Whole-Genome Sequencing for Characterization of Capsule Locus and Prediction of Serogroup of Invasive Meningococcal Isolates.

Abstract:

:Invasive meningococcal disease is mainly caused by Neisseria meningitidis serogroups A, B, C, X, W, and Y. The serogroup is typically determined by slide agglutination serogrouping (SASG) and real-time PCR (RT-PCR). We describe a whole-genome sequencing (WGS)-based method to characterize the capsule polysaccharide synthesis (cps) locus, classify N. meningitidis serogroups, and identify mechanisms for nongroupability using 453 isolates from a global strain collection. We identified novel genomic organizations within functional cps loci, consisting of insertion sequence (IS) elements in unique positions that did not disrupt the coding sequence. Genetic mutations (partial gene deletion, missing genes, IS insertion, internal stop, and phase-variable off) that led to nongroupability were identified. The results of WGS and SASG were in 91% to 100% agreement for all serogroups, while the results of WGS and RT-PCR showed 99% to 100% agreement. Among isolates determined to be nongroupable by WGS (31 of 453), the results of all three methods agreed 100% for those without a capsule polymerase gene. However, 61% (WGS versus SASG) and 36% (WGS versus RT-PCR) agreements were observed for the isolates, particularly those with phase variations or internal stops in cps loci, which warrant further characterization by additional tests. Our WGS-based serogrouping method provides comprehensive characterization of the N. meningitidis capsule, which is critical for meningococcal surveillance and outbreak investigations.

journal_name

J Clin Microbiol

authors

Marjuki H,Topaz N,Rodriguez-Rivera LD,Ramos E,Potts CC,Chen A,Retchless AC,Doho GH,Wang X

doi

10.1128/JCM.01609-18

subject

Has Abstract

pub_date

2019-02-27 00:00:00

issue

3

eissn

0095-1137

issn

1098-660X

pii

JCM.01609-18

journal_volume

57

pub_type

杂志文章
  • Benefit of hepatitis C virus core antigen assay in prediction of therapeutic response to interferon and ribavirin combination therapy.

    abstract::A highly sensitive second-generation hepatitis C virus (HCV) core antigen assay has recently been developed. We compared viral disappearance and first-phase kinetics between commercially available core antigen (Ag) assays, Lumipulse Ortho HCV Ag (Lumipulse-Ag), and a quantitative HCV RNA PCR assay, Cobas Amplicor HCV ...

    journal_title:Journal of clinical microbiology

    pub_type: 临床试验,杂志文章

    doi:10.1128/JCM.43.1.186-191.2005

    authors: Takahashi M,Saito H,Higashimoto M,Atsukawa K,Ishii H

    更新日期:2005-01-01 00:00:00

  • Effect of aerobic and anaerobic atmospheres on isolation of organisms from blood cultures.

    abstract::Blood was cultured in two vacuum bottles containing Columbia broth. Filtered air was admitted to one bottle (aerobic); the unvented bottle was considered anaerobic. Cultures were incubated at 35 C until growth occurred or for at least 7 days. Of 744 organisms isolated, 50% were isolated from both bottles, 30% from the...

    journal_title:Journal of clinical microbiology

    pub_type: 杂志文章

    doi:10.1128/JCM.1.2.154-156.1975

    authors: Blazevic DJ,Stemper JE,Matsen JM

    更新日期:1975-02-01 00:00:00

  • Reverse transcription-PCR detection of hepatitis G virus.

    abstract::Hepatitis G virus (HGV) was recently identified as a new member of the Flaviviridae, but its clinical significance is still unclear. Since no immunoassay for the diagnosis of HGV is available, we developed a sensitive reverse transcription-PCR (RT-PCR) assay to facilitate the detection of the viral genome by mass scre...

    journal_title:Journal of clinical microbiology

    pub_type: 杂志文章

    doi:10.1128/JCM.34.11.2660-2664.1996

    authors: Schlueter V,Schmolke S,Stark K,Hess G,Ofenloch-Haehnle B,Engel AM

    更新日期:1996-11-01 00:00:00

  • Evaluation and comparison of molecular techniques for epidemiological typing of Salmonella enterica subsp. enterica serovar dublin.

    abstract::A total of 28 unrelated isolates of the Salmonella enterica subsp. enterica serovar dublin (S. dublin) collected during a 6-year period, as well as four samples of the S. dublin live vaccine strain Bovisaloral and its prototype strain S. dublin 442/039, were investigated by different molecular typing methods for the f...

    journal_title:Journal of clinical microbiology

    pub_type: 杂志文章

    doi:10.1128/JCM.34.3.641-646.1996

    authors: Liebisch B,Schwarz S

    更新日期:1996-03-01 00:00:00

  • Discrimination between scrapie and bovine spongiform encephalopathy in sheep by molecular size, immunoreactivity, and glycoprofile of prion protein.

    abstract::A procedure for discrimination between scrapie and bovine spongiform encephalopathy (BSE) in sheep is of importance for establishing whether BSE has entered the sheep population. Since BSE has not yet been found in sheep at the farm level, such discrimination procedures can be developed only with experimental sheep BS...

    journal_title:Journal of clinical microbiology

    pub_type: 杂志文章

    doi:10.1128/jcm.42.3.972-980.2004

    authors: Thuring CM,Erkens JH,Jacobs JG,Bossers A,Van Keulen LJ,Garssen GJ,Van Zijderveld FG,Ryder SJ,Groschup MH,Sweeney T,Langeveld JP

    更新日期:2004-03-01 00:00:00

  • Comparison of Hybribio GenoArray and Roche human papillomavirus (HPV) linear array for HPV genotyping in anal swab samples.

    abstract::Human papillomavirus (HPV) is causally associated with anal cancer, as HPV DNA is detected in up to 90% of anal intraepithelial neoplasias and anal cancers. With the gradual increase of anal cancer rates, there is a growing need to establish reliable and clinically relevant methods to detect anal cancer precursors. In...

    journal_title:Journal of clinical microbiology

    pub_type: 杂志文章

    doi:10.1128/JCM.02274-14

    authors: Low HC,Silver MI,Brown BJ,Leng CY,Blas MM,Gravitt PE,Woo YL

    更新日期:2015-02-01 00:00:00

  • Evaluation of the four-hour Micro-ID technique for direct identification of oxidase-negative, Gram-negative rods from blood cultures.

    abstract::A 4-h Micro-ID technique for direct identification of oxidase-negative gram-negative rods from positive blood cultures was compared to subculture and species identification of single colonies by API 20E and Micro-ID, using standardized inocula. A total of 127 patients (220 positive cultures) were studied. Isolates inc...

    journal_title:Journal of clinical microbiology

    pub_type: 杂志文章

    doi:10.1128/JCM.12.4.533-537.1980

    authors: Appelbaum PC,Schick SF,Kellogg JA

    更新日期:1980-10-01 00:00:00

  • Multicenter evaluation of five commercial rubella virus immunoglobulin G kits which report in international units per milliliter.

    abstract::In a multicenter study, the consistency of international units expressed by five commercially available rubella virus immunoglobulin G kits was evaluated. The linearity and within-run and between-run precision were determined for each kit. All kits demonstrated good linearity and had within-run and between-run precisi...

    journal_title:Journal of clinical microbiology

    pub_type: 杂志文章

    doi:10.1128/JCM.30.3.633-641.1992

    authors: Dimech W,Bettoli A,Eckert D,Francis B,Hamblin J,Kerr T,Ryan C,Skurrie I

    更新日期:1992-03-01 00:00:00

  • Methicillin-Resistant Staphylococcus aureus spa Type t002 Outbreak in Horses and Staff at a Veterinary Teaching Hospital after Its Presumed Introduction by a Veterinarian.

    abstract::Methicillin-resistant Staphylococcus aureus (MRSA) infection and colonization, involving MRSA strains which differ from common human health care-associated clones, have become serious emerging conditions in equine veterinary hospitals. In 2010, MRSA spa type t535 caused an outbreak involving both horses and personnel ...

    journal_title:Journal of clinical microbiology

    pub_type: 杂志文章

    doi:10.1128/JCM.00090-15

    authors: Steinman A,Masarwa S,Tirosh-Levy S,Gleser D,Kelmer G,Adler A,Carmeli Y,Schwaber MJ

    更新日期:2015-09-01 00:00:00

  • Numerical analysis of electrophoretic protein patterns of methicillin-resistant strains of Staphylococcus aureus.

    abstract::A total of 50 strains of Staphylococcus aureus, including 41 methicillin-resistant S. aureus (MRSA) strains, were characterized by one-dimensional sodium dodecyl sulfate-polyacrylamide gel electrophoresis of whole-cell proteins. The protein patterns contained 40-50 discrete bands and were highly reproducible. Partial ...

    journal_title:Journal of clinical microbiology

    pub_type: 杂志文章

    doi:10.1128/JCM.27.11.2574-2581.1989

    authors: Costas M,Cookson BD,Talsania HG,Owen RJ

    更新日期:1989-11-01 00:00:00

  • Rapid and accurate identification of human isolates of Pasteurella and related species by sequencing the sodA gene.

    abstract::The identification of Pasteurella and related bacteria remains a challenge. Here, a 449- to 473-bp fragment (sodA(int)) internal to the sodA gene, encoding the manganese-dependent superoxide dismutase, was amplified and sequenced with a single pair of degenerate primers from the type strains of Pasteurella (18 strains...

    journal_title:Journal of clinical microbiology

    pub_type: 杂志文章

    doi:10.1128/JCM.43.5.2307-2314.2005

    authors: Gautier AL,Dubois D,Escande F,Avril JL,Trieu-Cuot P,Gaillot O

    更新日期:2005-05-01 00:00:00

  • Rapid identification of bacteria in blood cultures by using fluorescently labeled oligonucleotide probes.

    abstract::The applicability of whole-cell hybridization for the identification of pathogenic bacteria in blood from septic patients was examined. Oligonucleotide probes, fluorescently labeled with fluorescein isothiocyanate, directed against the variable regions of the 16S rRNAs of the following bacterial species and/or genera ...

    journal_title:Journal of clinical microbiology

    pub_type: 杂志文章

    doi:10.1128/JCM.38.2.814-817.2000

    authors: Jansen GJ,Mooibroek M,Idema J,Harmsen HJ,Welling GW,Degener JE

    更新日期:2000-02-01 00:00:00

  • Discrimination of antibody to herpes B virus from antibody to herpes simplex virus types 1 and 2 in human and macaque sera.

    abstract::The antigenic cross-reactive characteristics of herpes B virus and herpes simplex virus (HSV) type 1 (HSV-1) and HSV-2 are responsible for false-positive diagnoses by serological assays in humans and macaques. In the present study, we developed a fluorometric indirect enzyme-linked immunosorbent assay (ELISA) with rec...

    journal_title:Journal of clinical microbiology

    pub_type: 杂志文章

    doi:10.1128/JCM.00342-07

    authors: Fujima A,Ochiai Y,Saito A,Omori Y,Noda A,Kazuyama Y,Shoji H,Tanabayashi K,Ueda F,Yoshikawa Y,Hondo R

    更新日期:2008-01-01 00:00:00

  • 16S ribosomal DNA typing for identification of pathogens in patients with bacterial keratitis.

    abstract::The identification of pathogens in patients with bacterial keratitis remains problematic because standard diagnostic tests are negative for 40 to 60% of patients. A cross-sectional study was undertaken to determine if PCR and sequence analysis of 16S ribosomal DNA (rDNA) could be used to detect bacterial pathogens in ...

    journal_title:Journal of clinical microbiology

    pub_type: 杂志文章

    doi:10.1128/JCM.36.12.3492-3496.1998

    authors: Knox CM,Cevellos V,Dean D

    更新日期:1998-12-01 00:00:00

  • Persistence of Escherichia coli O157 isolates on bovine farms in England and Wales.

    abstract::We performed pulsed-field gel electrophoresis on Escherichia coli O157 isolates (n = 318) from 199 healthy animals in a longitudinal study carried out on nine farms. Investigation of the restriction types proved that at the farm level, the same clones can be detected on sampling occasions separated by as much as 17 mo...

    journal_title:Journal of clinical microbiology

    pub_type: 杂志文章

    doi:10.1128/JCM.43.2.898-902.2005

    authors: Liebana E,Smith RP,Batchelor M,McLaren I,Cassar C,Clifton-Hadley FA,Paiba GA

    更新日期:2005-02-01 00:00:00

  • Adiaspiromycosis causing respiratory failure and a review of human infections due to Emmonsia and Chrysosporium spp.

    abstract::We report a case of a 27-year-old male who presented with respiratory distress that required mechanical ventilation. Transbronchial biopsy revealed adiaspores of the fungus Emmonsia crescens within granulomata, a condition known as adiaspiromycosis. The patient received amphotericin products and corticosteroids, follo...

    journal_title:Journal of clinical microbiology

    pub_type: 杂志文章,评审

    doi:10.1128/JCM.00226-11

    authors: Anstead GM,Sutton DA,Graybill JR

    更新日期:2012-04-01 00:00:00

  • Fatal family outbreak of Bacillus cereus-associated food poisoning.

    abstract::Bacillus cereus is a well-known cause of food-borne illness, but infection with this organism is not commonly reported because of its usually mild symptoms. A fatal case due to liver failure after the consumption of pasta salad is described and demonstrates the possible severity of the emetic syndrome. ...

    journal_title:Journal of clinical microbiology

    pub_type: 杂志文章

    doi:10.1128/JCM.43.8.4277-4279.2005

    authors: Dierick K,Van Coillie E,Swiecicka I,Meyfroidt G,Devlieger H,Meulemans A,Hoedemaekers G,Fourie L,Heyndrickx M,Mahillon J

    更新日期:2005-08-01 00:00:00

  • Development and Evaluation of Novel Real-Time Reverse Transcription-PCR Assays with Locked Nucleic Acid Probes Targeting Leader Sequences of Human-Pathogenic Coronaviruses.

    abstract::Based on findings in small RNA-sequencing (Seq) data analysis, we developed highly sensitive and specific real-time reverse transcription (RT)-PCR assays with locked nucleic acid probes targeting the abundantly expressed leader sequences of Middle East respiratory syndrome coronavirus (MERS-CoV) and other human corona...

    journal_title:Journal of clinical microbiology

    pub_type: 杂志文章

    doi:10.1128/JCM.01224-15

    authors: Chan JF,Choi GK,Tsang AK,Tee KM,Lam HY,Yip CC,To KK,Cheng VC,Yeung ML,Lau SK,Woo PC,Chan KH,Tang BS,Yuen KY

    更新日期:2015-08-01 00:00:00

  • Comparison of 17 genome types of adenovirus type 3 identified among strains recovered from six continents.

    abstract::Restriction endonucleases BamHI, BclI, BglI, BglII, BstEII, EcoRI, HindIII, HpaI, SalI, SmalI, XbalI, and XholI were used to analyze 61 selected strains of adenovirus type 3 (Ad3) isolated from Africa, Asia, Australia, Europe, North America, and South America. It was noted that the use of BamHI, BclI, BglII, HpaI, Sal...

    journal_title:Journal of clinical microbiology

    pub_type: 杂志文章

    doi:10.1128/JCM.26.5.1009-1015.1988

    authors: Li QG,Wadell G

    更新日期:1988-05-01 00:00:00

  • Impact of a Rapid Herpes Simplex Virus PCR Assay on Duration of Acyclovir Therapy.

    abstract::Herpes simplex virus (HSV) infections of the central nervous system (CNS) are associated with significant morbidity and mortality rates in children. This study assessed the impact of a direct HSV (dHSV) PCR assay on the time to result reporting and the duration of acyclovir therapy for children with signs and symptoms...

    journal_title:Journal of clinical microbiology

    pub_type: 杂志文章

    doi:10.1128/JCM.02559-16

    authors: Van TT,Mongkolrattanothai K,Arevalo M,Lustestica M,Dien Bard J

    更新日期:2017-05-01 00:00:00

  • Detection of Legionella pneumophila capsular-like envelope antigens by counterimmunoelectrophoresis.

    abstract::The capsular-like envelope of Legionella pneumophila strains Togus 1 (serotype 2) and Philadelphia 1 (serotype 1) was isolated and purified by column chromatography on Sepharose 6B. Antibody raised in rabbits to these two antigenic materials did not cross-react in gel diffusion. Upon electrophoresis followed by gel di...

    journal_title:Journal of clinical microbiology

    pub_type: 杂志文章

    doi:10.1128/JCM.13.4.637-642.1981

    authors: Smith RA,DiGiorgio S,Darner J,Wilhelm A

    更新日期:1981-04-01 00:00:00

  • Ciprofloxacin-resistant Salmonella enterica serovar typhi from Kuwait with novel mutations in gyrA and parC genes.

    abstract::Blood isolates of Salmonella enterica serovar Typhi from two recently returned Bangladeshi patients in Kuwait were ciprofloxacin resistant, with ciprofloxacin MICs of 12 mg/liter for both isolates. Both isolates had three novel gyrA mutations (55-Leu-->Trp, 87-Asp-->Ala, and 106-Gln-->Arg) and three novel parC mutatio...

    journal_title:Journal of clinical microbiology

    pub_type: 杂志文章

    doi:10.1128/JCM.01161-08

    authors: Dimitrov T,Dashti AA,Albaksami O,Udo EE,Jadaon MM,Albert MJ

    更新日期:2009-01-01 00:00:00

  • Simple colorimetric microtiter plate hybridization assay for detection of amplified Mycobacterium leprae DNA.

    abstract::The detection of amplified products resulting from polymerase chain reactions (PCRs) remains a complicated process. To simplify the detection procedures, we developed a colorimetric microtiter plate hybridization assay for the specific detection of 5'-biotinylated PCR fragments of Mycobacterium leprae DNA. For this as...

    journal_title:Journal of clinical microbiology

    pub_type: 杂志文章

    doi:10.1128/JCM.31.3.665-670.1993

    authors: van der Vliet GM,Hermans CJ,Klatser PR

    更新日期:1993-03-01 00:00:00

  • Protease phenotypes of Pseudomonas aeruginosa isolated from patients with cystic fibrosis.

    abstract::The protease phenotypes expressed by isolates of Pseudomonas aeruginosa from cystic fibrosis (CF) patients were evaluated. The majority of isolates tested produced elastase (65%) or alkaline protease (64%) or both. The mucoid phenotype expressed by many CF isolates of P. aeruginosa did not absolutely restrict the expr...

    journal_title:Journal of clinical microbiology

    pub_type: 杂志文章

    doi:10.1128/JCM.17.1.55-59.1983

    authors: Jagger KS,Bahner DR,Warren RL

    更新日期:1983-01-01 00:00:00

  • Characterization of multidrug-resistant Escherichia coli isolates associated with nosocomial infections in dogs.

    abstract::Multidrug-resistant opportunistic pathogens have become endemic to the veterinary hospital environment. Escherichia coli isolates resistant to 12 antibiotics were isolated from two dogs that were housed in the intensive care unit at The University of Georgia Veterinary Teaching Hospital within 48 h of each other. Revi...

    journal_title:Journal of clinical microbiology

    pub_type: 杂志文章

    doi:10.1128/jcm.40.10.3586-3595.2002

    authors: Sanchez S,McCrackin Stevenson MA,Hudson CR,Maier M,Buffington T,Dam Q,Maurer JJ

    更新日期:2002-10-01 00:00:00

  • Correlation of cefoxitin MICs with the presence of mecA in Staphylococcus spp.

    abstract::This report describes the results of an 11-laboratory study to determine if a cefoxitin broth microdilution MIC test could predict the presence of mecA in staphylococci. Using breakpoints of < or = 4 microg/ml for mecA-negative and > or = 6 or 8 microg/ml for mecA-positive isolates, sensitivity and specificity based o...

    journal_title:Journal of clinical microbiology

    pub_type: 杂志文章,多中心研究

    doi:10.1128/JCM.02304-08

    authors: Swenson JM,Brasso WB,Ferraro MJ,Hardy DJ,Knapp CC,Lonsway D,McAllister S,Reller LB,Sader HS,Shortridge D,Skov R,Weinstein MP,Zimmer BL,Patel JB

    更新日期:2009-06-01 00:00:00

  • PCR-based diagnosis of Helicobacter pylori infection and real-time determination of clarithromycin resistance directly from human gastric biopsy samples.

    abstract::A novel PCR detection assay that amplifies the Helicobacter pylori-specific vacuolating cytotoxin gene (vacA) and thus enables rapid diagnosis of infection is described. Additionally, a real-time probe hybridization melting point analysis assay to detect all three mutations in the 23S rRNA gene associated with clarith...

    journal_title:Journal of clinical microbiology

    pub_type: 杂志文章

    doi:10.1128/JCM.39.4.1217-1220.2001

    authors: Chisholm SA,Owen RJ,Teare EL,Saverymuttu S

    更新日期:2001-04-01 00:00:00

  • Use of pulsed-field gel electrophoresis typing to study an outbreak of infection due to Serratia marcescens in a neonatal intensive care unit.

    abstract::Serratia marcescens is a well-known cause of nosocomial infections and outbreaks, particularly in critically ill neonates and immunocompromised patients. Numerous methods have been proposed for typing. We used pulsed-field gel electrophoresis (PFGE) typing to analyze an outbreak in a neonatal intensive care unit (NICU...

    journal_title:Journal of clinical microbiology

    pub_type: 杂志文章

    doi:10.1128/JCM.34.12.3138-3141.1996

    authors: Miranda G,Kelly C,Solorzano F,Leanos B,Coria R,Patterson JE

    更新日期:1996-12-01 00:00:00

  • Improved version of the exoantigen test for identification of Coccidioides immitis and Histoplasma capsulatum cultures.

    abstract::A rapid and simple method for extracting specific cell-free antigens of Coccidioides immitis and Histoplasma capsulatum from agar slant cultures was developed. The extracts were analyzed in immunodiffusion tests for the presence of C. immitis or H. capsulatum specific antigens. These extracts were compared with cultur...

    journal_title:Journal of clinical microbiology

    pub_type: 杂志文章

    doi:

    authors: Kaufman L,Standard P

    更新日期:1978-07-01 00:00:00

  • Nested PCR for rapid detection of mumps virus in cerebrospinal fluid from patients with neurological diseases.

    abstract::In this study, we have developed a reverse transcription (RT)-nested polymerase chain reaction (n-PCR) for the detection of mumps virus RNA in cerebrospinal fluid (CSF) from patients with neurological infections. A specific 112-bp fragment was amplified by this method with primers from the nucleoprotein of the mumps v...

    journal_title:Journal of clinical microbiology

    pub_type: 杂志文章

    doi:

    authors: Poggio GP,Rodriguez C,Cisterna D,Freire MC,Cello J

    更新日期:2000-01-01 00:00:00