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

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”.

scholarly journals Genetic diversity in Italian Lactobacillus sanfranciscensis strains assessed by multilocus sequence typing and pulsed-field gel electrophoresis analyses

Microbiology ◽  
2010 ◽  
Vol 156 (7) ◽  
pp. 2035-2045 ◽  
Author(s):  
Claudia Picozzi ◽  
Gaia Bonacina ◽  
Ileana Vigentini ◽  
Roberto Foschino
Keyword(s):  
Multilocus Sequence Typing ◽  
Geographical Area ◽  
Housekeeping Genes ◽  
Processing Conditions ◽  
Clonal Population ◽  
Factors Affecting ◽  
Lactobacillus Sanfranciscensis ◽  
Mlst Scheme ◽  
Sequence Types

Lactobacillus sanfranciscensis is a lactic acid bacterium that characterizes the sourdough environment. The genetic differences of 24 strains isolated in different years from sourdoughs, mostly collected in Italy, were examined and compared by PFGE and multilocus sequence typing (MLST). The MLST scheme, based on the analysis of six housekeeping genes (gdh, gyrA, mapA, nox, pgmA and pta) was developed for this study. PFGE with the restriction enzyme ApaI proved to have higher discriminatory power, since it revealed 22 different pulsotypes, while 19 sequence types were recognized through MLST analysis. Notably, restriction profiles generated from three isolates collected from the same firm but in three consecutive years clustered in a single pulsotype and showed the same sequence type, emphasizing the fact that the main factors affecting the dominance of a strain are correlated with processing conditions and the manufacturing environment rather than the geographical area. All results indicated a limited recombination among genes and the presence of a clonal population in L. sanfranciscensis. The MLST scheme proposed in this work can be considered a useful tool for characterization of isolates and for in-depth examination of the strain diversity and evolution of this species.

scholarly journals Invasiveness of Serotypes and Clones of Streptococcus pneumoniae among Children in Finland

2005 ◽  
Vol 73 (1) ◽  
pp. 431-435 ◽  
Author(s):  
William P. Hanage ◽  
Tarja H. Kaijalainen ◽  
Ritva K. Syrjänen ◽  
Kari Auranen ◽  
Maija Leinonen ◽  
...  
Keyword(s):  
Streptococcus Pneumoniae ◽  
Confidence Interval ◽  
Multilocus Sequence Typing ◽  
Invasive Disease ◽  
Invasive Infection ◽  
Data Set ◽  
Dramatic Effect ◽  
Life Threatening ◽  
The Difference ◽  
Sequence Types

ABSTRACT Streptococcus pneumoniae (the pneumococcus) causes diseases from otitis media to life-threatening invasive infection. The species is extremely antigenically and clonally diverse. We wished to determine odds ratios (ORs) for serotypes and clones of S. pneumoniae that cause invasive disease in Finland. A total of 224 isolates of S. pneumoniae from cases of invasive disease in children <2 years of age in Finland between 1995 and 1999 were serotyped, and sequence types (STs) were determined by multilocus sequence typing. These STs were compared with a previously published carriage data set. STs from invasive disease were significantly less diverse than those from carriage (invasive disease, 0.038 ± 0.01; carriage, 0.019 ± 0.005). The ORs of serotypes 14, 18C, 19A, and 6B were significantly greater than 1, indicating association with invasive disease. The ORs of 6A and 11A were significantly less than 1. The difference between 6A and 6B is significant, which suggests that relatively subtle changes in the capsule may have a dramatic effect upon disease potential. We found that ST 156, the Spain9V-3 clone which mainly expressed serotype 14 in Finland, is strongly associated with invasive disease (OR, 10.1; 95% confidence interval, 1.3 to 79.5). Significant associations with invasive disease were also detected for STs 482, 191, 124, and 138, and associations with carriage were detected for STs 485 and 62. These results demonstrate the invasive phenotype of the serotype 14 variant of the Spain9V-3 clone and differences between members of the same serogroup in invasive disease potential.

scholarly journals Determination of Molecular Phylogenetics of Vibrio parahaemolyticus Strains by Multilocus Sequence Typing

2008 ◽  
Vol 190 (8) ◽  
pp. 2831-2840 ◽  
Author(s):  
Narjol González-Escalona ◽  
Jaime Martinez-Urtaza ◽  
Jaime Romero ◽  
Romilio T. Espejo ◽  
Lee-Ann Jaykus ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Multilocus Sequence Typing ◽  
Vibrio Parahaemolyticus ◽  
Molecular Phylogenetics ◽  
Clonal Complex ◽  
Housekeeping Genes ◽  
The United States ◽  
Health Concern ◽  
Mlst Scheme

ABSTRACT Vibrio parahaemolyticus is an important human pathogen whose transmission is associated with the consumption of contaminated seafood. There is a growing public health concern due to the emergence of a pandemic strain causing severe outbreaks worldwide. Many questions remain unanswered regarding the evolution and population structure of V. parahaemolyticus. In this work, we describe a multilocus sequence typing (MLST) scheme for V. parahaemolyticus based on the internal fragment sequences of seven housekeeping genes. This MLST scheme was applied to 100 V. parahaemolyticus strains isolated from geographically diverse clinical (n = 37) and environmental (n = 63) sources. The sequences obtained from this work were deposited and are available in a public database (http://pubmlst.org/vparahaemolyticus ). Sixty-two unique sequence types were identified, and most (50) were represented by a single isolate, suggesting a high level of genetic diversity. Three major clonal complexes were identified by eBURST analysis. Separate clonal complexes were observed for V. parahaemolyticus isolates originating from the Pacific and Gulf coasts of the United States, while a third clonal complex consisted of strains belonging to the pandemic clonal complex with worldwide distribution. The data reported in this study indicate that V. parahaemolyticus is genetically diverse with a semiclonal population structure and an epidemic structure similar to that of Vibrio cholerae. Genetic diversity in V. parahaemolyticus appears to be driven primarily by frequent recombination rather than mutation, with recombination ratios estimated at 2.5:1 and 8.8:1 by allele and site, respectively. Application of this MLST scheme to more V. parahaemolyticus strains and by different laboratories will facilitate production of a global picture of the epidemiology and evolution of this pathogen.

scholarly journals The Variability of the Order Burkholderiales Representatives in the Healthcare Units

2015 ◽  
Vol 2015 ◽  
pp. 1-9 ◽  
Author(s):  
Olga L. Voronina ◽  
Marina S. Kunda ◽  
Natalia N. Ryzhova ◽  
Ekaterina I. Aksenova ◽  
Andrey N. Semenov ◽  
...  
Keyword(s):  
Cystic Fibrosis ◽  
Intensive Care Unit ◽  
Intensive Care ◽  
Lung Diseases ◽  
Burkholderia Cenocepacia ◽  
Bacteria Detection ◽  
Phylogenetic Position ◽  
Mlst Scheme ◽  
Chronic Lung Diseases ◽  
Sequence Types

Background and Aim. The order Burkholderiales became more abundant in the healthcare units since the late 1970s; it is especially dangerous for intensive care unit patients and patients with chronic lung diseases. The goal of this investigation was to reveal the real variability of the order Burkholderiales representatives and to estimate their phylogenetic relationships.Methods.16S rDNAand genes of theBurkholderia cenocepaciacomplex (Bcc) Multi Locus Sequence Typing (MLST) scheme were used for the bacteria detection.Results. A huge diversity of genome size and organization was revealed in the order Burkholderiales that may prove the adaptability of this taxon’s representatives. The following variability of the Burkholderiales in Russian healthcare units has been revealed: Burkholderiaceae (Burkholderia,Pandoraea, andLautropia), Alcaligenaceae (Achromobacter), and Comamonadaceae (Variovorax). TheBurkholderiagenus was the most diverse and was represented by 5 species and 16 sequence types (ST). ST709 and 728 were transmissible and often encountered in cystic fibrosis patients and in hospitals.A. xylosoxidanswas estimated by 15 genotypes. The strains of first and second ones were the most numerous.Conclusions. Phylogenetic position of the genusLautropiawith smaller genome is ambiguous. The Bcc MLST scheme is applicable for all Burkholderiales representatives for resolving the epidemiological problems.

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

2008 ◽  
Vol 74 (18) ◽  
pp. 5817-5821 ◽  
Author(s):  
Morten Enersen ◽  
Ingar Olsen ◽  
Dominique A. Caugant
Keyword(s):  
Genetic Diversity ◽  
Porphyromonas Gingivalis ◽  
Multilocus Sequence Typing ◽  
Sequence Types

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.

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

2013 ◽  
Vol 2013 ◽  
pp. 1-6 ◽  
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.

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

2013 ◽  
Vol 57 (11) ◽  
pp. 5697-5700 ◽  
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.

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

2019 ◽  
Vol 31 (6) ◽  
pp. 899-904 ◽  
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.

scholarly journals A multilocus sequence typing scheme of Pseudomonas putida for clinical and environmental isolates

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Kohei Ogura ◽  
Kayo Shimada ◽  
Tohru Miyoshi-Akiyama
Keyword(s):  
Pseudomonas Putida ◽  
Multilocus Sequence Typing ◽  
Haplotype Network ◽  
Significant Linkage Disequilibrium ◽  
Environmental Isolates ◽  
Single Nucleotide ◽  
Mlst Scheme ◽  
Network Tree ◽  
Significant Linkage ◽  
Sequence Types

Abstract Pseudomonas putida is a bacterium commonly found in soils, water and plants. Although P. putida group strains are considered to have low virulence, several nosocomial isolates with carbapenem- or multidrug-resistance have recently been reported. In the present study, we developed a multilocus sequence typing (MLST) scheme for P. putida. MLST loci and primers were selected and designed using the genomic information of 86 clinical isolates sequenced in this study as well as the sequences of 20 isolates previously reported. The genomes were categorised into 68 sequence types (STs). Significant linkage disequilibrium was detected for the 68 STs, indicating that the P. putida isolates are clonal. The MLST tree was similar to the haplotype network tree based on single nucleotide morphisms, demonstrating that our MLST scheme reflects the genetic diversity of P. putida group isolated from both clinical and environmental sites.

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