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Wyllie AL, Rots NY, Wijmenga-Monsuur AJ, van Houten MA, Sanders EAM, Trzciński K. Saliva as an alternative sample type for detection of pneumococcal carriage in young children. MICROBIOLOGY (READING, ENGLAND) 2023; 169:001394. [PMID: 37819029 PMCID: PMC10634364 DOI: 10.1099/mic.0.001394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 09/14/2023] [Indexed: 10/13/2023]
Abstract
For children, the gold standard for the detection of pneumococcal carriage is conventional culture of a nasopharyngeal swab. Saliva, however, has a history as one of the most sensitive methods for surveillance of pneumococcal colonization and has recently been shown to improve carriage detection in older age groups. Here, we compared the sensitivity of paired nasopharyngeal and saliva samples from PCV7-vaccinated 24-month-old children for pneumococcal carriage detection using conventional and molecular detection methods. Nasopharyngeal and saliva samples were collected from 288 24-month-old children during the autumn/winter, 2012/2013. All samples were first processed by conventional diagnostic culture. Next, DNA extracted from all plate growth was tested by qPCR for the presence of the pneumococcal genes piaB and lytA and a subset of serotypes. By culture, 161/288 (60 %) nasopharyngeal swabs tested positive for pneumococcus, but detection was not possible from saliva due to abundant polymicrobial growth on culture plates. By qPCR, 155/288 (54 %) culture-enriched saliva samples and 187/288 (65 %) nasopharyngeal swabs tested positive. Altogether, 219/288 (76 %) infants tested positive for pneumococcus, with qPCR-based carriage detection of culture-enriched nasopharyngeal swabs detecting significantly more carriers compared to either conventional culture (P<0.001) or qPCR detection of saliva (P=0.002). However, 32/219 (15 %) carriers were only positive in saliva, contributing significantly to the overall number of carriers detected (P=0.002). While testing nasopharyngeal swabs by qPCR proved most sensitive for pneumococcal detection in infants, saliva sampling could be considered as complementary to provide additional information on carriage and serotypes that may not be detected in the nasopharynx and may be particularly useful in longitudinal studies, requiring repeated sampling of study participants.
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Affiliation(s)
- Anne L. Wyllie
- Paediatric Immunology and Infectious Diseases, Wilhelmina Children’s Hospital, University Medical Center Utrecht, Utrecht, The Netherlands
- Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
| | - Nynke Y. Rots
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Alienke J. Wijmenga-Monsuur
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | | | - Elisabeth A. M. Sanders
- Paediatric Immunology and Infectious Diseases, Wilhelmina Children’s Hospital, University Medical Center Utrecht, Utrecht, The Netherlands
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Krzysztof Trzciński
- Paediatric Immunology and Infectious Diseases, Wilhelmina Children’s Hospital, University Medical Center Utrecht, Utrecht, The Netherlands
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Càmara J, Grau I, González-Díaz A, Tubau F, Calatayud L, Cubero M, Domínguez MÁ, Liñares J, Yuste J, Pallarés R, Ardanuy C. A historical perspective of MDR invasive pneumococcal disease in Spanish adults. J Antimicrob Chemother 2021; 76:507-515. [PMID: 33254238 DOI: 10.1093/jac/dkaa465] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 10/11/2020] [Indexed: 11/12/2022] Open
Abstract
OBJECTIVES To analyse the clonal dynamics and clinical characteristics of adult invasive pneumococcal disease (IPD) caused by MDR and penicillin-non-susceptible (PNS) pneumococci in Spain. METHODS All adult IPD episodes were prospectively collected (1994-2018). Streptococcus pneumoniae isolates were serotyped, genotyped and tested for antimicrobial susceptibility. Changes in the incidence of IPD were analysed and risk factors contributing to MDR were assessed by logistic regression. RESULTS Of 2095 IPD episodes, 635 (30.3%) were caused by MDR/PNS isolates. Over the study period, the incidence of MDR/PNS-IPD decreased (IRR 0.70; 95% CI 0.53-0.93) whereas that of susceptible isolates remained stable (IRR 0.96; 95% CI 0.80-1.16). A reduction of resistance rates to penicillin (-19.5%; 95% CI -37% to 2%) and cefotaxime (-44.5%; 95% CI -64% to -15%) was observed. Two clones, Spain9V-ST156 and Denmark14-ST230, accounted for 50% of current resistant disease. Among current MDR/PNS isolates, 45.8% expressed serotypes not covered by the upcoming PCV15/PCV20 vaccines. MDR/PNS episodes were associated with older patients with comorbidities, nosocomial acquisition and higher 30 day mortality. MDR/PNS pneumococci were not independently associated with 30 day mortality in multivariate analysis [OR 0.826 (0.648-1.054)]. CONCLUSIONS Our study shows an overall reduction of MDR/PNS isolates in adults after the introduction of pneumococcal conjugate vaccines. However, a significant proportion of current resistant isolates are not covered by any of the upcoming PCV15/PCV20 vaccines. The burden of resistant disease is related to older patients with underlying conditions and caused by two major clones. Our data show that MDR is not a statistically significant factor related to increased mortality.
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Affiliation(s)
- Jordi Càmara
- Microbiology Department, Hospital Universitari de Bellvitge, University of Barcelona, IDIBELL, Barcelona, Spain.,Ciber de Enfermedades Respiratorias (CIBERes), ISCIII, Madrid, Spain
| | - Inmaculada Grau
- Ciber de Enfermedades Respiratorias (CIBERes), ISCIII, Madrid, Spain.,Infectious Diseases Department, Hospital Universitari de Bellvitge, University of Barcelona. IDIBELL, Barcelona, Spain
| | - Aida González-Díaz
- Microbiology Department, Hospital Universitari de Bellvitge, University of Barcelona, IDIBELL, Barcelona, Spain.,Ciber de Enfermedades Respiratorias (CIBERes), ISCIII, Madrid, Spain
| | - Fe Tubau
- Microbiology Department, Hospital Universitari de Bellvitge, University of Barcelona, IDIBELL, Barcelona, Spain.,Ciber de Enfermedades Respiratorias (CIBERes), ISCIII, Madrid, Spain
| | - Laura Calatayud
- Microbiology Department, Hospital Universitari de Bellvitge, University of Barcelona, IDIBELL, Barcelona, Spain.,Ciber de Enfermedades Respiratorias (CIBERes), ISCIII, Madrid, Spain
| | - Meritxell Cubero
- Microbiology Department, Hospital Universitari de Bellvitge, University of Barcelona, IDIBELL, Barcelona, Spain.,Ciber de Enfermedades Respiratorias (CIBERes), ISCIII, Madrid, Spain
| | - M Ángeles Domínguez
- Microbiology Department, Hospital Universitari de Bellvitge, University of Barcelona, IDIBELL, Barcelona, Spain.,Spanish Network for Research in Infectious Diseases (REIPI), Instituto de Salud Carlos III, Madrid, Spain.,Departament of Pathology and Experimental Therapeutics, University of Barcelona, Barcelona, Spain
| | - Josefina Liñares
- Microbiology Department, Hospital Universitari de Bellvitge, University of Barcelona, IDIBELL, Barcelona, Spain.,Ciber de Enfermedades Respiratorias (CIBERes), ISCIII, Madrid, Spain
| | - José Yuste
- Ciber de Enfermedades Respiratorias (CIBERes), ISCIII, Madrid, Spain.,Pneumococcal Reference Laboratory. Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Román Pallarés
- Ciber de Enfermedades Respiratorias (CIBERes), ISCIII, Madrid, Spain.,Infectious Diseases Department, Hospital Universitari de Bellvitge, University of Barcelona. IDIBELL, Barcelona, Spain
| | - Carmen Ardanuy
- Microbiology Department, Hospital Universitari de Bellvitge, University of Barcelona, IDIBELL, Barcelona, Spain.,Ciber de Enfermedades Respiratorias (CIBERes), ISCIII, Madrid, Spain.,Departament of Pathology and Experimental Therapeutics, University of Barcelona, Barcelona, Spain
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3
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Zemlickova H, Jakubu V, Fridrichova M, Malisova L, Trojanek M. The association of pili with the emergence and replacement of the major antibiotic resistant pneumococcal clones. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2019; 53:690-695. [PMID: 31010747 DOI: 10.1016/j.jmii.2019.03.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 02/20/2019] [Accepted: 03/20/2019] [Indexed: 11/18/2022]
Abstract
BACKGROUND The aim of this study was to evaluate the presence of pilus islet 1 (PI-1) and to determine its clade type in pneumococcal isolates with reduced susceptibility to penicillin (penicillin non-susceptible pneumococci - PNSP) and/or resistant to macrolides isolated prior to and after the introduction of pneumococcal conjugate vaccines (PCVs) in the Czech Republic. METHODS Clinical isolates of serotypes 9V (n = 68) and 19A (n = 89) were examined. Isolates were characterised by multilocus sequence typing (MLST). The presence of PI-1 was determined by screening for the sortase B, C, and D genes located within PI-1. In the presence of PI-1 pilus, clade types were classified by PCR. RESULTS In the pre-PCV period (2000-2007), the prevalence of PNSP was 3.9% and 2.7% of isolates were resistant to erythromycin. During 2012-2015 (post-PCV period), the rates of PNSP remained stable (3.6%), but resistance to erythromycin increased to 8.3%. While in 2000-2007, resistance to antibiotics was associated mainly with serotype 9V, in 2012-2015, it was replaced by serotype 19A. PI-1 positive isolates were seen in both serotypes. All isolates (68) of serotype 9V belonged to the Spain9V-3 (CC156) clone and carried PI-1 of clade type I while 96.5% (56/58) of isolates of 19A serotype belonged to the Netherlands15B-37 (CC199) clone and carried PI-1 of clade type II. CONCLUSIONS Both major antibiotic resistant clones carried PI-1, although they differ in the clade type. Thus the role of PI-1 should be evaluated in further studies and potentially considered in the spread of antibiotic resistant clones.
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Affiliation(s)
- Helena Zemlickova
- Centre for Epidemiology and Microbiology, National Institute of Public Health, Prague, Czech Republic; Department of Clinical Microbiology, Faculty of Medicine and University Hospital, Charles University, Hradec Kralove, Czech Republic.
| | - Vladislav Jakubu
- Centre for Epidemiology and Microbiology, National Institute of Public Health, Prague, Czech Republic
| | - Marta Fridrichova
- Centre for Epidemiology and Microbiology, National Institute of Public Health, Prague, Czech Republic
| | - Lucia Malisova
- Centre for Epidemiology and Microbiology, National Institute of Public Health, Prague, Czech Republic
| | - Milan Trojanek
- Department of Infectious Diseases, Faculty of Medicine, Charles University in Prague, Budínova 2, 180 81 Prague, Czech Republic; Department of Infectious, Parasitic and Tropical Diseases, Na Bulovce Hospital, Budínova 2, 180 81 Prague, Czech Republic
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4
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Wyllie AL, Pannekoek Y, Bovenkerk S, van Engelsdorp Gastelaars J, Ferwerda B, van de Beek D, Sanders EAM, Trzciński K, van der Ende A. Sequencing of the variable region of rpsB to discriminate between Streptococcus pneumoniae and other streptococcal species. Open Biol 2018; 7:rsob.170074. [PMID: 28931649 PMCID: PMC5627049 DOI: 10.1098/rsob.170074] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 08/11/2017] [Indexed: 01/08/2023] Open
Abstract
The vast majority of streptococci colonizing the human upper respiratory tract are commensals, only sporadically implicated in disease. Of these, the most pathogenic is Mitis group member, Streptococcus pneumoniae Phenotypic and genetic similarities between streptococci can cause difficulties in species identification. Using ribosomal S2-gene sequences extracted from whole-genome sequences published from 501 streptococci, we developed a method to identify streptococcal species. We validated this method on non-pneumococcal isolates cultured from cases of severe streptococcal disease (n = 101) and from carriage (n = 103), and on non-typeable pneumococci from asymptomatic individuals (n = 17) and on whole-genome sequences of 1157 pneumococcal isolates from meningitis in the Netherlands. Following this, we tested 221 streptococcal isolates in molecular assays originally assumed specific for S. pneumoniae, targeting cpsA, lytA, piaB, ply, Spn9802, zmpC and capsule-type-specific genes. Cluster analysis of S2-sequences showed grouping according to species in line with published phylogenies of streptococcal core genomes. S2-typing convincingly distinguished pneumococci from non-pneumococcal species (99.2% sensitivity, 100% specificity). Molecular assays targeting regions of lytA and piaB were 100% specific for S. pneumoniae, whereas assays targeting cpsA, ply, Spn9802, zmpC and selected serotype-specific assays (but not capsular sequence typing) showed a lack of specificity. False positive results were over-represented in species associated with carriage, although no particular confounding signal was unique for carriage isolates.
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Affiliation(s)
- Anne L Wyllie
- Department of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Yvonne Pannekoek
- Department of Medical Microbiology, Academic Medical Center, Amsterdam, the Netherlands
| | - Sandra Bovenkerk
- Department of Medical Microbiology, Academic Medical Center, Amsterdam, the Netherlands
| | - Jody van Engelsdorp Gastelaars
- Department of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Bart Ferwerda
- Department of Neurology, Academic Medical Center, Amsterdam Neuroscience, Amsterdam, the Netherlands
| | - Diederik van de Beek
- Department of Neurology, Academic Medical Center, Amsterdam Neuroscience, Amsterdam, the Netherlands
| | - Elisabeth A M Sanders
- Department of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, the Netherlands.,Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Krzysztof Trzciński
- Department of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Arie van der Ende
- Department of Medical Microbiology, Academic Medical Center, Amsterdam, the Netherlands.,The Netherlands Reference Laboratory for Bacterial Meningitis, Academic Medical Center, Amsterdam, the Netherlands
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Matsuyama T, Fukuda Y, Sakai T, Tanimoto N, Nakanishi M, Nakamura Y, Takano T, Nakayasu C. Clonal structure in Ichthyobacterium seriolicida, the causative agent of bacterial haemolytic jaundice in yellowtail, Seriola quinqueradiata, inferred from molecular epidemiological analysis. JOURNAL OF FISH DISEASES 2017; 40:1065-1075. [PMID: 28000932 DOI: 10.1111/jfd.12586] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Revised: 10/14/2016] [Accepted: 10/17/2016] [Indexed: 06/06/2023]
Abstract
Bacterial haemolytic jaundice caused by Ichthyobacterium seriolicida has been responsible for mortality in farmed yellowtail, Seriola quinqueradiata, in western Japan since the 1980s. In this study, polymorphic analysis of I. seriolicida was performed using three molecular methods: amplified fragment length polymorphism (AFLP) analysis, multilocus sequence typing (MLST) and multiple-locus variable-number tandem repeat analysis (MLVA). Twenty-eight isolates were analysed using AFLP, while 31 isolates were examined by MLST and MLVA. No polymorphisms were identified by AFLP analysis using EcoRI and MseI, or by MLST of internal fragments of eight housekeeping genes. However, MLVA revealed variation in repeat numbers of three elements, allowing separation of the isolates into 16 sequence types. The unweighted pair group method using arithmetic averages cluster analysis of the MLVA data identified four major clusters, and all isolates belonged to clonal complexes. It is likely that I. seriolicida populations share a common ancestor, which may be a recently introduced strain.
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Affiliation(s)
- T Matsuyama
- National Research Institute of Aquaculture, Fisheries Research Agency, Research Center for Fish Diseases, Minami-Ise, Mie, Japan
| | - Y Fukuda
- Fisheries Research Institute, Oita Prefectural Agriculture, Forestry and Fisheries Research Center, Kamiura, Oita, Japan
| | - T Sakai
- National Research Institute of Aquaculture, Fisheries Research Agency, Research Center for Fish Diseases, Minami-Ise, Mie, Japan
| | - N Tanimoto
- Fisheries Technology Department, Kyoto Prefectural Agriculture, Forestry and Fisheries Technology Center, Miyazu, Kyoto, Japan
| | - M Nakanishi
- Fisheries Technology Department, Kyoto Prefectural Agriculture, Forestry and Fisheries Technology Center, Miyazu, Kyoto, Japan
| | - Y Nakamura
- National Research Institute of Fisheries Science, Fisheries Research Agency, Research Center for Bioinformatics and Biosciences, Yokohama, Kanagawa, Japan
| | - T Takano
- National Research Institute of Aquaculture, Fisheries Research Agency, Research Center for Fish Diseases, Minami-Ise, Mie, Japan
| | - C Nakayasu
- National Research Institute of Aquaculture, Fisheries Research Agency, Research Center for Fish Diseases, Minami-Ise, Mie, Japan
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Polysaccharide Capsule Composition of Pneumococcal Serotype 19A Subtypes Is Unaltered among Subtypes and Independent of the Nutritional Environment. Infect Immun 2016; 84:3152-3160. [PMID: 27550933 DOI: 10.1128/iai.00474-16] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Accepted: 08/12/2016] [Indexed: 11/20/2022] Open
Abstract
Serotype 19A strains have emerged as a cause of invasive pneumococcal disease after the introduction of the 7-valent pneumococcal conjugate vaccine (PCV7), and serotype 19A has now been included in the recent 13-valent vaccine (PCV13). Genetic analysis has revealed at least three different capsular serotype 19A subtypes, and nutritional environment-dependent variation of the 19A capsule structure has been reported. Pneumococcal vaccine effectiveness and serotyping accuracy might be impaired by structural differences in serotype 19A capsules. We therefore analyzed the distribution of 19A subtypes collected within a Swiss national surveillance program and determined capsule composition under different nutritional conditions with high-performance liquid chromatography (HPLC), gas chromatography-mass spectrometry (GC-MS), and nuclear magnetic resonance (NMR) spectroscopy. After the introduction of PCV7, a significant relative increase of subtype 19A-II and decrease of 19A-I occurred. Chemical analyses showed no difference in the composition as well as the linkage of 19A subtype capsular saccharides grown in defined and undefined growth media, which is consistent with a trisaccharide repeat unit composed of rhamnose, N-acetyl-mannosamine, and glucose. In summary, our study suggests that no structural variance dependent of the nutritional environment or the subtype exists. The serotype 19A subtype shift observed after the introduction of the PCV7 can therefore not be explained by selection of a capsule structure variant. However, capsule composition analysis of emerging 19A clones is recommended in cases where there is no other explanation for a selective advantage, such as antibiotic resistance or loss or acquisition of other virulence factors.
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7
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Krone CL, Oja AE, van de Groep K, Sanders EAM, Bogaert D, Trzciński K. Dried Saliva Spots: A Robust Method for Detecting Streptococcus pneumoniae Carriage by PCR. Int J Mol Sci 2016; 17:343. [PMID: 26959014 PMCID: PMC4813204 DOI: 10.3390/ijms17030343] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Revised: 02/23/2016] [Accepted: 03/01/2016] [Indexed: 01/29/2023] Open
Abstract
The earliest studies in the late 19th century on Streptococcus pneumoniae (S. pneumoniae) carriage used saliva as the primary specimen. However, interest in saliva declined after the sensitive mouse inoculation method was replaced by conventional culture, which made isolation of pneumococci from the highly polymicrobial oral cavity virtually impossible. Here, we tested the feasibility of using dried saliva spots (DSS) for studies on pneumococcal carriage. Saliva samples from children and pneumococcus-spiked saliva samples from healthy adults were applied to paper, dried, and stored, with and without desiccant, at temperatures ranging from -20 to 37 °C for up to 35 days. DNA extracted from DSS was tested with quantitative-PCR (qPCR) specifically for S. pneumoniae. When processed immediately after drying, the quantity of pneumococcal DNA detected in spiked DSS from adults matched the levels in freshly spiked raw saliva. Furthermore, pneumococcal DNA was stable in DSS stored with desiccant for up to one month over a broad range of temperatures. There were no differences in the results when spiking saliva with varied pneumococcal strains. The collection of saliva can be a particularly useful in surveillance studies conducted in remote settings, as it does not require trained personnel, and DSS are resilient to various transportation conditions.
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Affiliation(s)
- Cassandra L Krone
- Pediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital, University Medical Center Utrecht, 3508 AB Utrecht, The Netherlands.
| | - Anna E Oja
- Pediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital, University Medical Center Utrecht, 3508 AB Utrecht, The Netherlands.
| | - Kirsten van de Groep
- Pediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital, University Medical Center Utrecht, 3508 AB Utrecht, The Netherlands.
| | - Elisabeth A M Sanders
- Pediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital, University Medical Center Utrecht, 3508 AB Utrecht, The Netherlands.
| | - Debby Bogaert
- Pediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital, University Medical Center Utrecht, 3508 AB Utrecht, The Netherlands.
| | - Krzysztof Trzciński
- Pediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital, University Medical Center Utrecht, 3508 AB Utrecht, The Netherlands.
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8
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Hanincova K, Mukherjee P, Ogden NH, Margos G, Wormser GP, Reed KD, Meece JK, Vandermause MF, Schwartz I. Multilocus sequence typing of Borrelia burgdorferi suggests existence of lineages with differential pathogenic properties in humans. PLoS One 2013; 8:e73066. [PMID: 24069170 PMCID: PMC3775742 DOI: 10.1371/journal.pone.0073066] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Accepted: 07/17/2013] [Indexed: 11/18/2022] Open
Abstract
The clinical manifestations of Lyme disease, caused by Borrelia burgdorferi, vary considerably in different patients, possibly due to infection by strains with varying pathogenicity. Both rRNA intergenic spacer and ospC typing methods have proven to be useful tools for categorizing B. burgdorferi strains that vary in their tendency to disseminate in humans. Neither method, however, is suitable for inferring intraspecific relationships among strains that are important for understanding the evolution of pathogenicity and the geographic spread of disease. In this study, multilocus sequence typing (MLST) was employed to investigate the population structure of B. burgdorferi recovered from human Lyme disease patients. A total of 146 clinical isolates from patients in New York and Wisconsin were divided into 53 sequence types (STs). A goeBURST analysis, that also included previously published STs from the northeastern and upper Midwestern US and adjoining areas of Canada, identified 11 major and 3 minor clonal complexes, as well as 14 singletons. The data revealed that patients from New York and Wisconsin were infected with two distinct, but genetically and phylogenetically closely related, populations of B. burgdorferi. Importantly, the data suggest the existence of B. burgdorferi lineages with differential capabilities for dissemination in humans. Interestingly, the data also indicate that MLST is better able to predict the outcome of localized or disseminated infection than is ospC typing.
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Affiliation(s)
- Klara Hanincova
- Department of Microbiology and Immunology, New York Medical College, Valhalla, New York, United States of America
- * E-mail:
| | - Priyanka Mukherjee
- Department of Microbiology and Immunology, New York Medical College, Valhalla, New York, United States of America
| | - Nicholas H. Ogden
- Zoonoses Division, Centre for Food-borne, Environmental and Zoonotic Infectious Diseases, Public Health Agency of Canada, Ottawa, Ontario, Canada
| | - Gabriele Margos
- Institute for Infectious Diseases and Zoonoses, Ludwig-Maximilians-University Munich and National Reference Centre for Borrelia at the Bavarian Health and Food Safety Authority, Oberschleissheim, Germany
| | - Gary P. Wormser
- Division of Infectious Diseases, Department of Medicine, New York Medical College, Valhalla, New York, United States of America
| | - Kurt D. Reed
- Department of Pathology and Laboratory Medicine, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Jennifer K. Meece
- Marshfield Clinic Research Foundation, Marshfield, Wisconsin, United States of America
| | - Mary F. Vandermause
- Marshfield Clinic Research Foundation, Marshfield, Wisconsin, United States of America
| | - Ira Schwartz
- Department of Microbiology and Immunology, New York Medical College, Valhalla, New York, United States of America
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Abstract
BACKGROUND Vaccination against 7 serotypes of Streptococcus pneumoniae has led to the near extinction of vaccine serotypes in both disease and asymptomatic carriage. In carriage, vaccine serotypes have been replaced by nonvaccine serotypes. METHODS We used multilocus sequence typing to analyze a sample of 294 isolates of S. pneumoniae carried by Massachusetts children (aged, 3 months-7 years) and examine the results for serotype switching and association with antimicrobial resistance. RESULTS Eighty-six distinct sequence types (STs) were found, 10 of which exhibited a serotype other than that which would be expected from previous carriage samples. We interpret this as evidence of past or recent serotype switching. Switched variants include ST 320, which is a common and increasing source of multidrug resistance in this community. Switching events within serogroups were more common than expected by chance (P = 0.043 by a Monte Carlo approach). Using multilocus sequence typing data and eBURST analysis, we also describe clonal dynamics within the important replacement serotypes 19A, 15B/C, 35B, and the recently described 6C. CONCLUSIONS Some strains generated by serotype switching are increasingly important parts of the carriage population. In the case of 19A, it appears that the majority of increase is due to ST 320, a recently reported switched variant. This may have consequences for the STs causing invasive pneumococcal disease.
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10
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Sugimoto N, Shima K, Hinenoya A, Asakura M, Matsuhisa A, Watanabe H, Yamasaki S. Evaluation of a PCR-restriction fragment length polymorphism (PCR-RFLP) assay for molecular epidemiological study of Shiga toxin-producing Escherichia coli. J Vet Med Sci 2011; 73:859-67. [PMID: 21321474 DOI: 10.1292/jvms.11-0008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
In this study, we have evaluated our recently developed polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) assay for the molecular subtyping of Shiga toxin-producing Escherichia coli (STEC). A total of 200 STEC strains including O157 (n=100), O26 (n=50), O111 (n=10), and non-O26/O111/O157 (n=40) serogroups isolated during 2005-2006 in Japan, which were identified to be clonally different by pulsed-field gel electrophoresis (PFGE) were further analyzed by the PCR-RFLP assay in comparison to PFGE. Ninety-five of O157, 48 of O26, five of O111 and 19 of non-O26/O111/O157 STEC strains yielded one to three amplicons ranging from 6.0 to 15.5 kb in size by the specific primer set targeting region V which is located in the upstream of stx genes. These strains were classified into 41 (O157), 8 (O26), 4 (O111) and 17 (non-O26/O111/O157) groups based on the RFLP patterns obtained by subsequent restriction digestion, respectively. Although the discriminatory power of PCR-RFLP assay was somewhat less than that of PFGE, it is more convenient for molecular subtyping of STEC strains especially for O157, the most important serogroup implicated in human diseases, as well as to identify the outbreak-associated isolates because of its simplicity, rapidity, ease and good reproducibility.
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Affiliation(s)
- Norihiko Sugimoto
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Osaka, Japan
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Liñares J, Ardanuy C, Pallares R, Fenoll A. Changes in antimicrobial resistance, serotypes and genotypes in Streptococcus pneumoniae over a 30-year period. Clin Microbiol Infect 2010; 16:402-10. [DOI: 10.1111/j.1469-0691.2010.03182.x] [Citation(s) in RCA: 219] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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12
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Expansion and evolution of the Streptococcus pneumoniae Spain9V-ST156 clonal complex in Poland. Antimicrob Agents Chemother 2010; 54:1720-7. [PMID: 20194703 DOI: 10.1128/aac.01340-09] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In this study, we analyzed 118 penicillin-nonsusceptible Streptococcus pneumoniae (PNSP) isolates (MICs, >or=0.12 microg/ml) recovered in Poland in 2003 to 2005 from patients with respiratory tract diseases and invasive infections. Seven different serotypes (14, 9V, 23F, 19F, 6B, 19A, and 6A, in order of descending frequency), seven alleles of the murM gene (murMA, murMB6, and the new murMB12 to -16 alleles), and 31 multilocus sequence types (STs) were observed. The vast majority of the PNSP isolates (90.7%) belonged to the international multiresistant clones, and among these, the Spain(9V)-ST156 clonal complex was the most prevalent (56 isolates) and was significantly overrepresented in invasive infections. The clone has been evolving rapidly, as demonstrated by the observed number of STs, the diversity in multiple-locus variable-number-tandem-repeat analysis (MLVA) types, and the polymorphism of pbp and pspA genes (coding for penicillin-binding proteins and the pneumococcal surface protein A, respectively). The presence and structure of the rlrA islet (encoding the pneumococcal pilus) were very well conserved. The Spain(9V)-ST156 clonal complex has been largely responsible for a decreasing susceptibility to penicillin among pneumococci in Poland in recent years, in spite of a relatively moderate antimicrobial use.
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Xu Q, Pichichero ME, Casey JR, Zeng M. Novel type of Streptococcus pneumoniae causing multidrug-resistant acute otitis media in children. Emerg Infect Dis 2009; 15:547-51. [PMID: 19331730 PMCID: PMC2671439 DOI: 10.3201/eid1504.071704] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
A new multidrug-resistant strain of serotype 19A has been characterized in upstate New York. After our recent discovery of a Streptococcus pneumoniae 19A “superbug” (Legacy strain) that is resistant to all Food and Drug Administration–approved antimicrobial drugs for treatment of acute otitis media (AOM) in children, other S. pneumoniae isolates from children with AOM were characterized by multilocus sequence typing (MLST). Among 40 isolates studied, 16 (40%) were serotype 19A, and 9 (23%) were resistant to multiple antimicrobial drugs. Two others had unreported sequence types (STs) that expressed the 19A capsule, and 8 (88%) of the 9 multidrug-resistant strains were serotype 19A, including the Legacy strain with the new ST-2722. In genetic relatedness, ST-2722 belonged to a cluster of reported strains of S. pneumoniae in which all strains had 6 of the same alleles as ST-156. The multidrug-resistant strains related to ST-156 expressed different capsular serotypes: 9V, 14, 11A, 15C, and 19F.
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Affiliation(s)
- Qingfu Xu
- University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
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15
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Abstract
The molecular epidemiology of infectious diseases uses a variety of techniques to assay the relatedness of disease-causing organisms to identify strains responsible for outbreaks or associated with particular phenotypes of interest (such as antibiotic resistance) and, it is hoped, provide insights into where and how these strains have emerged. The correct analysis of such data requires that we understand how the assayed variation accumulates. We discuss this with specific reference to three classes of methods: those based on gel electrophoresis of fragments generated by restriction enzymes or polymerase chain reaction (PCR), those based on microsatellites and other repeat elements, and raw sequence data from protein-coding genes. We also provide a simple example of how the likely origin of an apparently novel antibiotic-resistant strain may be identified and conclude with a discussion of some popular analysis packages and the more interesting prospects for the future in this rapidly developing field.
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Zapun A, Contreras-Martel C, Vernet T. Penicillin-binding proteins and beta-lactam resistance. FEMS Microbiol Rev 2008; 32:361-85. [PMID: 18248419 DOI: 10.1111/j.1574-6976.2007.00095.x] [Citation(s) in RCA: 386] [Impact Index Per Article: 24.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
A number of ways and means have evolved to provide resistance to eubacteria challenged by beta-lactams. This review is focused on pathogens that resist by expressing low-affinity targets for these antibiotics, the penicillin-binding proteins (PBPs). Even within this narrow focus, a great variety of strategies have been uncovered such as the acquisition of an additional low-affinity PBP, the overexpression of an endogenous low-affinity PBP, the alteration of endogenous PBPs by point mutations or homologous recombination or a combination of the above.
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Affiliation(s)
- André Zapun
- Laboratoire d'Ingénierie des Macromolécules, Institut de Biologie Structurale Jean-Pierre Ebel, UMR 5075-CNRS, CEA, Université Joseph Fourier, Grenoble, France
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Obert CA, Gao G, Sublett J, Tuomanen EI, Orihuela CJ. Assessment of molecular typing methods to determine invasiveness and to differentiate clones of Streptococcus pneumoniae. INFECTION GENETICS AND EVOLUTION 2007; 7:708-16. [PMID: 17768094 PMCID: PMC2128056 DOI: 10.1016/j.meegid.2007.07.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2007] [Revised: 06/27/2007] [Accepted: 07/23/2007] [Indexed: 11/29/2022]
Abstract
In the United States, Streptococcus pneumoniae is the leading cause of community-acquired pneumonia and invasive bacterial disease. As antimicrobial resistance increases, it will become critical to determine if strains circulating in a population are likely to cause invasive pneumococcal disease (IPD). This is possible by comparison of an isolate's genotype to strains known to be invasive. In this work, we compared pulse-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST), comparative genomic hybridization (CGH) and multi-invasive-locus sequence typing (MILST) for their ability to distinguish between known IPD causing and carrier strains using phylogenetic analyses. In addition, we assess the ability of these techniques to determine true clones from highly related strains. The resulting trees suggest that despite similar overall topologies, the clearest picture of invasiveness and genetic relatedness can be viewed when typing methods are used collectively.
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Affiliation(s)
- Caroline A Obert
- Hartwell Center for Bioinformatics and Biotechnology, St. Jude Children's Research Hospital, 332 North Lauderdale, Memphis, TN 38105, United States.
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18
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Sjöström K, Blomberg C, Fernebro J, Dagerhamn J, Morfeldt E, Barocchi MA, Browall S, Moschioni M, Andersson M, Henriques F, Albiger B, Rappuoli R, Normark S, Henriques-Normark B. Clonal success of piliated penicillin nonsusceptible pneumococci. Proc Natl Acad Sci U S A 2007; 104:12907-12. [PMID: 17644611 PMCID: PMC1929012 DOI: 10.1073/pnas.0705589104] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Antibiotic resistance in pneumococci is due to the spread of strains belonging to a limited number of clones. The Spain(9V)-3 clone of sequence type (ST)156 is one of the most successful clones with reduced susceptibility to penicillin [pneumococci nonsusceptible to penicillin (PNSP)]. In Sweden during 2000-2003, a dramatic increase in the number of PNSP isolates was observed. Molecular characterization of these isolates showed that a single clone of sequence type ST156 increased from 40% to 80% of all serotype 14, thus causing the serotype expansion. Additionally, during the same time period, we examined the clonal composition of two serotypes 9V and 19F: all 9V and 20% of 19F isolates belonged to the clonal cluster of ST156, and overall approximately 50% of all PNSP belonged to the ST156 clonal cluster. Moreover, microarray and PCR analysis showed that all ST156 isolates, irrespective of capsular type, carried the rlrA pilus islet. This islet was also found to be present in the penicillin-sensitive ST162 clone, which is believed to be the drug-susceptible ancestor of ST156. Competitive experiments between related ST156 serotype 19F strains confirmed that those containing the rlrA pilus islet were more successful in an animal model of carriage. We conclude that the pilus island is an important biological factor common to ST156 isolates and other successful PNSP clones. In Sweden, a country where the low antibiotic usage does not explain the spread of resistant strains, at least 70% of all PNSP isolates collected during year 2003 carried the pilus islet.
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Affiliation(s)
- K. Sjöström
- *Department of Bacteriology, Swedish Institute for Infectious Disease Control, SE-171 82 Solna, Sweden
- Department of Microbiology, Tumor Biology, and Cell Biology, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | - C. Blomberg
- *Department of Bacteriology, Swedish Institute for Infectious Disease Control, SE-171 82 Solna, Sweden
- Department of Microbiology, Tumor Biology, and Cell Biology, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | - J. Fernebro
- *Department of Bacteriology, Swedish Institute for Infectious Disease Control, SE-171 82 Solna, Sweden
- Department of Microbiology, Tumor Biology, and Cell Biology, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | - J. Dagerhamn
- *Department of Bacteriology, Swedish Institute for Infectious Disease Control, SE-171 82 Solna, Sweden
- Department of Microbiology, Tumor Biology, and Cell Biology, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | - E. Morfeldt
- *Department of Bacteriology, Swedish Institute for Infectious Disease Control, SE-171 82 Solna, Sweden
| | | | - S. Browall
- *Department of Bacteriology, Swedish Institute for Infectious Disease Control, SE-171 82 Solna, Sweden
| | | | - M. Andersson
- *Department of Bacteriology, Swedish Institute for Infectious Disease Control, SE-171 82 Solna, Sweden
| | - F. Henriques
- *Department of Bacteriology, Swedish Institute for Infectious Disease Control, SE-171 82 Solna, Sweden
| | - B. Albiger
- Department of Microbiology, Tumor Biology, and Cell Biology, Karolinska Institutet, SE-171 77 Stockholm, Sweden
- Department of Clinical Microbiology, Lund University, SE-221 00 Malmö, Sweden
| | - Rino Rappuoli
- Novartis Vaccines, 53100 Siena, Italy; and
- To whom correspondence may be addressed. E-mail: or
| | - S. Normark
- *Department of Bacteriology, Swedish Institute for Infectious Disease Control, SE-171 82 Solna, Sweden
- Department of Microbiology, Tumor Biology, and Cell Biology, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | - B. Henriques-Normark
- *Department of Bacteriology, Swedish Institute for Infectious Disease Control, SE-171 82 Solna, Sweden
- Department of Microbiology, Tumor Biology, and Cell Biology, Karolinska Institutet, SE-171 77 Stockholm, Sweden
- To whom correspondence may be addressed. E-mail: or
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Calatayud L, Ardanuy C, Cercenado E, Fenoll A, Bouza E, Pallares R, Martín R, Liñares J. Serotypes, Clones, and Mechanisms of Resistance of Erythromycin-Resistant Streptococcus pneumoniae Isolates Collected in Spain. Antimicrob Agents Chemother 2007; 51:3240-6. [PMID: 17606677 PMCID: PMC2043242 DOI: 10.1128/aac.00157-07] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The aim of this study was to analyze the distributions of antibiotic susceptibility patterns, serotypes, phenotypes, genotypes, and macrolide resistance genes among 125 nonduplicated erythromycin-resistant Streptococcus pneumoniae clinical isolates collected in a Spanish point prevalence study. The prevalence of resistance to macrolides in this study was 34.7%. Multiresistance (to three or more antimicrobials) was observed in 81.6% of these strains. Among 15 antimicrobials studied, cefotaxime, moxifloxacin, telithromycin, and quinupristin-dalfopristin were the most active drugs. The most frequent serotypes of erythromycin-resistant isolates were 19F (25%), 19A (17%), 6B (12%), 14 (10%), and 23F (10%). Of the 125 strains, 109 (87.2%) showed the MLS(B) phenotype [103 had the erm(B) gene and 6 had both erm(B) and mef(E) genes]. Sixteen (12.8%) strains showed the M phenotype [14 with mef(E) and 2 with mef(A)]. All isolates were tested by PCR for the presence of the int, xis, tnpR, and tnpA genes associated with conjugative transposons (Tn916 family and Tn917). Positive detection of erm(B), tet(M), int, and xis genes related to the Tn916 family was found in 77.1% of MLS(B) phenotype strains. In 16 strains, only the tndX, erm(B), and tet(M) genes were detected, suggesting the presence of Tn1116, a transposon recently described for Streptococcus pyogenes. Five clones, namely, Sweden(15A)-25, clone(19F) ST87, Spain(23F)-1, Spain(6B)-2, and clone(19A) ST276, accounted for half of the MLS(B) strains. In conclusion, the majority of erythromycin-resistant pneumococci isolated in Spain had the MLS(B) phenotype, belonged to multiresistant international clones, and carried the erm(B), tet(M), xis, and int genes, suggesting the spread of transposons of the Tn916 family.
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Affiliation(s)
- Laura Calatayud
- Servicio de Microbiología, Hospital Universitario de Bellvitge, Feixa Llarga S/N 08907, L'Hospitalet de Llobregat, Barcelona, Spain
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20
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Reinert RR, van der Linden M, Seegmüller I, Al-Lahham A, Siedler A, Weissmann B, Toschke AM, von Kries R. Molecular epidemiology of penicillin-non-susceptible Streptococcus pneumoniae isolates from children with invasive pneumococcal disease in Germany. Clin Microbiol Infect 2007; 13:363-8. [PMID: 17359319 DOI: 10.1111/j.1469-0691.2006.01676.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A population-based nationwide surveillance of antibiotic resistance associated with invasive pneumococcal disease (IPD) in children and adolescents (aged<16 years) was performed in Germany between 1997 and 2004. In total, 1517 isolates were collected, of which 5.1% and 1.1% were intermediately- or fully-resistant, respectively, to penicillin G. During the 8-year study period, an increase in resistance to both penicillin G and erythromycin A was observed, and the frequency of isolates exhibiting reduced susceptibility to penicillin G or erythromycin A increased from 1.4% and 11.1%, respectively, in 1997, to 8.7% and 29.0%, respectively, in 2004. Among the penicillin non-susceptible pneumococcal isolates, serotypes 14 (24.5% of isolates), 23F (16.0%) and 6B (16.0%) were found most frequently. Multilocus sequence typing of 58 (62%) penicillin G non-susceptible isolates revealed that sequence type (ST) 156 (Spain9V-3 clone) and its single-locus variant ST 557 were widespread in Germany. Moreover, 17 new penicillin G non-susceptible STs were defined for the first time. The study illustrated the genetic heterogeneity of antibiotic-resistant pneumococcal isolates in Germany.
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Affiliation(s)
- R R Reinert
- Institute of Medical Microbiology, National Reference Centre for Streptococci, University Hospital (RWTH), Aachen, Germany.
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21
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Blossom DB, Cordeiro SM, Bajaksouzian S, Joloba ML, Kityo C, Whalen CC, Salata RA, Jacobs MR. Characterization of Penicillin Intermediate Serotypes ofStreptococcus pneumoniaeCarried by Human Immunodeficiency Virus-Infected Adults and Healthy Children in Uganda. Microb Drug Resist 2007; 13:21-8. [PMID: 17536930 DOI: 10.1089/mdr.2006.9993] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
There are little data on the genetic relatedness between antibiotic-resistant pneumococcal isolates colonizing the Ugandan population. Penicillin-intermediate pneumococci of serogroups or serotypes rarely or not previously reported as being penicillin nonsusceptible were selected out of 166 isolates representing 26 capsular serogroups or serotypes isolated from Ugandan children in 1995 and human immunodeficiency virus (HIV) infected Ugandan adults in 2004-2005. Pairs of penicillin-intermediate pneumococci of the same serogroup or serotype present in both patient populations were characterized further by pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST). Seven such pairs of isolates were found and included serogroups 7, 11, 15B/C, and 16 as well as serotypes 13, 21, and 35B. PFGE of these seven pairs showed no clonality between serogroups or serotypes, and clonality only within serogroup 11 and serotype 13. MLST of the 14 individual isolates revealed 13 different sequence types (STs), 11 of which had not previously been recorded. Comparisons with all known STs revealed that most of these strains were related only to strains of the same serotype in other countries, with these related strains frequently also being penicillin intermediate. These findings suggest that penicillin nonsusceptibility in Uganda is likely due to the introduction of antibiotic-resistant pneumococcal clones into Uganda rather than development of resistance within the country.
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Affiliation(s)
- D B Blossom
- Case Western Reserve University, 11100 Euclid Avenue, Cleveland, OH 44106, USA.
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22
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Sadowy E, Izdebski R, Skoczynska A, Grzesiowski P, Gniadkowski M, Hryniewicz W. Phenotypic and molecular analysis of penicillin-nonsusceptible Streptococcus pneumoniae isolates in Poland. Antimicrob Agents Chemother 2007; 51:40-7. [PMID: 17043125 PMCID: PMC1797676 DOI: 10.1128/aac.01072-06] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2006] [Accepted: 10/03/2006] [Indexed: 11/20/2022] Open
Abstract
beta-Lactams are the drugs of choice for the treatment of infections caused by the important bacterial pathogen Streptococcus pneumoniae. The recent growth of resistance of this organism to penicillin observed worldwide is of the highest concern. In this study, using 887 surveillance pneumococcal isolates recovered in Poland from 1998 to 2002, we observed the increase in penicillin nonsusceptibility from 8.7% to 20.3%. All of the 109 penicillin-nonsusceptible S. pneumoniae (PNSP) isolates identified, together with 22 archival PNSP isolates from 1995 to 1997, were subsequently analyzed by susceptibility testing, serotyping, profiling of pbp genes, pulsed-field gel electrophoresis, and multilocus sequence typing (MLST). Four predominant serotypes, serotypes 6B, 9V, 14, and 23F, characterized 85.5% of the isolates. MLST revealed the presence of 34 sequence types, 15 of which were novel types. Representatives of seven multiresistant international clones (Spain(23F)-1, Spain(6B)-2, Spain(9V)-3, Taiwan(23F)-15, Poland(23F)-16, Poland(6B)-20, and Sweden(15A)-25) or their closely related variants comprised the majority of the study isolates. The spread of Spain(9V)-3 and its related clone of serotype 14/ST143 has remarkably contributed to the recent increase in penicillin resistance in pneumococci in the country.
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Affiliation(s)
- Ewa Sadowy
- Department of Molecular Microbiology, National Institute of Public Health, Ul. Chełmska 30/34, 00-725 Warsaw, Poland.
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23
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Sullivan CB, Diggle MA, Clarke SC. Multilocus sequence typing: Data analysis in clinical microbiology and public health. Mol Biotechnol 2006; 29:245-54. [PMID: 15767702 DOI: 10.1385/mb:29:3:245] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Numerous computer-based statistical packages have been developed in recent years and it has become easier to analyze nucleotide sequence data and gather subsequent information that would not normally be available. Multilocus sequence typing (MLST) is used for characterizing isolates of bacterial and fungal species and uses nucleotide sequences of internal fragments of housekeeping genes. This method is finding a place in clinical microbiology and public health by providing data for epidemiological surveillance and development of vaccine policy. It adds greatly to our knowledge of the genetic variation that can occur within a species and has therefore been used for studies of population biology. Analysis requires the detailed interpretation of nucleotide sequence data obtained from housekeeping and nonhousekeeping genes. This is due to the amount of data generated from nucleotide sequencing and the information generated from an array of analytical tools improves our understanding of bacterial pathogens. This can benefit public health interventions and the development of enhanced therapies and vaccines. This review concentrates on the analytical tools used in MLST and their use in the clinical microbiology and public health fields.
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Affiliation(s)
- Christopher B Sullivan
- Scottish Meningococcus and Pneumococcus Reference Laboratory North Glasgow University Hospital NHS Trust, Glasgow, UK
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24
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Pai R, Gertz RE, Whitney CG, Beall B. Clonal association between Streptococcus pneumoniae serotype 23A, circulating within the United States, and an internationally dispersed clone of serotype 23F. J Clin Microbiol 2005; 43:5440-4. [PMID: 16272467 PMCID: PMC1287803 DOI: 10.1128/jcm.43.11.5440-5444.2005] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2005] [Revised: 06/24/2005] [Accepted: 08/09/2005] [Indexed: 11/20/2022] Open
Abstract
Streptococcus pneumoniae is an important pathogen in the United States and is associated with significant morbidity and mortality. Since the introduction of the seven-valent conjugate vaccine, a significant decline in pneumococcal disease has been reported. However, surveillance for pneumococcal disease remains essential, as the extent of cross protection against vaccine-related serotypes is still unclear. Further, any increase in non-vaccine-related serotypes also needs monitoring. We report on a new clonal association between a vaccine-related serotype, serotype 23A, obtained as part of the Active Bacterial Core surveillance, with an established internationally dispersed Pneumococcal Molecular Epidemiology Network (PMEN) clone, clone Colombia(23F)-26. Sixty-two isolates of serotype 23A collected from sterile sites during a 2-year period (2002 and 2003) were characterized. Twenty-one (34%) isolates were penicillin nonsusceptible, although none were fully resistant. Pulsed-field gel electrophoresis and multilocus sequence typing analysis showed that 24 (39%) of the serotype 23A isolates shared either genetic identity or high genetic relatedness with PMEN clone Colombia(23F)-26. Extensive variability was noted within the sequenced region of pbp2b in two penicillin-nonsusceptible isolates as well as in PMEN clone Colombia(23F)-26, suggesting that these isolates probably acquired penicillin resistance independently. The emergence of such new serotype and genotype associations highlights the dynamic nature of the pneumococcal population, necessitating continuous monitoring in the post-vaccine era.
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Affiliation(s)
- Rekha Pai
- CDC Respiratory Diseases Branch, Mailstop C02, 1600 Clifton Rd., NE, Atlanta, GA 30333, USA
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25
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Littauer P, Sangvik M, Caugant DA, Høiby EA, Simonsen GS, Sundsfjord A. Molecular epidemiology of macrolide-resistant isolates of Streptococcus pneumoniae collected from blood and respiratory specimens in Norway. J Clin Microbiol 2005; 43:2125-32. [PMID: 15872231 PMCID: PMC1153744 DOI: 10.1128/jcm.43.5.2125-2132.2005] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Norway has a low prevalence of antimicrobial resistance, including macrolide-resistant Streptococcus pneumoniae (MRSP). In a nationwide surveillance program, a total of 2,200 S. pneumoniae isolates were collected from blood cultures and respiratory tract specimens. Macrolide resistance was detected in 2.7%. M-type macrolide resistance was found in 60% of resistant isolates, and these were mainly mef(A)-positive, serotype-14 invasive isolates. The erm(B)-encoded macrolide-lincosamide-streptogramin B (MLS(B)) type dominated among the noninvasive isolates. One strain had an A2058G mutation in the 23S rRNA gene. Coresistance to other antibiotics was seen in 96% of the MLS(B)-type isolates, whereas 92% of the M-type isolates were susceptible to other commonly used antimicrobial agents. Serotypes 14, 6B, and 19F accounted for 84% of the macrolide-resistant isolates, with serotype 14 alone accounting for 67% of the invasive isolates. A total of 29 different sequence types (STs) were detected by multilocus sequence typing. Twelve STs were previously reported international resistant clones, and 75% of the macrolide-resistant isolates had STs identical or closely related to these clones. Eleven isolates displayed 10 novel STs, and 7/11 of these "Norwegian strains" coexpressed MLS(B) and tetracycline resistance, indicating the presence of Tn1545. The invasive serotype-14 isolates were all classified as ST9 or single-locus variants of this clone. ST9 is a mef-positive M-type clone, commonly known as England(14)-9, reported from several European countries. These observations suggest that the import of major international MRSP clones and the local spread of Tn1545 are the major mechanisms involved in the evolution and dissemination of MRSP in Norway.
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Affiliation(s)
- P Littauer
- University Hospital of North Norway (UNN), Department of Microbiology and Virology, Faculty of Medicine, Institute for Medical Biology, University of Tromsø, N-9037 Tromsø, Norway
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26
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Fakhr MK, Nolan LK, Logue CM. Multilocus sequence typing lacks the discriminatory ability of pulsed-field gel electrophoresis for typing Salmonella enterica serovar Typhimurium. J Clin Microbiol 2005; 43:2215-9. [PMID: 15872244 PMCID: PMC1153745 DOI: 10.1128/jcm.43.5.2215-2219.2005] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Nontyphoidal salmonellae are among the leading causes of food-borne disease in the United States. Because of the importance of Salmonella enterica in food-borne disease, numerous typing methodologies have been developed. Among the several molecular typing methods, pulsed-field gel electrophoresis (PFGE) is currently considered the "gold standard" technique in typing Salmonella. The aim of this study was to compare the discriminatory power of PFGE to multilocus sequence typing (MLST) in typing Salmonella enterica serovar Typhimurium clinical isolates. A total of 85 Salmonella Typhimurium clinical isolates from cattle were used in this study. PFGE using XbaI was performed on the 85 isolates by the Centers for Disease Control and Prevention method, and data were analyzed using the BioNumerics software package. Fifty PFGE profiles were observed among the isolates, and these grouped into three major clusters. For the MLST analysis, the manB, pduF, glnA, and spaM genes were amplified by PCR from the same 85 isolates. DNA sequencing of these four genes, manB, pduF, glnA, and spaM, showed no genetic diversity among the isolates tested, with a 100% identity in nucleotide sequence. Moreover, the DNA sequences of the aforementioned genes showed 100% identity to the sequence reported in GenBank for the S. enterica serovar Typhimurium LT2 strain. Therefore, MLST, using these genes, lacks the discriminatory power of PFGE for typing Salmonella enterica serovar Typhimurium.
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Affiliation(s)
- Mohamed K Fakhr
- Department of Veterinary and Microbiological Sciences, North Dakota State University, Fargo, ND 58105, USA
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27
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Spratt BG, Hanage WP, Li B, Aanensen DM, Feil EJ. Displaying the relatedness among isolates of bacterial species -- the eBURST approach. FEMS Microbiol Lett 2005; 241:129-34. [PMID: 15598523 DOI: 10.1016/j.femsle.2004.11.015] [Citation(s) in RCA: 158] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2004] [Revised: 11/05/2004] [Accepted: 11/05/2004] [Indexed: 11/18/2022] Open
Abstract
Determining the most appropriate way to represent the relationships between bacterial isolates is complicated by the differing rates of recombination within species. In many cases, a bifurcating tree can be positively misleading. The recently described program eBURST can be used with multilocus data to define groups or clonal complexes of related isolates derived from a common ancestor, the patterns of descent linking them together, and the ancestral genotype. eBURST has recently been extensively updated to include additional tools for exploring the relationships between isolates. We discuss the advantages of this approach and describe its use to explore patterns of descent within clonal complexes identified using multilocus sequence typing.
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Affiliation(s)
- Brian G Spratt
- Department of Infectious Disease Epidemiology, Faculty of Medicine, Imperial College London, St. Mary's Hospital, Old Medical School Building, London W2 1PG, UK.
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Bean DC, Klena JD. Characterization of major clones of antibiotic-resistant Streptococcus pneumoniae in New Zealand by multilocus sequence typing. J Antimicrob Chemother 2005; 55:375-8. [PMID: 15681581 DOI: 10.1093/jac/dki001] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVES To determine the relationship between New Zealand isolates of antibiotic-resistant Streptococcus pneumoniae and internationally widespread resistant clones. METHODS Fifty-nine isolates representing both invasive and non-invasive pneumococci from multiple locations, serotypes and years were analysed by multilocus sequence typing. RESULTS Major international clones, including Spain(23F)-1, France(9V)-3 and Taiwan(19F)-14, were found to be present in New Zealand. A one-allele variant of the Taiwan(19F)-14 clone (aroE 15-->4, ST 271) was particularly prominent. CONCLUSIONS Antibiotic-resistant pneumococci have not evolved de novo in New Zealand, but were introduced to the country during the early 1990s.
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Affiliation(s)
- David C Bean
- Plant and Microbial Science Department, University of Canterbury, Christchurch, New Zealand.
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Birtles A, Virgincar N, Sheppard CL, Walker RA, Johnson AP, Warner M, Edwards-Jones V, George RC. Antimicrobial resistance of invasive Streptococcus pneumoniae isolates in a British district general hospital: the international connection. J Med Microbiol 2004; 53:1241-1246. [PMID: 15585504 DOI: 10.1099/jmm.0.45763-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Between January 2000 and March 2001,Streptococcus pneumoniaewere isolated from the blood of 56 patients admitted to a single district general hospital in the South-East of England. The serotype and antibiotic susceptibility were determined for all isolates and, for those resistant to erythromycin, the presence or absence of themef(A) anderm(B) genes was determined by PCR. Multi-locus sequence typing, along with PFGE, was undertaken on all isolates resistant to penicillin or erythromycin and a group of antibiotic-susceptible isolates, to identify whether globally distributed pneumococcal clones, as described by the Pneumococcal Molecular Epidemiology Network (PMEN), were present in the study population. Three serotype 9V penicillin-resistant isolates were identified as belonging to the Spain9V-3 clone, while 14 erythromycin-resistant isolates of serotype 14 belonged to the England14-9 clone. A single multi-resistant isolate of serotype 6B, was found to be a single-locus variant of the Spain6B-2 clone. All 14 erythromycin-resistant serotype 14 isolates possessed themef(A) gene, while the single multi-resistant isolate possessed theerm(B) gene. These findings confirm the wide distribution and clinical impact of PMEN clones, which accounted for all of the penicillin and erythromycin resistance observed amongst invasive isolates in a district general hospital over a 15-month period.
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Affiliation(s)
- Andrew Birtles
- Respiratory and Systemic Infection Laboratory1 and Antibiotic Resistance Monitoring and Reference Laboratory3, Specialist and Reference Microbiology Division, Health Protection Agency, London NW9 5HT, UK 2Reading Public Health Laboratory, London Road, Reading RG1 5AN, UK 4Department of Biological Sciences, Manchester Metropolitan University, Chester Street, Manchester M1 5GD, UK
| | - Nilangi Virgincar
- Respiratory and Systemic Infection Laboratory1 and Antibiotic Resistance Monitoring and Reference Laboratory3, Specialist and Reference Microbiology Division, Health Protection Agency, London NW9 5HT, UK 2Reading Public Health Laboratory, London Road, Reading RG1 5AN, UK 4Department of Biological Sciences, Manchester Metropolitan University, Chester Street, Manchester M1 5GD, UK
| | - Carmen L Sheppard
- Respiratory and Systemic Infection Laboratory1 and Antibiotic Resistance Monitoring and Reference Laboratory3, Specialist and Reference Microbiology Division, Health Protection Agency, London NW9 5HT, UK 2Reading Public Health Laboratory, London Road, Reading RG1 5AN, UK 4Department of Biological Sciences, Manchester Metropolitan University, Chester Street, Manchester M1 5GD, UK
| | - Rachel A Walker
- Respiratory and Systemic Infection Laboratory1 and Antibiotic Resistance Monitoring and Reference Laboratory3, Specialist and Reference Microbiology Division, Health Protection Agency, London NW9 5HT, UK 2Reading Public Health Laboratory, London Road, Reading RG1 5AN, UK 4Department of Biological Sciences, Manchester Metropolitan University, Chester Street, Manchester M1 5GD, UK
| | - Alan P Johnson
- Respiratory and Systemic Infection Laboratory1 and Antibiotic Resistance Monitoring and Reference Laboratory3, Specialist and Reference Microbiology Division, Health Protection Agency, London NW9 5HT, UK 2Reading Public Health Laboratory, London Road, Reading RG1 5AN, UK 4Department of Biological Sciences, Manchester Metropolitan University, Chester Street, Manchester M1 5GD, UK
| | - Marina Warner
- Respiratory and Systemic Infection Laboratory1 and Antibiotic Resistance Monitoring and Reference Laboratory3, Specialist and Reference Microbiology Division, Health Protection Agency, London NW9 5HT, UK 2Reading Public Health Laboratory, London Road, Reading RG1 5AN, UK 4Department of Biological Sciences, Manchester Metropolitan University, Chester Street, Manchester M1 5GD, UK
| | - Valerie Edwards-Jones
- Respiratory and Systemic Infection Laboratory1 and Antibiotic Resistance Monitoring and Reference Laboratory3, Specialist and Reference Microbiology Division, Health Protection Agency, London NW9 5HT, UK 2Reading Public Health Laboratory, London Road, Reading RG1 5AN, UK 4Department of Biological Sciences, Manchester Metropolitan University, Chester Street, Manchester M1 5GD, UK
| | - Robert C George
- Respiratory and Systemic Infection Laboratory1 and Antibiotic Resistance Monitoring and Reference Laboratory3, Specialist and Reference Microbiology Division, Health Protection Agency, London NW9 5HT, UK 2Reading Public Health Laboratory, London Road, Reading RG1 5AN, UK 4Department of Biological Sciences, Manchester Metropolitan University, Chester Street, Manchester M1 5GD, UK
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30
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Trad S, Allignet J, Frangeul L, Davi M, Vergassola M, Couve E, Morvan A, Kechrid A, Buchrieser C, Glaser P, El-Solh N. DNA macroarray for identification and typing of Staphylococcus aureus isolates. J Clin Microbiol 2004; 42:2054-64. [PMID: 15131170 PMCID: PMC404631 DOI: 10.1128/jcm.42.5.2054-2064.2004] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A DNA macroarray containing 465 intragenic amplicons was designed to identify Staphylococcus aureus at the species level and to type S. aureus isolates. The genes selected included those encoding (i) S. aureus-specific proteins, (ii) staphylococcal and enterococcal proteins mediating antibiotic resistance and factors involved in their expression, (iii) putative virulence proteins and factors controlling their expression, and (iv) proteins produced by mobile elements. The macroarray was hybridized with the cellular DNAs of 80 S. aureus clinical isolates that were previously typed by analyses of their antibiograms and SmaI patterns. The set selected contained unrelated, endemic, and outbreak-related isolates belonging to 45 SmaI genotypes. In a gene content dendrogram, the 80 isolates were distributed into 52 clusters. The outbreak-related isolates were linked in the same or a closely related cluster(s). Clustering based on gene content provided a better discrimination than SmaI pattern analysis for the tested mecA(+) isolates that were endemic to Europe. All of the antibiotic resistance genes detected could be correlated with their corresponding phenotypes, except for one isolate which carried a mecA gene without being resistant. The 16 isolates responsible for bone infections were distinguishable from the 12 isolates from uninfected nasal carriers by a significantly higher prevalence of the sdrD gene coding for a putative SD (serine-aspartate) adhesin (in 15 and 7 isolates, respectively). In conclusion, the macroarray designed for this study offers an attractive and rapid typing method which has the advantage of providing additional information concerning the gene content of the isolate of interest.
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Affiliation(s)
- Salim Trad
- Département Ecosystèmes et Epidémiologie des Maladies Infectieuses, Institut Pasteur, Paris, France
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31
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Feil EJ, Li BC, Aanensen DM, Hanage WP, Spratt BG. eBURST: inferring patterns of evolutionary descent among clusters of related bacterial genotypes from multilocus sequence typing data. J Bacteriol 2004; 186:1518-30. [PMID: 14973027 PMCID: PMC344416 DOI: 10.1128/jb.186.5.1518-1530.2004] [Citation(s) in RCA: 1426] [Impact Index Per Article: 71.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
The introduction of multilocus sequence typing (MLST) for the precise characterization of isolates of bacterial pathogens has had a marked impact on both routine epidemiological surveillance and microbial population biology. In both fields, a key prerequisite for exploiting this resource is the ability to discern the relatedness and patterns of evolutionary descent among isolates with similar genotypes. Traditional clustering techniques, such as dendrograms, provide a very poor representation of recent evolutionary events, as they attempt to reconstruct relationships in the absence of a realistic model of the way in which bacterial clones emerge and diversify to form clonal complexes. An increasingly popular approach, called BURST, has been used as an alternative, but present implementations are unable to cope with very large data sets and offer crude graphical outputs. Here we present a new implementation of this algorithm, eBURST, which divides an MLST data set of any size into groups of related isolates and clonal complexes, predicts the founding (ancestral) genotype of each clonal complex, and computes the bootstrap support for the assignment. The most parsimonious patterns of descent of all isolates in each clonal complex from the predicted founder(s) are then displayed. The advantages of eBURST for exploring patterns of evolutionary descent are demonstrated with a number of examples, including the simple Spain(23F)-1 clonal complex of Streptococcus pneumoniae, "population snapshots" of the entire S. pneumoniae and Staphylococcus aureus MLST databases, and the more complicated clonal complexes observed for Campylobacter jejuni and Neisseria meningitidis.
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Affiliation(s)
- Edward J Feil
- Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, United Kingdom.
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32
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Noller AC, McEllistrem MC, Pacheco AGF, Boxrud DJ, Harrison LH. Multilocus variable-number tandem repeat analysis distinguishes outbreak and sporadic Escherichia coli O157:H7 isolates. J Clin Microbiol 2004; 41:5389-97. [PMID: 14662916 PMCID: PMC308975 DOI: 10.1128/jcm.41.12.5389-5397.2003] [Citation(s) in RCA: 160] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Escherichia coli O157:H7 is a major cause of food-borne illness in the United States. Outbreak detection involves traditional epidemiological methods and routine molecular subtyping by pulsed-field gel electrophoresis (PFGE). PFGE is labor-intensive, and the results are difficult to analyze and not easily transferable between laboratories. Multilocus variable-number tandem repeat (VNTR) analysis (MLVA) is a fast, portable method that analyzes multiple VNTR loci, which are areas of the bacterial genome that evolve quickly. Eighty isolates, including 21 isolates from five epidemiologically well-characterized outbreaks from Pennsylvania and Minnesota, were analyzed by PFGE and MLVA. Strains in PFGE clusters were defined as strains that differed by less than or equal to one band by using XbaI and the confirmatory enzyme SpeI. MLVA was performed by comparing the number of tandem repeats at seven loci. From 6 to 30 alleles were found at the seven loci, resulting in 64 MLVA types among the 80 isolates. MLVA correctly identified the isolates from all five outbreaks if only a single-locus variant was allowed. MLVA differentiated strains with unique PFGE types. Additionally, MLVA discriminated strains within PFGE-defined clusters that were not known to be part of an outbreak. In addition to being a simple and validated method for E. coli O157:H7 outbreak detection, MLVA appears to have a sensitivity equal to that of PFGE and a specificity superior to that of PFGE.
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Affiliation(s)
- Anna C Noller
- Infectious Diseases Epidemiology Research Unit, University of Pittsburgh Graduate School of Public Health and School of Medicine, Pittsburgh, Pennsylvania 15261, USA
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33
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Reinert RR, Muckel S, Al-Lahham A, Spratt BG, Brueggemann AB, Hakenbeck R, Lütticken R. Characterization of German penicillin non-susceptible serotype 23F pneumococci using multilocus sequence typing. J Med Microbiol 2003; 52:981-987. [PMID: 14532343 DOI: 10.1099/jmm.0.05216-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Three nationwide multicentre studies (n = 5071) showed an increase in antibiotic resistance in pneumococci in Germany. Serotype 23F was the predominant serotype (n = 45, 22.4 %), followed by 6B (n = 30, 14.9 %) and 9V (n = 19, 9.5 %). Multilocus sequence typing was used to characterize 45 serotype 23F strains with reduced penicillin susceptibility. The Spanish(23F)-1 clone [profile 4-4-2-4-4-1-1, sequence type (ST) 81] contributes significantly to the emergence of penicillin resistance in Germany (n = 21, 46.7 % of all penicillin non-susceptible serotype 23F isolates). Isolates of ST 277 (profile 7-13-8-6-6-12-8), which has been found previously in the Netherlands, are also observed, particularly in western Germany (n = 8, 17.8 %). A high proportion of strains (n = 11, 24.4 %) have sequence types that have not been reported to date from other countries (STs 353-362). The major penicillin-resistant clones are present in Germany, a country with relatively low levels of beta-lactam resistance.
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Affiliation(s)
- Ralf René Reinert
- Institute of Medical Microbiology, National Reference Center for Streptococci, University Hospital, D-52057 Aachen, Germany 2Department of Infectious Disease Epidemiology, Imperial College School of Medicine, St Mary's Campus, London W2 1PG, UK 3Department of Microbiology, University of Oxford, and Department of Public Health & Primary Care, John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK 4Institute of Microbiology, University of Kaiserslautern, Germany
| | - Stefanie Muckel
- Institute of Medical Microbiology, National Reference Center for Streptococci, University Hospital, D-52057 Aachen, Germany 2Department of Infectious Disease Epidemiology, Imperial College School of Medicine, St Mary's Campus, London W2 1PG, UK 3Department of Microbiology, University of Oxford, and Department of Public Health & Primary Care, John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK 4Institute of Microbiology, University of Kaiserslautern, Germany
| | - Adnan Al-Lahham
- Institute of Medical Microbiology, National Reference Center for Streptococci, University Hospital, D-52057 Aachen, Germany 2Department of Infectious Disease Epidemiology, Imperial College School of Medicine, St Mary's Campus, London W2 1PG, UK 3Department of Microbiology, University of Oxford, and Department of Public Health & Primary Care, John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK 4Institute of Microbiology, University of Kaiserslautern, Germany
| | - Brian G Spratt
- Institute of Medical Microbiology, National Reference Center for Streptococci, University Hospital, D-52057 Aachen, Germany 2Department of Infectious Disease Epidemiology, Imperial College School of Medicine, St Mary's Campus, London W2 1PG, UK 3Department of Microbiology, University of Oxford, and Department of Public Health & Primary Care, John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK 4Institute of Microbiology, University of Kaiserslautern, Germany
| | - Angela B Brueggemann
- Institute of Medical Microbiology, National Reference Center for Streptococci, University Hospital, D-52057 Aachen, Germany 2Department of Infectious Disease Epidemiology, Imperial College School of Medicine, St Mary's Campus, London W2 1PG, UK 3Department of Microbiology, University of Oxford, and Department of Public Health & Primary Care, John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK 4Institute of Microbiology, University of Kaiserslautern, Germany
| | - Regine Hakenbeck
- Institute of Medical Microbiology, National Reference Center for Streptococci, University Hospital, D-52057 Aachen, Germany 2Department of Infectious Disease Epidemiology, Imperial College School of Medicine, St Mary's Campus, London W2 1PG, UK 3Department of Microbiology, University of Oxford, and Department of Public Health & Primary Care, John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK 4Institute of Microbiology, University of Kaiserslautern, Germany
| | - Rudolf Lütticken
- Institute of Medical Microbiology, National Reference Center for Streptococci, University Hospital, D-52057 Aachen, Germany 2Department of Infectious Disease Epidemiology, Imperial College School of Medicine, St Mary's Campus, London W2 1PG, UK 3Department of Microbiology, University of Oxford, and Department of Public Health & Primary Care, John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK 4Institute of Microbiology, University of Kaiserslautern, Germany
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34
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Sadowy E, Zhou J, Meats E, Gniadkowski M, Spratt BG, Hryniewicz W. Identification of multidrug-resistant Streptococcus pneumoniae strains isolated in Poland by multilocus sequence typing. Microb Drug Resist 2003; 9:81-6. [PMID: 12705686 DOI: 10.1089/107662903764736373] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Multilocus sequence typing (MLST) of 35 isolates of multidrug-resistant Streptococcus pneumoniae recovered in Poland during 1995-1996 distinguished 10 different sequence types (ST). The majority of the isolates were assigned to two Polish clones of serotypes 6B and 23F, although the international clones, Spain23F-1 and Spain9V-3, were also identified. Similar results were obtained using pulsed-field gel electrophoresis (PFGE), providing a direct comparison of these two typing methods.
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Affiliation(s)
- Ewa Sadowy
- Sera & Vaccines Central Research Laboratory, 00-725 Warsaw, Poland.
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35
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Gaia V, Fry NK, Harrison TG, Peduzzi R. Sequence-based typing of Legionella pneumophila serogroup 1 offers the potential for true portability in legionellosis outbreak investigation. J Clin Microbiol 2003; 41:2932-9. [PMID: 12843023 PMCID: PMC165343 DOI: 10.1128/jcm.41.7.2932-2939.2003] [Citation(s) in RCA: 77] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Seven gene loci of Legionella pneumophila serogroup 1 were analyzed as potential epidemiological typing markers to aid in the investigation of legionella outbreaks. The genes chosen included four likely to be selectively neutral (acn, groES, groEL, and recA) and three likely to be under selective pressure (flaA, mompS, and proA). Oligonucleotide primers were designed to amplify 279- to 763-bp fragments from each gene. Initial sequence analysis of the seven loci from 10 well-characterized isolates of L. pneumophila serogroup 1 gave excellent reproducibility (R) and epidemiological concordance (E) values (R = 1.00; E = 1.00). The three loci showing greatest discrimination and nucleotide variation, flaA, mompS, and proA, were chosen for further study. Indices of discrimination (D) were calculated using a panel of 79 unrelated isolates. Single loci gave D values ranging from 0.767 to 0.857, and a combination of all three loci resulted in a D value of 0.924. When all three loci were combined with monoclonal antibody subgrouping, the D value was 0.971. Sequence-based typing of L. pneumophila serogroup 1 using only three loci is epidemiologically concordant and highly discriminatory and has the potential to become the new "gold standard" for the epidemiological typing of L. pneumophila.
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Affiliation(s)
- Valeria Gaia
- Istituto Cantonale di Microbiologia, Lugano, Switzerland.
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36
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Noller AC, McEllistrem MC, Stine OC, Morris JG, Boxrud DJ, Dixon B, Harrison LH. Multilocus sequence typing reveals a lack of diversity among Escherichia coli O157:H7 isolates that are distinct by pulsed-field gel electrophoresis. J Clin Microbiol 2003; 41:675-9. [PMID: 12574266 PMCID: PMC149678 DOI: 10.1128/jcm.41.2.675-679.2003] [Citation(s) in RCA: 132] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Escherichia coli O157:H7 is a major cause of foodborne illness in the United States. Pulsed-field gel electrophoresis (PFGE) is the molecular epidemiologic method mostly commonly used to identify food-borne outbreaks. Although PFGE is a powerful epidemiologic tool, it has disadvantages that make a DNA sequence-based approach potentially attractive. Multilocus sequence typing (MLST) analyzes the internal fragments of housekeeping genes to establish genetic relatedness between isolates. We sequenced selected portions of seven housekeeping genes and two membrane protein genes (ompA and espA) of 77 isolates that were diverse by PFGE to determine whether there was sufficient sequence variation to be useful as an epidemiologic tool. There was no DNA sequence diversity in the sequenced portions of the seven housekeeping genes and espA. For ompA, all but five isolates had sequence identical to that of the reference strains. E. coli O157:H7 has a striking lack of genetic diversity in the genes we explored, even among isolates that are clearly distinct by PFGE. Other approaches to identify improved molecular subtyping methods for E. coli 0157:H7 are needed.
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Affiliation(s)
- Anna C Noller
- Department of Infectious Diseases and Microbiology, University of Pittsburgh Graduate School of Public Health and School of Medicine, Pittsburgh, Pennsylvania, USA
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37
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Abstract
Bacterial systematics has not yet reached a consensus for defining the fundamental unit of biological diversity, the species. The past half-century of bacterial systematics has been characterized by improvements in methods for demarcating species as phenotypic and genetic clusters, but species demarcation has not been guided by a theory-based concept of species. Eukaryote systematists have developed a universal concept of species: A species is a group of organisms whose divergence is capped by a force of cohesion; divergence between different species is irreversible; and different species are ecologically distinct. In the case of bacteria, these universal properties are held not by the named species of systematics but by ecotypes. These are populations of organisms occupying the same ecological niche, whose divergence is purged recurrently by natural selection. These ecotypes can be discovered by several universal sequence-based approaches. These molecular methods suggest that a typical named species contains many ecotypes, each with the universal attributes of species. A named bacterial species is thus more like a genus than a species.
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Affiliation(s)
- Frederick M Cohan
- Department of Biology, Wesleyan University, Middletown, Connecticut 06459-0170, USA.
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38
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Parry CM, Duong NM, Zhou J, Mai NTH, Diep TS, Thinh LQ, Wain J, Van Vinh Chau N, Griffiths D, Day NPJ, White NJ, Hien TT, Spratt BG, Farrar JJ. Emergence in Vietnam of Streptococcus pneumoniae resistant to multiple antimicrobial agents as a result of dissemination of the multiresistant Spain(23F)-1 clone. Antimicrob Agents Chemother 2002; 46:3512-7. [PMID: 12384358 PMCID: PMC128725 DOI: 10.1128/aac.46.11.3512-3517.2002] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2002] [Revised: 07/02/2002] [Accepted: 07/30/2002] [Indexed: 11/20/2022] Open
Abstract
Surveillance for Streptococcus pneumoniae resistant to penicillin and other antimicrobial agents is necessary to define the optimal empirical antibiotic therapy for meningitis in resource-poor countries such as Vietnam. The clinical and microbiological features of 100 patients admitted to the Centre for Tropical Diseases in Ho Chi Minh City, Vietnam, between 1993 and 2002 with invasive pneumococcal disease were studied. A penicillin-nonsusceptible pneumococcus (MIC, > or =0.1 micro g/ml) was isolated from the blood or cerebrospinal fluid of 8% of patients (2 of 24) between 1993 and 1995 but 56% (20 of 36) during 1999 to 2002 (P < 0.0001). Pneumococcal isolates resistant to penicillin (MIC, > or =2.0 micro g/ml) increased from 0% (0 of 24) to 28% (10 of 36) (P = 0.002). Only one isolate was ceftriaxone resistant (MIC, 2.0 micro g/ml). Penicillin-nonsusceptible pneumococci were isolated from 78% of children younger than 15 years (28 of 36) compared with 25% of adults (16 of 64) (P = 0.0001). Isolation of a penicillin-nonsusceptible pneumococcus in adults with meningitis was independently associated with referral from another hospital (P = 0.005) and previous antibiotic therapy (P = 0.025). Multilocus sequence typing showed that 86% of the invasive penicillin-resistant pneumococcus isolates tested (12 of 14) were of the Spain(23F)-1 clone. The serotypes of >95% of the penicillin-nonsusceptible pneumococci were included in the currently available pneumococcal vaccines. Our findings point to the recent introduction and spread of the Spain(23F)-1 clone of penicillin-resistant pneumococci in Vietnam. Simple clinical predictors can be used to guide empirical antibiotic therapy of meningitis. Pneumococcal vaccination may help to control this problem.
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39
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Ziglam HM, Finch RG. Penicillin-resistant pneumococci-implications for management of community-acquired pneumonia and meningitis. Int J Infect Dis 2002; 6 Suppl 1:S14-20. [PMID: 12044285 DOI: 10.1016/s1201-9712(02)90150-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Abstract
Penicillin-nonsusceptible Streptococcus pneumoniae isolates have become increasingly prevalent worldwide. They are well-known agents of community-acquired infections such as otitis media, pneumonia and bacterial meningitis. Therapy of pneumococcal infections is made difficult by the emergence and spread of bacterial resistance to penicillin and other beta-lactams, as well as other antimicrobials such as macrolides. This article reviews current concepts of epidemiology and the implications of penicillin-nonsusceptible pneumococci for management of community-acquired pneumonia and meningitis.
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40
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Abstract
The population structures of bacterial species are complex and often controversial. To a large extent, this is due to uncertainty about the frequency and impact of recombination in bacteria. The existence of clones within bacterial populations, and of linkage disequilibrium between alleles at different loci, is often cited as evidence for low rates of recombination. However, clones and linkage disequilibrium are almost inevitable in species that divide by binary fission and can be present in populations where recombination is frequent. In recent years, it has become possible to directly compare rates of recombination in different species. These studies indicate that in many bacterial species, including Neisseria meningitidis, Streptococcus pneumoniae, and Staphylococcus aureus, evolutionary change at neutral (housekeeping) loci is more likely to occur by recombination than mutation and can result in the elimination of any deep-rooted phylogenetic signal. In such species, the long-term evolution of the population is dominated by recombination, but this does not occur at a sufficiently high frequency to prevent the emergence of adaptive clones, although these are relatively short-lived and rapidly diversify.
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Affiliation(s)
- E J Feil
- Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, United Kingdom.
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41
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McGee L, McDougal L, Zhou J, Spratt BG, Tenover FC, George R, Hakenbeck R, Hryniewicz W, Lefévre JC, Tomasz A, Klugman KP. Nomenclature of major antimicrobial-resistant clones of Streptococcus pneumoniae defined by the pneumococcal molecular epidemiology network. J Clin Microbiol 2001; 39:2565-71. [PMID: 11427569 PMCID: PMC88185 DOI: 10.1128/jcm.39.7.2565-2571.2001] [Citation(s) in RCA: 381] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2001] [Accepted: 04/22/2001] [Indexed: 11/20/2022] Open
Abstract
The emergence of disease caused by penicillin-resistant and multidrug-resistant pneumococci has become a global concern, necessitating the identification of the epidemiological spread of such strains. The Pneumococcal Molecular Epidemiology Network was established in 1997 under the auspices of the International Union of Microbiological Societies with the aim of characterizing, standardizing, naming, and classifying antimicrobial agent-resistant pneumococcal clones. Here we describe the nomenclature for 16 pneumococcal clones that have contributed to the increase in antimicrobial resistance worldwide. Guidelines for the recognition of these clones using molecular typing procedures (pulsed-field gel electrophoresis, BOX-PCR, and multilocus sequence typing) are presented, as are the penicillin-binding profiles and macrolide resistance determinants for the 16 clones. This network can serve as a prototype for the collaboration of scientists in identifying clones of important human pathogens and as a model for the development of other networks.
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Affiliation(s)
- L McGee
- MRC/SAIMR/WITS Pneumococcal Diseases Research Unit, Johannesburg, South Africa.
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42
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Feil EJ, Smith JM, Enright MC, Spratt BG. Estimating recombinational parameters in Streptococcus pneumoniae from multilocus sequence typing data. Genetics 2000; 154:1439-50. [PMID: 10747043 PMCID: PMC1461021 DOI: 10.1093/genetics/154.4.1439] [Citation(s) in RCA: 206] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Multilocus sequence typing (MLST) is a highly discriminatory molecular typing method that defines isolates of bacterial pathogens using the sequences of approximately 450-bp internal fragments of seven housekeeping genes. This technique has been applied to 575 isolates of Streptococcus pneumoniae and identifies a number of discrete clonal complexes. These clonal complexes are typically represented by a single group of isolates sharing identical alleles at all seven loci, plus single-locus variants that differ from this group at only one out of the seven loci. As MLST is highly discriminatory, the members of each clonal complex can be assumed to have a recent common ancestor, and the molecular events that give rise to the single-locus variants can be used to estimate the relative contributions of recombination and mutation to clonal divergence. By comparing the sequences of the variant alleles within each clonal complex with the allele typically found within that clonal complex, we estimate that recombination has generated new alleles at a frequency approximately 10-fold higher than mutation, and that a single nucleotide site is approximately 50 times more likely to change through recombination than mutation. We also demonstrate how to estimate the average length of recombinational replacements from MLST data.
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Affiliation(s)
- E J Feil
- Wellcome Trust Centre for the Epidemiology of Infectious Disease, Department of Zoology, University of Oxford, United Kingdom.
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