scholarly journals Diversity of cwp loci in clinical isolates of Clostridium difficile

2013 ◽  
Vol 62 (9) ◽  
pp. 1444-1452 ◽  
Author(s):  
Manuele Biazzo ◽  
Rossella Cioncada ◽  
Luigi Fiaschi ◽  
Vittorio Tedde ◽  
Patrizia Spigaglia ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Clostridium Difficile ◽  
Total Cell ◽  
The Other ◽  
Clinical Isolates ◽  
Cell Wall Proteins ◽  
High Genetic Diversity ◽  
Cell Extracts ◽  
Number Of Genes ◽  
Genes Encoding

An increased incidence of Clostridium difficile infection (CDI) is associated with the emergence of epidemic strains characterized by high genetic diversity. Among the factors that may have a role in CDI is a family of 29 paralogues, the cell-wall proteins (CWPs), which compose the outer layer of the bacterial cell and are likely to be involved in colonization. Previous studies have shown that 12 of the 29 cwp genes are clustered in the same region, named after slpA (cwp1), the slpA locus, whereas the remaining 17 paralogues are distributed throughout the genome. The variability of 14 of these 17 cwp paralogues was determined in 40 C. difficile clinical isolates belonging to six of the currently prevailing PCR ribotypes. Based on sequence conservation, these cwp genes were divided into two groups, one comprising nine cwp loci having highly conserved sequences in all isolates, and the other five loci showing low genetic conservation among isolates of the same PCR ribotype, as well as between different PCR ribotypes. Three conserved CWPs, Cwp16, Cwp18 and Cwp25, and two variable ones, Cwp26 and Cwp27, were characterized further by Western blot analysis of total cell extracts or surface-layer preparations of the C. difficile clinical isolates. Expression of genetically invariable CWPs was well conserved in all isolates, whilst genetically variable CWPs were not always expressed at comparable levels, even in strains containing identical sequences but belonging to different PCR ribotypes. This is the first report on the distribution and variability of a number of genes encoding CWPs in C. difficile.

scholarly journals Morphological and Genetic Diversity of Temperate Phages in Clostridium difficile

2007 ◽  
Vol 73 (22) ◽  
pp. 7358-7366 ◽  
Author(s):  
Louis-Charles Fortier ◽  
Sylvain Moineau
Keyword(s):  
Electron Microscopy ◽  
Genetic Diversity ◽  
Clostridium Difficile ◽  
Dna Hybridization ◽  
Southern Hybridization ◽  
The Other ◽  
Restriction Profile ◽  
Transmission Electron ◽  
The Family ◽  
Genes Encoding

ABSTRACT Eight temperate phages were characterized after mitomycin C induction of six Clostridium difficile isolates corresponding to six distinct PCR ribotypes. The hypervirulent C. difficile strain responsible for a multi-institutional outbreak (NAP1/027 or QCD-32g58) was among these prophage-containing strains. Observation of the crude lysates by transmission electron microscopy (TEM) revealed the presence of three phages with isometric capsids and long contractile tails (Myoviridae family), as well as five phages with long noncontractile tails (Siphoviridae family). TEM analyses also revealed the presence of a significant number of phage tail-like particles in all the lysates. Southern hybridization experiments with restricted prophage DNA showed that C. difficile phages belonging to the family Myoviridae are highly similar and most likely related to previously described prophages φC2, φC5, and φCD119. On the other hand, members of the Siphoviridae phage family are more genetically divergent, suggesting that they originated from distantly related ancestors. Our data thus suggest that there are at least three genetically distinct groups of temperate phages in C. difficile; one group is composed of highly related myophages, and the other two groups are composed of more genetically heterogeneous siphophages. Finally, no gene homologous to genes encoding C. difficile toxins or toxin regulators could be identified in the genomes of these phages using DNA hybridization. Interestingly, each unique phage restriction profile correlated with a specific C. difficile PCR ribotype.

scholarly journals In Vitro Activities of Doripenem and Comparator Agents against 364 Anaerobic Clinical Isolates

2005 ◽  
Vol 49 (10) ◽  
pp. 4413-4417 ◽  
Author(s):  
Hannah M. Wexler ◽  
Adrian E. Engel ◽  
Daniel Glass ◽  
Calida Li
Keyword(s):  
Clostridium Difficile ◽  
Bacteroides Fragilis ◽  
The Other ◽  
Clinical Isolates ◽  
Excellent Activity

ABSTRACT The in vitro activities of doripenem against 364 anaerobic isolates were measured and compared to those of ertapenem, imipenem, meropenem, ceftriaxone, and levofloxacin. All of the carbapenems were active against nearly all Bacteroides fragilis group isolates. Doripenem was either comparable to or slightly less active than imipenem and meropenem against most isolates but more active than the other penems against Clostridium difficile. Doripenem appears to have excellent activity against a broad range of anaerobes.

scholarly journals Genetic Diversity and Population Structure of Vibrio parahaemolyticus Isolated From Clinical and Food Sources

2021 ◽  
Vol 12 ◽  
Author(s):  
Min He ◽  
Tao Lei ◽  
Fufeng Jiang ◽  
Jumei Zhang ◽  
Haiyan Zeng ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Vibrio Parahaemolyticus ◽  
Large Scale ◽  
Foodborne Pathogen ◽  
Guangdong Province ◽  
Housekeeping Genes ◽  
Clinical Isolates ◽  
Food Sources ◽  
Clinical Samples ◽  
High Genetic Diversity

Vibrio parahaemolyticus is a common foodborne pathogen that causes gastroenteritis worldwide. Determining its prevalence and genetic diversity will minimize the risk of infection and the associated economic burden. Multilocus sequence typing (MLST) is an important tool for molecular epidemiology and population genetic studies of bacteria. Here, we analyzed the genetic and evolutionary relationships of 162 V. parahaemolyticus strains isolated in the Guangdong Province, China, using MLST. In the study, 120 strains were isolated from food samples, and 42 strains were isolated from clinical samples. All strains were categorized into 100 sequence types (STs), of which 58 were novel (48 from the food isolates and 10 from the clinical isolates). ST415 was the most prevalent ST among the food isolates, while ST3 was the most prevalent ST among the clinical isolates. Further, 12 clonal complexes, 14 doublets, and 73 singletons were identified in all ST clusters, indicating high genetic diversity of the analyzed strains. At the concatenated sequence level, non-synonymous sites in both, food and clinical isolates, were associated with purifying selection. Of note, the dN/dS ration was greater than 1 for some housekeeping genes in all isolates. This is the first time that some loci under positive selection were identified. These observations confirm frequent recombination events in V. parahaemolyticus. Recombination was much more important than mutation for genetic heterogeneity of the food isolates, but the probabilities of recombination and mutations were almost equal for the clinical isolates. Based on the phylogenetic analysis, the clinical isolates were concentrated in the maximum-likelihood tree, while the food isolates were heterogeneously distributed. In conclusion, the food and clinical isolates of V. parahaemolyticus from the Guangdong Province are similar, but show different evolutionary trends. This may help prevent large-scale spread of highly virulent strains and provides a genetic basis for the discovery of microevolutionary relationships in V. parahaemolyticus populations.

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.

Prevalence and Genotyping of Commensal Neisseria with Reduced Susceptibility to Penicillin

2015 ◽  
Vol 25 (1) ◽  
pp. 11-15 ◽  
Author(s):  
Arij Mechergui ◽  
Wafa Achour ◽  
Assia Ben Hassen
Keyword(s):  
Genetic Diversity ◽  
Elevated Level ◽  
Clinical Isolates ◽  
Penicillin Resistance ◽  
High Genetic Diversity ◽  
Clonal Relationship ◽  
Neutropenic Patients

We analyzed 85 <i>Neisseria </i>spp. strains collected by swabbing from neutropenic patients to determine the prevalence of reduced susceptibility to penicillin and to ascertain the clonal relationship between these strains. High genetic diversity and an elevated level of penicillin resistance were found among commensal <i>Neisseria </i>clinical isolates.

scholarly journals STUDY OF GENETIC DIVERSITY AND ANALYSIS OF THE DEGREE OF SIMILARITY IN SOME APPLE AND PLUM VARIETIES USING RAPD MARKERS

2021 ◽  
Vol 37 (37) ◽  
pp. 19-26
Author(s):  
Adina Iancu ◽  
◽  
Mihai Chivu ◽  
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Rapd Markers ◽  
The Other ◽  
Ex Situ ◽  
Allelic Polymorphism ◽  
High Genetic Diversity ◽  
Ex Situ Collection ◽  
Plum Varieties ◽  
Degree Of Similarity

Molecular evaluation of germplasm is an important step in breeding programs, and the application of molecular biological techniques has led to important results in terms of both within- and between-species variability of traits. The RAPD technique has been successfully used to reveal allelic polymorphism as well as to measure genetic similarity. In this study, the genetic diversity of 25 genotypes and cultivars for apple species and 26 genotypes and cultivars for plum species was assessed with six RAPD markers. All these cultivars belong to the ex situ collection of apple and the ex situ collection of plum at the Research Institute for Fruit Growing Pitesti. The average number of amplified bands was 19.2 for apple and 17.66 for plum. Statistical analysis of intraspecific allelic polymorphism was expressed using the PIC (Polymorphic Information Content) index, which takes into account the allelic frequency. Two statistical indices were used to quantify genetic diversity: the Shannon index and the Simpson index. The degree of similarity between varieties was analyzed using the NTSYSpc version 2.1. Following RAPD analyses, the allele sizes of the analyzed varieties were within the range quoted in the literature, the genetic profiles of the studied varieties suggesting a medium to high genetic diversity, except for markers OPBC-04 and OPBB-05 for plum species, which expressed a high genetic diversity. Genetic distances calculated based on polymorphism of migrated bands in agarose gel confirmed the known genealogies of the apple and plum varieties studied. Thus, the smallest genetic distance for apple species was found between 'Jonagold' and 'Golden Delicious', 'Pionier' and 'Rustic', 'Jonathan' and 'Idared', 'Wagener Premiat' and 'Granny Smith', 'Remar' and 'Aura', 'Romus 3' and 'Rome Beauty', and the largest between Malus floribunda and the other genotypes studied. In plum, the smallest genetic distance was found between 'Dani' and 'Tita', 'Roman' and 'Tuleu gras', 'Dara' and 'Haganta', 'Romanța' and 'Stanley', 'Anna Spath' and 'Renclod Violet', and the largest between 'Lama', 'Black Diamond' and the other genotypes studied.

scholarly journals Genetic diversity of Streptococcus suis clinical isolates from pigs and humans in Italy (2003-2007)

2009 ◽  
Vol 14 (33) ◽  
Author(s):  
M S Princivalli ◽  
C Palmieri ◽  
G Magi ◽  
C Vignaroli ◽  
A Manzin ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Antibiotic Resistance Genes ◽  
Streptococcus Suis ◽  
Invasive Disease ◽  
Clinical Isolates ◽  
High Genetic Diversity ◽  
Pork Products ◽  
Genotypic Analysis ◽  
Common Clinical Presentation ◽  
Industrialised Countries

Streptococcus suis, a major porcine pathogen, is emerging as a zoonotic agent capable of causing severe invasive disease in humans exposed to pigs or pork products. S. suis infection is rare in industrialised countries and usually arises as sporadic cases, with meningitis the most common clinical presentation in humans. Recent reports of two cases of meningitis in Sardinia and north-eastern Italy prompted this first characterisation of Italian S. suis isolates. Fifty-nine S. suis strains, the two recent human strains and 57 swine clinical isolates collected between 2003 and 2007 from different Italian herds and regions, were tested for antimicrobial susceptibility, PCR-screened for virulence and antibiotic resistance genes, and subjected to molecular typing. Phenotypic and genotypic analysis demonstrated an overall high genetic diversity among isolates, the majority of which were resistant to macrolides (78%) and tetracyclines (90%). The erm(B), tet(O), mosaic tet(O/W/32/O), tet(W), and tet(M) genes were detected. The tet(O/W/32/O) gene, the most frequent tet gene after tet(O), had never been described in the genus Streptococcus before. In addition, a virulent cps2, erm(B) tet(O) clone, belonging to sequence type 1 (ST1) of the ST1 complex, was found to be prevalent and persistent in Italian swine herds. Finally, the two human isolates (both ST1) carrying cps2, erm(B) and tet(W) were seen to be closely related to each other.

scholarly journals Genetic diversity and molecular analysis of metallo beta lactamases among imipenem resistant clinical isolates of Pseudomonas aeruginosa from Peshawar, Pakistan

2021 ◽  
Vol 37 (7) ◽  
Author(s):  
Amjad Ali ◽  
Kafeel Ahmad ◽  
Shaista Rahat ◽  
Israr Ahmad
Keyword(s):  
Genetic Diversity ◽  
Pseudomonas Aeruginosa ◽  
Molecular Analysis ◽  
Opportunistic Pathogen ◽  
Clinical Isolates ◽  
High Genetic Diversity ◽  
Beta Lactamases ◽  
Creative Commons ◽  
High Prevalence ◽  
Control And Prevention

Objectives: Pseudomonas aeruginosa is an opportunistic pathogen with remarkable adaptation ability to thrive in diverse environmental conditions. This study aimed at phenotypic and molecular analysis of metallo beta lactamases (blaIMP, blaVIM, blaNDM-1 and blaSPM-1) and genetic diversity analysis among imipenem resistant clinical isolates of Pseudomonas aeruginosa. Methods: This study was conducted from May 2017 to June 2018. The study included 187 Pseudomonas aeruginosa isolates collected from different clinical specimens from Peshawar, Pakistan. The isolates were analyzed for resistance to imipenem. Combined disc test (CDT) was then performed for phenotypic detection of metallo beta lactamases among imipenem resistant isolates of Pseudomonas aeruginosa. Molecular detection of metallo beta lactamases genes i.e. blaIMP, blaVIM, blaNDM-1 and blaSPM-1 was analyzed through polymerase chain reaction. Genetic diversity was determined through RAPD-PCR. Results: MBL production was observed in 76% (n=19) isolates. The occurrence of MBL genes blaIMP, blaNDM-1 and blaVIM was 68% (n=17), 48% (n=12), and 4% (n=1) respectively. The blaSPM-1 gene was not detected. High genetic diversity was observed in current study. Out of 182 isolates 171 isolates showed different RAPD profiles (93.95% polymorphism); 160 were unique RAPD strains and based on similarity coefficient ≥ 80%, 22 isolates were clustered into 11 distinct clones. Conclusion: A high prevalence of blaIMP and blaNDM-1 among imipenem resistant isolates of Pseudomonas aeruginosa is alarming that calls for proper control and prevention strategies. RAPD technique was found to be a good genotyping technique when limited resources are available. doi: https://doi.org/10.12669/pjms.37.7.4303 How to cite this:Ali A, Ahmad K, Rahat S, Ahmad I. Genetic diversity and molecular analysis of metallo beta lactamases among imipenem resistant clinical isolates of Pseudomonas aeruginosa from Peshawar, Pakistan. Pak J Med Sci. 2021;37(7):---------.  doi: https://doi.org/10.12669/pjms.37.7.4303 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

scholarly journals Genetic diversity and structure of Chinese grass shrimp, Palaemonetes sinensis, inferred from transcriptome-derived microsatellite markers

BMC Genetics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Yingying Zhao ◽  
Xiaochen Zhu ◽  
Zhi Li ◽  
Weibin Xu ◽  
Jing Dong ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Markers ◽  
In Situ Conservation ◽  
Grass Shrimp ◽  
The Other ◽  
Fixation Index ◽  
High Genetic Diversity ◽  
Genetic Diversity And Structure ◽  
Polymorphic Microsatellite ◽  
Two Populations

Abstract Background The Chinese grass shrimp, Palaemonetes sinensis, is an economically important freshwater shrimp in China, and the study of genetic diversity and structure can positively contribute to the exploration of germplasm resources and assist in the understanding of P. sinensis aquaculture. Microsatellite markers are widely used in research of genetic backgrounds since it is considered an important molecular marker for the analyses of genetic diversity and structure. Hence, the aim of this study was to evaluate the genetic diversity and structure of wild P. sinensis populations in China using the polymorphic microsatellite makers from the transcriptome. Results Sixteen polymorphic microsatellite markers were developed for P. sinensis from transcriptome, and analyzed for differences in genetic diversity and structure in multiple wild P. sinensis populations in China. Totally of 319 individual shrimps from seven different populations were genotyped to find that allelic polymorphisms varied in two to thirteen alleles seen in the entire loci. Compared to other populations analyzed, the two populations including LD and SJ showed lower genetic diversity. Both the genetic distance (D) and Wrights fixation index (FST) comparing any two populations also indicated that LD and SJ populations differed from the other five populations. An UPGMA tree analysis showed three main clusters containing SJ, LD and other populations which were also confirmed using STRUCTURE analysis. Conclusion This is the first study where polymorphic microsatellite markers from the transcriptome were used to analyze genetic diversity and structures of different wild P. sinensis populations. All the polymorphic microsatellite makers are believed useful for evaluating the extent of the genetic diversity and population structure of P. sinensis. Compared to the other five populations, the LD and SJ populations exhibited lower genetic diversity, and the genetic structure was differed from the other five populations. Therefore, they needed to be protected against further declines in genetic diversity. The other five populations, LP, LA, LSL, LSY and LSH, are all belonging to Liaohe River Drainage with a relatively high genetic diversity, and hence can be considered as hot spots for in-situ conservation of P. sinensis as well as sources of desirable alleles for breeding values.

scholarly journals Clostridium difficile clade 3 (RT023) have a modified cell surface and contain a large transposable island with novel cargo

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Helen Alexandra Shaw ◽  
Ladan Khodadoost ◽  
Mark D. Preston ◽  
Jeroen Corver ◽  
Peter Mullany ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Clostridium Difficile ◽  
Abc Transporters ◽  
Reference Strain ◽  
Whole Genome ◽  
Bacterial Strains ◽  
Live Attenuated Vaccines ◽  
Clostridioides Difficile ◽  
Niche Adaptation ◽  
Genes Encoding

Abstract The major global pathogen Clostridium difficile (recently renamed Clostridioides difficile) has large genetic diversity including multiple mobile genetic elements. In this study, whole genome sequencing of 86 strains from the poorly characterised clade 3, predominantly PCR ribotype (RT)023, of C. difficile revealed distinctive surface architecture characteristics and a large mobile genetic island. These strains have a unique sortase substrate phenotype compared with well-characterised strains of C. difficile, and loss of the phage protection protein CwpV. A large genetic insertion (023_CTnT) comprised of three smaller elements (023_CTn1-3) is present in 80/86 strains analysed in this study, with genes common among other bacterial strains in the gut microbiome. Novel cargo regions of 023_CTnT include genes encoding a sortase, putative sortase substrates, lantibiotic ABC transporters and a putative siderophore biosynthetic cluster. We demonstrate the excision of 023_CTnT and sub-elements 023_CTn2 and 023_CTn3 from the genome of RT023 reference strain CD305 and the transfer of 023_CTn3 to a non-toxigenic C. difficile strain, which may have implications for the use of non-toxigenic C. difficile strains as live attenuated vaccines. Finally, we show that the genes within the island are expressed in a regulated manner in C. difficile RT023 strains conferring a distinct “niche adaptation”.

Sign in / Sign up

Export Citation Format

Share Document