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de Souza Santos DR, do Carmo CN, de Filippis I. High-Resolution Melting (HRM) for rapid MLST analysis of Neisseria meningitidis. METHODS IN MICROBIOLOGY 2022; 200:106557. [PMID: 35964773 DOI: 10.1016/j.mimet.2022.106557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Revised: 08/08/2022] [Accepted: 08/08/2022] [Indexed: 10/15/2022]
Abstract
The genetic characterization of meningococcal isolates is extremely important for the epidemiological monitoring of meningococcal disease, through the identification of circulating epidemic clones, with the purpose of supporting specific actions of Health Surveillance to contain outbreaks. The objective of this work is to determine a strategy for the epidemiological control of Neisseria meningitidis (Nm) through the detection of genetic signatures of Multilocus Sequence Typing (MLST) genes, by the method of high-resolution DNA melting analysis (qPCR-HRM), to identify the main hypervirulent clones circulating in the country. We analyzed 65 cc103 strains, 19 cc11, 38 cc32 and 8 cc41/44 and 17 were not associated to a specific cc. For the abcZ gene a total of 112 strains were tested, 79 for adk and gdh genes, 87 for aroE, 27 for fumC and 70 strains for pdhC gene. The results obtained were compared and validated with nucleotide sequencing. The percentage of correct allele detection for each clonal complex ranged between 77% and 100%. After an active search in PubMLST, it was found that by inserting results from at least 4 alleles in the MLST database, it is possible to determine the clonal complex of 99% to 100% of the deposited samples. The results obtained in this study suggest that it is possible to identify Nm clonal complexes by a combination analysis of melting curves (TM) of four constitutional genes included in the MLST scheme by qPCR-HRM.
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Affiliation(s)
| | - Cleber Nascimento do Carmo
- Departamento de Epidemiologia e Métodos Quantitativos em Saúde, Escola Nacional de Saúde Pública, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, Brazil
| | - Ivano de Filippis
- Instituto Nacional de Controle de Qualidade em Saúde, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, Brazil
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Moura ARSS, Kretz CB, Ferreira IE, Nunes AMPB, de Moraes JC, Reis MG, McBride AJA, Wang X, Campos LC. Molecular characterization of Neisseria meningitidis isolates recovered from 11-19-year-old meningococcal carriers in Salvador, Brazil. PLoS One 2017; 12:e0185038. [PMID: 28931058 PMCID: PMC5607198 DOI: 10.1371/journal.pone.0185038] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2017] [Accepted: 09/04/2017] [Indexed: 11/18/2022] Open
Abstract
Characterization of meningococci isolated from the pharynx is essential towards understanding the dynamics of meningococcal carriage and disease. Meningococcal isolates, collected from adolescents resident in Salvador, Brazil during 2014, were characterized by multilocus sequence typing, genotyping or whole-genome sequencing. Most were nongroupable (61.0%), followed by genogroups B (11.9%) and Y (8.5%). We identified 34 different sequence types (STs), eight were new STs, distributed among 14 clonal complexes (cc), cc1136 represented 20.3% of the nongroupable isolates. The porA and fetA genotypes included P1.18,25-37 (11.9%), P1.18-1,3 (10.2%); F5-5 (23.7%), F4-66 (16.9%) and F1-7 (13.6%). The porB class 3 protein and the fHbp subfamily A (variants 2 and 3) genotypes were found in 93.0 and 71.0% of the isolates, respectively. NHBA was present in all isolates, and while most lacked NadA (94.9%), we detected the hyperinvasive lineages B:P1.19,15:F5-1:ST-639 (cc32); C:P1.22,14-6:F3-9:ST-3780 (cc103) and W:P1.5,2:F1-1:ST-11 (cc11). This is the first report on the genetic diversity and vaccine antigen prevalence among N. meningitidis carriage isolates in the Northeast of Brazil. This study highlights the need for ongoing characterization of meningococcal isolates following the introduction of vaccines and for determining public health intervention strategies.
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Affiliation(s)
| | - Cécilia Batmalle Kretz
- Meningitis and Vaccine Preventable Diseases Branch, Division of Bacterial Diseases, Centers for Disease Control and Prevention, Atlanta, United States of America
| | - Italo Eustáquio Ferreira
- Laboratório de Patologia e Biologia Molecular, Instituto Gonçalo Moniz, FIOCRUZ-BA, Salvador, Bahia, Brazil
| | | | | | - Mitermayer Galvão Reis
- Laboratório de Patologia e Biologia Molecular, Instituto Gonçalo Moniz, FIOCRUZ-BA, Salvador, Bahia, Brazil
| | - Alan John Alexander McBride
- Laboratório de Patologia e Biologia Molecular, Instituto Gonçalo Moniz, FIOCRUZ-BA, Salvador, Bahia, Brazil
- Núcleo de Biotecnologia, Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas, Rio Grande do Sul, Brazil
| | - Xin Wang
- Meningitis and Vaccine Preventable Diseases Branch, Division of Bacterial Diseases, Centers for Disease Control and Prevention, Atlanta, United States of America
| | - Leila Carvalho Campos
- Laboratório de Patologia e Biologia Molecular, Instituto Gonçalo Moniz, FIOCRUZ-BA, Salvador, Bahia, Brazil
- * E-mail:
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Zahner V, Silva ACTDCE, Moraes GPD, McIntosh D, Filippis ID. Extended genetic analysis of Brazilian isolates of Bacillus cereus and Bacillus thuringiensis. Mem Inst Oswaldo Cruz 2013; 108:65-72. [PMID: 23440117 PMCID: PMC3974328 DOI: 10.1590/s0074-02762013000100011] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2012] [Accepted: 07/17/2012] [Indexed: 11/22/2022] Open
Abstract
Multiple locus sequence typing (MLST) was undertaken to extend the genetic characterization of 29 isolates of Bacillus cereus and Bacillus thuringiensis previously characterized in terms of presence/absence of sequences encoding virulence factors and via variable number tandem repeat (VNTR). Additional analysis involved polymerase chain reaction for the presence of sequences (be, cytK, inA, pag, lef, cya and cap), encoding putative virulence factors, not investigated in the earlier study. MLST analysis ascribed novel and unique sequence types to each of the isolates. A phylogenetic tree was constructed from a single sequence of 2,838 bp of concatenated loci sequences. The strains were not monophyletic by analysis of any specific housekeeping gene or virulence characteristic. No clear association in relation to source of isolation or to genotypic profile based on the presence or absence of putative virulence genes could be identified. Comparison of VNTR profiling with MLST data suggested a correlation between these two methods of genetic analysis. In common with the majority of previous studies, MLST was unable to provide clarification of the basis for pathogenicity among members of the B. cereus complex. Nevertheless, our application of MLST served to reinforce the notion that B. cereus and B. thuringiensis should be considered as the same species.
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Affiliation(s)
- Viviane Zahner
- Laboratório de Transmissores de Leishmanioses, Setor de Entomologia Médica Forense, Instituto Oswaldo Cruz, Rio de Janeiro, RJ, Brasil.
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Bratcher HB, Bennett JS, Maiden MCJ. Evolutionary and genomic insights into meningococcal biology. Future Microbiol 2012; 7:873-85. [PMID: 22827308 PMCID: PMC3492750 DOI: 10.2217/fmb.12.62] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Epidemic disease caused by Neisseria meningitidis, the meningococcus, has been recognized for two centuries, but remains incompletely controlled and understood. There have been dramatic reductions in serogroup A and C meningococcal disease following the introduction of protein-polysaccharide conjugate vaccines, but there is currently no comprehensive vaccine against serogroup B meningococci. Genetic analyses of meningococcal populations have provided many insights into the biology, evolution and pathogenesis of this important pathogen. The meningococcus, and its close relative the gonococcus, are the only pathogenic members of the genus Neisseria, and the invasive propensity of meningococci varies widely, with approximately a dozen 'hyperinvasive lineages' responsible for most disease. Despite this, attempts to identify a 'pathogenome', a subset of genes associated with the invasive phenotypes, have failed; however, genome-wide studies of representative meningococcal isolates using high-throughput sequencing are beginning to provide details on the relationship of invasive phenotype and genotype in this fascinating organism and how this relationship has evolved.
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de Filippis I, de Lemos APS, Hostetler JB, Wollenberg K, Sacchi CT, Harrison LH, Bash MC, Prevots DR. Molecular epidemiology of Neisseria meningitidis serogroup B in Brazil. PLoS One 2012; 7:e33016. [PMID: 22431994 PMCID: PMC3303791 DOI: 10.1371/journal.pone.0033016] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2011] [Accepted: 02/03/2012] [Indexed: 11/23/2022] Open
Abstract
Background Neisseria meningitidis serogroup B has been predominant in Brazil, but no broadly effective vaccine is available to prevent endemic meningococcal disease. To understand genetic diversity among serogroup B strains in Brazil, we selected a nationally representative sample of clinical disease isolates from 2004, and a temporally representative sample for the state of São Paulo (1988–2006) for study (n = 372). Methods We performed multi-locus sequence typing (MLST) and sequence analysis of five outer membrane protein (OMP) genes, including novel vaccine targets fHbp and nadA. Results In 2004, strain B:4:P1.15,19 clonal complex ST-32/ET-5 (cc32) predominated throughout Brazil; regional variation in MLST sequence type (ST), fetA, and porB was significant but diversity was limited for nadA and fHbp. Between 1988 and 1996, the São Paulo isolates shifted from clonal complex ST-41/44/Lineage 3 (cc41/44) to cc32. OMP variation was associated with but not predicted by cc or ST. Overall, fHbp variant 1/subfamily B was present in 80% of isolates and showed little diversity. The majority of nadA were similar to reference allele 1. Conclusions A predominant serogroup B lineage has circulated in Brazil for over a decade with significant regional and temporal diversity in ST, fetA, and porB, but not in nadA and fHbp.
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Affiliation(s)
- Ivano de Filippis
- National Quality Control Institute (INCQS), Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, Brazil
- Laboratory of Bacterial Polysaccharides, Center for Biologics Evaluation and Research (CBER), Food and Drug Administration (FDA), Bethesda, Maryland, United States of America
- Epidemiology Unit, Laboratory of Clinical Infectious Diseases, Division of Intramural Research, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, Maryland, United States of America
| | | | | | - Kurt Wollenberg
- Office of Cyberinfrastructure and Computational Biology (OCICB), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, Maryland, United States of America
| | | | - Lee H. Harrison
- Infectious Diseases Epidemiology Research Unit, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Margaret C. Bash
- Laboratory of Bacterial Polysaccharides, Center for Biologics Evaluation and Research (CBER), Food and Drug Administration (FDA), Bethesda, Maryland, United States of America
| | - D. Rebecca Prevots
- Epidemiology Unit, Laboratory of Clinical Infectious Diseases, Division of Intramural Research, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, Maryland, United States of America
- * E-mail:
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Fatal meningococcal meningitis in a HIV-infected patient caused by serogroup C Neisseria meningitidis belonging to the non-hypervirulent clonal complex ST-60 (cc60). Braz J Infect Dis 2011. [DOI: 10.1016/s1413-8670(11)70168-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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The elusive meningococcal meningitis serogroup: a systematic review of serogroup B epidemiology. BMC Infect Dis 2010; 10:175. [PMID: 20565757 PMCID: PMC2894839 DOI: 10.1186/1471-2334-10-175] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2009] [Accepted: 06/17/2010] [Indexed: 11/23/2022] Open
Abstract
Background Invasive meningococcal disease (IMD), is a widely distributed, complex human disease affecting all age categories. The causative agent, Neisseria meningitidis, is spread through aerosol respiratory droplets. 13 different serogroups have been identified, each with varying epidemiological features including prevalence, virulence, immunogenicity, geographical and temporal distribution. Although preventative measures are available for several of the serogroups, meningococcal disease caused by serogroup B is of particular interest due to the challenge it presents concerning vaccine development. Methods A systematic review of peer reviewed studies and reports, the collection of data from national and international health resources, along with the analysis of the Multi Locus Sequence Typing database was carried out aimed at collecting information concerning serogroup B IMD and the epidemiology attached to it. Results A continuous output of related and novel STs occurring worldwide in terms of the hypervirulent clonal complexes was observed both in published studies and the MLST database in this case using the eburst software, which highlights the genetically diverse nature of serogroup B strains. Conclusions With the recent dominance of serogroup B IMD seen in many countries, along with the presence of antibiotic resistance, vaccine development needs to target areas of the bacterium which tackle this widespread and heterogeneous aspect of meningococcal meningitis disease.
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The genetic structure of Neisseria meningitidis populations in Cuba before and after the introduction of a serogroup BC vaccine. INFECTION GENETICS AND EVOLUTION 2010; 10:546-54. [DOI: 10.1016/j.meegid.2010.02.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2009] [Revised: 02/04/2010] [Accepted: 02/05/2010] [Indexed: 11/20/2022]
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Clonal distribution of disease-associated and healthy carrier isolates of Neisseria meningitidis between 1983 and 2005 in Cuba. J Clin Microbiol 2009; 48:802-10. [PMID: 20042619 DOI: 10.1128/jcm.01653-09] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In response to epidemic levels of serogroup B meningococcal disease in Cuba during the 1980s, the VA-MENGOC-BC vaccine was developed and introduced into the National Infant Immunization Program in 1991. Since then the incidence of meningococcal disease in Cuba has returned to the low levels recorded before the epidemic. A total of 420 Neisseria meningitidis strains collected between 1983 and 2005 in Cuba were analyzed by multilocus sequence typing (MLST). The set of strains comprised 167 isolated from disease cases and 253 obtained from healthy carriers. By MLST analysis, 63 sequence types (STs) were identified, and 32 of these were reported to be a new ST. The Cuban isolates were associated with 12 clonal complexes; and the most common were ST-32 (246 isolates), ST-53 (86 isolates), and ST-41/44 (36 isolates). This study also showed that the application of VA-MENGOC-BC, the Cuban serogroup B and C vaccine, reduced the frequency and diversity of hypervirulent clonal complexes ST-32 (vaccine serogroup B type-strain) and ST-41/44 and also affected other lineages. Lineages ST-8 and ST-11 were no longer found during the postvaccination period. The vaccine also affected the genetic composition of the carrier-associated meningococcal isolates. The number of carrier isolates belonging to hypervirulent lineages decreased significantly after vaccination, and ST-53, a sequence type common in carriers, became the predominant ST.
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Weidlich L, Baethgen LF, Mayer LW, Moraes C, Klein CC, Nunes LS, Rios SDS, Kmetzsch CI, Rossetti ML, Zaha A. High prevalence of Neisseria meningitidis hypervirulent lineages and emergence of W135:P1.5,2:ST-11 clone in Southern Brazil. J Infect 2008; 57:324-31. [DOI: 10.1016/j.jinf.2008.07.014] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2008] [Revised: 07/25/2008] [Accepted: 07/29/2008] [Indexed: 11/17/2022]
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Baethgen LF, Weidlich L, Moraes C, Klein C, Nunes LS, Cafrune PI, Lemos AP, Rios SS, Abreu MF, Kmetzsch C, Sperb AF, Riley LW, Rossetti MLR, Zaha A. Epidemiology of meningococcal disease in southern Brazil from 1995 to 2003, and molecular characterization of Neisseria meningitidis using multilocus sequence typing. Trop Med Int Health 2008; 13:31-40. [DOI: 10.1111/j.1365-3156.2007.01970.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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de Filippis I, de Andrade CF, de Almeida AECC, Clementino MM, Fernandes CACM, de Carvalho ML, Vicente ACP. Neisseria meningitidis PorA variable regions: rapid detection of P1.7 and P1.19 variants by PCR. Lett Appl Microbiol 2007; 45:426-31. [PMID: 17897387 DOI: 10.1111/j.1472-765x.2007.02205.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
AIM Rapid characterization of variable region (VR)1 variants of the porA gene among invasive strains is crucial for outbreak management and epidemiology studies. Recent sequence analysis studies in Brazil showed that the VR1 P1.7 and P1.19 variants are highly prevalent, accounting for 68%, of the total number of VR1 variants characterized. The aim of this work is to develop a rapid polymerase chain reaction (PCR)-based method for genosubtyping Neisseria meningitidis by detection of porA variable regions P1.7 and P1.19. METHODS AND RESULTS PCR primers for the detection of porA VR1 P1.7 and P1.19 were designed and tested using 198 clinical N. meningitidis isolates that had been previously evaluated by porA sequencing. All 50 strains with VR1 P1.7 and all 65 strains with VR1 P1.19 were positively identified by the respective VR-specific PCR and no false-positive reactions occurred. CONCLUSIONS VR-specific PCR amplification accurately identified VR P1.7 and P1.19 strains. SIGNIFICANCE AND IMPACT OF THE STUDY To overcome the disadvantages of serosubtyping and sequencing for typing the porA VR1 segment of N. meningitidis, we developed a PCR-based method to rapidly and accurately detect VR1 P1.7 and P1.19 variants. This approach is highly specific and sensitive; moreover it may allow for genotype determination of culture-negative samples.
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Affiliation(s)
- I de Filippis
- Microbiology Dept., National Institute for Quality Control of Health, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil.
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de Filippis I, de Andrade CF, Silva L, Prevots DR, Vicente ACP. PorA variable antigenic regions VR1, VR2, and VR3 of Neisseria meningitidis serogroups B and C isolated in Brazil from 1999 to 2004. Infect Immun 2007; 75:3683-5. [PMID: 17502397 PMCID: PMC1932963 DOI: 10.1128/iai.01721-06] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2006] [Revised: 01/24/2007] [Accepted: 05/02/2007] [Indexed: 11/20/2022] Open
Abstract
The high genetic diversity found among the PorA regions VR1 and VR2 of 101 Neisseria meningitidis isolates from patients with meningococcal disease and healthy carriers in Brazil contrasts with the stability found in the PorA VR3 of these isolates. The presence of VR3 epitope variant 35 or 36 on the surfaces of 87% of the strains analyzed suggests that these antigens should be considered for inclusion in new formulations of vaccines against serogroup B meningococci in Brazil.
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Affiliation(s)
- Ivano de Filippis
- National Institute for Quality Control of Health, Fundacao Oswaldo Cruz, Avenida Brasil 4365, Manguinhos, Rio de Janeiro 21045-900, Brazil.
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Abstract
Multilocus sequence typing (MLST) was proposed in 1998 as a portable, universal, and definitive method for characterizing bacteria, using the human pathogen Neisseria meningitidis as an example. In addition to providing a standardized approach to data collection, by examining the nucleotide sequences of multiple loci encoding housekeeping genes, or fragments of them, MLST data are made freely available over the Internet to ensure that a uniform nomenclature is readily available to all those interested in categorizing bacteria. At the time of writing, over thirty MLST schemes have been published and made available on the Internet, mostly for pathogenic bacteria, although there are schemes for pathogenic fungi and some nonpathogenic bacteria. MLST data have been employed in epidemiological investigations of various scales and in studies of the population biology, pathogenicity, and evolution of bacteria. The increasing speed and reduced cost of nucleotide sequence determination, together with improved web-based databases and analysis tools, present the prospect of increasingly wide application of MLST.
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Affiliation(s)
- Martin C J Maiden
- Peter Medawar Building for Pathogen Research and Department of Zoology, University of Oxford, Oxford, OX1 3SY, United Kingdom.
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