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1.  Clinical Prediction and Diagnosis of Neurosyphilis in HIV-Infected Patients with Early Syphilis 
Journal of Clinical Microbiology  2013;51(12):4060-4066.
The diagnosis of neurosyphilis (NS) is a challenge, especially in HIV-infected patients, and the criteria for deciding when to perform a lumbar puncture (LP) in HIV-infected patients with syphilis are controversial. We retrospectively reviewed demographic, clinical, and laboratory data from 122 cases of HIV-infected patients with documented early syphilis who underwent an LP to rule out NS, and we evaluated 3 laboratory-developed validated real-time PCR assays, the Treponema pallidum particle agglutination (TPPA) assay, the fluorescent treponemal antibody absorption (FTA-ABS) assay, and the line immunoassay INNO-LIA Syphilis, for the diagnosis of NS from cerebrospinal fluid (CSF) samples of these patients. NS was defined by a reactive CSF-VDRL test result and/or a CSF white blood cell (WBC) count of >20 cells/μl. Thirty of the 122 patients (24.6%) had early NS. Headache, visual symptoms, a CD4 cell count of <500 cells/μl, and viremia, as defined by an HIV-1 RNA count of ≥50 copies/ml, were associated with NS in multivariate analysis (P = <0.001 for each factor). Blood serum rapid plasma reagin (RPR) titers were not associated with early NS (P = 0.575). For the diagnosis of NS, the PCR, FTA-ABS, TPPA, and INNO-LIA assays had sensitivities of 58%, 100%, 68%, and 100%, specificities of 67%, 12%, 49%, and 13%, and negative predictive values of 85%, 100%, 84%, and 100%, respectively. Visual disturbances, headache, uncontrolled HIV-1 viremia, and a CD4 cell count of <500 cells/μl were predictors of NS in HIV-infected patients with early syphilis, while blood serum RPR titers were not; therefore, RPR titers should not be used as the sole criterion for deciding whether to perform an LP in early syphilis. When applied to CSF samples, the INNO-LIA Syphilis assay easily helped rule out NS.
doi:10.1128/JCM.01989-13
PMCID: PMC3838065  PMID: 24088852
2.  Invasive Potential of Nonencapsulated Disease Isolates of Neisseria meningitidis 
Infection and Immunity  2012;80(7):2346-2353.
The capsule of Neisseria meningitidis is the major virulence factor that enables this bacterium to overcome host immunity elicited by complement and phagocytes, rendering it capable of surviving in blood. As such, nonencapsulated N. meningitidis isolates are generally considered nonpathogenic. Here, we consider the inherent virulence of two nonencapsulated N. meningitidis isolates obtained from our national surveillance of infected blood cultures in Canada. Capsule deficiency of both strains was confirmed by serology and PCR for the ctrA to ctrD genes and siaA to siaC genes, as well as siaD genes specific to serogroups B, C, Y, and W135. In both strains, the capsule synthesis genes were replaced by the capsule null locus, cnl-2. In accordance with a lack of capsule, both strains were fully susceptible to killing by both human and baby rabbit complement. However, in the presence of cytidine-5′ monophospho-N-acetylneuraminic acid (CMP-NANA), allowing for lipooligosaccharide (LOS) sialylation, a significant increase of resistance to complement killing was observed. Mass spectrometry of purified LOS did not reveal any uncommon modifications that would explain their invasive phenotype. Finally, in a mouse intraperitoneal challenge model, these nonencapsulated isolates displayed enhanced virulence relative to an isogenic mutant of serogroup B strain MC58 lacking capsule (MC58ΔsiaD). Virulence of all nonencapsulated isolates tested was below that of encapsulated serogroup B strains MC58 and B16B6. However, whereas no mortality was observed with MC58ΔsiaD, 5/10 mice succumbed to infection with strain 2275 and 2/11 mice succumbed to strain 2274. Our results suggest the acquisition of a new virulence phenotype by these nonencapsulated strains.
doi:10.1128/IAI.00293-12
PMCID: PMC3416473  PMID: 22508859
3.  Immune Response to Haemophilus influenzae Type b Vaccination in Patients with Chronic Renal Failure 
Adult chronic renal failure patients undergoing hemodialysis are at an increased risk of invasive Haemophilus influenzae type b (Hib) disease due to the lack of functionally active anti-Hib antibodies. The pediatric Hib polysaccharide-protein conjugate vaccine is highly immunogenic in these patients and can provide protection against invasive Hib infection for at least 1 year.
doi:10.1128/CVI.00101-12
PMCID: PMC3370432  PMID: 22539472
4.  Invasive Serogroup B Neisseria meningitidis in Québec, Canada, 2003 to 2010: Persistence of the ST-269 Clone Since It First Emerged in 2003 
Journal of Clinical Microbiology  2012;50(5):1545-1551.
In the era after the introduction of the meningococcal serogroup C conjugate vaccine, from 1 January 2003 to 31 December 2010, serogroup B meningococci were the major cause of invasive meningococcal disease in the province of Québec, Canada, being responsible for 72% of all meningococcal disease cases. Of the 334 invasive serogroup B Neisseria meningitidis strains analyzed, 53.9% belonged to the ST-269 clonal complex (CC). Since it first emerged in 2003, the percentage of invasive serogroup B isolates that belonged to the ST-269 CC had increased from 35% in 2003 to 76% in 2010. Among the 180 meningococci in the ST-269 CC, 91.7% belonged to a single ST (ST-269). The most common PorA genotypes identified in the ST-269 CC were (i) VR1 19-1, VR2 15-11, VR3 36 (84%) and (ii) VR1 18-7, VR2 9, VR3 35-1 (9%). Cases of invasive disease due to the ST-269 CC were commonly found in those aged 11 to 19 years (30.5%) and 20 to 40 years (25.5%). Meningococci of the ST-269 CC were uncommon in other Canadian provinces. In contrast to the ST-269 CC, invasive serogroup B meningococci that belonged to the ST-41/44 CC were much more diverse genetically. However, one ST (ST-571), which is uncommon in the United States, accounted for 35% of all cases due to this CC. The current finding suggests that the ST-269 clone may indeed represent an emerging hypervirulent clone of meningococci.
doi:10.1128/JCM.06835-11
PMCID: PMC3347115  PMID: 22337990
5.  International Circumpolar Surveillance Interlaboratory Quality Control Program for Serotyping Haemophilus influenzae and Serogrouping Neisseria meningitidis, 2005 to 2009 
Journal of Clinical Microbiology  2012;50(3):651-656.
The International Circumpolar Surveillance (ICS) program was initiated in 1999 to conduct population-based surveillance for invasive pneumococcal disease in select regions of the Arctic. The program was expanded to include the surveillance of invasive diseases caused by Neisseria meningitidis and Haemophilus influenzae. An interlaboratory quality control (QC) program to monitor laboratory proficiencies in the serogrouping of N. meningitidis and serotyping of H. influenzae strains was codeveloped by the Arctic Investigations Program (Anchorage, AK) and the Public Health Agency of Canada National Microbiology Laboratory (Winnipeg, Manitoba, Canada) and introduced into the ICS program in 2005. Other participating laboratories included the Provincial Laboratory for Public Health (Edmonton, Alberta, Canada), Laboratoire Santé Publique du Québec (Sainte-Anne-de-Bellevue, Québec, Canada), and Statens Serum Institut (Copenhagen, Denmark). From 2005 through 2009, 50 isolates (24 N. meningitidis and 26 H. influenzae isolates) were distributed among the five participating laboratories. The overall serogroup concordance for N. meningitidis strains was 92.3% (96/104), without including three isolates that were found to express both serogroup Y and W135 specificities. Concordant results were obtained for serogroups A, B, C, and Y among all laboratories. Discrepancies were observed most frequently for serogroups W135, X, Z, and 29E. The overall serotype concordance for H. influenzae was 98% (125/127 attempts). The two discrepant results involved a serotype c strain and a serotype e strain, and in both cases, the serotypeable H. influenzae isolates were misidentified as being nontypeable. These data demonstrate a high degree of concordance for serogroup and serotype determinations of N. meningitidis and H. influenzae isolates, respectively, among the five laboratories participating in this quality control program.
doi:10.1128/JCM.05084-11
PMCID: PMC3295160  PMID: 22170933
7.  Homologous Recombination Drives Both Sequence Diversity and Gene Content Variation in Neisseria meningitidis 
Genome Biology and Evolution  2013;5(9):1611-1627.
The study of genetic and phenotypic variation is fundamental for understanding the dynamics of bacterial genome evolution and untangling the evolution and epidemiology of bacterial pathogens. Neisseria meningitidis (Nm) is among the most intriguing bacterial pathogens in genomic studies due to its dynamic population structure and complex forms of pathogenicity. Extensive genomic variation within identical clonal complexes (CCs) in Nm has been recently reported and suggested to be the result of homologous recombination, but the extent to which recombination contributes to genomic variation within identical CCs has remained unclear. In this study, we sequenced two Nm strains of identical serogroup (C) and multi-locus sequence type (ST60), and conducted a systematic analysis with an additional 34 Nm genomes. Our results revealed that all gene content variation between the two ST60 genomes was introduced by homologous recombination at the conserved flanking genes, and 94.25% or more of sequence divergence was caused by homologous recombination. Recombination was found in genes associated with virulence factors, antigenic outer membrane proteins, and vaccine targets, suggesting an important role of homologous recombination in rapidly altering the pathogenicity and antigenicity of Nm. Recombination was also evident in genes of the restriction and modification systems, which may undermine barriers to DNA exchange. In conclusion, homologous recombination can drive both gene content variation and sequence divergence in Nm. These findings shed new light on the understanding of the rapid pathoadaptive evolution of Nm and other recombinogenic bacterial pathogens.
doi:10.1093/gbe/evt116
PMCID: PMC3787668  PMID: 23902748
horizontal gene transfer; homologous recombination; clonal complex; MLST; nonvertical gene; restriction modification systems
8.  Molecular Characterization of Syphilis in Patients in Canada: Azithromycin Resistance and Detection of Treponema pallidum DNA in Whole-Blood Samples versus Ulcerative Swabs▿  
Journal of Clinical Microbiology  2009;47(6):1668-1673.
Although detection of Treponema pallidum DNA in whole-blood specimens of syphilis patients has been reported, it is uncertain at what stage of the disease such specimens are most suitable for the molecular diagnosis of syphilis. Also, few studies have directly compared the different gene targets for routine laboratory diagnostic usage in PCR assays. We examined 87 specimens from 68 patients attending two urban sexually transmitted disease clinics in Alberta, Canada. PCR was used to amplify the T. pallidum tpp47, bmp, and polA genes as well as a specific region of the 23S rRNA gene linked to macrolide antibiotic susceptibility. In primary syphilis cases, PCR was positive exclusively (75% sensitivity rate) in ulcerative swabs but not in blood specimens, while in secondary syphilis cases, 50% of the blood specimens were positive by PCR. Four out of 14 (28.6%) of our PCR-positive syphilis cases were found to be caused by an azithromycin-resistant strain(s). Our results confirmed that swabs from primary ulcers are the specimens of choice for laboratory diagnostic purposes. However, further research is required to determine what specimen(s) would be most appropriate for molecular investigation of syphilis in secondary and latent syphilis.
doi:10.1128/JCM.02392-08
PMCID: PMC2691066  PMID: 19339468
9.  Antibiotic Susceptibility of Invasive Haemophilus influenzae Strains in Canada▿  
Canadian invasive Haemophilus influenzae isolates from 1990 to 2006 were examined for antibiotic susceptibility: 42 strains (17.8%) were resistant to ampicillin by β-lactamase production, 5.5% were β-lactamase negative ampicillin intermediate, and 2.5% were intermediate to only the 2-μg ampicillin disk. An increase in β-lactamase-negative ampicillin-intermediate strains has been found.
doi:10.1128/AAC.01580-07
PMCID: PMC2292521  PMID: 18227189
10.  Serotyping and Population Genetics of Invasive Haemophilus influenzae  
doi:10.1128/JCM.02166-07
PMCID: PMC2268342  PMID: 18326837
12.  Genetic and Antigenic Analysis of Invasive Serogroup Y Neisseria meningitidis Isolates Collected from 1999 to 2003 in Canada▿ † 
Journal of Clinical Microbiology  2007;45(6):1753-1758.
One hundred forty serogroup Y Neisseria meningitidis isolates recovered from patients with invasive meningococcal disease (IMD) in Canada from 1999 to 2003 were analyzed by genetic and serological methods. Seventy-four isolates (52.9%) belonged to serotype 2c, and most have serosubtype antigen P1.5,2 (37 isolates, 26%) or P1.5 (31 isolates, 22%). Forty-eight isolates (34.3%) belonged to serotype 14 and have serosubtype antigen P1.5,2 (13 isolates, 9%) or P1.5 (7 isolates, 5%) or were nonserosubtypeable (27 isolates, 19%). Thirteen isolates (9.3%) were nonserotypeable. Multilocus sequence typing identified two unrelated clonal populations of serogroup Y meningococci causing invasive disease in Canada: ST-23 and ST-167 clonal complexes. Almost all ST-167-related isolates were typed as 2c:P1.5, while strains of the ST-23 clonal complex were either serotype 14 or 2c but with the serosubtype antigen P1.5,2. In contrast to previous reports that patients with serogroup Y disease are usually older, 26% of the Canadian serogroup Y cases were found in the 10-to-19-year-old age group and another 11% were in the 20-to-39-year-old age group.
doi:10.1128/JCM.02134-06
PMCID: PMC1933026  PMID: 17442798
13.  Nucleotide Sequence Diversity of the bexA Gene in Serotypeable Haemophilus influenzae Strains Recovered from Invasive Disease Patients in Canada▿ † 
Journal of Clinical Microbiology  2007;45(6):1996-1999.
The bexA genes of 36 Haemophilus influenzae isolates were sequenced to reveal their nucleotide sequence diversity, which divided them into two groups, similar to clonal divisions I and II. This sequence diversity may lead to false-negative PCR results for H. influenzae infections if bexA is the chosen gene target.
doi:10.1128/JCM.00612-07
PMCID: PMC1933025  PMID: 17460059
14.  Invasive Meningococcal Disease in Québec, Canada, Due to an Emerging Clone of ST-269 Serogroup B Meningococci with Serotype Antigen 17 and Serosubtype Antigen P1.19 (B:17:P1.19) 
Journal of Clinical Microbiology  2006;44(8):2743-2749.
During periods of endemic meningococcal disease, serogroup B Neisseria meningitidis is responsible for a significant percentage of invasive diseases, and no particular clone or strain predominates (F. E. Ashton and D. A. Caugant, Can. J. Microbiol. 47: 293-289, 2001), However, in the winter of 2004 to 2005, a cluster of serogroup B meningococcal disease occurred in one region in the province of Québec, Canada. The N. meningitidis strain responsible for this cluster of cases was identified as sequence type ST-269 with the antigenic formula B:17:P1.19. Retrospective analysis of isolates from 2000 onwards showed that this clone first emerged in the province of Québec in 2003. The emergence of this clone of serogroup B meningococci occurred after a mass vaccination against serogroup C N. meningitidis, suggesting possible capsule replacement.
doi:10.1128/JCM.00601-06
PMCID: PMC1594649  PMID: 16891487
15.  Invasive Haemophilus influenzae in Manitoba, Canada, in the Postvaccination Era 
Journal of Clinical Microbiology  2006;44(4):1530-1535.
Fifty-two Haemophilus influenzae isolates from patients with invasive disease in the province of Manitoba, Canada, were examined for serotype, biotype, genotype, and antibiotic susceptibility. Half of the 52 isolates were found to be serotype a, and 38.5% (20 isolates) were found to be nonserotypeable (NST). There were only three serotype b strains and one each for serotypes c, d, and f. All 26 serotype a isolates belonged to biotype II and demonstrated identical or highly similar DNA fingerprints by pulsed-field gel electrophoresis. An analysis of these isolates by multilocus sequence typing showed that they belong to the clonal complex ST-23. While 69% (18 of 26) of the serotype a cases were found in males, only 9 (45%) of the 20 patients with NST isolates were males. Twenty (77%) of the 26 serotype a isolates were from patients who were ≤24 months old. Twelve (63%) of the NST isolates were from adult or adolescent patients. In contrast to the clonal nature of serotype a isolates, the 20 NST isolates were found to belong to 18 different sequence types. Most of these 18 different sequence types were unrelated to each other, with the exception of 7 sequence types grouped into three clonal groups. Two (6.25%) out of 32 serotypeable isolates (1 serotype a and 1 serotype b) and 6 (30%) of 20 NST isolates were resistant to ampicillin due to β-lactamase production. These results suggest a change in the epidemiology of H. influenzae disease, with the majority of invasive H. influenzae isolates being associated with serotype a and NST strains.
doi:10.1128/JCM.44.4.1530-1535.2006
PMCID: PMC1448631  PMID: 16597886
16.  Use of Monoclonal Antibodies To Serotype Bordetella pertussis Isolates: Comparison of Results Obtained by Indirect Whole-Cell Enzyme-Linked Immunosorbent Assay and Bacterial Microagglutination Methods 
Journal of Clinical Microbiology  2005;43(5):2449-2451.
Sixty-one Bordetella pertussis isolates were tested blindly in two laboratories to determine their serotype nature by monoclonal antibodies using two independent methods: the standard bacterial microagglutination assay and an indirect whole-cell enzyme-linked immunosorbent assay. Both methods gave concordant results in 60 of the 61 isolates.
doi:10.1128/JCM.43.5.2449-2451.2005
PMCID: PMC1153803  PMID: 15872280
17.  Serological Specificities of Murine Hybridoma Monoclonal Antibodies against Neisseria meningitidis Serogroups B, C, Y, and W135 and Evaluation of Their Usefulness as Serogrouping Reagents by Indirect Whole-Cell Enzyme-Linked Immunosorbent Assay 
Murine hybridoma monoclonal antibodies (MAbs) were produced against the capsular antigens of serogroups B, C, Y, and W135 meningococci. Each serogroup-specific MAb reacted with the extracted capsular polysaccharide from its homologous serogroup only and did not react with capsules from the other three serogroups. The application of these MAbs for serogroup identification of meningococci was demonstrated by their abilities to correctly identify 183 clinical isolates of 185 meningococci recovered from individual invasive meningococcal disease (IMD) patients during routine surveillance in 2002. The remaining two meningococci were identified by PCR grouping as C in one case and Y in another, but neither isolate was positive by bacterial agglutination using rabbit antisera or by enzyme-linked immunosorbent assay using MAbs. The specificities of the anti-Y and anti-W135 MAbs were further assessed by tests with 37 serogroup W135 and 106 serogroup Y meningococci recovered from IMD cases during 1999 to 2001 and 2003. All 143 meningococci except one serogroup Y isolate were correctly identified by positive reactions with the corresponding MAbs that identified their homologous serogroups. The single serogroup Y isolate was received as nonagglutinable and tested as negative with both rabbit anti-Y antiserum and anti-Y MAb but was positive for the serogroup Y-specific siaD gene. The advantage of using MAbs for serogrouping of meningococci is discussed.
doi:10.1128/CDLI.12.1.152-156.2005
PMCID: PMC540207  PMID: 15643000
18.  Polymorphisms of the Fimbria fim3 Gene of Bordetella pertussis Strains Isolated in Canada 
Journal of Clinical Microbiology  2004;42(11):5364-5367.
The fim genes which code for the fimbria protective antigens present in both the inactivated whole-cell and acellular vaccines were analyzed in 86 Canadian Bordetella pertussis isolates. At least one of the novel mutations identified was found to involve a surface epitope that has been mapped by serum antibodies from infected or vaccinated subjects.
doi:10.1128/JCM.42.11.5364-5367.2004
PMCID: PMC525145  PMID: 15528744
19.  DNA Sequence Analysis of the PorB Protein of Nonserotypeable Serogroup C ET-15 Meningococci Suggests a Potential Mutational Hot Spot on Their Serotype Antigens 
Journal of Clinical Microbiology  2004;42(6):2718-2723.
The nucleotide sequences of the PorB proteins from 28 nonserotypeable serogroup C ET-15 meningococci recovered from invasive meningococcal disease cases were determined. PCR amplification of the porB genes responsible for encoding the serotype antigen was used for DNA sequence determination and identification of the nature of the serotype antigen. DNA sequencing revealed that three strains were of serotype 2a, and of the remaining 25 strains, 20 were found to have an identical single point mutation in the region of the VR3 gene, which encodes surface-exposed loop VI, where the serotype 2a epitope resides. This nonsynonymous mutation was confirmed by synthetic peptide immunochemical analysis to confer new serospecificity to these serotype 2a mutants. This finding of a potential novel mutational hot spot on the PorB proteins of meningococci may have implications for pathogenesis and vaccine development.
doi:10.1128/JCM.42.6.2718-2723.2004
PMCID: PMC427874  PMID: 15184458
20.  Phenotypic and Genetic Characterization of a Unique Variant of Serogroup C ET-15 Meningococci (with the Antigenic Formula C:2a:P1.7,1) Causing Invasive Meningococcal Disease in Quebec, Canada 
Journal of Clinical Microbiology  2004;42(4):1460-1465.
Serogroup C Neisseria meningitidis belonging to the electrophoretic type (ET) ET-15, a variant of ET-37, is endemic in Canada. Like other serogroup C ET-37 meningococci, the endemic ET-15 strains are usually found to carry the serotype and serosubtype antigens of 2a:P1.5,2. In 2001, a sudden increase in the number of cases of serogroup C meningococcal disease in Quebec, Canada, was caused by an antigenic variant of the ET-15 strain. This antigenic variant carries the unique serosubtype marker of P1.7,1. Strains of C:2a:P1.7,1 meningococci were not isolated in Canada in large numbers prior to 2001, and the characteristics of these meningococcal strains linked to an outbreak in Quebec, Canada, are described in the present study.
doi:10.1128/JCM.42.4.1460-1465.2004
PMCID: PMC387618  PMID: 15070989
21.  Nonencapsulated Neisseria meningitidis Strain Produces Amylopectin from Sucrose: Altering the Concept for Differentiation between N. meningitidis and N. polysaccharea 
Journal of Clinical Microbiology  2003;41(1):273-278.
Neisseria meningitidis is the causative agent of meningococcal sepsis and meningitis. Neisseria polysaccharea is a nonpathogenic species. N. polysaccharea is able to use sucrose to produce amylopectin, a starch-like polysaccharide, which distinguishes it biochemically from the pathogenic species N. meningitidis. The data presented here indicate that this may be an insufficient criterion to distinguish between these two species. The nonencapsulated Neisseria strain 93246 expressed a phenotype of amylopectin production similar to that of N. polysaccharea. However, strain 93246 reacted with N. meningitidis serotype 4 and serosubtype P1.14 monoclonal antibodies and showed the N. meningitidis L1(8) lipo-oligosaccharide immunotype. Further analyses were performed on four genetic loci in strain 93246, and the results were compared with 7 N. meningitidis strains, 13 N. polysaccharea strains, and 2 N. gonorrhoeae strains. Three genetic loci, opcA, siaD, and lgt-1 in strain 93246, were the same as in N. meningitidis. Particularly, the siaD gene encoding polysialyltransferase responsible for biosynthesis of N. meningitidis group B capsule was detected in strain 93246. This siaD gene was inactivated by a frameshift mutation at the poly(C) tract, which makes strain 93246 identical to other nonencapsulated N. meningitidis strains. As expected, the ams gene encoding amylosucrase, responsible for production of amylopectin from sucrose, was detected in strain 93246 and all 13 N. polysaccharea strains but not in N. meningitidis and N. gonorrhoeae strains. These data suggest that strain 93246 is nonencapsulated N. meningitidis but has the ability to produce extracellular amylopectin from sucrose. The gene for amylopectin production in strain 93246 was likely imported from N. polysaccharea by horizontal genetic exchange. Therefore, we conclude that genetic analysis is required to complement the traditional phenotypic classification for the nonencapsulated Neisseria strains.
doi:10.1128/JCM.41.1.273-278.2003
PMCID: PMC149584  PMID: 12517860
22.  Flagella as a Potential Marker for Campylobacter jejuni Strains Associated with Guillain-Barré Syndrome 
Journal of Clinical Microbiology  2001;39(2):762-764.
Campylobacter jejuni recovered from patients with Guillain-Barré syndrome (GBS) in different geographical locations and bearing different heat-labile and heat-stable antigens were found to have identical amino acid sequences in their flagellar flaA short variable region, suggesting that it may be a potentially useful marker for GBS association.
doi:10.1128/JCM.39.2.762-764.2001
PMCID: PMC87815  PMID: 11158146
24.  Extensive Genomic Variation within Clonal Complexes of Neisseria meningitidis 
Genome Biology and Evolution  2011;3:1406-1418.
Meningococcal disease is a widely distributed complex disease affecting all age categories. It can cause severe meningitis and septicemia, especially in unvaccinated infants and young children. The causative agent, Neisseria meningitidis (Nm), can be phenotypically and genetically differentiated into serogroups and sequence types (STs) and has a highly dynamic population structure. To obtain a deeper understanding of the epidemiology of Nm, we sequenced seven Nm genomes. Large-scale genomic analysis was conducted with these 7 Nm genomes, 27 additional Nm genomes from GenBank, and 4 other Neisseria genomes. We observed extensive homologous recombination in all gene functional categories among different Nm genomes. Homologous recombination is so frequent that it has resulted in numerous chimeric open reading frames, including genes in the capsule biosynthesis cluster and loci targeted by commercial vaccines. Our results reveal that, despite widespread use, evolutionary relationships inferred from the standard seven-gene multilocus sequence typing (MLST) method could not predict virulence gene content or strain phenotype. In fact, up to 28% of the virulence-associated genes could differ between strains of identical STs. Consistent with previous studies, we found that allelic recombination is also associated with alterations in antibiotic susceptibility. Overall, these findings emphasize the extensive genomic plasticity of Nm and the limitations of standard molecular methods to quantify this genotypic and phenotypic diversity.
doi:10.1093/gbe/evr119
PMCID: PMC3242501  PMID: 22084315
homologous recombination; horizontal gene transfer; genome evolution; multilocus sequence typing; virulence gene
25.  Global Population Structure and Evolution of Bordetella pertussis and Their Relationship with Vaccination 
mBio  2014;5(2):e01074-14.
ABSTRACT
Bordetella pertussis causes pertussis, a respiratory disease that is most severe for infants. Vaccination was introduced in the 1950s, and in recent years, a resurgence of disease was observed worldwide, with significant mortality in infants. Possible causes for this include the switch from whole-cell vaccines (WCVs) to less effective acellular vaccines (ACVs), waning immunity, and pathogen adaptation. Pathogen adaptation is suggested by antigenic divergence between vaccine strains and circulating strains and by the emergence of strains with increased pertussis toxin production. We applied comparative genomics to a worldwide collection of 343 B. pertussis strains isolated between 1920 and 2010. The global phylogeny showed two deep branches; the largest of these contained 98% of all strains, and its expansion correlated temporally with the first descriptions of pertussis outbreaks in Europe in the 16th century. We found little evidence of recent geographical clustering of the strains within this lineage, suggesting rapid strain flow between countries. We observed that changes in genes encoding proteins implicated in protective immunity that are included in ACVs occurred after the introduction of WCVs but before the switch to ACVs. Furthermore, our analyses consistently suggested that virulence-associated genes and genes coding for surface-exposed proteins were involved in adaptation. However, many of the putative adaptive loci identified have a physiological role, and further studies of these loci may reveal less obvious ways in which B. pertussis and the host interact. This work provides insight into ways in which pathogens may adapt to vaccination and suggests ways to improve pertussis vaccines.
IMPORTANCE
Whooping cough is mainly caused by Bordetella pertussis, and current vaccines are targeted against this organism. Recently, there have been increasing outbreaks of whooping cough, even where vaccine coverage is high. Analysis of the genomes of 343 B. pertussis isolates from around the world over the last 100 years suggests that the organism has emerged within the last 500 years, consistent with historical records. We show that global transmission of new strains is very rapid and that the worldwide population of B. pertussis is evolving in response to vaccine introduction, potentially enabling vaccine escape.
doi:10.1128/mBio.01074-14
PMCID: PMC3994516  PMID: 24757216

Results 1-25 (27)