Analysis of genetic diversity amongStaphylococcus aureusisolates from patients with deep-seated and superficial staphylococcal infections using pulsed-field gel electrophoresis

2006 ◽  
Vol 38 (6-7) ◽  
pp. 418-426 ◽  
Author(s):  
Ashok Kumar ◽  
Pallab Ray ◽  
Mamta Kanwar ◽  
Meera Sharma ◽  
Subhash Varma
Keyword(s):  
Genetic Diversity ◽  
Gel Electrophoresis ◽  
Pulsed Field Gel Electrophoresis ◽  
Pulsed Field ◽  
Staphylococcal Infections

scholarly journals Investigation of genetic diversity of Salmonella enterica strains isolated from patients by Pulsed Field Gel Electrophoresis

2011 ◽  
Vol 5 (S1) ◽  
Author(s):  
Mohsen Ghafari ◽  
Bita Bakhshi ◽  
Mohamad Reza Pour Shafi ◽  
Nour Amir Mozafari ◽  
Mona Salimi ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Gel Electrophoresis ◽  
Salmonella Enterica ◽  
Pulsed Field Gel Electrophoresis ◽  
Pulsed Field

scholarly journals Association of IS1016 with the hia Adhesin Gene and Biotypes V and I in Invasive Nontypeable Haemophilus influenzae

2008 ◽  
Vol 76 (11) ◽  
pp. 5221-5227 ◽  
Author(s):  
Sarah W. Satola ◽  
Brooke Napier ◽  
Monica M. Farley
Keyword(s):  
Genetic Diversity ◽  
Haemophilus Influenzae ◽  
Gel Electrophoresis ◽  
Pulsed Field Gel Electrophoresis ◽  
Division I ◽  
Emerging Infections ◽  
Nontypeable Haemophilus Influenzae ◽  
Insertion Element ◽  
Pulsed Field ◽  
Slide Agglutination

ABSTRACT A subset of invasive nontypeable Haemophilus influenzae (NTHI) strains has evidence of IS1016, an insertion element associated with division I H. influenzae capsule serotypes. We examined IS1016-positive invasive NTHI isolates collected as part of Active Bacterial Core Surveillance within the Georgia Emerging Infections Program for the presence or absence of hmw1 and hmw2 (two related adhesin genes that are common in NTHI but absent in encapsulated H. influenzae) and hia (homologue of hsf, an encapsulated H. influenzae adhesin gene). Isolates were serotyped using slide agglutination, confirmed as NTHI strains using PCR capsule typing, and biotyped. Two hundred twenty-nine invasive NTHI isolates collected between August 1998 and December 2006 were screened for IS1016; 22/229 (9.6%) were positive. Nineteen of 201 previously identified IS1016-positive invasive NTHI isolates collected between January 1989 and July 1998 were also examined. Forty-one IS1016-positive and 56 randomly selected IS1016-negative invasive NTHI strains were examined. The hia adhesin was present in 39 of 41 (95%) IS1016-positive NTHI strains and 1 of 56 (1.8%) IS1016-negative NTHI strains tested; hmw (hmw1, hmw2, or both) was present in 50 of 56 (89%) IS1016-negative NTHI isolates but in only 5 of 41 (12%; all hmw2) IS1016-positive NTHI isolates. IS1016-positive NTHI strains were more often biotype V (P < 0.001) or biotype I (P = 0.04) than IS1016-negative NTHI strains, which were most often biotype II. Pulsed-field gel electrophoresis revealed the expected genetic diversity of NTHI with some clustering based on IS1016, hmw or hia, and biotypes. A significant association of IS1016 with biotypes V and I and the presence of hia adhesins was found among invasive NTHI. IS1016-positive NTHI strains may represent a unique subset of NTHI strains, with characteristics more closely resembling those of encapsulated H. influenzae.

Detection and Genotyping of Leuconostoc spp. in a Sausage Processing Plant

2015 ◽  
Vol 78 (12) ◽  
pp. 2170-2176 ◽  
Author(s):  
J. J. PADILLA-FRAUSTO ◽  
L. G. CEPEDA-MARQUEZ ◽  
L. M. SALGADO ◽  
M. H. ITURRIAGA ◽  
S. M. ARVIZU-MEDRANO
Keyword(s):  
Genetic Diversity ◽  
Lactic Acid ◽  
Lactic Acid Bacteria ◽  
Gel Electrophoresis ◽  
Pulsed Field Gel Electrophoresis ◽  
Processing Plant ◽  
Randomly Amplified Polymorphic Dna ◽  
Pulsed Field ◽  
Two Samples ◽  
Conveyor Belts

Some Leuconostoc spp. have the ability to produce slime and undesirable compounds in cooked sausage. The objectives of this research were to identify Leuconostoc sources in a Vienna-type sausage processing plant and to evaluate the genetic diversity of the isolated strains. Three hundred and two samples of sausage batter, sausages during processing, spoiled sausage, equipment surfaces, chilling brine, workers' gloves and aprons, and used casings were collected (March to November 2008 and February to April 2010) from a sausage processing plant. Lactic acid bacteria (LAB) were quantified, and Leuconostoc were detected using PCR. Strains were isolated and identified in Leuconostoc-positive samples. Leuconostoc strains were genotyped using randomly amplified polymorphic DNA and pulsed-field gel electrophoresis. LAB content of nonspoiled and spoiled sausage ranged from &lt;0.8 to 4.4 log CFU/g and from 4.9 to 8.3 log CFU/g, respectively. LAB levels on equipment surfaces ranged from &lt;1.3 to 4.8 log CFU/100 cm2. Leuconostoc was detected in 35% of the samples, and 88 Leuconostoc spp. strains were isolated and genotyped. The main Leuconostoc spp. isolated were L. mesenteroides (37 genotypes), L. fallax (29 genotypes), and L. lactis (6 genotypes). Some strains of Leuconostoc isolated from equipment surfaces and sausages showed the same genotype. One L. lactis genotype included strains isolated from spoiled sausages analyzed in April 2008 and March to April 2010. Equipment and conveyor belts constitute Leuconostoc contamination sources. Leuconostoc persistence in the sausage processing environment and in the final product suggests the existence of microbial reservoirs, possibly on equipment surfaces.

scholarly journals Use of Pulsed-Field Gel Electrophoresis for Molecular Epidemiologic and Population Genetic Studies ofMycobacterium tuberculosis †

1999 ◽  
Vol 37 (6) ◽  
pp. 1927-1931 ◽  
Author(s):  
Samir P. Singh ◽  
Hugh Salamon ◽  
Carol J. Lahti ◽  
Mehran Farid-Moyer ◽  
Peter M. Small
Keyword(s):  
Genetic Diversity ◽  
Molecular Epidemiology ◽  
Gel Electrophoresis ◽  
Population Biology ◽  
Rflp Analysis ◽  
Analytical Techniques ◽  
Restriction Enzymes ◽  
Pulsed Field Gel Electrophoresis ◽  
Molecular Biology Technique ◽  
Pulsed Field

Pulsed-field gel electrophoresis (PFGE) is a powerful molecular biology technique which has provided important insights into the epidemiology and population biology of many pathogens. However, few studies have used PFGE for the molecular epidemiology ofMycobacterium tuberculosis. A laboratory protocol was developed to determine the typeability, stability, and reproducibility of PFGE typing of M. tuberculosis. Formal data-analytical techniques were used to assess the genetic diversity elucidated by PFGE analyses using four separate restriction enzymes and by IS6110 RFLP analyses, as well as to assess the concordance among these typing methods. One hundred epidemiologically characterized clinical isolates of M. tuberculosis were genotyped with four different PFGE enzymes (AseI, DraI,SpeI, and XbaI), as well as by RFLP analysis with IS6110. Identical patterns were found among 34 isolates known to be genetically related, suggesting that the PFGE protocol is robust and reproducible. Among 66 isolates representing population-sampled cases, heterozygosity and information content dependency estimates indicate that all five genotyping systems capture quantitatively similar levels of genetic diversity. Nevertheless, comparisons between PFGE analyses and IS6110 typing reveals that PFGE provided more discrimination among isolates with fewer than five copies of IS6110 and less clustering in isolates with five or more copies. The comparisons confirm the hypothesis that the resolution of IS6110 RFLP genotyping is dependent upon the number of IS6110 elements in the genome of isolates. The general concordance among the results obtained with four independent enzymes suggests that M. tuberculosis is a clonal organism. The availability of a robust genotyping technique largely independent of repetitive elements has implications for the molecular epidemiology of M. tuberculosis.

scholarly journals Prevalence of Clostridium botulinum in Finnish Trout Farms: Pulsed-Field Gel Electrophoresis Typing Reveals Extensive Genetic Diversity among Type E Isolates

1998 ◽  
Vol 64 (11) ◽  
pp. 4161-4167 ◽  
Author(s):  
Sebastian Hielm ◽  
Johanna Björkroth ◽  
Eija Hyytiä ◽  
Hannu Korkeala
Keyword(s):  
Genetic Diversity ◽  
Gel Electrophoresis ◽  
Clostridium Botulinum ◽  
Pulsed Field Gel Electrophoresis ◽  
Most Probable Number ◽  
Probable Number ◽  
Pulsed Field ◽  
Pfge Typing ◽  
Specific Pcr ◽  
Trout Farms

ABSTRACT The distribution of Clostridium botulinum serotypes A, B, E, and F in Finnish trout farms was examined. A total of 333 samples were tested with a neurotoxin-specific PCR assay. C. botulinum type E was found in 68% of the farm sediment samples, in 15% of the fish intestinal samples, and in 5% of the fish skin samples. No other serotypes were found. The spore counts determined by the most-probable-number method were considerably higher for the sediments than for the fish intestines and skin; the average values were 2,020, 166, and 310 C. botulinum type E spores kg−1, respectively. The contamination rates in traditional freshwater ponds and marine net cages were high, but in concrete ponds equipped with sediment suction devices the contamination rates were significantly lower. Pulsed-field gel electrophoresis (PFGE) typing of 42 isolates obtained in this survey and 12 North American reference strains generated 28 pulsotypes upon visual inspection, suggesting that there was extensive genetic diversity and that the discriminatory power of PFGE typing in C. botulinum type E was high. A numerical analysis of SmaI-XmaI macrorestriction profiles confirmed these findings, as it divided the 54 isolates into 15 clusters at a similarity level of 76%. For this material, this level of similarity corresponded to a three-band difference in the macrorestriction profiles, which indicated that there is no genotypic proof of a close epidemiological relationship among the clusters.

scholarly journals Intermediately virulent Rhodococcus equi isolates from pigs in Slovenia: discovery of new plasmid types and assessment of genetic diversity by pulsed-field gel electrophoresis

2009 ◽  
Vol 54 (No. 3) ◽  
pp. 111-117 ◽  
Author(s):  
M. Pate ◽  
M. Ocepek ◽  
I. Zdovc ◽  
C. Minato ◽  
Y. Ohtsu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Gel Electrophoresis ◽  
Detailed Comparison ◽  
Rhodococcus Equi ◽  
Pulsed Field Gel Electrophoresis ◽  
High Genetic Diversity ◽  
Pulsed Field ◽  
Large Plasmids ◽  
Multiple Strains ◽  
Pfge Profiles

The presence of large plasmids in 30 <I>Rhodococcus equi</I> strains isolated from pig lymph nodes with granulomatous changes was investigated. Plasmid DNAs were isolated and digested with the restriction endonucleases <I>Bam</I>HI, <I>Eco</I>RI, <I>Eco</I>T22I and <I>Hind</I>III for detailed comparison and estimation of plasmid sizes. A total of nine isolates were identified as intermediately virulent (VapB-positive), harbouring large plasmids of type 5 (<I>n</I> = 5) and four new variants that we tentatively designated as type 19 (<I>n</I> = 1), 20 (<I>n</I> = 1), 21 (<I>n</I> = 1) and 24 (<I>n</I> = 1). All isolates were subjected to genotyping with pulsed-field gel electrophoresis (PFGE). High genetic diversity was observed: 21 distinct genotypes were detected; five were found in multiple isolates and the others were unique. Isolates of the same plasmid type exhibited different PFGE profiles and vice versa. In a few cases, multiple strains from certain farms were analysed, the majority of which exhibited diverse PFGE profiles. Our findings demonstrate the presence of a wide variety of <I>R. equi</I> strains even in small confined environments such as farms. This is the first molecular epidemiology study of intermediately virulent <I>R. equi</I> isolates from Slovenian pigs.

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