05/15/2023] Open
Abstract
The genetic mechanisms of resistance, clonal composition, and the occurrence of pili were analyzed in 39 pneumococcal strains isolated from healthy children in the southeastern region of Poland. Strains with resistance to combinations of erythromycin, clindamycin, and tetracycline were found in clonal groups (CGs) related to Tennessee 23F-4 and Taiwan 19F-14 clones. Capsular switching possibly occurred in the Spain 9V-3 clone and its variants to serotypes 35B and 6A, as well as DLVs of Tennessee 23F-4 to serotype 23A. The double-locus variants of Colombia 23F-26 presented serotype 23B. The major transposons carrying the erythromycin and tetracycline resistance genes were Tn6002 (66.6%), followed by Tn916 (22.2%) and Tn2009 (11.1%). The macrolide efflux genetic assembly (MEGA) element was found in 41.7% of all erythromycin-resistant isolates. The majority of the isolates carrying the PI-1 gene belonged to the CGs related to the Spain 9V-3 clone expressing serotypes 35B and 6A, and the presence of both PI-1 and PI-2 was identified in CG4 consisting of the isolates related to the Taiwan 19F-14 clone expressing serotypes 19F and 19A. Importantly, in the nearest future, the piliated strains of serogroups 23B, 23A, and 35B may be of concern, being a possible origin of the emerging clones of piliated non-vaccine pneumococcal serotypes in Poland. This study reveals that nasopharyngeal carriage in children is an important reservoir for the selection and spreading of new drug-resistant pneumococcal clones in the community after the elimination of vaccine serotypes.
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Affiliation(s)
- Karolina Kielbik
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Medical University of Lublin, 20-093 Lublin, Poland
| | - Ewelina Grywalska
- Department of Clinical Immunology, Faculty of Medicine, Medical University of Lublin, 20-093 Lublin, Poland
| | - Andrzej Glowniak
- Department of Cardiology, Medical University of Lublin, 20-093 Lublin, Poland
| | - Grażyna Mielnik-Niedzielska
- Department of Pediatric Otolaryngology, Phoniatrics and Audiology, Medical University of Lublin, 20-093 Lublin, Poland
| | - Izabela Korona-Glowniak
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Medical University of Lublin, 20-093 Lublin, Poland
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3
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Smaoui H, Tali-Maamar H, Zouhair S, Bouheraoua S, Mefteh K, Bouskraoui M, Amiche A, Khris M, Deghmane AE, Taha MK. Implementation of a prospective study for enhancing surveillance of invasive bacterial infections in North Africa. Int J Infect Dis 2021; 115:101-105. [PMID: 34843957 DOI: 10.1016/j.ijid.2021.11.036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 11/12/2021] [Accepted: 11/23/2021] [Indexed: 02/02/2023] Open
Abstract
OBJECTIVES We implemented a project named MENINGSTOP in three countries of North Africa (Algeria, Morocco and Tunisia). The main objective was to use real-time PCR to detect, identify and type the three main agents (Neisseria meningitidis, Streptococcus pneumoniae and Haemophilus influenzae) responsible for invasive bacterial infections (IBI). METHODS The protocol of WHO and US CDC for real-time PCR was used to detect and type the three bacterial agents in clinical samples. We also designated two quality exercises using an external interlaboratory study and cross-testing of 10% of randomly selected samples. RESULTS Among the 752 samples tested, 18% were positive for one of the three agents. N. meningitidis was the most frequent globally reaching 9% of all samples (7% to 17% range) followed by S. pneumoniae 8% of all samples (6% to 15%). Group B meningococci was the most frequent (74% of all positive samples for meningococci and ranging from 50% to 90%). Quality assurance showed >85% correlation scores. CONCLUSIONS Real-time PCR can help improving epidemiological surveillance. Data confirm the prevalence of meningococci B. Our project adds a reliable tool to enhance surveillance and to help decision making in vaccination strategies against IBI.
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Affiliation(s)
- Hanen Smaoui
- University of Tunis El Manar, Faculty of Medicine of Tunis; Children's Hospital Béchir Hamza of Tunis, Laboratory of Microbiology, Tunis, Tunisia
| | | | - Saïd Zouhair
- Faculty of Medicine and Pharmacy of Marrakech, University of Cadi Ayyad, Marrakech, Morocco
| | - Selma Bouheraoua
- Université d'Alger 1; Institut Pasteur of Algeria, Algiers, Algeria
| | - Khaoula Mefteh
- University of Tunis El Manar, Faculty of Medicine of Tunis; Children's Hospital Béchir Hamza of Tunis, Laboratory of Microbiology, Tunis, Tunisia
| | - Mohammed Bouskraoui
- Faculty of Medicine and Pharmacy of Marrakech, University of Cadi Ayyad, Marrakech, Morocco; Hospital of Mère-Enfant, Teaching hospital of Mohammed VI Marrakech, Marrakech, Morocco
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Nwogu IB, Jones M, Langley T. Economic evaluation of meningococcal serogroup B (MenB) vaccines: A systematic review. Vaccine 2021; 39:2201-2213. [PMID: 33744052 DOI: 10.1016/j.vaccine.2021.02.049] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 02/18/2021] [Accepted: 02/19/2021] [Indexed: 10/21/2022]
Abstract
BACKGROUND Meningococcal serogroup B (MenB) has emerged as the leading cause of invasive meningococcal disease (IMD) in several countries following the release of effective vaccines against serogroups A, C, W, and Y. In 2013, however, the first multicomponent MenB vaccine (Bexsero®) was licensed in Europe. AIM To review the evidence on the cost-effectiveness of vaccination against MenB. METHODS Searches were performed in MEDLINE, EMBASE, Web of Science, NHS EED, Econlit, Tufts CEA registry, and HTA. Three reviewers independently screened and selected studies. Using a narrative synthesis, studies were categorized by vaccination strategies. The quality of included studies was assessed using the Comparative Health Economics Evaluation Reporting Standards (CHEERS) checklist. RESULTS 13 studies were included. Ten studies were conducted in the European region and three in the Americas. None of the vaccination strategies were considered cost-effective. Including herd effects improved value for money for MenB vaccines. Routine infant vaccination was the most effective short-term strategy, however, adolescent strategies offered the best value for money. Without herd immunity, routine infant vaccination had the lowest incremental cost-effectiveness ratio estimates. CONCLUSION Routine MenB vaccination does not offer substantial value for money, mainly due to high vaccine costs and low disease incidence.
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Affiliation(s)
- Ifechukwu B Nwogu
- Division of Epidemiology and Public Health, School of Medicine, University of Nottingham, UK.
| | - Matthew Jones
- Division of Primary Care, School of Medicine, University of Nottingham, UK
| | - Tessa Langley
- Division of Epidemiology and Public Health, School of Medicine, University of Nottingham, UK
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Diallo K, Feteh VF, Ibe L, Antonio M, Caugant DA, du Plessis M, Deghmane AE, Feavers IM, Fernandez K, Fox LM, Rodrigues CMC, Ronveaux O, Taha MK, Wang X, Brueggemann AB, Maiden MCJ, Harrison OB. Molecular diagnostic assays for the detection of common bacterial meningitis pathogens: A narrative review. EBioMedicine 2021; 65:103274. [PMID: 33721818 PMCID: PMC7957090 DOI: 10.1016/j.ebiom.2021.103274] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 02/19/2021] [Accepted: 02/22/2021] [Indexed: 11/29/2022] Open
Abstract
Bacterial meningitis is a major global cause of morbidity and mortality. Rapid identification of the aetiological agent of meningitis is essential for clinical and public health management and disease prevention given the wide range of pathogens that cause the clinical syndrome and the availability of vaccines that protect against some, but not all, of these. Since microbiological culture is complex, slow, and often impacted by prior antimicrobial treatment of the patient, molecular diagnostic assays have been developed for bacterial detection. Distinguishing between meningitis caused by Neisseria meningitidis (meningococcus), Streptococcus pneumoniae (pneumococcus), Haemophilus influenzae, and Streptococcus agalactiae and identifying their polysaccharide capsules is especially important. Here, we review methods used in the identification of these bacteria, providing an up-to-date account of available assays, allowing clinicians and diagnostic laboratories to make informed decisions about which assays to use.
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Affiliation(s)
- Kanny Diallo
- Department of Zoology, University of Oxford, South Parks Rd, Oxford OX1 3SY, United Kingdom; Centre Suisse de Recherches Scientifiques en Côte d'Ivoire, Abidjan, Cote d'Ivoire
| | - Vitalis F Feteh
- Department of Zoology, University of Oxford, South Parks Rd, Oxford OX1 3SY, United Kingdom; Nuffield Department of Population Health, Big Data Institute, University of Oxford, Oxford OX3 7LF, United Kingdom
| | - Lilian Ibe
- Department of Zoology, University of Oxford, South Parks Rd, Oxford OX1 3SY, United Kingdom; Nuffield Department of Population Health, Big Data Institute, University of Oxford, Oxford OX3 7LF, United Kingdom
| | - Martin Antonio
- WHO Collaborating Centre for New Vaccines Surveillance, Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Atlantic Boulevard, Fajara, PO Box 273, Banjul, Gambia; Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Dominique A Caugant
- WHO Collaborating Center for Reference and Research on Meningococci, Norwegian Institute of Public Health, Oslo N-0213, Norway
| | - Mignon du Plessis
- A division of the National Health Laboratory Service (NHLS), National Institute for Communicable Diseases (NICD), Johannesburg, South Africa
| | | | - Ian M Feavers
- Department of Zoology, University of Oxford, South Parks Rd, Oxford OX1 3SY, United Kingdom
| | | | - LeAnne M Fox
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Division of Bacterial Diseases, Meningitis and Vaccine Preventable Diseases Branch, United States
| | - Charlene M C Rodrigues
- Department of Zoology, University of Oxford, South Parks Rd, Oxford OX1 3SY, United Kingdom; Department of Paediatric Infectious Diseases, St George's University Hospitals NHS Foundation Trust, London, United Kingdom
| | | | | | - Xin Wang
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Division of Bacterial Diseases, Meningitis and Vaccine Preventable Diseases Branch, United States
| | - Angela B Brueggemann
- Nuffield Department of Population Health, Big Data Institute, University of Oxford, Oxford OX3 7LF, United Kingdom
| | - Martin C J Maiden
- Department of Zoology, University of Oxford, South Parks Rd, Oxford OX1 3SY, United Kingdom
| | - Odile B Harrison
- Department of Zoology, University of Oxford, South Parks Rd, Oxford OX1 3SY, United Kingdom.
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6
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Tsang RSW. A Narrative Review of the Molecular Epidemiology and Laboratory Surveillance of Vaccine Preventable Bacterial Meningitis Agents: Streptococcus pneumoniae, Neisseria meningitidis, Haemophilus influenzae and Streptococcus agalactiae. Microorganisms 2021; 9:449. [PMID: 33671611 PMCID: PMC7926440 DOI: 10.3390/microorganisms9020449] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 02/16/2021] [Accepted: 02/16/2021] [Indexed: 12/23/2022] Open
Abstract
This narrative review describes the public health importance of four most common bacterial meningitis agents, Streptococcus pneumoniae, Neisseria meningitidis, Haemophilus influenzae, and S. agalactiae (group B Streptococcus). Three of them are strict human pathogens that normally colonize the nasopharynx and may invade the blood stream to cause systemic infections and meningitis. S. agalactiae colonizes the genito-gastrointestinal tract and is an important meningitis agent in newborns, but also causes invasive infections in infants or adults. These four bacteria have polysaccharide capsules that protect them against the host complement defense. Currently licensed conjugate vaccines (against S. pneumoniae, H. influenza, and N. meningitidis only but not S. agalactiae) can induce protective serum antibodies in infants as young as two months old offering protection to the most vulnerable groups, and the ability to eliminate carriage of homologous serotype strains in vaccinated subjects lending further protection to those not vaccinated through herd immunity. However, the serotype-specific nature of these vaccines have driven the bacteria to adapt by mechanisms that affect the capsule antigens through either capsule switching or capsule replacement in addition to the possibility of unmasking of strains or serotypes not covered by the vaccines. The post-vaccine molecular epidemiology of vaccine-preventable bacterial meningitis is discussed based on findings obtained with newer genomic laboratory surveillance methods.
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Affiliation(s)
- Raymond S W Tsang
- Laboratory for Vaccine Preventable Bacterial Diseases, National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, MB R3E 3R2, Canada
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7
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Ceyhan M, Ozsurekci Y, Lucidarme J, Borrow R. Characterization of invasive Neisseria meningitidis isolates recovered from children in Turkey during a period of increased serogroup B disease, 2013-2017. Vaccine 2020; 38:3545-3552. [PMID: 32199701 DOI: 10.1016/j.vaccine.2020.03.024] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 02/03/2020] [Accepted: 03/09/2020] [Indexed: 01/24/2023]
Abstract
Diverse Neisseria meningitidis strains belonging to various serogroups and clonal complexes cause epidemic and endemic life-threatening disease worldwide. This study aimed to investigate the genetic diversity of recent invasive meningococci in Turkey with respect to multilocus sequence type (MLST) and also meningococcal serogroup B (MenB) vaccine antigens to enable assessment of potential MenB strain coverage using the genetic Meningococcal Antigen Typing System (gMATS). Fifty-four isolates, representing 37.5% of all pediatric (ages 0-18 years) invasive meningococcal disease cases in Turkey from January 2013 to December 2017, underwent genome sequence analysis. Thirty-six (66.7%) isolates were MenB, 10 (18.5%) were serogroup W (MenW), 4 (7.4%) were serogroup A (MenA), 3 (5.6%) were serogroup Y (MenY) and 1 (1.8%) was serogroup X (MenX). The MenB isolates were diverse with cc35 (19.4%), cc41/44 (19.4%) and cc32 (13.8%) as the most prevalent clonal complexes. The MenW isolates (n = 10) comprised cc11 (n = 5), ST-2754 (cc-unassigned; n = 4) and cc22 (n = 1). gMATS was indicative of high 4CMenB coverage (72.2-79.1%) of Turkish invasive MenB strains from pediatric patients. Strain coverage of several clonal complexes differed from that seen elsewhere in Europe highlighting the importance of performing local assessments and also the use of phenotypic methods, i.e. MATS, where possible. All of the isolates possessed in-frame fhbp alleles and so were potentially covered by MenB-fHbp. Continued surveillance is essential to guide recommendations for current and future vaccines as well as understanding changes in epidemiology.
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Affiliation(s)
- Mehmet Ceyhan
- Hacettepe University, Faculty of Medicine, Department of Pediatric Infectious Diseases, Ankara, Turkey
| | - Yasemin Ozsurekci
- Hacettepe University, Faculty of Medicine, Department of Pediatric Infectious Diseases, Ankara, Turkey.
| | - Jay Lucidarme
- Meningococcal Reference Unit, Public Health England, Manchester, United Kingdom
| | - Ray Borrow
- Meningococcal Reference Unit, Public Health England, Manchester, United Kingdom
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8
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Azarsa M, Ohadian Moghadam S, Rahbar M, Baseri Z, Pourmand MR. Molecular serotyping and genotyping of penicillin non-susceptible pneumococci: the introduction of new sequence types, Tehran, Iran. New Microbes New Infect 2019; 32:100597. [PMID: 31641513 PMCID: PMC6796605 DOI: 10.1016/j.nmni.2019.100597] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 08/25/2019] [Accepted: 08/30/2019] [Indexed: 12/04/2022] Open
Abstract
The emergence of penicillin non-susceptible Streptococcus pneumoniae (PNSP) isolates can pose significant challenges to today's health-care system. Resistant clonal isolates are disseminated in different regions and countries, and this study was focused on the description of the epidemiological spread of these strains. Clinical samples were collected from individuals admitted to hospitals affiliated to the Tehran University of Medical Sciences, Iran. To investigate the molecular characteristics of PNSP isolates, they were subjected to molecular typing using multi-locus sequence typing (MLST). Serotype distributions of S. pneumoniae isolates were also evaluated by multiplex PCR assay. The most prevalent serotypes in the PNSP isolates were 23F, 19F, 14, 3 and 9V. Two isolates were considered as a non-vaccine serotype. The MLST analysis showed that PNSP isolates belonged to five different clonal complexes (CC180, CC217, CC81, CC63 and CC320) and 42% (5/12) of the sequence types were novel (12936, 12937, 12938, 12939 and 12940). This study indicates the high level of heterogeneity that is present among PNSP isolates. Unexpected high genetic diversity in small populations indicates consecutive diversification of resistant strains.
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Affiliation(s)
- M Azarsa
- Department of Microbiology, Khoy University of Medical Sciences, Khoy, Iran
| | - S Ohadian Moghadam
- Uro-Oncology Research Centre, Tehran University of Medical Sciences, Tehran, Iran
| | - M Rahbar
- Department of Microbiology, Reference Health Laboratories Research Centre, Ministry of Health and Medical Education, Tehran, Iran
| | - Z Baseri
- Central Laboratory of Shariati Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - M R Pourmand
- Department of Pathobiology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
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9
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Diallo K, Coulibaly MD, Rebbetts LS, Harrison OB, Lucidarme J, Gamougam K, Tekletsion YK, Bugri A, Toure A, Issaka B, Dieng M, Trotter C, Collard JM, Sow SO, Wang X, Mayer LW, Borrow R, Greenwood BM, Maiden MCJ, Manigart O. Development of a PCR algorithm to detect and characterize Neisseria meningitidis carriage isolates in the African meningitis belt. PLoS One 2018; 13:e0206453. [PMID: 30517103 PMCID: PMC6281270 DOI: 10.1371/journal.pone.0206453] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Accepted: 10/12/2018] [Indexed: 12/25/2022] Open
Abstract
Improved methods for the detection and characterization of carried Neisseria meningitidis isolates are needed. We evaluated a multiplex PCR algorithm for the detection of a variety of carriage strains in the meningitis belt. To further improve the sensitivity and specificity of the existing PCR assays, primers for gel-based PCR assays (sodC, H, Z) and primers/probe for real-time quantitative PCR (qPCR) assays (porA, cnl, sodC, H, E, Z) were modified or created using Primer Express software. Optimized multiplex PCR assays were tested on 247 well-characterised carriage isolates from six countries of the African meningitis belt. The PCR algorithm developed enabled the detection of N. meningitidis species using gel-based and real-time multiplex PCR targeting porA, sodC, cnl and characterization of capsule genes through sequential multiplex PCR assays for genogroups (A, W, X, then B, C, Y and finally H, E and Z). Targeting both porA and sodC genes together allowed the detection of meningococci with a sensitivity of 96% and 89% and a specificity of 78% and 67%, for qPCR and gel-based PCR respectively. The sensitivity and specificity ranges for capsular genogrouping of N. meningitidis are 67% - 100% and 98%-100% respectively for gel-based PCR and 90%-100% and 99%-100% for qPCR. We developed a PCR algorithm that allows simple, rapid and systematic detection and characterisation of most major and minor N. meningitidis capsular groups, including uncommon capsular groups (H, E, Z).
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Affiliation(s)
- Kanny Diallo
- Centre pour le Développement des Vaccins (CVD), Bamako, Mali
- University of Oxford (Department of Zoology), Oxford, United Kingdom
| | | | - Lisa S. Rebbetts
- University of Oxford (Department of Zoology), Oxford, United Kingdom
| | - Odile B. Harrison
- University of Oxford (Department of Zoology), Oxford, United Kingdom
| | - Jay Lucidarme
- Public Health England, (PHE–Vaccine Evaluation Unit), Manchester, United Kingdom
| | - Kadidja Gamougam
- Centre de Support en Santé Internationale (CSSI), Ndjamena, Chad
| | | | - Akalifa Bugri
- Navrongo Health Research Centre (NHRC), Navrongo, Ghana
| | - Aliou Toure
- Centre pour le Développement des Vaccins (CVD), Bamako, Mali
| | - Bassira Issaka
- Centre de Recherche Médicale et Sanitaire (CERMES), Niamey, Niger
| | - Marietou Dieng
- Institut de Recherche pour le Développement (IRD), Dakar, Senegal
| | - Caroline Trotter
- University of Cambridge (Disease Dynamics Unit -Department of Veterinary Medicine), Cambridge, United Kingdom
| | | | - Samba O. Sow
- Centre pour le Développement des Vaccins (CVD), Bamako, Mali
| | - Xin Wang
- Centers for Disease Control and Prevention, Division of Bacterial Diseases, Atlanta, United States of America
| | - Leonard W. Mayer
- Centers for Disease Control and Prevention, Division of Bacterial Diseases, Atlanta, United States of America
| | - Ray Borrow
- Public Health England, (PHE–Vaccine Evaluation Unit), Manchester, United Kingdom
| | - Brian M. Greenwood
- London School of Hygiene and Tropical Medicine (LSHTM), London, United Kingdom
| | | | - Olivier Manigart
- London School of Hygiene and Tropical Medicine (LSHTM), London, United Kingdom
- * E-mail:
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10
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Whaley MJ, Joseph SJ, Retchless AC, Kretz CB, Blain A, Hu F, Chang HY, Mbaeyi SA, MacNeil JR, Read TD, Wang X. Whole genome sequencing for investigations of meningococcal outbreaks in the United States: a retrospective analysis. Sci Rep 2018; 8:15803. [PMID: 30361650 PMCID: PMC6202316 DOI: 10.1038/s41598-018-33622-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 09/13/2018] [Indexed: 01/14/2023] Open
Abstract
Although rare in the U.S., outbreaks due to Neisseria meningitidis do occur. Rapid, early outbreak detection is important for timely public health response. In this study, we characterized U.S. meningococcal isolates (N = 201) from 15 epidemiologically defined outbreaks (2009-2015) along with temporally and geographically matched sporadic isolates using multilocus sequence typing, pulsed-field gel electrophoresis (PFGE), and six whole genome sequencing (WGS) based methods. Recombination-corrected maximum likelihood (ML) and Bayesian phylogenies were reconstructed to identify genetically related outbreak isolates. All WGS analysis methods showed high degree of agreement and distinguished isolates with similar or indistinguishable PFGE patterns, or the same strain genotype. Ten outbreaks were caused by a single strain; 5 were due to multiple strains. Five sporadic isolates were phylogenetically related to 2 outbreaks. Analysis of 9 outbreaks using timed phylogenies identified the possible origin and estimated the approximate time that the most recent common ancestor emerged for outbreaks analyzed. U.S. meningococcal outbreaks were caused by single- or multiple-strain introduction, with organizational outbreaks mainly caused by a clonal strain and community outbreaks by divergent strains. WGS can infer linkage of meningococcal cases when epidemiological links are uncertain. Accurate identification of outbreak-associated cases requires both WGS typing and epidemiological data.
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Affiliation(s)
- Melissa J Whaley
- Meningitis and Vaccine Preventable Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Sandeep J Joseph
- Meningitis and Vaccine Preventable Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Adam C Retchless
- Meningitis and Vaccine Preventable Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Cecilia B Kretz
- Meningitis and Vaccine Preventable Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Amy Blain
- Meningitis and Vaccine Preventable Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Fang Hu
- Meningitis and Vaccine Preventable Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - How-Yi Chang
- Meningitis and Vaccine Preventable Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Sarah A Mbaeyi
- Meningitis and Vaccine Preventable Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Jessica R MacNeil
- Meningitis and Vaccine Preventable Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Timothy D Read
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Xin Wang
- Meningitis and Vaccine Preventable Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA.
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11
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Hao L, Holden MTG, Wang X, Andrew L, Wellnitz S, Hu F, Whaley M, Sammons S, Knipe K, Frace M, McNamara LA, Liberator P, Anderson AS. Distinct evolutionary patterns of Neisseria meningitidis serogroup B disease outbreaks at two universities in the USA. Microb Genom 2018; 4. [PMID: 29616896 PMCID: PMC5989579 DOI: 10.1099/mgen.0.000155] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Neisseria meningitidis serogroup B (MnB) was responsible for two independent meningococcal disease outbreaks at universities in the USA during 2013. The first at University A in New Jersey included nine confirmed cases reported between March 2013 and March 2014. The second outbreak occurred at University B in California, with four confirmed cases during November 2013. The public health response to these outbreaks included the approval and deployment of a serogroup B meningococcal vaccine that was not yet licensed in the USA. This study investigated the use of whole-genome sequencing(WGS) to examine the genetic profile of the disease-causing outbreak isolates at each university. Comparative WGS revealed differences in evolutionary patterns between the two disease outbreaks. The University A outbreak isolates were very closely related, with differences primarily attributed to single nucleotide polymorphisms/insertion-deletion (SNP/indel) events. In contrast, the University B outbreak isolates segregated into two phylogenetic clades, differing in large part due to recombination events covering extensive regions (>30 kb) of the genome including virulence factors. This high-resolution comparison of two meningococcal disease outbreaks further demonstrates the genetic complexity of meningococcal bacteria as related to evolution and disease virulence.
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Affiliation(s)
- Li Hao
- 1Vaccine Research & Development, Pfizer Inc, 401 N. Middletown Rd, Pearl River, NY 10965, USA
| | | | - Xin Wang
- 3Division of Bacterial Diseases, Centers for Diseases Control and Prevention, Atlanta, Georgia, USA
| | - Lubomira Andrew
- 1Vaccine Research & Development, Pfizer Inc, 401 N. Middletown Rd, Pearl River, NY 10965, USA
| | - Sabine Wellnitz
- 1Vaccine Research & Development, Pfizer Inc, 401 N. Middletown Rd, Pearl River, NY 10965, USA
| | - Fang Hu
- 3Division of Bacterial Diseases, Centers for Diseases Control and Prevention, Atlanta, Georgia, USA
| | - Melissa Whaley
- 3Division of Bacterial Diseases, Centers for Diseases Control and Prevention, Atlanta, Georgia, USA
| | - Scott Sammons
- 3Division of Bacterial Diseases, Centers for Diseases Control and Prevention, Atlanta, Georgia, USA
| | - Kristen Knipe
- 3Division of Bacterial Diseases, Centers for Diseases Control and Prevention, Atlanta, Georgia, USA
| | - Mike Frace
- 3Division of Bacterial Diseases, Centers for Diseases Control and Prevention, Atlanta, Georgia, USA
| | - Lucy A McNamara
- 3Division of Bacterial Diseases, Centers for Diseases Control and Prevention, Atlanta, Georgia, USA
| | - Paul Liberator
- 1Vaccine Research & Development, Pfizer Inc, 401 N. Middletown Rd, Pearl River, NY 10965, USA
| | - Annaliesa S Anderson
- 1Vaccine Research & Development, Pfizer Inc, 401 N. Middletown Rd, Pearl River, NY 10965, USA
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Nejati F, Fateh A, Nojoumi SA, Rahbar M, Behrouzi A, Vaziri F, Siadat SD. MLVA typing of Haemophilus influenzae isolated from two Iranian university hospitals. IRANIAN JOURNAL OF MICROBIOLOGY 2018; 10:30-36. [PMID: 29922416 PMCID: PMC6004631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
BACKGROUND AND OBJECTIVES Different serotypes of Haemophilus influenzae is now divided into 2 divisions: encapsulated and unencapsulated. Multiple locus variable number tandem repeat analysis (MLVA) includes such specifications as the extra power of separation, ease of data interpretation, and epidemiological data accordance, which have made it an appropriate molecular device for good typing and phylogenetic analysis of bacterial pathogens. MATERIALS AND METHODS In this research, cultured samples were studied and strains identified through biochemical tests were recognized. Moreover, DNA was extracted and studied qualitatively and quantitatively. Four pairs of specialized primers related to H. influenzae variable number tandem repeats (VNTR) and preparation of PCR were designed according to the regulated program. Also, electrophoresis of PCR products was performed. Finally, the interpretation of electrophoresis gel was done with respect to the observable bands showing the presence or absence of the required sequence in the samples related to every primer. RESULTS This study was the first MLVA typing of the unencapsulated H. influenzae in Iran. In this research, the VNTR sequences were tested in 30 strains without the unencapsulated H. influenzae. Among 30 mentioned strains, for which MLVA profile was obtained in this research, 25 different MLVA types were observed. Likewise, there was no repetition in VNTR sequences resulting from PCR in few H. influenzae. In all these cases, the number of repetitions in MLVA profile was determined as 0, except for one of the primers in 4 strains, which was 16%. However, this did not occur for the other VNTRs. CONCLUSION The highest diversity of the repeats was for VNTR5 (7 types), followed by VNTR6 with 6 types of repeats, and VNTR12-1 and VNTR12-2 with 3 different types.
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Affiliation(s)
- Faranak Nejati
- Department of Mycobacteriology & Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
| | - Abolfazl Fateh
- Department of Mycobacteriology & Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran,Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Seyed Ali Nojoumi
- Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Mohammad Rahbar
- Department of Microbiology, Reference Health Laboratories Research Center, Ministry of Health and Medical Education, Tehran, Iran
| | - Ava Behrouzi
- Department of Mycobacteriology & Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
| | - Farzam Vaziri
- Department of Mycobacteriology & Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran,Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran,Corresponding authors: Farzam Vaziri & Seyed Davar Siadat, PhD, Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran; Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran. Tel: +982166968853, Fax: +982166496721
| | - Seyed Davar Siadat
- Department of Mycobacteriology & Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran,Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran,Corresponding authors: Farzam Vaziri & Seyed Davar Siadat, PhD, Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran; Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran. Tel: +982166968853, Fax: +982166496721
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Tagini F, Greub G. Bacterial genome sequencing in clinical microbiology: a pathogen-oriented review. Eur J Clin Microbiol Infect Dis 2017; 36:2007-2020. [PMID: 28639162 PMCID: PMC5653721 DOI: 10.1007/s10096-017-3024-6] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 05/22/2017] [Indexed: 12/11/2022]
Abstract
In recent years, whole-genome sequencing (WGS) has been perceived as a technology with the potential to revolutionise clinical microbiology. Herein, we reviewed the literature on the use of WGS for the most commonly encountered pathogens in clinical microbiology laboratories: Escherichia coli and other Enterobacteriaceae, Staphylococcus aureus and coagulase-negative staphylococci, streptococci and enterococci, mycobacteria and Chlamydia trachomatis. For each pathogen group, we focused on five different aspects: the genome characteristics, the most common genomic approaches and the clinical uses of WGS for (i) typing and outbreak analysis, (ii) virulence investigation and (iii) in silico antimicrobial susceptibility testing. Of all the clinical usages, the most frequent and straightforward usage was to type bacteria and to trace outbreaks back. A next step toward standardisation was made thanks to the development of several new genome-wide multi-locus sequence typing systems based on WGS data. Although virulence characterisation could help in various particular clinical settings, it was done mainly to describe outbreak strains. An increasing number of studies compared genotypic to phenotypic antibiotic susceptibility testing, with mostly promising results. However, routine implementation will preferentially be done in the workflow of particular pathogens, such as mycobacteria, rather than as a broadly applicable generic tool. Overall, concrete uses of WGS in routine clinical microbiology or infection control laboratories were done, but the next big challenges will be the standardisation and validation of the procedures and bioinformatics pipelines in order to reach clinical standards.
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Affiliation(s)
- F Tagini
- Institute of Microbiology, Department of Laboratory, University of Lausanne & University Hospital, Lausanne, Switzerland
| | - G Greub
- Institute of Microbiology, Department of Laboratory, University of Lausanne & University Hospital, Lausanne, Switzerland.
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Investigation of Kingella kingae Invasive Infection Outbreaks in Day Care Facilities: Assessment of a Rapid Genotyping Tool Targeting the DNA Uptake Sequence. J Clin Microbiol 2017; 55:2422-2430. [PMID: 28539344 DOI: 10.1128/jcm.00271-17] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 05/16/2017] [Indexed: 11/20/2022] Open
Abstract
Outbreaks of Kingella kingae invasive infections have recently been reported in day care centers. Pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST) revealed that although the invasive strains had widespread dissemination in the day care population, less virulent strains were also circulating in the facilities. However, these typing tools are costly, time-consuming, and labor-intensive and provide delayed results. A study was conducted to assess the performance of a rapid and cost-effective genotyping tool targeting the DNA uptake sequence (DUS) in the investigation of outbreaks of K. kingae disease. DUS typing (DUST) patterns of each strain from 7 different clusters were compared to distinguish genotypically linked strains from others. PFGE and, when available, MLST results were used as gold standards. DUST was assessed on 80 K. kingae isolates from Nir-Itzhak (n = 14), Tel-Nof (n = 14), Palmahim (n = 5), Umm-al-Fahm (n = 7), Eilat (n = 8), Nevatim (n = 15) in Israel and Paris, France (n = 17). A unique DUST pattern was involved in the Nir-Itzhak, Palmahim, Umm-al-Fahm, and Paris episodes. Two DUST patterns were found in Eilat, whereas at least 3 were identified in the Tel-Nof and Nevatim episodes. In total, 11 (13.8%) children carried a K. kingae isolate that differed from the outbreak strain. These results were concordant with those obtained with the traditional PFGE and MLST methods. DUST appears to be sensitive and specific in distinguishing the invasive outbreak strain from others in asymptomatic carriers and could be useful to limit unnecessary exposure of the entire day care population to selective antibiotic pressure.
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15
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Barnwal RP, Loh E, Godin KS, Yip J, Lavender H, Tang CM, Varani G. Structure and mechanism of a molecular rheostat, an RNA thermometer that modulates immune evasion by Neisseria meningitidis. Nucleic Acids Res 2016; 44:9426-9437. [PMID: 27369378 PMCID: PMC5100586 DOI: 10.1093/nar/gkw584] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Revised: 05/24/2016] [Accepted: 06/18/2016] [Indexed: 11/15/2022] Open
Abstract
Neisseria meningitidis causes bacterial meningitis and septicemia. It evades the host complement system by upregulating expression of immune evasion factors in response to changes in temperature. RNA thermometers within mRNAs control expression of bacterial immune evasion factors, including CssA, in the 5'-untranslated region of the operon for capsule biosynthesis. We dissect the molecular mechanisms of thermoregulation and report the structure of the CssA thermometer. We show that the RNA thermometer acts as a rheostat, whose stability is optimized to respond in a small temperature range around 37°C as occur within the upper airways during infection. Small increases in temperature gradually open up the structure to allow progressively increased access to the ribosome binding site. Even small changes in stability induced by mutations of imperfect base pairs, as in naturally occurring polymorphisms, shift the thermometer response outside of the desired temperature range, suggesting that its activity could be modulated by pharmacological intervention.
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Affiliation(s)
| | - Edmund Loh
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
- Department of Microbiology, Tumor and Cell Biology (MTC), Mikrobiell Patogenes, Gustaf V, Karolinska Sjukhuset 171 76 Stockholm, Sweden
| | - Katherine S Godin
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA
| | - Jordan Yip
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA
| | - Hayley Lavender
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Christoph M Tang
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Gabriele Varani
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA
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16
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McNeil HC, Jefferies JMC, Clarke SC. Vaccine preventable meningitis in Malaysia: epidemiology and management. Expert Rev Anti Infect Ther 2016; 13:705-14. [PMID: 25962101 DOI: 10.1586/14787210.2015.1033401] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Worldwide bacterial meningitis accounts for more than one million cases and 135,000 deaths annually. Profound, lasting neurological complications occur in 9-25% of cases. This review confirms the greatest risk from bacterial meningitis is in early life in Malaysia. Much of the disease burden can be avoided by immunization, particularly against Haemophilus influenzae type b (Hib) and Streptococcus pneumoniae. Despite inclusion of the Hib vaccine in the National Immunisation Programme and the licensure of pneumococcal vaccines, these two species are the main contributors to bacterial meningitis in Malaysia, with Neisseria meningitidis and Mycobacterium tuberculosis, causing a smaller proportion of disease. The high Hib prevalence may partly be due to dated, small-scale studies limiting the understanding of the current epidemiological situation. This highlights the need for larger, better quality surveillance from Malaysia to evaluate the success of Hib immunization and to help guide immunization policy for vaccines against S. pneumoniae and N. meningitidis.
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Affiliation(s)
- Hannah C McNeil
- University of Southampton Malaysia Campus, No.3, Persiaran Canselor 1, Kota Ilmu, Educity, Iskandar, 79200 Nusajaya, Johor, Malaysia
| | - Johanna M C Jefferies
- Faculty of Medicine and Institute of Life Sciences, University of Southampton, Southampton, UK
| | - Stuart C Clarke
- University of Southampton Malaysia Campus, No.3, Persiaran Canselor 1, Kota Ilmu, Educity, Iskandar, 79200 Nusajaya, Johor, Malaysia.,Faculty of Medicine and Institute of Life Sciences, University of Southampton, Southampton, UK
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17
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SIGNORELLI C, CHIESA V, ODONE A. Meningococcal serogroup B vaccine in Italy: state-of-art, organizational aspects and perspectives. JOURNAL OF PREVENTIVE MEDICINE AND HYGIENE 2015; 56:E125-32. [PMID: 26788733 PMCID: PMC4755121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 08/28/2015] [Indexed: 10/26/2022]
Abstract
Neisseria meningitidis causes severe invasive meningococcal diseases (IMDs) in humans including meningitis and septicemia, responsible for serious clinical conditions and leading to life-long disabilities and death. Serogroup B dominates IMDs burden in Italy, accounting for over 60% of total cases. On January 2013 the European Medicine Agency (EMA) licensed the first serogroup B meningococcal (MenB) vaccine in Europe. A number of European countries and Regions have introduced the new MenB vaccine in their immunization schedule, including Italy. In this paper we present the state of art, related critical issues and future perspectives of MenB vaccine introduction in Italy, in the context of the most recent available epidemiological data. In particular, we systematically assess the ongoing processes in the 8 Italian regions and one autonomous province that have already introduced MenB vaccine. With the new 2014-2018 National Vaccine Prevention Plan including active MenB vaccine offer about to be adopted, it is of fundamental importance to gather further evidence on MenB vaccine clinical effectiveness, duration of protection and cost-effectiveness. Italian regions are called to organize and manage MenB immunization programs. Careful consideration will need to be devoted on timing, doses, and co-administration with other vaccines but also to economic assessments and strengthened communication to the general public. Our data will help to plan, implement and evaluate MenB immunization programmes in other Italian and international settings.
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Affiliation(s)
- C. SIGNORELLI
- Correspondence: Carlo Signorelli, Dipartimento di Scienze Biomediche, Biotecnologiche e Translazionali, Università degli studi di Parma, via Volturno, 39, 43125 Parma Italy - E-mail:
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18
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Law DKS, Lefebvre B, Gilca R, Deng S, Zhou J, De Wals P, Tsang RSW. Characterization of invasive Neisseria meningitidis strains from Québec, Canada, during a period of increased serogroup B disease, 2009-2013: phenotyping and genotyping with special emphasis on the non-carbohydrate protein vaccine targets. BMC Microbiol 2015; 15:143. [PMID: 26204985 PMCID: PMC4514445 DOI: 10.1186/s12866-015-0469-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Accepted: 06/19/2015] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND The epidemiology of invasive meningococcal disease (IMD) in Québec, Canada, has been dominated in the past decade by a clone of serogroup B (MenB) Neisseria meningitidis defined by multi-locus sequence typing (MLST) as sequence type (ST)-269. With the licensure of a new MenB vaccine Bexsero (4CMenB) in Canada, this study characterized invasive N. meningitidis recovered in Québec from 2009 to 2013, with an objective to examine the diversity of the 4CMenB vaccine antigens. Isolates were serogrouped by antisera and genogrouped by PCR, and further typed by whole cell ELISA for serotype and serosubtype antigens. Clonal analysis was done by MLST. Isolates were genotyped by analysis of their 4CMenB vaccine antigen genes of PorA, factor H binding protein (fHbp), Neisserial Heparin Binding Antigen (NHBA), and Neisseria Adhesin A (NadA). RESULTS Of the 263 IMD isolates analysed, 229, 16, 10, 7, and 1 belonged to MenB, MenY, MenW, MenC, and MenX, respectively. Of the 229 MenB, 159 (69.4 %) were typed as ST-269 clonal complex (CC); and they possessed a restricted number of three fHbp and five nhba gene alleles. Nine N. meningitidis isolates (eight MenB and one MenY) were found to possess at least one gene that encoded for an antigen that matched exactly with protein variants in the 4CMenB vaccine. Two MenB expressed PorA antigen P1.4 and possessed the nhba gene for peptide 2; four other MenB were predicted to have NHBA peptide 2; another two MenB were predicted to encode fHbp peptide 1.1; and a single MenY was found to have nadA gene for NadA peptide 8. In addition, another 172 isolates were found to possess genes for variant 1 fHbp peptides other than peptide 1.1 or NadA variant 1-2/3 peptides other than peptide 8; and therefore, may potentially be covered by 4CMenB. CONCLUSION The most prevalent clone of N. meningitidis in Quebec was ST-269 CC; and 96 % of the isolates in this CC were predicted to be covered by 4CMenB vaccine. Extensive genetic diversity was found in the other IMD isolates in Québec which might suggest a lower coverage by the vaccine when compared to the ST-269 MenB.
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Affiliation(s)
- Dennis K S Law
- Vaccine Preventable Bacterial Diseases, National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, R3E 3R2, Winnipeg, MB, Canada.
| | - Brigitte Lefebvre
- Laboratoire de santé publique du Québec, Institut national de santé publique du Québec, 20045 chemin Sante-Marie, Ste-Anne-de-Bellevue, H9X 3R5, Québec, Canada.
| | - Rodica Gilca
- Institut national de santé publique du Québec, Centre de Recherche du CHUL-CHUQ, Québec, Canada.
- Département de Médecine Sociale et Préventive de I'Université Laval, Québec, Canada.
| | - Saul Deng
- Vaccine Preventable Bacterial Diseases, National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, R3E 3R2, Winnipeg, MB, Canada.
| | - Jianwei Zhou
- Vaccine Preventable Bacterial Diseases, National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, R3E 3R2, Winnipeg, MB, Canada.
| | - Philippe De Wals
- Institut national de santé publique du Québec, Centre de Recherche du CHUL-CHUQ, Québec, Canada.
- Département de Médecine Sociale et Préventive de I'Université Laval, Québec, Canada.
| | - Raymond S W Tsang
- Vaccine Preventable Bacterial Diseases, National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, R3E 3R2, Winnipeg, MB, Canada.
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Bartsch MS, Edwards HS, Lee D, Moseley CE, Tew KE, Renzi RF, Van de Vreugde JL, Kim H, Knight DL, Sinha A, Branda SS, Patel KD. The rotary zone thermal cycler: a low-power system enabling automated rapid PCR. PLoS One 2015; 10:e0118182. [PMID: 25826708 PMCID: PMC4380418 DOI: 10.1371/journal.pone.0118182] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Accepted: 01/09/2015] [Indexed: 12/17/2022] Open
Abstract
Advances in molecular biology, microfluidics, and laboratory automation continue to expand the accessibility and applicability of these methods beyond the confines of conventional, centralized laboratory facilities and into point of use roles in clinical, military, forensic, and field-deployed applications. As a result, there is a growing need to adapt the unit operations of molecular biology (e.g., aliquoting, centrifuging, mixing, and thermal cycling) to compact, portable, low-power, and automation-ready formats. Here we present one such adaptation, the rotary zone thermal cycler (RZTC), a novel wheel-based device capable of cycling up to four different fixed-temperature blocks into contact with a stationary 4-microliter capillary-bound sample to realize 1-3 second transitions with steady state heater power of less than 10 W. We demonstrate the utility of the RZTC for DNA amplification as part of a highly integrated rotary zone PCR (rzPCR) system that uses low-volume valves and syringe-based fluid handling to automate sample loading and unloading, thermal cycling, and between-run cleaning functionalities in a compact, modular form factor. In addition to characterizing the performance of the RZTC and the efficacy of different online cleaning protocols, we present preliminary results for rapid single-plex PCR, multiplex short tandem repeat (STR) amplification, and second strand cDNA synthesis.
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Affiliation(s)
- Michael S. Bartsch
- Sandia National Laboratories, Livermore, CA, United States of America
- * E-mail:
| | | | - Daniel Lee
- Sandia National Laboratories, Livermore, CA, United States of America
| | | | - Karen E. Tew
- Sandia National Laboratories, Livermore, CA, United States of America
| | - Ronald F. Renzi
- Sandia National Laboratories, Livermore, CA, United States of America
| | | | - Hanyoup Kim
- Sandia National Laboratories, Livermore, CA, United States of America
| | | | - Anupama Sinha
- Sandia National Laboratories, Livermore, CA, United States of America
| | - Steven S. Branda
- Sandia National Laboratories, Livermore, CA, United States of America
| | - Kamlesh D. Patel
- Sandia National Laboratories, Livermore, CA, United States of America
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Tsang RSW, Hoang L, Tyrrell G, Horsman G, Wylie J, Jamieson FB, Lefebvre B, Taha MK. Genetic and antigenic characterization of Canadian invasive Neisseria meningitidis serogroup C (MenC) case isolates in the post-MenC conjugate vaccine era, 2009–2013. J Med Microbiol 2015. [DOI: 10.1099/jmm.0.000006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Affiliation(s)
- Raymond S. W. Tsang
- Vaccine Preventable Bacterial Diseases, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Linda Hoang
- BC Public Health Microbiology and Reference Laboratory, Vancouver, British Columbia, Canada
| | - Gregory Tyrrell
- Provincial Laboratory for Public Health, Edmonton, Alberta, Canada
| | - Greg Horsman
- Saskatchewan Disease Control Laboratory, Regina, Saskatchewan, Canada
| | - John Wylie
- Cadham Provincial Public Health Laboratory, Winnipeg, Manitoba, Canada
| | - Frances B. Jamieson
- Faculty of Medicine, University of Toronto, Ontario, Canada
- Public Health Ontario Laboratory, Public Health Ontario, Ontario, Canada
| | - Brigitte Lefebvre
- Laboratoire de Santé Publique du Québec, Institut National de Santé Publique du Québec, Sainte-Anne-de-Bellevue, Québec, Canada
| | - Muhamed-Kheir Taha
- Institut Pasteur, Invasive Bacterial Infections Unit and National Reference Centre for Meningococci, Paris, France
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Skaare D, Anthonisen IL, Caugant DA, Jenkins A, Steinbakk M, Strand L, Sundsfjord A, Tveten Y, Kristiansen BE. Multilocus sequence typing and ftsI sequencing: a powerful tool for surveillance of penicillin-binding protein 3-mediated beta-lactam resistance in nontypeable Haemophilus influenzae. BMC Microbiol 2014; 14:131. [PMID: 24884375 PMCID: PMC4039647 DOI: 10.1186/1471-2180-14-131] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Accepted: 05/14/2014] [Indexed: 12/26/2022] Open
Abstract
Background Beta-lactam resistance in Haemophilus influenzae due to ftsI mutations causing altered penicillin-binding protein 3 (PBP3) is increasing worldwide. Low-level resistant isolates with the N526K substitution (group II low-rPBP3) predominate in most geographical regions, while high-level resistant isolates with the additional S385T substitution (group III high-rPBP3) are common in Japan and South Korea. Knowledge about the molecular epidemiology of rPBP3 strains is limited. We combined multilocus sequence typing (MLST) and ftsI/PBP3 typing to study the emergence and spread of rPBP3 in nontypeable H. influenzae (NTHi) in Norway. Results The prevalence of rPBP3 in a population of 795 eye, ear and respiratory isolates (99% NTHi) from 2007 was 15%. The prevalence of clinical PBP3-mediated resistance to ampicillin was 9%, compared to 2.5% three years earlier. Group II low-rPBP3 predominated (96%), with significant proportions of isolates non-susceptible to cefotaxime (6%) and meropenem (20%). Group III high-rPBP3 was identified for the first time in Northern Europe. Four MLST sequence types (ST) with characteristic, highly diverging ftsI alleles accounted for 61% of the rPBP3 isolates. The most prevalent substitution pattern (PBP3 type A) was present in 41% of rPBP3 isolates, mainly carried by ST367 and ST14. Several unrelated STs possessed identical copies of the ftsI allele encoding PBP3 type A. Infection sites, age groups, hospitalization rates and rPBP3 frequencies differed between STs and phylogenetic groups. Conclusions This study is the first to link ftsI alleles to STs in H. influenzae. The results indicate that horizontal gene transfer contributes to the emergence of rPBP3 by phylogeny restricted transformation. Clonally related virulent rPBP3 strains are widely disseminated and high-level resistant isolates emerge in new geographical regions, threatening current empiric antibiotic treatment. The need of continuous monitoring of beta-lactam susceptibility and a global system for molecular surveillance of rPBP3 strains is underlined. Combining MLST and ftsI/PBP3 typing is a powerful tool for this purpose.
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Affiliation(s)
- Dagfinn Skaare
- Department of Microbiology, Vestfold Hospital Trust, Tønsberg, Norway.
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Abstract
Spread of antibiotic resistance is mediated by clonal lineages of bacteria that besides being resistant also possess other properties promoting their success. Some vaccines already in use, such as the pneumococcal conjugate vaccines, have had an effect on these successful clones, but at the same time have allowed for the expansion and resistance evolution of previously minor clones not covered by the vaccine. Since resistance frequently is horizontally transferred it will be difficult to generate a vaccine that covers all possible genetic lineages prone to develop resistance unless the vaccine target(s) is absolutely necessary for spread and/or disease development. Targeting the resistance mechanism itself by a vaccine is an interesting but hitherto unexplored approach.
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Affiliation(s)
- Birgitta Henriques-Normark
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 171 77 Stockholm, Sweden
- Karolinska University Hospital, 171 76 Stockholm, Sweden
| | - Staffan Normark
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 171 77 Stockholm, Sweden
- Karolinska University Hospital, 171 76 Stockholm, Sweden
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Soriano-Gabarró M, Wolter J, Hogea C, Vyse A. Carriage ofNeisseria meningitidisin Europe: a review of studies undertaken in the region. Expert Rev Anti Infect Ther 2014; 9:761-74. [DOI: 10.1586/eri.11.89] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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Hajia M, Farzanehkhah M, Hajihashemi B, Dolatyar A, Imani M, Saburian R, Rahnamaye Farzami M, Rahbar M. Real-Time Assay as A Tool for Detecting lytA Gene in Streptococcus pneumoniae Isolates. CELL JOURNAL 2014; 16:141-6. [PMID: 24567943 PMCID: PMC4072081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2013] [Accepted: 06/01/2013] [Indexed: 11/23/2022]
Abstract
OBJECTIVE In-time diagnosis of Streptococcus pneumoniae (S. pneumonia) can play a significant role in decreasing morbidity and mortality rate. Applying molecular methods has gained popularity due to the existing limits of routine diagnostic methods. Examining the expression of different genes of this bacterium through different molecular methods suggests that lytA gene has a higher sensitivity and specificity in diagnosis of Streptococcus pneumoniae. The aim of this study was to evalutate lytA gene expression in diagnosis of invasive S. pneumonia in culture positive specimens by real-time polymerase chain reaction (PCR). MATERIALS AND METHODS IIn this a descriptive study, All received specimens were isolated to identify S. pneumoniae. DNA was then extracted and after optimizing the test and determining the detection limit, samples were tested by real-time PCR using lytA gene primers. RESULTS Twenty seven isolates were diagnosed as S. pneumoniae. In all, the extracted DNA was positive in real-time method. The electrophoresis of the products also confirmed the presence of single product b along with the 53 base pair fragment. The detection limit of the test was less 6 colony forming unit (CFU). CONCLUSION Real-Time PCR seems to provide reliable and rapid results. We suggest that this test should be conducted on the preliminary isolated specimens, since applying various biochemical tests need one extra working day.
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Affiliation(s)
- Masoud Hajia
- Reference Health Laboratories Research Center, Ministry of Health & Medical Education,
Tehran, Iran
| | - Mohammad Farzanehkhah
- Science and Research Branch, Islamic Azad University, Arak, Iran,P.O. Box: 1587695815Science and Research BranchIslamic Azad UniversityArakIran
| | | | - AliReza Dolatyar
- Reference Health Laboratories Research Center, Ministry of Health & Medical Education,
Tehran, Iran
| | - Mohsen Imani
- Reference Health Laboratories Research Center, Ministry of Health & Medical Education,
Tehran, Iran
| | - Roghieh Saburian
- Reference Health Laboratories Research Center, Ministry of Health & Medical Education,
Tehran, Iran
| | - Marjan Rahnamaye Farzami
- Reference Health Laboratories Research Center, Ministry of Health & Medical Education,
Tehran, Iran
| | - Mohammad Rahbar
- Reference Health Laboratories Research Center, Ministry of Health & Medical Education,
Tehran, Iran
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Hong E, Giuliani MM, Deghmane AE, Comanducci M, Brunelli B, Dull P, Pizza M, Taha MK. Could the multicomponent meningococcal serogroup B vaccine (4CMenB) control Neisseria meningitidis capsular group X outbreaks in Africa? Vaccine 2013; 31:1113-6. [DOI: 10.1016/j.vaccine.2012.12.022] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2012] [Revised: 12/06/2012] [Accepted: 12/08/2012] [Indexed: 02/03/2023]
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Jamieson FB, Rawte P, Deeks SL, Zhou J, Law DKS, Deng S, Tsang RSW. Genetic and antigenic characterization of invasive endemic serogroup B Neisseria meningitidis from Ontario, Canada, in 2001-2010. J Med Microbiol 2012; 62:46-55. [PMID: 23038803 DOI: 10.1099/jmm.0.050369-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
This study examined the antigenic and genetic diversity of serogroup B Neisseria meningitidis (MenB) recovered from invasive meningococcal disease (IMD) cases in Ontario, Canada, over the period 2001-2010 during which no MenB outbreaks had occurred. MenB was found to be responsible for 39 % of all IMD cases, with the remaining cases caused mainly by serogroups Y (28 %), C (23.5 %) and W135 (8 %). One hundred and ninety-three individual MenB case isolates were collected and characterized. Of the 88 sequence types (STs) identified, 75 were grouped into 14 known clonal complexes (CCs), whilst 13 STs were not assigned to any known CC. Fifty-seven different PorA genotypes and 88 STs defined the diversity of invasive MenB in Ontario, which supported the endemic nature of MenB disease in Ontario. Despite the presence of the hypervirulent ST-41/44 and ST-32 CCs, no single ST was predominant and responsible for a large number of IMD cases. Although the Québec outbreak clone of ST-269 was also found in Ontario, the 20 case isolates were genetically diverse: they grouped into seven STs and did not have a predominant PorA genotype. eburst analysis identified a new CC responsible for 14.5 % of the MenB case isolates. The six most common PorA variable region 2 (VR2) genotypes (VR2-9, -4, -14, -16, -13-1 and -16-3) were found in 67 % of invasive MenB isolates.
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Affiliation(s)
- Frances B Jamieson
- Faculty of Medicine, University of Toronto, Ontario, Canada.,Public Health Ontario Laboratory, Public Health Ontario, Ontario, Canada
| | - Prasad Rawte
- Public Health Ontario Laboratory, Public Health Ontario, Ontario, Canada
| | - Shelley L Deeks
- Dalla Lana School of Public Health, University of Toronto, Ontario, Canada.,Surveillance and Epidemiology, Public Health Ontario, Ontario, Canada
| | - Jianwei Zhou
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Dennis K S Law
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Saul Deng
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Raymond S W Tsang
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
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Ion torrent personal genome machine sequencing for genomic typing of Neisseria meningitidis for rapid determination of multiple layers of typing information. J Clin Microbiol 2012; 50:1889-94. [PMID: 22461678 DOI: 10.1128/jcm.00038-12] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Neisseria meningitidis causes invasive meningococcal disease in infants, toddlers, and adolescents worldwide. DNA sequence-based typing, including multilocus sequence typing, analysis of genetic determinants of antibiotic resistance, and sequence typing of vaccine antigens, has become the standard for molecular epidemiology of the organism. However, PCR of multiple targets and consecutive Sanger sequencing provide logistic constraints to reference laboratories. Taking advantage of the recent development of benchtop next-generation sequencers (NGSs) and of BIGSdb, a database accommodating and analyzing genome sequence data, we therefore explored the feasibility and accuracy of Ion Torrent Personal Genome Machine (PGM) sequencing for genomic typing of meningococci. Three strains from a previous meningococcus serogroup B community outbreak were selected to compare conventional typing results with data generated by semiconductor chip-based sequencing. In addition, sequencing of the meningococcal type strain MC58 provided information about the general performance of the technology. The PGM technology generated sequence information for all target genes addressed. The results were 100% concordant with conventional typing results, with no further editing being necessary. In addition, the amount of typing information, i.e., nucleotides and target genes analyzed, could be substantially increased by the combined use of genome sequencing and BIGSdb compared to conventional methods. In the near future, affordable and fast benchtop NGS machines like the PGM might enable reference laboratories to switch to genomic typing on a routine basis. This will reduce workloads and rapidly provide information for laboratory surveillance, outbreak investigation, assessment of vaccine preventability, and antibiotic resistance gene monitoring.
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