Multilocus Sequence Typing of Non-JP2 Serotype b Aggregatibacter actinomycetemcomitans Strains of Ghanaian and Swedish Origin

Objective and MethodsThe Gram-negative bacterium, Aggregatibacter actinomycetemcomitans is associated with periodontitis affecting young individuals. The geographic dissemination of the highly leukotoxic JP2 genotype of serotype b of this species was previously studied by multilocus sequence typing (MLST). Here, we have used MLST to genetically characterize non-JP2 genotype strains of serotype b, isolated from individuals living in Ghana (n=41), and in Sweden (n=13), respectively.ResultsThe MLST analysis revealed a total of nine sequence types (ST). Both Ghanaian and Swedish isolates were distributed in ST 1-3. ST 5 and 6 were only identified among the Ghanaian strains, whereas ST 4, 7, 8 and 9 were uniquely represented among the Swedish strains. Previously, we characterized these non-JP2 genotype strains of A. actinomycetemcomitans serotype b by arbitrarily-primed (AP)-PCR, which distributed them into three groups, AP-PCR type 1, 2, and 3, respectively. AP-PCR type 1 strains are generally highly leukotoxic, and are associated with progression of periodontal attachment loss. As AP-PCR type 1 includes both JP2 genotype strains and a proportion of non-JP2 genotype strains of serotype b, a straightforward diagnostic procedure has been sought. This has revealed a gene, cagE, which appears to be conserved only in this AP-PCR type. According to our results, MLST was not a highly discriminatory method to identify AP-PCR type 1, as strains of this AP-PCR type could be found within three different ST: ST 2, ST 3 and ST 8.ConclusionAccording to MLST, a geographic dissemination of non-JP2 genotype A. actinomycetemcomitans serotype b appears to exist. However, aiming to identify carriers of AP-PCR type 1, non-JP2 genotype serotype b, PCR with cagE-specific primers is likely the most efficient diagnostic procedure known today.

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Analysis of Genetic Relatedness of Haemophilus influenzae Isolates by Multilocus Sequence Typing

Journal of Bacteriology ◽

10.1128/jb.01207-07 ◽

2007 ◽

Vol 190 (4) ◽

pp. 1473-1483 ◽

Cited By ~ 58

Author(s):

Alice L. Erwin ◽

Sara A. Sandstedt ◽

Paul J. Bonthuis ◽

Jennifer L. Geelhood ◽

Kevin L. Nelson ◽

...

Keyword(s):

Haemophilus Influenzae ◽

Multilocus Sequence Typing ◽

Genetic Relatedness ◽

Geographic Origin ◽

Maximum Parsimony Analysis ◽

Negative Bacterium ◽

Phylogenetic Groups ◽

Capsule Production ◽

Metabolic Reactions ◽

Sequence Types

ABSTRACT The gram-negative bacterium Haemophilus influenzae is a human-restricted commensal of the nasopharynx that can also be associated with disease. The majority of H. influenzae respiratory isolates lack the genes for capsule production and are nontypeable (NTHI). Whereas encapsulated strains are known to belong to serotype-specific phylogenetic groups, the structure of the NTHI population has not been previously described. A total of 656 H. influenzae strains, including 322 NTHI strains, have been typed by multilocus sequence typing and found to have 359 sequence types (ST). We performed maximum-parsimony analysis of the 359 sequences and calculated the majority-rule consensus of 4,545 resulting equally most parsimonious trees. Eleven clades were identified, consisting of six or more ST on a branch that was present in 100% of trees. Two additional clades were defined by branches present in 91% and 82% of trees, respectively. Of these 13 clades, 8 consisted predominantly of NTHI strains, three were serotype specific, and 2 contained distinct NTHI-specific and serotype-specific clusters of strains. Sixty percent of NTHI strains have ST within one of the 13 clades, and eBURST analysis identified an additional phylogenetic group that contained 20% of NTHI strains. There was concordant clustering of certain metabolic reactions and putative virulence loci but not of disease source or geographic origin. We conclude that well-defined phylogenetic groups of NTHI strains exist and that these groups differ in genetic content. These observations will provide a framework for further study of the effect of genetic diversity on the interaction of NTHI with the host.

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Characterization of Neisseria meningitidis isolates collected from 1974 to 2003 in Japan by multilocus sequence typing

Journal of Medical Microbiology ◽

10.1099/jmm.0.45541-0 ◽

2004 ◽

Vol 53 (7) ◽

pp. 657-662 ◽

Cited By ~ 37

Author(s):

Hideyuki Takahashi ◽

Toshiro Kuroki ◽

Yuko Watanabe ◽

Hiroshi Tanaka ◽

Hiroo Inouye ◽

...

Keyword(s):

Statistical Analysis ◽

Neisseria Meningitidis ◽

Multilocus Sequence Typing ◽

Clonal Complex ◽

The Other ◽

Mlst Database ◽

Mlst Analysis ◽

The Past ◽

Sequence Types

Analysis of 182 Neisseria meningitidis strains isolated over the past 30 years in Japan by serogroup typing and multilocus sequence typing (MLST) was performed. The serogroups of the 182 Japanese isolates were B (103 isolates), Y (39), W135 (1) and non-groupable (39). By MLST analysis, 65 different sequence types (ST) were identified, 42 of which were not found in the MLST database as of January 2004 and seemed to be unique to Japan. Statistical analysis of the MLST results revealed that, although the Japanese isolates seemed to be genetically divergent, they were classified into six major clonal complexes and other minor complexes. Among these isolates, well-documented ST complexes found worldwide were present, such as ST-23 complex (49 isolates), ST-44 complex (41 isolates) and ST-32 complex (8 isolates). On the other hand, a new clonal complex designated ST-2046 complex (28 isolates), which has not been identified in other countries, was also found, suggesting that this clone was indigenous to Japan. Taken together, it was speculated that meningococcal isolates in Japan comprised heterogeneous clones, which were derived both from clones identified in other countries and clones unique to Japan.

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Multilocus sequence typing (MLST) analysis of 104Clostridium difficilestrains isolated from China

Epidemiology and Infection ◽

10.1017/s0950268812000453 ◽

2012 ◽

Vol 141 (1) ◽

pp. 195-199 ◽

Cited By ~ 39

Author(s):

Q. YAN ◽

J. ZHANG ◽

C. CHEN ◽

H. ZHOU ◽

P. DU ◽

...

Keyword(s):

Genetic Diversity ◽

Clostridium Difficile ◽

Multilocus Sequence Typing ◽

Geographical Origin ◽

Host Population ◽

High Genetic Diversity ◽

Dominant Type ◽

Mlst Analysis ◽

Phylogenetic Lineages ◽

Sequence Types

SUMMARYThe phylogenetic and epidemic relationships of 104 clinical isolatesof Clostridium difficilefrom three hospitals of different geographical and population sources in China were investigated by multilocus sequence typing. Twenty-two sequence types (STs) were identified, four of which, ST117, ST118, ST119 and ST129, were novel. No geographically specific and host population-specific phylogenetic lineages were found and there was no correlation between geographical origin or host population and strain genotype. ST37 was the dominant type in our survey but the four novel STs underline the high genetic diversity and unique polymorphisms inC. difficilefrom China.

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Multilocus Sequence Typing of Aggregatibacter actinomycetemcomitans Competently Depicts the Population Structure of the Species

Microbiology Spectrum ◽

10.1128/spectrum.01085-21 ◽

2021 ◽

Author(s):

Signe Nedergaard ◽

Anne B. Jensen ◽

Dorte Haubek ◽

Niels Nørskov-Lauritsen

Keyword(s):

Population Structure ◽

Multilocus Sequence Typing ◽

Housekeeping Genes ◽

Aggregatibacter Actinomycetemcomitans ◽

Content Type ◽

Typing Scheme ◽

Sequence Types

We developed a multilocus sequence typing scheme (MLST) for Aggregatibacter actinomycetemcomitans based on seven housekeeping genes, adk , atpG , frdB , mdh , pgi , recA , and zwf . A total of 188 strains of seven serotypes were separated into 57 sequence types.

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Comparison ofArcobacterIsolation Methods, and Diversity ofArcobacterspp. in Cheshire, United Kingdom

Applied and Environmental Microbiology ◽

10.1128/aem.01964-10 ◽

2010 ◽

Vol 77 (5) ◽

pp. 1646-1650 ◽

Cited By ~ 37

Author(s):

J. Y. Merga ◽

A. J. H. Leatherbarrow ◽

C. Winstanley ◽

M. Bennett ◽

C. A. Hart ◽

...

Keyword(s):

United Kingdom ◽

Multilocus Sequence Typing ◽

Specific Method ◽

Fecal Samples ◽

Mlst Analysis ◽

Isolation Methods ◽

Arcobacter Butzleri ◽

High Level ◽

Sequence Types ◽

Animal Feces

ABSTRACTThe aims of this study were, firstly, to compare five published methods for the isolation ofArcobacterspp. from animal feces in order to determine the most sensitive and specific method. Second, we analyzed the resulting isolates by multilocus sequence typing (MLST) in order to investigate the diversity of the isolates recovered. Third, we investigated the ability to recoverArcobacterspp. from frozen fecal samples. Seventy-seven fecal samples from cattle, sheep, and badgers were subjected to five isolation methods, based on published methods for the isolation ofArcobacterandCampylobacterspp. Thirty-nineArcobacter butzleriisolates were analyzed using a multilocus sequence typing scheme. The survival ofArcobacterspp. in frozen samples was investigated by freezing the fecal samples at −80°C for 7 days and then applying the same five isolation methods. The most sensitive and specific method used anArcobacter-specific broth in conjunction with modified charcoal cefoperazone deoxycholate agar (mCCDA) with added antibiotics. Freezing of fecal samples led to a reduction in the recovery ofArcobacterspp. by approximately 50%. The 39 allelic profiles obtained by MLST could be divided into 11 sequence types (STs). We have identified the most sensitive and specific method for the isolation ofArcobacterspp. from animal feces and demonstrated that the freezing of fecal samples prior to isolation reduces arcobacter recovery. MLST analysis of the isolates revealed a high level of diversity.

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Genetic Profiling of Aggregatibacter actinomycetemcomitans Serotype B Isolated from Periodontitis Patients Living in Sweden

Pathogens ◽

10.3390/pathogens8030153 ◽

2019 ◽

Vol 8 (3) ◽

pp. 153 ◽

Cited By ~ 7

Author(s):

Anders Johansson ◽

Rolf Claesson ◽

Carola Höglund Åberg ◽

Dorte Haubek ◽

Mark Lindholm ◽

...

Keyword(s):

Diagnostic Marker ◽

Aggregatibacter Actinomycetemcomitans ◽

Conventional Polymerase Chain Reaction ◽

Chain Reaction ◽

Genetic Profiling ◽

Attachment Loss ◽

Polymerase Chain ◽

Serotype B ◽

Periodontal Attachment Loss ◽

Potential Use

The bacterium Aggregatibacter actinomycetemcomitans is associated with aggressive forms of periodontitis and with systemic diseases, such as endocarditis. By assessing a Ghanaian longitudinal adolescent cohort, we earlier recognized the cagE gene as a possible diagnostic marker for a subgroup of JP2 and non-JP2 genotype serotype b A. actinomycetemcomitans strains, associated with high leukotoxicity as determined in a semi-quantitative cell assay. This group of A. actinomycetemcomitans is associated with the progression of attachment loss. In the present work, we used conventional polymerase chain reaction (PCR) and quantitative PCR to perform the cagE genotyping of our collection of 116 selected serotype b A. actinomycetemcomitans strains, collected over a period of 15 years from periodontitis patients living in Sweden. The A. actinomycetemcomitans strains carrying cagE (referred to as cagE+; n = 49) were compared to the cagE-negative strains (n = 67), present at larger proportions in the subgingival plaque samples, and were also much more prevalent in the young (≤35 years) compared to in the old (>35 years) group of patients. Our present results underline the potential use of cagE genotyping in the risk assessment of the development of periodontal attachment loss in Swedish adolescents.

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Prevalence, genetic diversity and recombination of species G enteroviruses infecting pigs in Vietnam

Journal of General Virology ◽

10.1099/vir.0.061978-0 ◽

2014 ◽

Vol 95 (3) ◽

pp. 549-556 ◽

Cited By ~ 23

Author(s):

Nguyen Van Dung ◽

Pham Hong Anh ◽

Nguyen Van Cuong ◽

Ngo Thi Hoa ◽

Juan Carrique-Mas ◽

...

Keyword(s):

Genetic Diversity ◽

Untranslated Region ◽

Study Group ◽

Group Comparison ◽

Specific Primers ◽

Sequence Comparisons ◽

Detection Rates ◽

High Frequencies ◽

Faecal Samples

Picornaviruses infecting pigs, described for many years as ‘porcine enteroviruses’, have recently been recognized as distinct viruses within three distinct genera (Teschovirus, Sapelovirus and Enterovirus). To better characterize the epidemiology and genetic diversity of members of the Enterovirus genus, faecal samples from pigs from four provinces in Vietnam were screened by PCR using conserved enterovirus (EV)-specific primers from the 5′ untranslated region (5′ UTR). High rates of infection were recorded in pigs on all farms, with detection frequencies of approximately 90 % in recently weaned pigs but declining to 40 % in those aged over 1 year. No differences in EV detection rates were observed between pigs with and without diarrhoea [74 % (n = 70) compared with 72 % (n = 128)]. Genetic analysis of consensus VP4/VP2 and VP1 sequences amplified from a subset of EV-infected pigs identified species G EVs in all samples. Among these, VP1 sequence comparisons identified six type 1 and seven type 6 variants, while four further VP1 sequences failed to group with any previously identified EV-G types. These have now been formally assigned as EV-G types 8–11 by the Picornavirus Study Group. Comparison of VP1, VP4/VP2, 3Dpol and 5′ UTRs of study samples and those available on public databases showed frequent, bootstrap-supported differences in their phylogenies indicative of extensive within-species recombination between genome regions. In summary, we identified extremely high frequencies of infection with EV-G in pigs in Vietnam, substantial genetic diversity and recombination within the species, and evidence for a much larger number of circulating EV-G types than currently described.

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Phenotypic and Molecular Analysis of Penicillin-Nonsusceptible Streptococcus pneumoniae Isolates in Poland

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.01072-06 ◽

2006 ◽

Vol 51 (1) ◽

pp. 40-47 ◽

Cited By ~ 13

Author(s):

Ewa Sadowy ◽

Radosław Izdebski ◽

Anna Skoczyńska ◽

Paweł Grzesiowski ◽

Marek Gniadkowski ◽

...

Keyword(s):

Streptococcus Pneumoniae ◽

Molecular Analysis ◽

Gel Electrophoresis ◽

Multilocus Sequence Typing ◽

Susceptibility Testing ◽

Bacterial Pathogen ◽

Pulsed Field Gel Electrophoresis ◽

Pulsed Field ◽

Related Clone ◽

Sequence Types

ABSTRACT β-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 (Spain23F-1, Spain6B-2, Spain9V-3, Taiwan23F-15, Poland23F-16, Poland6B-20, and Sweden15A-25) or their closely related variants comprised the majority of the study isolates. The spread of Spain9V-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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Population Genetics and Characterization ofCampylobacter jejuniIsolates from Western Jackdaws and Game Birds in Finland

Applied and Environmental Microbiology ◽

10.1128/aem.02365-18 ◽

2018 ◽

Vol 85 (4) ◽

Cited By ~ 3

Author(s):

Sara Kovanen ◽

Mirko Rossi ◽

Mari Pohja-Mykrä ◽

Timo Nieminen ◽

Mirja Raunio-Saarnisto ◽

...

Keyword(s):

Host Specificity ◽

Campylobacter Jejuni ◽

Multilocus Sequence Typing ◽

Wild Birds ◽

Whole Genome ◽

Mallard Duck ◽

Content Type ◽

Game Birds ◽

Hygienic Measures ◽

Sequence Types

ABSTRACTPoultry are considered a major reservoir and source of human campylobacteriosis, but the roles of environmental reservoirs, including wild birds, have not been assessed in depth. In this study, we isolated and characterizedCampylobacter jejunifrom western jackdaws (n= 91, 43%), mallard ducks (n= 82, 76%), and pheasants (n= 9, 9%). Most of the western jackdaw and mallard duckC. jejuniisolates represented multilocus sequence typing (MLST) sequence types (STs) that diverged from those previously isolated from human patients and various animal species, whereas all pheasant isolates represented ST-19, a common ST among human patients and other hosts worldwide. Whole-genome MLST revealed that mallard duck ST-2314 and pheasant ST-19 isolates represented bacterial clones that were genetically highly similar to human isolates detected previously. Further analyses revealed that in addition to a divergent ClonalFrame genealogy, certain genomic characteristics of the western jackdawC. jejuniisolates, e.g., a novelcdtABCgene cluster and the type VI secretion system (T6SS), may affect their host specificity and virulence. Game birds may thus pose a risk for acquiring campylobacteriosis; therefore, hygienic measures during slaughter and meat handling warrant special attention.IMPORTANCEThe roles of environmental reservoirs, including wild birds, in the molecular epidemiology ofCampylobacter jejunihave not been assessed in depth. Our results showed that game birds may pose a risk for acquiring campylobacteriosis, because they hadC. jejunigenomotypes highly similar to human isolates detected previously. Therefore, hygienic measures during slaughter and meat handling warrant special attention. On the contrary, a unique phylogeny was revealed for the western jackdaw isolates, and certain genomic characteristics identified among these isolates are hypothesized to affect their host specificity and virulence. Comparative genomics within sequence types (STs), using whole-genome multilocus sequence typing (wgMLST), and phylogenomics are efficient methods to analyze the genomic relationships ofC. jejuniisolates.

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Nonencapsulated or nontypeableHaemophilus influenzaeare more likely than their encapsulated or serotypeable counterparts to have mutations in their fucose operon

Canadian Journal of Microbiology ◽

10.1139/w11-017 ◽

2011 ◽

Vol 57 (12) ◽

pp. 982-986 ◽

Cited By ~ 14

Author(s):

Michelle L. Shuel ◽

Kathleen E. Karlowsky ◽

Dennis K.S. Law ◽

Raymond S.W. Tsang

Keyword(s):

Nucleotide Sequence ◽

Haemophilus Influenzae ◽

Dna Sequencing ◽

Multilocus Sequence Typing ◽

Population Biology ◽

Housekeeping Genes ◽

Sequence Variations ◽

Sequence Types ◽

Complete Deletion

Population biology of Haemophilus influenzae can be studied by multilocus sequence typing (MLST), and isolates are assigned sequence types (STs) based on nucleotide sequence variations in seven housekeeping genes, including fucK. However, the ST cannot be assigned if one of the housekeeping genes is absent or cannot be detected by the current protocol. Occasionally, strains of H. influenzae have been reported to lack the fucK gene. In this study, we examined the prevalence of this mutation among our collection of H. influenzae isolates. Of the 704 isolates studied, including 282 encapsulated and 422 nonencapsulated isolates, nine were not typeable by MLST owing to failure to detect the fucK gene. All nine fucK-negative isolates were nonencapsulated and belonged to various biotypes. DNA sequencing of the fucose operon region confirmed complete deletion of genes in the operon in seven of the nine isolates, while in the remaining two isolates, some of the genes were found intact or in parts. The significance of these findings is discussed.

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