Genetic Diversity of Porphyromonas gingivalis Isolates Recovered from Single “Refractory” Periodontitis Sites

ABSTRACT Multilocus sequence typing and fimA genotyping were performed on Porphyromonas gingivalis isolates from 15 subjects with “refractory” periodontitis. Several sequence types were detected for most individual pockets. The variation indicated recombination at the recA and pepO genes. The prevalence of fimA genotypes II and IV confirmed their association with periodontitis.

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High Genetic Diversity ofEnterococcus faeciumandEnterococcus faecalisClinical Isolates by Pulsed-Field Gel Electrophoresis and Multilocus Sequence Typing from a Hospital in Malaysia

BioMed Research International ◽

10.1155/2013/938937 ◽

2013 ◽

Vol 2013 ◽

pp. 1-6 ◽

Cited By ~ 23

Author(s):

Poh Leng Weng ◽

Ramliza Ramli ◽

Mariana Nor Shamsudin ◽

Yoke-Kqueen Cheah ◽

Rukman Awang Hamat

Keyword(s):

Genetic Diversity ◽

Gel Electrophoresis ◽

Multilocus Sequence Typing ◽

Genetic Relatedness ◽

Pulsed Field Gel Electrophoresis ◽

High Genetic Diversity ◽

Pulsed Field ◽

Susceptibility Profiles ◽

Sequence Types ◽

Multiple Antibiotics

Little is known on the genetic relatedness and potential dissemination of particular enterococcal clones in Malaysia. We studied the antibiotic susceptibility profiles ofEnterococcus faeciumandEnterococcus faecalisand subjected them to pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST).E. faeciumandE. faecalisdisplayed 27 and 30 pulsotypes, respectively, and 10 representativeE. faeciumandE. faecalisisolates (five each) yielded few different sequence types (STs): ST17 (2 isolates), ST78, ST203, and ST601 forE. faecium, and ST6, ST16, ST28, ST179, and ST399 forE. faecalis. Resistance to tazobactam-piperacillin and ampicillin amongstE. faeciumisolates was highly observed as compared toE. faecalisisolates. All of the isolates were sensitive to vancomycin and teicoplanin. The presence of epidemic and nosocomial strains of selectedE. faeciumSTs: 17, 78, and 203 andE. faecalisST6 as well as high rates of resistance to multiple antibiotics amongstE. faeciumisolates is of a particular concern.

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Multilocus Sequence Typing Reveals Extensive Genetic Diversity of the Emerging Fungal Pathogen Scedosporium aurantiacum

Frontiers in Cellular and Infection Microbiology ◽

10.3389/fcimb.2021.761596 ◽

2021 ◽

Vol 11 ◽

Author(s):

Azian Harun ◽

Alex Kan ◽

Katharina Schwabenbauer ◽

Felix Gilgado ◽

Haybrig Perdomo ◽

...

Keyword(s):

Genetic Diversity ◽

Cystic Fibrosis ◽

Multilocus Sequence Typing ◽

Fungal Pathogen ◽

Fungal Colonization ◽

Invasive Infection ◽

Mlst Scheme ◽

Australian Continent ◽

The World ◽

Sequence Types

Scedosporium spp. are the second most prevalent filamentous fungi after Aspergillus spp. recovered from cystic fibrosis (CF) patients in various regions of the world. Although invasive infection is uncommon prior to lung transplantation, fungal colonization may be a risk factor for invasive disease with attendant high mortality post-transplantation. Abundant in the environment, Scedosporium aurantiacum has emerged as an important fungal pathogen in a range of clinical settings. To investigate the population genetic structure of S. aurantiacum, a MultiLocus Sequence Typing (MLST) scheme was developed, screening 24 genetic loci for polymorphisms on a tester strain set. The six most polymorphic loci were selected to form the S. aurantiacum MLST scheme: actin (ACT), calmodulin (CAL), elongation factor-1α (EF1α), RNA polymerase subunit II (RPB2), manganese superoxide dismutase (SOD2), and β-tubulin (TUB). Among 188 global clinical, veterinary, and environmental strains, 5 to 18 variable sites per locus were revealed, resulting in 8 to 23 alleles per locus. MLST analysis observed a markedly high genetic diversity, reflected by 159 unique sequence types. Network analysis revealed a separation between Australian and non-Australian strains. Phylogenetic analysis showed two major clusters, indicating correlation with geographic origin. Linkage disequilibrium analysis revealed evidence of recombination. There was no clustering according to the source of the strains: clinical, veterinary, or environmental. The high diversity, especially amongst the Australian strains, suggests that S. aurantiacum may have originated within the Australian continent and was subsequently dispersed to other regions, as shown by the close phylogenetic relationships between some of the Australian sequence types and those found in other parts of the world. The MLST data are accessible at http://mlst.mycologylab.org. This is a joined publication of the ISHAM/ECMM working groups on “Scedosporium/Pseudallescheria Infections” and “Fungal Respiratory Infections in Cystic Fibrosis”.

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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 Reveals Genetic Diversity of Carbapenem- or Ceftazidime-Nonsusceptible Pseudomonas aeruginosa in China

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.00970-13 ◽

2013 ◽

Vol 57 (11) ◽

pp. 5697-5700 ◽

Cited By ~ 6

Author(s):

Jingshu Ji ◽

Jie Wang ◽

Zhihui Zhou ◽

Haiping Wang ◽

Yan Jiang ◽

...

Keyword(s):

Genetic Diversity ◽

Pseudomonas Aeruginosa ◽

Multilocus Sequence Typing ◽

Genetic Background ◽

Drug Resistant ◽

Content Type ◽

Novel Alleles ◽

Sequence Types

ABSTRACTIt is unclear whether the genetic background of drug-resistantPseudomonas aeruginosawas disseminated from a certain clone. Thus, we performed MLST (multilocus sequence typing) of 896P. aeruginosaisolates that were nonsusceptible to imipenem, meropenem, or ceftazidime. This revealed 254 sequence types (STs), including 104 new STs and 34 STs with novel alleles. Thirty-three clonal complexes and 404 singletons were found. In conclusion, drug-resistantP. aeruginosaclones can be developed from diverse genetic backgrounds.

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Comparison of multilocus sequence types found among North American isolates of Mycoplasma bovis from cattle, bison, and deer, 2007–2017

Journal of Veterinary Diagnostic Investigation ◽

10.1177/1040638719874848 ◽

2019 ◽

Vol 31 (6) ◽

pp. 899-904 ◽

Cited By ~ 5

Author(s):

Karen B. Register ◽

Murray D. Jelinski ◽

Matthew Waldner ◽

William D. Boatwright ◽

Tavis K. Anderson ◽

...

Keyword(s):

Genetic Diversity ◽

Health Status ◽

North America ◽

Host Specificity ◽

North American ◽

Multilocus Sequence Typing ◽

Mycoplasma Bovis ◽

Clear Association ◽

Sequence Types

A prior multilocus sequence typing (MLST) study reported that Mycoplasma bovis isolates from North American bison possess sequence types (STs) different from those found among cattle. The 42 bison isolates evaluated were obtained in 2007 or later, whereas only 19 of 94 (~20%) of the available cattle isolates, with only 1 from North America, were from that same time. We compared STs of additional, contemporary, North American cattle isolates with those from bison, as well as isolates from 2 North American deer, all originating during the same timeframe, to more definitively assess potential strain-related host specificity and expand our understanding of the genetic diversity of M. bovis. From 307 isolates obtained between 2007 and 2017 (209 from cattle, 96 from bison, 2 from deer), we identified 49 STs, with 39 found exclusively in cattle and 5 exclusively in bison. Four STs were shared between bison and cattle isolates; one ST was found in cattle and in a deer. There was no clear association between ST and the health status of the animal of origin. An MLST-based phylogeny including 41 novel STs identified in our study reveals that STs found in bison fall within several divergent lineages that include STs found exclusively in cattle.

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Multilocus Sequence Typing of Genital Chlamydia trachomatis in Norway Reveals Multiple New Sequence Types and a Large Genetic Diversity

PLoS ONE ◽

10.1371/journal.pone.0034452 ◽

2012 ◽

Vol 7 (3) ◽

pp. e34452 ◽

Cited By ~ 20

Author(s):

Kirsten Gravningen ◽

Linus Christerson ◽

Anne-Sofie Furberg ◽

Gunnar Skov Simonsen ◽

Kristina Ödman ◽

...

Keyword(s):

Genetic Diversity ◽

Chlamydia Trachomatis ◽

Multilocus Sequence Typing ◽

Sequence Types

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Genetic Diversity of Campylobacter jejuni Isolates from Farm Animals and the Farm Environment

Applied and Environmental Microbiology ◽

10.1128/aem.69.12.7409-7413.2003 ◽

2003 ◽

Vol 69 (12) ◽

pp. 7409-7413 ◽

Cited By ~ 116

Author(s):

F. M. Colles ◽

K. Jones ◽

R. M. Harding ◽

M. C. J. Maiden

Keyword(s):

Genetic Diversity ◽

Campylobacter Jejuni ◽

Human Disease ◽

Clonal Complex ◽

Food Samples ◽

Complex Model ◽

Farm Animals ◽

Significant Genetic Differentiation ◽

Sequence Types ◽

Retail Food

ABSTRACT The genetic diversity of Campylobacter jejuni isolates from farm animals and their environment was investigated by multilocus sequence typing (MLST). A total of 30 genotypes, defined by allelic profiles (assigned to sequence types [STs]), were found in 112 C. jejuni isolates originating in poultry, cattle, sheep, starlings, and slurry. All but two of these genotypes belonged to one of nine C. jejuni clonal complexes previously identified in isolates from human disease and retail food samples and one clonal complex previously associated with an environmental source. There was some evidence for the association of certain clonal complexes with particular farm animals: isolates belonging to the ST-45 complex predominated among poultry isolates but were absent among sheep isolates, while isolates belonging to the ST-61 and ST-42 complexes were predominant among sheep isolates but were absent from the poultry isolates. In contrast, ST-21 complex isolates were distributed among the different isolation sources. Comparison with MLST data from 91 human disease isolates showed small but significant genetic differentiation between the farm and human isolates; however, representatives of six clonal complexes were found in both samples. These data demonstrate that MLST and the clonal complex model can be used to identify and compare the genotypes of C. jejuni isolates from farm animals and the environment with those from retail food and human disease.

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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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Clonal analysis of the serogroup B meningococci causing New Zealand's epidemic

Epidemiology and Infection ◽

10.1017/s0950268805004954 ◽

2005 ◽

Vol 134 (2) ◽

pp. 377-383 ◽

Cited By ~ 26

Author(s):

K. H. DYET ◽

D. R. MARTIN

Keyword(s):

Genetic Diversity ◽

New Zealand ◽

16S Rrna ◽

Meningococcal Disease ◽

Common Ancestor ◽

Clonal Complex ◽

Clonal Analysis ◽

The Other ◽

Disease Rates ◽

Sequence Types

An epidemic of meningococcal disease caused by serogroup B meningococci expressing the P1.7-2,4 PorA protein began in New Zealand in 1991. The PorA type has remained stable. Different porB have been found in association with the P1.7-2,4 PorA, although type 4 has been most common. The clonal origins of B:P1.7-2,4 meningococci isolated from cases during 1990 to the end of 2003 were analysed. In 1990, the year immediately preceding the recognized increase in disease rates, all three subclones (ST-41, ST-42, and ST-154) of the ST-41/44 clonal complex occurred among the five isolates of B:P1.7-2,4. The two sequence types, ST-42 and ST-154, continued to cause most disease throughout New Zealand. Isolates belonging to subclone ST-41 were mostly identified early in the epidemic and in the South Island. 16S rRNA typing indicated that isolates belonging to the subclones ST-41 and ST-154 share a common ancestor, with those typing as ST-42 more distantly related with some genetically ambiguous. It is possible that ST-41 and ST-154 may have evolved one from the other but evolution to ST-42 is more difficult to explain. It is possible that one or more of the ST types could have been introduced into New Zealand prior to the first detection of clinical cases in 1990. Genetic diversity may have occurred during carriage in the community.

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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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