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

2010 ◽  
Vol 77 (5) ◽  
pp. 1646-1650 ◽  
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.

scholarly journals Temporal Variation and Host Association in the Campylobacter Population in a Longitudinal Ruminant Farm Study

2011 ◽  
Vol 77 (18) ◽  
pp. 6579-6586 ◽  
Author(s):  
Emma L. Sproston ◽  
Iain D. Ogden ◽  
Marion MacRae ◽  
John F. Dallas ◽  
Samuel K. Sheppard ◽  
...  
Keyword(s):  
Temporal Variation ◽  
Campylobacter Jejuni ◽  
Multilocus Sequence Typing ◽  
Host Association ◽  
Fecal Samples ◽  
Content Type ◽  
Sheep Farm ◽  
Sequence Types ◽  
Over Time ◽  
Cattle And Sheep

ABSTRACTCampylobacter jejuniandC. coliwere quantified and typed, using multilocus sequence typing (MLST), from fecal samples collected from a mixed cattle and sheep farm during summer. Cattle had a significantly higher prevalence than sheep (21.9% [74/338] and 14.0% [30/214], respectively), but both decreased over time. There were no differences in the averageCampylobacterconcentrations shed by cattle (600 CFU g−1) and sheep (820 CFU g−1), although sheep did show a significant temporal reduction in the number ofCampylobacterorganisms shed in their feces. A total of 21 different sequence types (STs) (97.7%C. jejuni, 2.3%C. coli) were isolated from cattle, and 9 different STs were isolated from sheep (40.6%C. jejuni, 59.4%C. coli). TheCampylobacterpopulation in cattle was relatively stable, and the frequencies of genotypes isolated showed little temporal variation. However, the composition of subtypes isolated from sheep did show significant temporal differences. The cattle and sheep consistently showed significant differences in their carriage ofCampylobacterspecies, STs, and CCs despite the fact that both were exposed to the same farming environment. This work has highlighted the patterns of aCampylobacterpopulation on a ruminant farm by identifying the existence of both temporal and between-host variations.

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

2004 ◽  
Vol 53 (7) ◽  
pp. 657-662 ◽  
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.

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

2012 ◽  
Vol 141 (1) ◽  
pp. 195-199 ◽  
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.

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

2021 ◽  
Vol 11 ◽  
Author(s):  
Rolf Claesson ◽  
Anders Johansson ◽  
Carola Höglund Åberg ◽  
Anders Esberg ◽  
Dorte Haubek ◽  
...  
Keyword(s):  
Multilocus Sequence Typing ◽  
Diagnostic Procedure ◽  
Aggregatibacter Actinomycetemcomitans ◽  
Negative Bacterium ◽  
Specific Primers ◽  
Mlst Analysis ◽  
Serotype B ◽  
Periodontal Attachment Loss ◽  
Sequence Types

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.

scholarly journals Multilocus Sequence Typing Scheme for Bacteria of the Bacillus cereus Group

2004 ◽  
Vol 70 (1) ◽  
pp. 191-201 ◽  
Author(s):  
Erlendur Helgason ◽  
Nicolas J. Tourasse ◽  
Roger Meisal ◽  
Dominique A. Caugant ◽  
Anne-Brit Kolstø
Keyword(s):  
Population Structure ◽  
Bacillus Cereus ◽  
Multilocus Sequence Typing ◽  
Sequence Data ◽  
Housekeeping Genes ◽  
Industrial Applications ◽  
Enzyme Electrophoresis ◽  
Mlst Scheme ◽  
High Level ◽  
Sequence Types

ABSTRACT In this study we developed a multilocus sequence typing (MLST) scheme for bacteria of the Bacillus cereus group. This group, which includes the species B. cereus, B. thuringiensis, B. weihenstephanensis, and B. anthracis, is known to be genetically very diverse. It is also very important because it comprises pathogenic organisms as well as bacteria with industrial applications. The MLST system was established by using 77 strains having various origins, including humans, animals, food, and soil. A total of 67 of these strains had been analyzed previously by multilocus enzyme electrophoresis, and they were selected to represent the genetic diversity of this group of bacteria. Primers were designed for conserved regions of housekeeping genes, and 330- to 504-bp internal fragments of seven such genes, adk, ccpA, ftsA, glpT, pyrE, recF, and sucC, were sequenced for all strains. The number of alleles at individual loci ranged from 25 to 40, and a total of 53 allelic profiles or sequence types (STs) were distinguished. Analysis of the sequence data showed that the population structure of the B. cereus group is weakly clonal. In particular, all five B. anthracis isolates analyzed had the same ST. The MLST scheme which we developed has a high level of resolution and should be an excellent tool for studying the population structure and epidemiology of the B. cereus group.

scholarly journals Application of Streptococcus uberis Multilocus Sequence Typing: Analysis of the Population Structure Detected among Environmental and Bovine Isolates from New Zealand and the United Kingdom

2006 ◽  
Vol 72 (2) ◽  
pp. 1429-1436 ◽  
Author(s):  
Gillian D. Pullinger ◽  
Mario López-Benavides ◽  
Tracey J. Coffey ◽  
John H. Williamson ◽  
Ray T. Cursons ◽  
...  
Keyword(s):  
United Kingdom ◽  
New Zealand ◽  
Multilocus Sequence Typing ◽  
Population Biology ◽  
Clonal Complex ◽  
Bovine Milk ◽  
Capsule Formation ◽  
The United Kingdom ◽  
Streptococcus Uberis ◽  
Sequence Types

ABSTRACT We recently developed a multilocus sequence typing (MLST) scheme to differentiate S. uberis isolates and facilitate an understanding of the population biology of this pathogen. The scheme was initially used to study a collection of 160 bovine milk isolates from the United Kingdom and showed that the majority of isolates were from one clonal complex (designated the ST-5 complex). Here we describe the MLST analysis of a collection of New Zealand isolates. These were obtained from diverse sources, including bovine milk, other bovine anatomical sites, and environmental sources. The complete allelic profiles of 253 isolates were determined. The collection was highly diverse and included 131 different sequence types (STs). The New Zealand and United Kingdom populations were distinct, since none of the 131 STs were represented within the previously studied collection of 160 United Kingdom S. uberis isolates. However, seven of the STs were members of the ST-5 clonal complex, the major complex within the United Kingdom collection. Two new clonal complexes were identified: ST-143 and ST-86. All three major complexes were isolated from milk, other bovine sites, and the environment. Carriage of the hasA gene, which is necessary for capsule formation, correlated with clonal complex and isolation from clinical cases of mastitis.

Visible Laser Probing (VLP) with GaP Solid Immersion Lens Demonstrating 110 nm Resolution in Common Laser Probing Applications

2016 ◽  
Author(s):  
Travis Eiles ◽  
Patrick Pardy
Keyword(s):  
Gallium Phosphide ◽  
Fault Isolation ◽  
Solid Immersion Lens ◽  
Laser Probing ◽  
Isolation Methods ◽  
Visible Laser ◽  
High Level ◽  
Industry Needs ◽  
Diameter Reduction ◽  
Better Than

Abstract This paper demonstrates a breakthrough method of visible laser probing (VLP), including an optimized 577 nm laser microscope, visible-sensitive detector, and an ultimate-resolution gallium phosphide-based solid immersion lens on the 10 nm node, showing a 110 nm resolution. This is 2x better than what is achieved with the standard suite of probing systems using typical infrared (IR) wavelengths today. Since VLP provides a spot diameter reduction of 0.5x over IR methods, it is reasonable, based simply on geometry, to project that VLP using the 577 nm laser will meet the industry needs for laser probing for both the 10 nm and 7 nm process nodes. Based on its high level of optimization, including high resolution and specialized solid immersion lens, it is highly likely that this VLP technology will be one of the last optically-based fault isolation methods successfully used.

scholarly journals Whole-Genome Phylogenomic Heterogeneity of Neisseria gonorrhoeae Isolates with Decreased Cephalosporin Susceptibility Collected in Canada between 1989 and 2013

2014 ◽  
Vol 53 (1) ◽  
pp. 191-200 ◽  
Author(s):  
Walter Demczuk ◽  
Tarah Lynch ◽  
Irene Martin ◽  
Gary Van Domselaar ◽  
Morag Graham ◽  
...  
Keyword(s):  
Neisseria Gonorrhoeae ◽  
Large Scale ◽  
Epidemiological Studies ◽  
23S Rrna ◽  
Genome Comparison ◽  
Whole Genome ◽  
Content Type ◽  
Genomic Epidemiology ◽  
High Level ◽  
Sequence Types

A large-scale, whole-genome comparison of CanadianNeisseria gonorrhoeaeisolates with high-level cephalosporin MICs was used to demonstrate a genomic epidemiology approach to investigate strain relatedness and dynamics. Although current typing methods have been very successful in tracing short-chain transmission of gonorrheal disease, investigating the temporal evolutionary relationships and geographical dissemination of highly clonal lineages requires enhanced resolution only available through whole-genome sequencing (WGS). Phylogenomic cluster analysis grouped 169 Canadian strains into 12 distinct clades. While someN. gonorrhoeaemultiantigen sequence types (NG-MAST) agreed with specific phylogenomic clades or subclades, other sequence types (ST) and closely related groups of ST were widely distributed among clades. Decreased susceptibility to extended-spectrum cephalosporins (ESC-DS) emerged among a group of diverse strains in Canada during the 1990s with a variety of nonmosaicpenAalleles, followed in 2000/2001 with thepenAmosaic X allele and then in 2007 with ST1407 strains with thepenAmosaic XXXIV allele. Five genetically distinct ESC-DS lineages were associated withpenAmosaic X, XXXV, and XXXIV alleles and nonmosaic XII and XIII alleles. ESC-DS with coresistance to azithromycin was observed in 5 strains with 23S rRNA C2599T or A2143G mutations. As the costs associated with WGS decline and analysis tools are streamlined, WGS can provide a more thorough understanding of strain dynamics, facilitate epidemiological studies to better resolve social networks, and improve surveillance to optimize treatment for gonorrheal infections.

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

2006 ◽  
Vol 51 (1) ◽  
pp. 40-47 ◽  
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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