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PFGE Patterns (pfge + pattern)
Kinds of PFGE Patterns Selected AbstractsGenotypic variability and persistence of Legionella pneumophila PFGE patterns in 34 cooling towers from two different areasENVIRONMENTAL MICROBIOLOGY, Issue 2 2008Inma Sanchez Summary Genotypic variability and clonal persistence are important concepts in molecular epidemiology as they facilitate the search for the source of sporadic cases or outbreaks of legionellosis. We studied the genotypic variability and persistence of Legionella pulsed-field gel electrophoresis (PFGE) patterns over time (period > 6 months) in 34 positive cooling towers from two different areas. In area A, radius of 70 km, 52 indistinguishable PFGE patterns were differentiated among the 27 cooling towers. In 13 cooling towers we observed , 2 PFGE patterns. Each cooling tower had its own indistinguishable Legionella PFGE pattern which was not shared with any other cooling tower. In area B, radius of 1 km, 10 indistinguishable PFGE patterns were obtained from the seven cooling towers. In four, we observed , 2 PFGE patterns. Three of these 10 indistinguishable PFGE patterns were shared by more than one cooling tower. In 27 of 34 cooling towers the same PFGE pattern was recovered after 6 months to up to 5 years of follow-up. The large genotypic diversity of Legionella observed in the cooling towers aids in the investigation of community outbreaks of Legionnaires' disease. However, shared patterns in small areas may confound the epidemiological investigation. The persistence of some PFGE patterns in cooling towers makes the recovery of the Legionella isolate causing the outbreak possible over time. [source] Genotypes of multidrug-resistant Salmonella enterica serotype typhimurium from two regions of KenyaFEMS IMMUNOLOGY & MEDICAL MICROBIOLOGY, Issue 1 2000Samuel Kariuki Abstract A combination of phage typing and pulsed-field gel electrophoresis of XbaI-digested chromosomal DNA has been used to study the epidemiological relationships of multidrug-resistant Salmonella enterica serotype typhimurium from Nairobi (64 isolates) and Kilifi (40 isolates) collected over the period 1994,1997. Isolates from Nairobi belonged to 11 definitive phage types (DTs) encompassing eight different PFGE patterns. In contrast, isolates from Kilifi were mainly DT 56 (60%) and all fell into a single PFGE pattern. The remaining isolates did not conform to a recognisable phage type. We conclude that multidrug-resistant S. typhimurium infections from Nairobi were caused by multiple strains while those from Kilifi were likely to be from a microepidemic caused by a single clone. [source] Genotyping of Campylobacter spp. from retail meats by pulsed-field gel electrophoresis and ribotypingJOURNAL OF APPLIED MICROBIOLOGY, Issue 1 2006B. Ge Abstract Aims:, To determine the genetic relatedness of Campylobacter spp. from retail meat products, and compare the discriminatory power of pulsed-field gel electrophoresis (PFGE) and automatic ribotyping. Methods and Results:, A total of 378 Campylobacter isolates recovered from 159 raw meats (130 chicken, 25 turkey, three pork and one beef) sampled from 50 retail grocery stores of four supermarket chains in the Maryland suburban area from August 1999 to July 2000 were analysed by PFGE with SmaI, 120 isolates of which were also characterized by ribotyping with PstI using RiboPrinter® system. A total of 148 unique PFGE patterns were identified, 91 of which were present in multiple Campylobacter isolates and 24 in multiple meat samples. Nineteen Campylobacter clones with identical PFGE patterns recurred frequently (up to nine times) throughout the sampling period. Comparing ribotyping with PFGE, we identified 44 PFGE patterns and 22 RiboGroups among the 120 isolates tested. Multiple PFGE patterns within one RiboGroup were commonly observed, as well as multiple RiboGroups within one PFGE pattern. Conclusions:, Although Campylobacter present in retail meats were genetically diverse, certain clones persisted in poultry meats. PFGE had a greater discriminatory power than ribotyping, and the two methods were complementary in genotyping Campylobacter. Significance and Impact of the Study:, Genomic DNA fingerprinting of Campylobacter confirmed diverse and recurrent Campylobacter clones in the retail meats, which provides additional data for a better understanding of the epidemiological aspect of Campylobacter infection. [source] Staphylococcus aureus as source of catheter-related bloodstream infection evaluated by PFGE and rep-PCR typing in a Brazilian hospital,APMIS, Issue 11 2008GERALDO SADOYAMA Staphylococci are a common cause of catheter-related bloodstream infection (CR-BSI), and epidemiological typing is an important tool for effective infection control. This study evaluated by PFGE and rep-PCR whether Staphylococcus aureus strains isolated from skin and catheter tips were related to specimens isolated from blood. A prospective observational study, carried out in a clinical surgical ward at a Brazilian hospital between September 2000 and November 2002, investigated non-tunneled central venous catheters from 179 patients. S. aureus isolates were mainly obtained from blood (41.4%), while coagulase-negative staphylococci strains were more often isolated from the skin at the catheter insertion site (49.7%) and from the catheter tip (57.5%). Among the 21 strains isolated from 9 patients at 2 or 3 sites simultaneously, 9 were methicillin-resistant S. aureus (MRSA) and 12 were methicillin-susceptible S. aureus (MSSA). Seven patients harbored the same S. aureus strain isolated from the skin, blood and/or catheter tip cultures. MRSA isolates belonged to one PFGE pattern (type A- subtypes A1, A2 and A3), and to two rep-PCR patterns (a and b). MSSA isolates were distinguished in five PFGE (B to F) and in three rep-PCR (c, d and e) patterns. Both PFGE and rep-PCR methods indicated that the skin at the catheter insertion site was the origin of CR-BSI caused by S. aureus. [source] Evaluating the usefulness of spa typing, in comparison with pulsed-field gel electrophoresis, for epidemiological typing of methicillin-resistant Staphylococcus aureus in a low-prevalence region in Sweden 2000,2004CLINICAL MICROBIOLOGY AND INFECTION, Issue 5 2010A. C. Petersson Clin Microbiol Infect 2010; 16: 456,462 Abstract The usefulness of spa typing was evaluated in relation to pulsed-field gel electrophoresis (PFGE), as a tool for epidemiological typing of methicillin-resistant Staphylococcus aureus (MRSA) in a low-prevalence region in southern Sweden. Bacterial isolates from 216 MRSA cases, newly identified in 2000,2004, were studied. The isolates were obtained from infected patients (31%), and from colonized individuals found by screening (69%). In total, 49 spa types and 73 PFGE patterns were identified. The discriminatory power of spa typing was lower (94.9 ± 1.8%) than that of PFGE (97.3 ± 1.2%). For two spa types (t002 and t008) the Panton,Valentine leukocidin results added useful discriminatory information. The most common spa types were t044 (n = 31; four PFGE patterns), t002 (n = 24; 10 PFGE patterns), t067 (n = 12; four PFGE patterns), t050 (n = 12; one PFGE pattern), and t324 (n = 11; one PFGE pattern). Epidemiological investigations identified 91 single cases and 39 transmission chains, each involving two to 13 cases. All the transmission chains were held together both by spa and PFGE typing. Among the 91 single-case isolates, 33 spa types and 50 PFGE patterns were unique (matchless) at the time of identification. The low prevalence of MRSA, the low number of outbreaks, and the wide spectrum of strains due to frequent acquisitions abroad (49% of the cases), makes spa typing a useful complement to epidemiological investigations in our setting. However, we still recommend the continued use of PFGE for further discrimination of isolates with identical spa types when epidemiological data can not exclude possible transmission. [source] Genotypic variability and persistence of Legionella pneumophila PFGE patterns in 34 cooling towers from two different areasENVIRONMENTAL MICROBIOLOGY, Issue 4 2008Inma Sanchez No abstract is available for this article. [source] Genotypic variability and persistence of Legionella pneumophila PFGE patterns in 34 cooling towers from two different areasENVIRONMENTAL MICROBIOLOGY, Issue 2 2008Inma Sanchez Summary Genotypic variability and clonal persistence are important concepts in molecular epidemiology as they facilitate the search for the source of sporadic cases or outbreaks of legionellosis. We studied the genotypic variability and persistence of Legionella pulsed-field gel electrophoresis (PFGE) patterns over time (period > 6 months) in 34 positive cooling towers from two different areas. In area A, radius of 70 km, 52 indistinguishable PFGE patterns were differentiated among the 27 cooling towers. In 13 cooling towers we observed , 2 PFGE patterns. Each cooling tower had its own indistinguishable Legionella PFGE pattern which was not shared with any other cooling tower. In area B, radius of 1 km, 10 indistinguishable PFGE patterns were obtained from the seven cooling towers. In four, we observed , 2 PFGE patterns. Three of these 10 indistinguishable PFGE patterns were shared by more than one cooling tower. In 27 of 34 cooling towers the same PFGE pattern was recovered after 6 months to up to 5 years of follow-up. The large genotypic diversity of Legionella observed in the cooling towers aids in the investigation of community outbreaks of Legionnaires' disease. However, shared patterns in small areas may confound the epidemiological investigation. The persistence of some PFGE patterns in cooling towers makes the recovery of the Legionella isolate causing the outbreak possible over time. [source] Genotypes of multidrug-resistant Salmonella enterica serotype typhimurium from two regions of KenyaFEMS IMMUNOLOGY & MEDICAL MICROBIOLOGY, Issue 1 2000Samuel Kariuki Abstract A combination of phage typing and pulsed-field gel electrophoresis of XbaI-digested chromosomal DNA has been used to study the epidemiological relationships of multidrug-resistant Salmonella enterica serotype typhimurium from Nairobi (64 isolates) and Kilifi (40 isolates) collected over the period 1994,1997. Isolates from Nairobi belonged to 11 definitive phage types (DTs) encompassing eight different PFGE patterns. In contrast, isolates from Kilifi were mainly DT 56 (60%) and all fell into a single PFGE pattern. The remaining isolates did not conform to a recognisable phage type. We conclude that multidrug-resistant S. typhimurium infections from Nairobi were caused by multiple strains while those from Kilifi were likely to be from a microepidemic caused by a single clone. [source] Mechanisms of antimicrobial resistance and genetic relatedness among enterococci isolated from dogs and cats in the United StatesJOURNAL OF APPLIED MICROBIOLOGY, Issue 6 2010C.R. Jackson Abstract Aims:, In this study, mechanisms of antimicrobial resistance and genetic relatedness among resistant enterococci from dogs and cats in the United States were determined. Methods and Results:, Enterococci resistant to chloramphenicol, ciprofloxacin, erythromycin, gentamicin, kanamycin, streptomycin, lincomycin, quinupristin/dalfopristin and tetracycline were screened for the presence of 15 antimicrobial resistance genes. Five tetracycline resistance genes [tet(M), tet(O), tet(L), tet(S) and tet(U)] were detected with tet(M) accounting for approx. 60% (130/216) of tetracycline resistance; erm(B) was also widely distributed among 96% (43/45) of the erythromycin-resistant enterococci. Five aminoglycoside resistance genes were also detected among the kanamycin-resistant isolates with the majority of isolates (25/36; 69%) containing aph(3,)-IIIa. The bifunctional aminoglycoside resistance gene, aac(6,)-Ie -aph(2,)-Ia, was detected in gentamicin-resistant isolates and ant(6)-Ia in streptomycin-resistant isolates. The most common gene combination among enterococci from dogs (n = 11) was erm(B), aac(6,)-Ie- aph(2,)-Ia, aph(3,)-IIIa, tet(M), while tet(O), tet(L) were most common among cats (n = 18). Using pulsed-field gel electrophoresis (PFGE), isolates clustered according to enterococcal species, source and antimicrobial gene content and indistinguishable patterns were observed for some isolates from dogs and cats. Conclusion:, Enterococci from dogs and cats may be a source of antimicrobial resistance genes. Significance and Impact of the Study:, Dogs and cats may act as reservoirs of antimicrobial resistance genes that can be transferred from pets to people. Although host-specific ecovars of enterococcal species have been described, identical PFGE patterns suggest that enterococcal strains may be exchanged between these two animal species. [source] Soil survival of Escherichia coli O157:H7 acquired by a child from garden soil recently fertilized with cattle manureJOURNAL OF APPLIED MICROBIOLOGY, Issue 2 2006A. Mukherjee Abstract Aims:, This investigation was conducted to determine the survival of a naturally occurring Escherichia coli O157:H7 in garden soil linked to a sporadic case of E. coli O157 infection in Minnesota. Methods and Results:, The presence and viability of E. coli O157:H7 was monitored in manure-contaminated garden soil for several weeks. Bacterial isolates were characterized using PCR and pulsed-field gel electrophoresis (PFGE). Isolates obtained from the patient and the garden plots during this investigation had indistinguishable PFGE patterns and had the same virulence factors (stx1, stx2, eaeA, ehxA). The E. coli O157:H7 levels obtained from the garden plots declined gradually for a period of 2 months, and on day 69 only one garden plot of four had detectable levels of pathogen. All plots were negative on day 92. The rate of decline in the soil samples stored at 4°C was faster compared with soil samples that remained in ambient conditions, and in refrigerated storage E. coli O157:H7 could not be detected after 10 days. Conclusions:,E. coli O157:H7 strains can survive on manure-amended soil for more than 2 months, and this survival could be reduced by low temperature. Significance and Impact of the Study:, This is one of the few reports that have investigated the survival of a proven virulent strain in naturally contaminated soil samples. This case stresses the importance of avoiding the use of raw cattle manure to amend soil for cultivation of foods, including soils in residential garden plots. [source] Genotyping of Campylobacter spp. from retail meats by pulsed-field gel electrophoresis and ribotypingJOURNAL OF APPLIED MICROBIOLOGY, Issue 1 2006B. Ge Abstract Aims:, To determine the genetic relatedness of Campylobacter spp. from retail meat products, and compare the discriminatory power of pulsed-field gel electrophoresis (PFGE) and automatic ribotyping. Methods and Results:, A total of 378 Campylobacter isolates recovered from 159 raw meats (130 chicken, 25 turkey, three pork and one beef) sampled from 50 retail grocery stores of four supermarket chains in the Maryland suburban area from August 1999 to July 2000 were analysed by PFGE with SmaI, 120 isolates of which were also characterized by ribotyping with PstI using RiboPrinter® system. A total of 148 unique PFGE patterns were identified, 91 of which were present in multiple Campylobacter isolates and 24 in multiple meat samples. Nineteen Campylobacter clones with identical PFGE patterns recurred frequently (up to nine times) throughout the sampling period. Comparing ribotyping with PFGE, we identified 44 PFGE patterns and 22 RiboGroups among the 120 isolates tested. Multiple PFGE patterns within one RiboGroup were commonly observed, as well as multiple RiboGroups within one PFGE pattern. Conclusions:, Although Campylobacter present in retail meats were genetically diverse, certain clones persisted in poultry meats. PFGE had a greater discriminatory power than ribotyping, and the two methods were complementary in genotyping Campylobacter. Significance and Impact of the Study:, Genomic DNA fingerprinting of Campylobacter confirmed diverse and recurrent Campylobacter clones in the retail meats, which provides additional data for a better understanding of the epidemiological aspect of Campylobacter infection. [source] Genetic characterization of Erwinia amylovora strains by amplified fragment length polymorphismJOURNAL OF APPLIED MICROBIOLOGY, Issue 2 2004A. Rico Abstract Aims:,Erwinia amylovora is one of the most important pathogens of pear and apple and is subject to strict quarantine regulations worldwide, although its patterns of dispersal are largely unknown. Previous attempts to fingerprint E. amylovora strains by molecular techniques have detected very little polymorphism because of the high genetic homogeneity of this bacterium. Our aim was to establish and test a typing method to quantify genetic diversity among strains of this plant pathogen. Methods and Results:, Twenty-two strains from different hosts and geographical locations were examined by PCR fingerprinting with four primers and by amplified fragment length polymorphism (AFLP) with four selected combinations of primers with a single base extension. PCR fingerprinting revealed little polymorphism producing the same amplification patterns for 17 strains, while the combined AFLP patterns yielded 78 polymorphic bands (34% of total bands) and allowed the differentiation of all but two strains. Clustering of strains in the resulting dendrogram was not correlated with host, year or country of isolation, and questions previous genealogies based on PFGE patterns. Conclusions:, The AFLP technique allowed the detection of an unprecedented number of genetic markers in E. amylovora and proved to be the most useful tool so far for discriminating among strains of this pathogen. The results obtained in this study strongly suggest the occurrence of multiple introductions of the pathogen in Spain and other European countries. Significance and Impact of the Study:, A major limitation in understanding the ecology of fire blight is the lack of typing techniques with a high power of discrimination. This study demonstrates the high resolution and the usefulness of the AFLP technique to differentiate among E. amylovora strains. [source] Discrimination of Staphylococcus aureus biotypes by pulsed-field gel electrophoresis of DNA macro-restriction fragmentsJOURNAL OF APPLIED MICROBIOLOGY, Issue 2 2003J.A. Hennekinne Abstract Aims: To examine whether pulsed-field gel electrophoresis (PFGE) of DNA macro-restriction fragments could provide better discrimination among the different biotypes previously described within the species Staphylococcus aureus than the traditional biochemical approach. Methods and Results: Seventy three Staph. aureus strains from various sources (human, animal or food origin) and belonging to eight biotypes, including the poultry-like biotype, tentatively designated as an ,abattoir' biotype, were genotyped by PFGE after SmaI digestion of DNA. The PFGE patterns were compared using the average linkage matching method (UPGMA) with the Dice coefficient. A total of 61 PFGE patterns were observed, showing between 31 and 100% similarity. In most cases, strains with the same biotype were grouped specifically into one, two or three separate sub-clusters. Strains from the ,abattoir' biotype were clustered in one separate sub-cluster. Conclusions: The PFGE typing is useful to distinguish the traditional biotypes of Staph. aureus and has a more discriminatory power than the biochemical typing. Significance and Impact of the Study: The PFGE typing confirms the ,abattoir' biotype as a separate group on a genetic level and is well suited to investigate modes of staphylococcal contamination of food. [source] Systemic neonatal candidosis: the karyotyping of Candida albicans strains isolated from neonates and health-workersMYCOSES, Issue 1 2010J. Ben Abdeljelil Summary Candida albicans has become an important cause of nosocomial infections in neonatal intensive care units (NICUs). The aim of the present study was to compare C. albicans strains isolated from neonates (NN) suffering from systemic candidosis and from nurses in order to determine the relatedness between NN and health workers' strains. Thirty-one C. albicans strains were isolated from 18 NN admitted to the NICU of the neonatology service of Farhat Hached Hospital of Sousse, Tunisia and suffering from systemic candidosis, together with five strains recovered from nurses suffering from C. albicans onychomycosis. Two additional strains were tested, one from an adult patient who developed a systemic candidosis and the second from an adult with inguinal intertrigo. All strains were karyotyped by pulsed-field gel electrophoresis (PFGE) with a CHEF-DR II system. Analysis of PFGE patterns yielded by the 38 strains tested led to the identification of three pulsotypes that were designated I, II and III, and consisted of six chromosomal bands with a size ranging from 700 to >2500 kbp. The most widespread was the pulsotype I, which was shared by 17 NN and the five nurses' strains. The identity between NN and nurses' strains is very suggestive of a nosocomial acquisition from health-workers. [source] Karyotyping of Candida albicans and Candida glabrata from patients with Candida sepsisMYCOSES, Issue 5-6 2000Klempp-Selb The aim of this study was to determine the relatedness of Candida strains from patients suffering from Candida septicaemia by typing of Candida isolates from blood cultures and different body sites by pulsed field gel electrophoresis (PFGE using a contour-clamped homogenous electric field, CHEF). We studied 17 isolates of Candida albicans and 10 isolates of Candida glabrata from six patients. Four patients suffered from a C. albicans septicaemia, one patient from a C. glabrata septicaemia, and one patient had a mixed septicaemia with C. albicans and C. glabrata. Eight isolates from blood cultures were compared with 19 isolates of other sites (stool six, urine four, genital swab four, tip of central venous catheter three, tracheal secretion one, sputum one). PFGE typing resulted in 10 different patterns, four with C. albicans and six with C. glabrata. Five of the six patients had strains of identical PFGE patterns in the blood and at other sites. Seven isolates of a 58-year-old female with a C. glabrata septicaemia fell into five different PFGE patterns. However, they showed minor differences only, which may be due to chromosomal rearrangements within a single strain. Thus it appears, that the colonizing Candida strains were identical to the circulating strains in the bloodstream in at least five of six patients. [source] Achromobacter xylosoxidans respiratory tract infections in cystic fibrosis patients,APMIS, Issue 9 2008TIZIANA RASO Achromobacter xylosoxidans is a ubiquitous Gram-negative non-fermenting rod, recently characterized as an emerging pathogen in cystic fibrosis (CF) patients. Its pathogenic potential and prevalent transmission routes are still unclear. This study investigated the PFGE genetic pattern and antimicrobial resistance profile of 42 A. xylosoxidans isolates obtained over 4 years from the respiratory tract of 22 CF patients. By genotypic analysis, 31 isolates were attributed to 8 distinct PFGE patterns (A,H), whereas 11 isolates were not typable because their DNA was not restricted by XbaI and DraI restriction enzymes. The majority of the isolates showed multidrug resistance; imipenem and piperacillin were the most active drugs. During the course of A. xylosoxidans chronic infection forced expiratory volume and body mass index values were not significantly lowered. The demonstration of widespread antibiotic resistance underscores the importance of antibiogram-directed therapy. Our data suggest that in some cases the infection may have been acquired from other patients or from a common contaminated source. Further epidemiological studies may be important for the design and implementation of prophylactic measures in CF centers. [source] Evaluating the usefulness of spa typing, in comparison with pulsed-field gel electrophoresis, for epidemiological typing of methicillin-resistant Staphylococcus aureus in a low-prevalence region in Sweden 2000,2004CLINICAL MICROBIOLOGY AND INFECTION, Issue 5 2010A. C. Petersson Clin Microbiol Infect 2010; 16: 456,462 Abstract The usefulness of spa typing was evaluated in relation to pulsed-field gel electrophoresis (PFGE), as a tool for epidemiological typing of methicillin-resistant Staphylococcus aureus (MRSA) in a low-prevalence region in southern Sweden. Bacterial isolates from 216 MRSA cases, newly identified in 2000,2004, were studied. The isolates were obtained from infected patients (31%), and from colonized individuals found by screening (69%). In total, 49 spa types and 73 PFGE patterns were identified. The discriminatory power of spa typing was lower (94.9 ± 1.8%) than that of PFGE (97.3 ± 1.2%). For two spa types (t002 and t008) the Panton,Valentine leukocidin results added useful discriminatory information. The most common spa types were t044 (n = 31; four PFGE patterns), t002 (n = 24; 10 PFGE patterns), t067 (n = 12; four PFGE patterns), t050 (n = 12; one PFGE pattern), and t324 (n = 11; one PFGE pattern). Epidemiological investigations identified 91 single cases and 39 transmission chains, each involving two to 13 cases. All the transmission chains were held together both by spa and PFGE typing. Among the 91 single-case isolates, 33 spa types and 50 PFGE patterns were unique (matchless) at the time of identification. The low prevalence of MRSA, the low number of outbreaks, and the wide spectrum of strains due to frequent acquisitions abroad (49% of the cases), makes spa typing a useful complement to epidemiological investigations in our setting. However, we still recommend the continued use of PFGE for further discrimination of isolates with identical spa types when epidemiological data can not exclude possible transmission. [source] Genetic relatedness between group B streptococci originating from bovine mastitis and a human group B streptococcus type V cluster displaying an identical pulsed-field gel electrophoresis patternCLINICAL MICROBIOLOGY AND INFECTION, Issue 9 2006I. C. M. Oliveira Abstract Twenty isolates of group B streptococcus (GBS) were recovered from the milk of cows with bovine mastitis on three farms located in the south and south-east of Brazil between 1987 and 1988. These isolates were characterised by molecular methods and compared with a collection of 103 human GBS isolates from colonised and infected patients in the same region between 1980 and 2003. Some of the bovine isolates shared identical or similar pulsed-field gel electrophoresis (PFGE) patterns with a PFGE clone of human GBS type V. In addition, these bovine and human isolates also possessed the same ribotype. Multilocus sequence typing (MLST) of representative isolates confirmed the genetic relationship between the human and bovine GBS isolates with identical PFGE patterns, which clustered in the same ST-26 clonal complex. These data support the hypothesis that some bovine GBS strains are related closely to human isolates and may infect humans, or vice versa. Further comparative genomic analyses of GBS isolates from bovine and human origins are required to investigate this hypothesis further. [source] | |||||||||||||