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Journal articles on the topic "Phage typing"
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Markowsky, George, Melvin Gershman, and Jacqueline Hunter. "Phage typing sets." Mathematical and Computer Modelling 16, no. 6-7 (June 1992): 113–19. http://dx.doi.org/10.1016/0895-7177(92)90156-f.
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Ward, L. R., J. D. H. de Sa, and B. Rowe. "A phage-typing scheme for Salmonella enteritidis." Epidemiology and Infection 99, no. 2 (October 1987): 291–94. http://dx.doi.org/10.1017/s0950268800067765.
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SUMMARYFor many years phage typing has proved invaluable in epidemiological studies on Salmonella typhi, S. paratyphi A and B, S. typhimurium and a few other serotypes. A phage-typing scheme for S. enteritidis is described. This scheme to date differentiates 27 types using 10 typing phages.
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Coward, Chris, Andrew J. Grant, Craig Swift, Jennifer Philp, Rebecca Towler, Mohammad Heydarian, Jennifer A. Frost, and Duncan J. Maskell. "Phase-Variable Surface Structures Are Required for Infection of Campylobacter jejuni by Bacteriophages." Applied and Environmental Microbiology 72, no. 7 (July 2006): 4638–47. http://dx.doi.org/10.1128/aem.00184-06.
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ABSTRACT This study characterizes the interaction between Campylobacter jejuni and the 16 phages used in the United Kingdom typing scheme by screening spontaneous mutants of the phage-type strains and transposon mutants of the sequenced strain NCTC 11168. We show that the 16 typing phages fall into four groups based on their patterns of activity against spontaneous mutants. Screens of transposon and defined mutants indicate that the phage-bacterium interaction for one of these groups appears to involve the capsular polysaccharide (CPS), while two of the other three groups consist of flagellatropic phages. The expression of CPS and flagella is potentially phase variable in C. jejuni, and the implications of these findings for typing and intervention strategies are discussed.
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Richardson, J. F., P. Aparicio, R. R. Marples, and B. D. Cookson. "Ribotyping ofStaphylococcus aureus: an assessment using well–defined strains." Epidemiology and Infection 112, no. 1 (February 1994): 93–101. http://dx.doi.org/10.1017/s0950268800057459.
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SummaryRibotyping, with homologous or heterologous (Escherichia coli) r–RNA, of the propagating strains for phages of the international set for strains ofStaphylococcus aureusof human origin was undertaken to determine the discrimination of this typing method. Ribotyping could distinguish between strains of different phage groups, but could not distinguish between seven phage group III strains of different phage type. Ribotyping may be a useful adjunct to phage typing inS. aureusbut is unlikely to replace it as the primary method of epidemiological typing.
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Ortel, S. "Phage-typing of Listeria." International Journal of Food Microbiology 8, no. 3 (June 1989): 241–43. http://dx.doi.org/10.1016/0168-1605(89)90019-6.
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Vindel, Ana, Cecilia Martín-Bourgon, Juan A. Saez-Nieto, and Saez Nieto. "Characterization of non-typable strains ofStaphylococcus aureusfrom cases of hospital infection." Epidemiology and Infection 99, no. 1 (August 1987): 191–200. http://dx.doi.org/10.1017/s0950268800067029.
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SUMMARYA high percentage of non-typable (NT)Staphylococcus aureusstrains was isolated in Spanish hospitals during 1984 and 1985. Several alternative methods of typing were employed to study these isolates. These were: phage-typing at 1000 × RTD, phage-typing after heat-treatment (48 °C), thermal shock (56 °C), reverse-typing and induction of additional phages. Using these methods the number of NT isolates was reducedby 60%. Best results were obtained with heat-treatment. Additional phages and reverse-typing were also useful.A scheme for the study of outbreaks and sporadic cases caused by NT strains is proposed using the methods described.
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Pereira, A. Torres, and J. A. G. Melo Cristino. "Phage typing of Staphylococcus saprophyticus." Epidemiology and Infection 107, no. 3 (December 1991): 557–63. http://dx.doi.org/10.1017/s0950268800049256.
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SUMMARYThis study included 502 staphylococcus strains; Staphylococcus saprophyticus (297 strains) S. cohnii (47), S. xylosus (10), S. epidermidis (67) and S. aureus (81). Mitomycin C induction was performed on 100 isolates of S. saprophyticus and all induced strains were reacted with each other. Twenty-six strains proved to be lysogenic. Phages were propagated and titrated. With 12 of the phages there were three frequent associations, named lytic groups A, B and C, which included 75% of all typable strains. Typability of the system was 45% and reproducibility was between 94.2% and 100%. Phages did not lyse S. aureus and S. epidermidis strains, but they lysed S. saprophyticus and only rare strains of other novobiocin resistant species. Effective S. saprophyticus typing serves ecological purposes and tracing the origin of urinary strains from the skin or mucous membranes. Phage typing in association with plasmid profiling previously described, are anticipated as complementary methods with strong discriminatory power for differentiating among S. saprophyticus strains.
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Threlfall, E. J., B. Rowe, and L. R. Ward. "Subdivision ofSalmonella enteritidisphage types by plasmid profile typing." Epidemiology and Infection 102, no. 3 (June 1989): 459–65. http://dx.doi.org/10.1017/s095026880003017x.
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SUMMARYDifferentiation ofSalmonella enteritidisby plasmid profile typing has been compared to differentiation by phage typing. Examination of the type strains of the 27S. enteritidisphage types showed that only 11 profile patterns could be identified. Moreover, two profile patterns were found in 15 of the type strains, including those of the two most common phage types in Britain, types 4 and 8. On this basis, plasmid profile typing is not as sensitive as phage typing for the primary subdivision ofS. enteritidis.When differentiation of 534 strains of the 27 phage types was attempted using plasmid profiles, variation in pattern suitable for epidemiologieal subdivision was found in 13 phage types and there were 9 profile patterns in strains of phage type 4. Plasmid profile typing can, therefore, be regarded as an effective adjunct to phage typing for the subdivision ofS. enteritidis
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MILLER, T., P. G. BRAUN, K. FEHLHABER, R. PRAGER, Y. PFEIFER, and W. RABSCH. "Typing ofSalmonella entericaserovar Infantis isolates from 51 outbreaks in Germany between 1974 and 2009 by a novel phage-typing scheme." Epidemiology and Infection 142, no. 1 (March 21, 2013): 75–83. http://dx.doi.org/10.1017/s095026881300037x.
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SUMMARYWe developed a new phage-typing method and evaluated its application in combination withXbaI macrorestriction analysis by pulsed-field gel electrophoresis (PFGE) as a useful tool for the long-term epidemiology ofSalmonella entericaserovar Infantis. In this study, we investigated 1008S.Infantis isolates recovered from humans, various animal species and food products from 1973 to 2009. The typing scheme is based on 17 typing phages, defining 61 different patterns within the strain collection. The experiments showed that phage typing is a reliable method for differentiation of outbreaks and sporadic clinical cases as well as for elucidation of chains of transmission. The combined analysis of phage typing and PFGE revealed the existence of epidemic clones with a high stability over time like PT29/XB27 which was identified in nosocomial salmonellosis, community outbreaks as well as in broiler chickens from 2002 to 2009.
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Khakhria, R., and H. Lior. "Extended phage-typing scheme forCampylobacter jejuniandCampylobacter coli." Epidemiology and Infection 108, no. 3 (June 1992): 403–14. http://dx.doi.org/10.1017/s0950268800049918.
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SUMMARYThe extended phage-typing scheme described forCampylobacter jejuniandCampylobacter colihas established 46 different phage types using 19 typing phages. Altogether 754 campylobacter isolates, 672C. jejuniand 82C. coli, isolated from human and non-human sources received from 17 different countries were phage-typed. Overall, 80·6% of the total isolates were typable. Among typable strains, 9 phage types (3, 5, 10, 11, 18, 19, 23, 26 and 44) represented 57·0% of the strains, 21·3% of the strains belonged to another 37 phage types and the remaining 2·3% of isolates were designated atypical. The most common phage type 11 (140/754) was frequently observed amongC. jejuniisolates from human (113/561) and non-human sources (18/111). whereas type 44 was frequent amongC. coliisolates from human (22/59) and from non-human sources (8/23). A study of the animal host-associations of common phage types showed that contaminated cattle and poultry appear to be the most common sources of human infection. The greatest variety of phage types was observed in Canada (24 phage types), followed by Portugal (17 types) and the UK (14 types), reflecting the larger sample sizes from these countries. Phage type 11 was encountered in 12 different countries and prevalence of other phage types varied from one country to another. The number of isolates typable with the scheme varied from 93·2% (261/280) in Canada to 61% (47/77) in Thailand. However, the number and diversity of phage types makes phage typing the method of choice in epidemiological studies of campylobacter infections.
Dissertations / Theses on the topic "Phage typing"
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Hu, Honghua. "Molecular typing and evolution of Salmonella enterica serovar Typhimurium." Thesis, The University of Sydney, 2005. http://hdl.handle.net/2123/704.
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Salmonella enterica serovar Typhimurium is a common cause of salmonellosis among humans and animals worldwide. In Australia, Typhimurium is responsible for over half of the salmonellosis cases. The Anderson phage-typing scheme is the primary means of long-term surveillance of Typhimurium outbreak isolates, and has played an important role in epidemiology. However, there exist quite a number of strains of Typhimurium that cannot be defined by the phage-typing scheme. Furthermore, the knowledge of evolutionary relationships among isolates of different phage types is still very limited and the genetic basis of phage type variation remains largely unknown. To address these issues, this study focused on molecular typing and evolution of Typhimurium. Fluorescent amplified-fragment length polymorphism (AFLP) was applied to 46 Typhimurium isolates comprising nine phage types in Australia using the restriction enzymes MseI and EcoRI and MseI +1 / EcoRI +1 primer pair combinations. The selected phage types, DT9, DT135, DT64, DT44, DT126, DT12a, DT1, DT141 and DT108, have been dominant or frequent phage types in animal and human infections in Australia in recent years. AFLP in the present study showed a very good discrimination power with Simpson index of diversity of 0.98, 35 different AFLP patterns were observed in the 46 isolates studied. The tree based on AFLP patterns showed good correlation with phage type, grouped most Typhimurium isolates by phage type, and differentiated all nine phage types. Furthermore, 84 phage-type specific polymorphic AFLP fragments, for which presence or absence correlated with phage type (including 25 with one exception to phage-type specificity) were observed in the 46 strains studied. Eighteen phage-type specific AFLP fragments were cloned and sequenced. Sixteen are of known genes or have a homologue in the databases. It was found a predominance of phage and plasmid genes rather than mutational changes in the AFLP fragments studied. Of the 18 cloned and sequenced AFLP fragments, only four relate to mutational changes in the S. enterica chromosome, the other 14 comprise DNA of mobile elements: nine are phage related, three are plasmid related and two are gain of DNA from unknown origin. Twelve of the 18 sequenced phage-type specific AFLP markers are polymorphic because the DNA is present or absent as indicated by Southern hybridization. Two of these markers were successfully used in preliminary PCR-based typing of 30 DT9 and 29 DT135 isolates from worldwide collections. 27 of the 30 DT9 isolates and all DT135 isolates tested were correctly categorized. The results implied a good potential to use the sequence of these fragments as the basis for a multiplex PCR or a microarray based molecular 'phage' typing method for Typhimurium. This thesis also studied the molecular evolutionary relationships among the same set of 46 Typhimurium isolates using mutational changes detected by AFLP, or analysis of intergenic regions and their flanking genes in genome sequences. The complete genome sequence of Typhimurium LT2 was analysed by computer modelled AFLP. The polymorphic AFLP fragments, which matched with the modelled LT2 AFLP fragments, were amplified and sequenced by LT2 genome based primers to determine the changes. Forty-nine intergenic regions with higher pairwise differences between LT2 and Typhi CT18 were amplified and sequenced using LT2 genome based primers for one isolate of each phage type. 51 polymorphic sites were detected consisting of 18 in AFLP fragments and 33 in intergenic regions or their flanking genes. PCR-RFLP (restriction fragment length polymorphism) and SNaPshot were used to further investigate the distribution of the single nucleotide polymorphisms (SNPs) detected in intergenic regions in all isolates studied. Of the 18 mutational changes detected in AFLP fragments, eight were indels (insertions / deletions) and ten single base substitutions. Of the eight indels, four were in genes, three in intergenic regions, and one covered adjacent intergenic and coding regions. The four indels in genes all caused frameshift mutations, including three single base indels and one 19 bp deletion. Of the ten substitutions, one was in an intergenic region and nine in genes comprising three synonymous and six non-synonymous substitutions. Of the 33 polymorphic sites detected from sequences of 23 intergenic regions and their flanking genes, one was IS200 insertion and 32 single nucleotide polymorphisms (SNPs), of which 30 were single base substitutions and two were single base indels. Nine of the 33 variations were found in the flanking genes, which were all single base substitutions comprising four synonymous, four non-synonymous substitutions and one non-sense mutation. More non-synonymous than synonymous substitutions were found for those in coding regions within Typhimurium, indicating that slightly deleterious intraspecies mutations can be fixed within clones, such as various lineages of Typhimurium. The 51 polymorphic sites, which were inferred from sequences of both mutation related AFLP fragments, and intergenic regions and their flanking genes, gave a single phylogenetic tree of the 46 Typhimurium isolates studied. All sequences involved were compared with the homologous sequences in the available S. enterica genome sequences for serovars Typhi, Paratyphi A, Gallinarum, Enteritidis and Pullorum and this enabled the determination of the direction of the mutational changes in the isolates studied and the root of the phylogenetic tree. There were only two events inferred to have occurred twice, the remaining 49 polymorphisms can be explained by a single event. The data indicated that Typhimurium has a very strong clonal structure with a very low level of recombination over the time for diversification of Typhimurium as majority of clonal variations are from point mutations rather than recombination. The phylogenetic tree based on mutational changes showed that most Typhimurium isolates of a given phage type are in the same evolutionary group, but that some phage types appear to have arisen more than once. Comparison of the phylogenetic tree with AFLP data gave examples of unrelated isolates of a given phage type having common AFLP fragments comprising plasmid or phage genes, supporting the view that phage type can be determined by presence of specific phages or plasmids. The mutation-based tree showed that six of the nine phage types studied appeared to have a single origin, at least for the isolates studied. It also found that DT1 and DT44 had two independent origins even for the limited set of strains used. The distribution of DT12a isolates into two groups could be explained that the group of three DT12a isolates were derived from the other group of four DT12a isolates, where the root of the tree might be. The data also confirmed that DT64 arose from DT9. The phylogenetic tree that was generated based on essentially mutational changes provides clear relationships of the closely related Typhimurium isolates with high level of consistency and reasonable confidence. This study provided one of the few analyses of relationships of isolates within a clone. Matching actual AFLP with computer modeled AFLP and sequencing intergenic regions provide very good new strategies to identify mutational polymorphisms and to study the molecular evolutionary relationships in the closely related isolates.
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Hu, Honghua. "Molecular typing and evolution of Salmonella enterica serovar Typhimurium." University of Sydney. School of Molecular and Microbial Biosciences, 2005. http://hdl.handle.net/2123/704.
Full textAbstract:
Salmonella enterica serovar Typhimurium is a common cause of salmonellosis among humans and animals worldwide. In Australia, Typhimurium is responsible for over half of the salmonellosis cases. The Anderson phage-typing scheme is the primary means of long-term surveillance of Typhimurium outbreak isolates, and has played an important role in epidemiology. However, there exist quite a number of strains of Typhimurium that cannot be defined by the phage-typing scheme. Furthermore, the knowledge of evolutionary relationships among isolates of different phage types is still very limited and the genetic basis of phage type variation remains largely unknown. To address these issues, this study focused on molecular typing and evolution of Typhimurium. Fluorescent amplified-fragment length polymorphism (AFLP) was applied to 46 Typhimurium isolates comprising nine phage types in Australia using the restriction enzymes MseI and EcoRI and MseI +1 / EcoRI +1 primer pair combinations. The selected phage types, DT9, DT135, DT64, DT44, DT126, DT12a, DT1, DT141 and DT108, have been dominant or frequent phage types in animal and human infections in Australia in recent years. AFLP in the present study showed a very good discrimination power with Simpson index of diversity of 0.98, 35 different AFLP patterns were observed in the 46 isolates studied. The tree based on AFLP patterns showed good correlation with phage type, grouped most Typhimurium isolates by phage type, and differentiated all nine phage types. Furthermore, 84 phage-type specific polymorphic AFLP fragments, for which presence or absence correlated with phage type (including 25 with one exception to phage-type specificity) were observed in the 46 strains studied. Eighteen phage-type specific AFLP fragments were cloned and sequenced. Sixteen are of known genes or have a homologue in the databases. It was found a predominance of phage and plasmid genes rather than mutational changes in the AFLP fragments studied. Of the 18 cloned and sequenced AFLP fragments, only four relate to mutational changes in the S. enterica chromosome, the other 14 comprise DNA of mobile elements: nine are phage related, three are plasmid related and two are gain of DNA from unknown origin. Twelve of the 18 sequenced phage-type specific AFLP markers are polymorphic because the DNA is present or absent as indicated by Southern hybridization. Two of these markers were successfully used in preliminary PCR-based typing of 30 DT9 and 29 DT135 isolates from worldwide collections. 27 of the 30 DT9 isolates and all DT135 isolates tested were correctly categorized. The results implied a good potential to use the sequence of these fragments as the basis for a multiplex PCR or a microarray based molecular �phage� typing method for Typhimurium. This thesis also studied the molecular evolutionary relationships among the same set of 46 Typhimurium isolates using mutational changes detected by AFLP, or analysis of intergenic regions and their flanking genes in genome sequences. The complete genome sequence of Typhimurium LT2 was analysed by computer modelled AFLP. The polymorphic AFLP fragments, which matched with the modelled LT2 AFLP fragments, were amplified and sequenced by LT2 genome based primers to determine the changes. Forty-nine intergenic regions with higher pairwise differences between LT2 and Typhi CT18 were amplified and sequenced using LT2 genome based primers for one isolate of each phage type. 51 polymorphic sites were detected consisting of 18 in AFLP fragments and 33 in intergenic regions or their flanking genes. PCR-RFLP (restriction fragment length polymorphism) and SNaPshot were used to further investigate the distribution of the single nucleotide polymorphisms (SNPs) detected in intergenic regions in all isolates studied. Of the 18 mutational changes detected in AFLP fragments, eight were indels (insertions / deletions) and ten single base substitutions. Of the eight indels, four were in genes, three in intergenic regions, and one covered adjacent intergenic and coding regions. The four indels in genes all caused frameshift mutations, including three single base indels and one 19 bp deletion. Of the ten substitutions, one was in an intergenic region and nine in genes comprising three synonymous and six non-synonymous substitutions. Of the 33 polymorphic sites detected from sequences of 23 intergenic regions and their flanking genes, one was IS200 insertion and 32 single nucleotide polymorphisms (SNPs), of which 30 were single base substitutions and two were single base indels. Nine of the 33 variations were found in the flanking genes, which were all single base substitutions comprising four synonymous, four non-synonymous substitutions and one non-sense mutation. More non-synonymous than synonymous substitutions were found for those in coding regions within Typhimurium, indicating that slightly deleterious intraspecies mutations can be fixed within clones, such as various lineages of Typhimurium. The 51 polymorphic sites, which were inferred from sequences of both mutation related AFLP fragments, and intergenic regions and their flanking genes, gave a single phylogenetic tree of the 46 Typhimurium isolates studied. All sequences involved were compared with the homologous sequences in the available S. enterica genome sequences for serovars Typhi, Paratyphi A, Gallinarum, Enteritidis and Pullorum and this enabled the determination of the direction of the mutational changes in the isolates studied and the root of the phylogenetic tree. There were only two events inferred to have occurred twice, the remaining 49 polymorphisms can be explained by a single event. The data indicated that Typhimurium has a very strong clonal structure with a very low level of recombination over the time for diversification of Typhimurium as majority of clonal variations are from point mutations rather than recombination. The phylogenetic tree based on mutational changes showed that most Typhimurium isolates of a given phage type are in the same evolutionary group, but that some phage types appear to have arisen more than once. Comparison of the phylogenetic tree with AFLP data gave examples of unrelated isolates of a given phage type having common AFLP fragments comprising plasmid or phage genes, supporting the view that phage type can be determined by presence of specific phages or plasmids. The mutation-based tree showed that six of the nine phage types studied appeared to have a single origin, at least for the isolates studied. It also found that DT1 and DT44 had two independent origins even for the limited set of strains used. The distribution of DT12a isolates into two groups could be explained that the group of three DT12a isolates were derived from the other group of four DT12a isolates, where the root of the tree might be. The data also confirmed that DT64 arose from DT9. The phylogenetic tree that was generated based on essentially mutational changes provides clear relationships of the closely related Typhimurium isolates with high level of consistency and reasonable confidence. This study provided one of the few analyses of relationships of isolates within a clone. Matching actual AFLP with computer modeled AFLP and sequencing intergenic regions provide very good new strategies to identify mutational polymorphisms and to study the molecular evolutionary relationships in the closely related isolates.
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Cambray-Young, Joanna Claire. "Characterisation of a virulent bacteriophage from the UK Campylobacter phage-typing scheme." Thesis, University of Cambridge, 2011. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.609423.
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Rusin, Patricia Anne. "Antibiotic resistance, heavy metal resistance, chlorine resistance and phage typing patterns of fecal coliforms isolated from secondary effluent." Diss., The University of Arizona, 1989. http://hdl.handle.net/10150/184925.
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Antibiotic resistance profiles of fecal coliform isolated from unchlorinated and chlorinated secondary effluent were determined. Of 332 fecal coliforms isolated from chlorinated effluent a mean of 48% were multiply antibiotic resistant. In contrast, of 347 fecal coliforms isolated from unchlorinated effluent a mean of 29% were multiply antibiotic resistant. Resistance to ampicillin, cephalothin, and carbenicillin were significantly higher in the former than the latter. Randomly selected isolates survived and/or grew in sterile and unsterile effluent retaining resistance patterns for 40 days. Resistance factors were transferred in laboratory medium at frequencies from 0 to 1.2 x 10⁻² (number of recombinants/number of recipients) and in sterile neutralized tertiary effluent at frequencies from 0 to 1.0 x 10⁻⁴. Resuscitative techniques were necessary for optimal recovery of fecal coliforms from effluent using selective media. Antibiotic resistance patterns of fecal coliforms isolated from unchlorinated and chlorinated effluent was not associated with chlorine or heavy metal resistance. Multiply antibiotic resistant fecal coliforms from chlorinated effluent were significantly less sensitive to lytic phage than multiply antibiotic sensitive fecal coliforms from unchlorinated effluent (p < .05). Using group discriminate analysis of data, phage typing techniques were shown to be a potential tool for tracing fecal contamination of groundwater.
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Merrill, Bryan Douglas. "Advancing Phage Genomics and Honeybee Health Through Discovery and Characterization of Paenibacillaceae Bacteriophages." BYU ScholarsArchive, 2015. https://scholarsarchive.byu.edu/etd/5641.
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The Paenibacillaceae family of bacteria includes two species known to infect the hives of honeybees, Paenibacillus larvae and Brevibacillus laterosporus. P. larvae, the causative agent of American Foulbrood (AFB) causes a lethal infection of honeybee larvae, while B. laterosporus is a secondary invader following European Foulbrood (EFB) infection. Increasing antibiotic resistance of P. larvae bacteria has prompted a search for alternative treatment methods for this disease. Bacteriophages are the most diverse life forms on earth and can provide important insights about the bacterial hosts they infect. However, few Paenibacillaceae phages have been isolated or characterized. In this study, the first B. laterosporus phages are characterized with respect to host range, structural morphology, and sequence similarity. The isolation and characterization of many P. larvae field isolates together with 38 novel P. larvae phages made possible the first broad phage typing study of P. larvae. Phage typing data indicated that P. larvae strains tested could be categorized into one of two groups. Comparative genomics of bacteriophages was made easier by modifying Phamerator to make it broadly accessible and usable to phage researchers throughout the world. Additionally, raw sequencing data can now be used to identify phage DNA packaging strategies that are indicative of a phage’s physical ends. Using these data, phage genomes can be published in an orientation and complementarity that reflects the physical structure of the phage chromosome, providing order and consistency that will benefit all future phage researchers.
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Cowley, Lauren A. "Use of genome sequencing to investigate the molecular basis of bacteriaphage interaction of the Escherichia coli O157 typing phages and the elucidation of the biological and public health significance of phage type." Thesis, University of Edinburgh, 2017. http://hdl.handle.net/1842/23583.
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Background Shiga toxin producing Escherichia coli (STEC) O157 causes severe gastrointestinal disease and haemolytic uremic syndrome, and has a major impact on public health worldwide with regular outbreaks and sporadic infection. Phage typing, i.e. the susceptibility of STEC O157 strains to a bank of 16 bacteriophages, has been used in the UK to differentiate STEC O157 for the past 25 years and the phage type (PT) can be an epidemiological marker of strains associated with severe disease or associated with cases that occur from foreign travel. However, little is known about the molecular interactions between the typing phages (TP) and STEC O157. The aims of this thesis were to use whole genome sequencing to elucidate the genetic basis for phage typing of STEC O157 and through this understand genetic differences between strains relevant to disease severity and epidemiology. Results Sequencing the STEC O157 TPs revealed that they were clustered into 4 groups based on sequence similarity that corresponded with their infectivity. Long read sequencing revealed microevolutionary events occuring in STEC O157 genomes over a short time period (approximately 1 year), evidenced by the loss and gain of prophage regions and plasmids. An IncHI2 plasmid was found responsible for a change in Phage Type (PT) from PT8 to PT54 during two related outbreaks at the same restaurant. These changes resulted in a strain (PT54) that was fitter under certain growth conditions and associated with a much larger outbreak (140 as opposed to 4 cases). TraDIS (Transposon directed Insertion site sequencing) was used to identify 114 genes associated with phage sensitivity and 44 genes involved in phage resistance, emphasising the complex nature of identifying specific genetic markers of phage susceptibility or resistance. Further work is required to prove their phage-related functions but several are likely to encode novel phage receptors. Deletion of a Stx2a prophage from a PT21/28 strain led to a strain that typed as PT32, supporting the concept that the highly pathogenic PT21/28 lineage I strains emerged from Stx2c+ PT32 strains in the last two decades by acquisition of Stx2a-encoding prophages. Conclusions This body of work has highlighted the complexity of bacteriophage interaction and investigated the genetic basis for susceptibility and resistance in E. coli. The grouping of the TPs showed that resistance or susceptibility to all members of a typing group was likely to be caused by one mechanism. IncHI2 was identified as one of the markers for the PT54 phenotype. The Stx2a prophage region was associated with the switch from PT32 to PT21/28, although PT32 strains containing both Stx2a and Stx2c-encoding prophages have been isolated and can provide insights into phage variation underpinning the susceptibility to the relevant typing phages. The TraDIS results indicated that susceptibility or resistance was governed by multiple genetic factors and not controlled by a single gene. The significance of LPS for initial protection from phage adsorption was evident and a number of novel genes controlling phage susceptibility and resistance identified including the Sap operon and stringent starvation protein A respectively. While SNP-based typing provides an excellent indication of the evolution and relatedness of strains, phage typing can provide real insights into short term evolution of the bacteria as PTs can be altered by mobile elements such as prophages and plasmids. This study has shown that, although complex, genetic determinants for PT can be mined from the genome and allow us to understand the evolution of this zoonotic pathogen between host species and during outbreaks.
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LUCARELLI, CLAUDIA. "La multiresistenza in Salmonella: caratterizzazione molecolare di un nuovo clone emergente di Salmonella enterica sierotipo Typhimurium." Doctoral thesis, Università degli Studi di Roma "Tor Vergata", 2009. http://hdl.handle.net/2108/1089.
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Salmonella enterica sierotipo Typhimurium (STM) rappresenta la prevalente causa di gastroenterite trasmessa da alimenti in Italia, con la maggior parte degli isolati con resistenza multipla agli antibiotici, principalmente ad ampicillina (A), cloramfenicolo (C), streptomicina (S), sulfamidici (Su) e tetraciclina (T) (ACSSuT).
Un nuovo pattern di resistenza (R-type) ASSuT, mancante della resistenza a C, è recentemente emerso in Italia tra ceppi di STM e della sua variante monofasica, Salmonella enterica subspecie enterica sierotipo S. 4,[5],12:i:– .
L’obiettivo principale di questa tesi è stato la caratterizzazione di ceppi di STM e di S. 4,[5],12:i:– con R-type ASSuT, usando tecniche di tipizzazione molecolari e fenotipiche, quali l’elettroforesi in campo pulsato (PFGE) e la fagotipizzazione, allo scopo di valutare la loro origine clonale e la loro relazione con i ceppi ACSSuT. Usando il database Pulse-Net Europe è stata valutata la presenza di ceppi ASSuT in altre nazioni Europee al fine di allestire una collezione internazionale di ceppi. Questa collezione è stata ulteriormente caratterizzata, identificando i geni di resistenza, investigando la loro localizzazione, e determinando la regione di resistenza.
Sia tra ceppi di STM che di S. 4,[5],12:i:–, il principale profilo di PFGE è rappresentato da STYMXB.0079, mentre i ceppi STM ACSSuT appartengono ai profili STYMXB.0061 e STYMXB.0067. L’analisi dei profili di PFGE con il software Bionumerics ha mostrato che più del 90% dei ceppi ASSuT e ACSSuT appartenevano a due distinti clusters con un’omologia genetica del 73%, dati che dimostrano l’appartenenza dei ceppi ASSuT ad un'unica linea clonale differente da quella dei ceppi ACSSuT.
La maggior parte dei ceppi con profilo ASSuT non erano tipizzabili (DTNT) attraverso la fagotipizzazione o appartenevano al fagotipo U302. Al contrario i ceppi ACSSuT appartenevano principalmente al fagotipo DT104.
Successivamente, nel database Pulse-Net Europe, è stato possibile identificare ceppi ASSuT, sia STM che S. 4,[5],12:i:– isolati in Danimarca ed Inghilterra, con profili di PFGE identici o strettamente correlati a quelli dei ceppi italiani, dati che indicano che il clone ASSuT è presente anche in altri paesi Europei.
Al fine di identificare i geni responsabili della resistenza sono stati selezionati 64 ceppi di STM e S. 4,[5],12:i:– ASSuT, e 11 ceppi di STM con differenti R-type e profili di PFGE, usati come controlli. Tutti i ceppi provenivano da infezioni umane ed erano stati isolati in Italia, Danimarca e Inghilterra.
Tutti i ceppi ASSuT erano positivi per i seguenti geni di resistenza: blaTEM, strA-strB, sul2 and tet(B). Successivi esperimenti di localizzazione hanno dimostrato che i geni di resistenza ASSuT sono localizzati sul cromosoma
Infine, è stata determinata la sequenza completa del cluster di resistenza ASSuT. Questo cluster è composto da due isole di resistenza (RI1 e RI2) separate da DNA cromosomale. In particolare, RI1 è compresa tra due IS26 e contiene deltatnp3R, blaTEM-1, tnpB, seguito da strB, strA, sul2, repC, deltarepA ed un’atra IS26. RI2 è anch’essa compresa tra due IS26, comprendenti deltaIS10L, il gene di resistenza alla tetraciclina, IS1, l’operone per la resistenza al mercurio, il gene yaeA, e un’ ipotetica transposasi (tniAdelta). Entrambe le RIs mostrano il 99% di identità con due regioni adiacenti del plasmide pHCM1, presente nel ceppo di S. Typhi isolato in Vietnam. Le sequenze di inserzione IS26 potrebbero aver avuto un ruolo nella formazione di questo cluster di resistenza, ma quest’ipotesi deve essere ancora verificata.
In conclusione il lavoro di questa tesi indica che i ceppi ASSuT di STM e S. 4,[5],12:i:–, in aumento in Italia, appartengono ad un'unica linea clonale e che i ceppi S. 4,[5],12:i:– circolanti nella nostra nazione, derivano principalmente da questa linea clonale di STM. Inoltre il clone ASSuT è diffuso anche in Danimarca ed Inghilterra. Il pattern di antibiotico resistenza conferito da un’isola di resistenza cromosomale, con un’organizzazione simile ad altri cluster precedentemente descritti, suscita preoccupazione poichè la resistenza può essere mantenuta stabilmente in assenza di pressione selettiva.Salmonella enterica serovar Typhimurium (STM) represents the prevalent cause of foodborne gastroenteritis in Italy with the majority of isolates exhibiting multidrug resistance, mainly to ampicillin (A), chloramphenicol (C), streptomycin (S), sulfonamide (Su) and tetracycline (T) (ACSSuT). However, a new resistance pattern (R-type) ASSuT, lacking resistance to C, has recently emerged in Italy among strains of STM and of its monophasic variant, Salmonella enterica subspecie enterica serovar S. 4,[5],12:i:– . The main objective of this thesis has been the characterization of STM and S. 4,[5],12:i:– strains with R-type ASSuT, using both molecular and phenotypic typing technique, pulsed-field gel electrophoresis (PFGE) and phage typing, in order to evaluate their clonal origin and the relationships with the ACSSuT strains. In addition, by the use of the Pulse-Net database it was evaluated if ASSuT strains were present in other European countries in order to set up an international collection of these strains. This collection has been further characterized with the identification of resistance genes, the investigation of their localization, and determination of the resistance region. Among both the STM and S. 4,[5],12:i:– ASSuT strains, the predominant PFGE profile was STYMXB.0079, while the STM ACSSuT strains belonged to the STYMXB.0061 and STYMXB. 0067. Bionumerics cluster analysis of PFGE profiles showed that more than 90% of ASSuT and ACSSuT resistant strains were included in two distinct clusters with a genetic homology of 73% each other, suggesting that the ASSuT resistant strains belong to a same clonal lineage different from that of the ACSSuT strains. Phage typing showed that both STM and S. 4,[5],12:i:– ASSuT strains were not typeable (DTNT) or U302. A different figure was observed for the ACSSuT strains: the STM strains mostly belonged to DT104. The Pulse-Net Europe database, allowed us to identify ASSuT strains, both STM and S. enterica 4,[5],12:i:–, isolated in Denmark and UK, with the same or very closely related PFGE patterns as the Italian strains, suggesting that the ASSuT clone is circulating in different European countries. The resistance genes were identified in 64 strains of STM and S. enterica 4,[5],12:i:–with ASSuT R-type and in 11 STM strains with different resistance patterns and PFGE profiles as controls. All strains were isolated from human infections in Italy, Denmark and UK. All the ASSuT strains were positive for the following resistance genes: blaTEM, strA-strB, sul2 and tet(B). The control strains showed the same gene pattern, in accordance with their resistance profiles. A variability of the genes conferring resistance to tetracycline was detected. Localization experiments demonstrated that the ASSuT resistance genes are chromosomally located. Finally, the complete sequence of ASSuT resistance cluster was determined. This cluster is composed by two resistance island (RI1 and RI2) divided by chromosomal DNA. In particular, RI1 is comprised between two IS26 and contains deltatnp3R, blaTEM-1, tnpB , followed by strB, strA, sul2, repC, DeltarepA and another IS26. RI2 is bracketed by two IS26, comprising deltaIS10L, tetracycline resistance gene, IS1, the operon for resistance to mercury, yaeA gene, and a putative transposase (tniAdelta). Both this RIs show 99% sequence identity to two adiacent region of pHCM1 plasmid, harbored in S. Typhi isolated in Vietnam. IS26 elements could have played a role in the assembly of this resistance cluster but it will be investigated more in detail. In conclusion the work of this thesis indicates that the tetra-resistant ASSuT strains of STM and S. 4,[5],12:i:–, increasingly isolated in Italy, belong to a same clonal lineage and that the S. 4,[5],12:i:– strains circulating in our country, mainly derive from this STM clonal lineage. ASSuT clone is also circulating in Denmark and United Kingdom. The antimicrobial resistance pattern conferred by a chromosomal island, with an organization similar to previously reported clusters, deserves concern since the resistance could be stably maintained even in the absence of selective pressure.
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Howard, Michael David. "Antigenic Characterization of Haemophilus somnus Lipooligosaccharide." Thesis, Virginia Tech, 1998. http://hdl.handle.net/10919/35378.
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Lipooligosaccharide (LOS) is the major outer membrane component of many Gram-negative bacteria inhabiting the mucosal membranes, including pathogenic species of Haemophilus and Neisseria. LOS phase variation is one mechanism by which some of these bacteria avoid the host immune response. To better understand LOS phase variation as a virulence mechanism of H. somnus, knowledge of the antigenic diversity of LOS epitopes must be increased. Monoclonal antibodies (MAbs) to H. somnus LOS were produced and used with cross-reacting MAbs to H. aegyptius LOS (MAb 5F5) and Neisseria gonorrhoeae LOS (MAb 3F11) in an ELISA to investigate LOS heterogeneity among forty-five strains of H. somnus. Using three MAbs, thirty-nine of these H. somnus strains were grouped into six antigenic types. Three groups, associated solely with the cross-reacting MAbs 5F5 and 3F11, included the majority (76%) of H. somnus strains. The anti-H. somnus LOS MAb 5D7 recognized a low frequency epitope associated with each of the remaining three groups, which included 11% of the H. somnus strains. Six strains (13%) were not recognized by any of these MAbs.
Inhibition ELISA experiments showed that the MAb 5F5 epitope contained phosphocholine (PCho) and this epitope was present in 56% of the strains tested. The MAb 5F5 epitope is phase variable in H. somnus LOS. How PCho negative variants could allow for systemic infection after initial colonization of the mucosa by PCho positive variants is discussed.
Master of Science
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Trojanek, Anne, Helge Fischer, and Matthias Heinz. "Auf die Typen kommt es an. Eine empirische Analyse studentischer Spielertypen." Saechsische Landesbibliothek- Staats- und Universitaetsbibliothek Dresden, 2018. http://nbn-resolving.de/urn:nbn:de:bsz:14-qucosa-234411.
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Aktuell streben Hochschulen nach Lösungen zur Senkung von Studienabbruchquoten, Anregung der Studienmotivation und Optimierung von Studieneingangsphasen. Diese hochschulpolitischen Ziele sind von großer Bedeutung für den demografischen Wandel und den steigenden Bedarf an hochqualifizierten Fachkräften. Viele verschiedene Konzepte versuchen diesen Zielen Rechnung zu tragen. Auch die Technische Universität Dresden (TUD) hat mit ihrem Gesamtkonzept zur Unterstützung des Studienerfolgs verschiedene Teilprojekte ins Leben gerufen. Eines davon ist das Studienassistenzsystem gOPAL, welches Studienanfängern der TUD beim Aufbau von Orientierungswissen und Kompetenzen der Studierfähigkeit unterstützt. [... aus dem Text]
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Trojanek, Anne, Helge Fischer, and Matthias Heinz. "Auf die Typen kommt es an. Eine empirische Analyse studentischer Spielertypen." TUDpress, 2017. https://tud.qucosa.de/id/qucosa%3A30890.
Full textAbstract:
Aktuell streben Hochschulen nach Lösungen zur Senkung von Studienabbruchquoten, Anregung der Studienmotivation und Optimierung von Studieneingangsphasen. Diese hochschulpolitischen Ziele sind von großer Bedeutung für den demografischen Wandel und den steigenden Bedarf an hochqualifizierten Fachkräften. Viele verschiedene Konzepte versuchen diesen Zielen Rechnung zu tragen. Auch die Technische Universität Dresden (TUD) hat mit ihrem Gesamtkonzept zur Unterstützung des Studienerfolgs verschiedene Teilprojekte ins Leben gerufen. Eines davon ist das Studienassistenzsystem gOPAL, welches Studienanfängern der TUD beim Aufbau von Orientierungswissen und Kompetenzen der Studierfähigkeit unterstützt. [... aus dem Text]
Book chapters on the topic "Phage typing"
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Chirakadze, Irina, Ann Perets, and Rafiq Ahmed. "Phage Typing." In Methods in Molecular Biology, 293–305. Totowa, NJ: Humana Press, 2009. http://dx.doi.org/10.1007/978-1-60327-565-1_17.
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Gooch, Jan W. "Phage Typing." In Encyclopedic Dictionary of Polymers, 914. New York, NY: Springer New York, 2011. http://dx.doi.org/10.1007/978-1-4419-6247-8_14469.
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Rowe, B., and J. A. Frost. "Vibrio Phages and Phage-Typing." In Cholera, 95–105. Boston, MA: Springer US, 1992. http://dx.doi.org/10.1007/978-1-4757-9688-9_5.
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Rabsch, Wolfgang. "Salmonella Typhimurium Phage Typing for Pathogens." In Methods in Molecular Biology, 177–211. Totowa, NJ: Humana Press, 2007. http://dx.doi.org/10.1007/978-1-59745-512-1_10.
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Jeshina, J., and Kuyyalil Surekha. "Epidemiological Typing of Methicillin-Resistant Staphylococcus aureus (MRSA) Isolated from Kerala Using Phage Typing." In Prospects in Bioscience: Addressing the Issues, 393–97. India: Springer India, 2012. http://dx.doi.org/10.1007/978-81-322-0810-5_46.
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Pausz, Clemens, Jessica L. Clasen, and Curtis A. Suttle. "Isolation Independent Methods of Characterizing Phage Communities 1: Strain Typing Using Fingerprinting Methods." In Methods in Molecular Biology, 255–78. Totowa, NJ: Humana Press, 2009. http://dx.doi.org/10.1007/978-1-60327-565-1_15.
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Ayana, N., and Kuyyalil Surekha. "Biotyping and Phage Typing of Salmonella enterica Serotype Typhi Isolates from Kerala, South India." In Prospects in Bioscience: Addressing the Issues, 405–10. India: Springer India, 2012. http://dx.doi.org/10.1007/978-81-322-0810-5_48.
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Syvänen, A. C., A. Sajantila, and M. Lukka. "Forensic DNA typing by the solid-phase minisequencing method." In DNA Fingerprinting: State of the Science, 275–82. Basel: Birkhäuser Basel, 1993. http://dx.doi.org/10.1007/978-3-0348-8583-6_25.
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Berger, Yvonne. "Typik Bildungsorientierungen: Milieuübergreifende Gemeinsamkeiten und Unterschiede der Phase Hochschule." In Biographische Orientierungen im Bildungsverlauf, 161–92. Wiesbaden: Springer Fachmedien Wiesbaden, 2020. http://dx.doi.org/10.1007/978-3-658-30433-1_6.
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Lima, C., H. V. Smith, R. A. B. Nichols, J. Greenman, and T. Paget. "Typing of Cryptosporidium Parvum Oocysts Using Phage-display Technology." In Cryptosporidium, 169–71. Elsevier, 2003. http://dx.doi.org/10.1016/b978-044451351-9/50022-7.
Full textConference papers on the topic "Phage typing"
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Rabsch, W., and H. Schmieger. "The biological base of Salmonella phage typing." In Fourth International Symposium on the Epidemiology and Control of Salmonella and Other Food Borne Pathogens in Pork. Iowa State University, Digital Press, 2001. http://dx.doi.org/10.31274/safepork-180809-1202.
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Gibson, K. J., Rita Prager, A. Liesegang, A. Fruth, Thomas G. Blaha, H. Tschäpe, and W. Rabsch. "Phage typing and clonal analysis of Salmonella Heidelberg strains isolated from animals and other sources from Minnesota (USA) and Germany." In Fourth International Symposium on the Epidemiology and Control of Salmonella and Other Food Borne Pathogens in Pork. Iowa State University, Digital Press, 2001. http://dx.doi.org/10.31274/safepork-180809-1137.
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Cadó Bessa, Marjo, Alessandra Sella, Jalusa Deon Kich, and Marisa Cardoso. "Characterization of porcine S. typhimurium strains isolated in the state of Rio Grande do Sul, Brazil, by phage typing, antimicrobial resistance profile, REP-PCR and ERIC-PCR." In Sixth International Symposium on the Epidemiology and Control of Foodborne Pathogens in Pork. Iowa State University, Digital Press, 2005. http://dx.doi.org/10.31274/safepork-180809-767.
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Hamon, G. "Two-Phase Flow Rock-Typing: Another Perspective." In SPE Annual Technical Conference and Exhibition. Society of Petroleum Engineers, 2003. http://dx.doi.org/10.2118/84035-ms.
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Ramli, Asari, Ayham Ashqar, and M. Azan Karim. "An Innovative Approach to Integrated Fluid Typing in Depleted Reservoirs." In International Petroleum Technology Conference. IPTC, 2021. http://dx.doi.org/10.2523/iptc-21215-ms.
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Abstract The economic value of completing a reservoir is strongly influenced by the fluid type. Wells drilled in developed brown field penetrate reservoirs with significant pressure loss due to offset production. A major challenge in evaluating mature reservoirs is the uncertainty introduced by pore fluids with unknown or varying petrophysical properties, such as change hydrocarbon gravity, diminishing pore pressures, and low to absent gas level indication. These are prone to error and uncertainty. Accurate understanding of reservoir fluid properties is therefore a key requirement for successful reservoir management. This manuscript illustrates a successful integrated workflow to ascertain. An integration between LWD triple combo data, near/far neutron, mud logs, pressure measurement, and production history of neighbouring wells, are critical to confirm fluid type within the drilled reservoirs. Cross plots, ratios and confidence analysis are required to ascertain the confidence level. Acquired data was ranked according to uncertainty associated with the acquisition technique, rate of penetration, lag time, mud type, and pre-test drawdown. Mobility was used as an indicator of fluid type or phase change in absence of any major rock type changes. Gas data were verified for any mud contamination and analysed using ratios to verify Hydrocarbon wetness. Data was ranked based on confidence factor determined through data precision and reservoir propertied. We also highlight the uncertainty in measurements. The fluid typing workflow used successfully identified the correct fluid typing, and reduced the reliance on single conventional method, or the need to run pre-test measurements. Data in intervals dominated with residual oil saturation showed misleading fluid type, same applies in high permeability sand, corrected gas data analysis gave a good indication of fluid type and mapped the change in fluid phase when combined with log data, while near/ far neutron aided to correlate the different sands, however due to its relationship with porosity, there is no one correlation could be derived. This paper illustrates that standard petrophysical techniques, such as analysis of density and neutron porosity logs, near/far neutrons, pretest can give misleading results if used in solo without consideration to the uncertainty associated with the measurement. The integration of fundamentally different data has resulted in identifying the fluid typing and its distribution in the reservoir and without integrating other measurements. A fluid typing systematic was developed to ensure the best and cost-effective model to assure the correct fluid type is identified. In this paper, a methodology is proposed which uses the geodesic transform, and integrate various source fundamentally different data, which is routinely acquired, then develop a systematic reasoning of confidence on data precision and accuracy. The system followed ensured the correct mapping of fluid typing in various reservoirs with different petrophysical properties. It is the first time such workflow is followed, and an integrated approach is consistently used in different sandstone reservoirs.
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Li, Jinqing, Xiaojun Chen, Dakui Wang, and Yuwei Li. "Enhancing Label Representations with Relational Inductive Bias Constraint for Fine-Grained Entity Typing." In Thirtieth International Joint Conference on Artificial Intelligence {IJCAI-21}. California: International Joint Conferences on Artificial Intelligence Organization, 2021. http://dx.doi.org/10.24963/ijcai.2021/529.
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Fine-Grained Entity Typing (FGET) is a task that aims at classifying an entity mention into a wide range of entity label types. Recent researches improve the task performance by imposing the label-relational inductive bias based on the hierarchy of labels or label co-occurrence graph. However, they usually overlook explicit interactions between instances and labels which may limit the capability of label representations. Therefore, we propose a novel method based on a two-phase graph network for the FGET task to enhance the label representations, via imposing the relational inductive biases of instance-to-label and label-to-label. In the phase 1, instance features will be introduced into label representations to make the label representations more representative. In the phase 2, interactions of labels will capture dependency relationships among them thus make label representations more smooth. During prediction, we introduce a pseudo-label generator for the construction of the two-phase graph. The input instances differ from batch to batch so that the label representations are dynamic. Experiments on three public datasets verify the effectiveness and stability of our proposed method and achieve state-of-the-art results on their testing sets.
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Al Subait, Ali, Kadhem Al-Nasser, Najm Alqahtani, and Ammar Agnia. "Enhanced Reservoir Characterization of Complex Carbonates by Integrating Diagenesis with Petrophysical Properties." In SPE Annual Technical Conference and Exhibition. SPE, 2022. http://dx.doi.org/10.2118/210457-ms.
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Abstract Carbonate reservoir characterization is often challenging due to variable mineralogy, pore-geometry, texture, and diagenetic processes that modified the rock fabric and its petrophysical properties affecting rock typing, reservoir-potential evaluation, and deliverability prediction. This work implements a multidisciplinary petrophysical discrimination scheme that draws upon the diagenetic history of the rock to resolve such characterization challenges and optimize field development practices. This study integrates sequence stratigraphy, core description, petrography, diagenetic analysis, mineralogy, routine core analysis (RCA), mercury injection capillary pressure (MICP) and wireline logs to define Diagenesis-Integrated Reservoir Rock Types (DI-RRT). The DI-RRT are established by delineating the continuous mineral phase, flow-dominant pore types, and main diagenetic processes. The data integration facilitated DI-RRT predictions, DI-RRT-constrained permeability and saturation-height modeling in all wells across the field. This rock typing scheme effectively classifies reservoir potential and delineates the contrast in the reservoir's flow and storage properties. Diagenesis, linked to lithological and pore attributes, serves as an effective discriminant for rocks of similar depositional and lithological settings but contrasting reservoir behavior. This is evident in reservoir intervals of high-energy depositional facies, which showed distinct petrophysical trends due to post-depositional modifications. Calcitic DI-RRT of mainly grain-dominated fabric and moldic porosity exhibits consistently low-to-modest potential that varied in response to the intensity of leaching, cementation and compaction. On the contrary, dolomitic DI-RRT manifest six distinctive behaviors distinguished by pore-type, texture, replacive dolomitization, dissolution and cementation. The reservoir quality is significantly enhanced where replacive dolomitization accompanied intensive dissolution, even with patchy anhydrite cementation. This scheme enabled the identification and mapping of these high-productivity zones in wells across the field. It further granted a good match between log- and core-based predictions of permeability and saturation. Integrating diagenesis with petrophysical rock types, wireline logs and field observations enhances reservoir characterization in complex carbonate reservoirs. It boosts current intellection of reservoir performance, identifies porosity-permeability and saturation trends with higher precision, and capitalizes on reservoir-quality zones during the field-development cycle. It further provides a roadmap to distribute petrophysical properties in uncored wells and 3D models optimizing subsequent static and dynamic models.
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Masalmeh, Shehadeh, Ali Al-Mesmari, S. Amir Farzaneh, and Mehran Sohrabi. "Trapped Gas Saturation Measurement in 2-phase and 3-phase Experiments to Support CCS and CO2 EOR Projects in Carbonate." In ADIPEC. SPE, 2022. http://dx.doi.org/10.2118/210878-ms.
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Abstract Trapped gas saturation (Sgt) is an important parameter for both CO2 storage (CCS) and Enhanced Oil Recovery (EOR) processes. Trapped gas saturation is affected by different parameters such as rock typing, wettability, saturation history, sequence of water and gas injection cycles, etc. This paper presents a comprehensive experimental study that aimed at measuring trapped gas saturation using carbonate rocks to provide measured data in support of CCS and EOR projects in carbonate reservoirs. The trapped gas experiments were performed using limestone reservoir cores taken from two different reservoirs, B and G. The experiments were performed under different injection strategies to investigate the impact of rock type, wettability and injection sequence. Moreover, the study compares trapped gas under 2-phase and 3-phase flow conditions. The study was performed using different gases, including methane and CO2 and also investigated the impact of the type of displacing fluid (water or oil) on trapped gas saturation. All experiments were performed using vertically oriented reservoir cores and both the gas and liquid phases were injected from the top of the core. A comprehensive data set has been produced in this study by performing both 2-phase and 3-phase coreflood experiments. The 3-phase experimental data showed that: 1- Trapped gas saturation is strongly dependent on the order of fluid injection sequence, Sgt is much higher during WAG experiments starting with water injection (WAG_W) compared to WAG experiments starting with gas injection (WAG_G), 2- A significant difference was measured between the trapped gas saturation in the core from reservoir G compared to the core from reservoir B, even though reservoir G has a higher permeability than reservoir B, 3- Trapped gas saturation measured using samples initialized at mobile water saturation (to mimic transition zone) increases as the initial water saturation increases and 4- Trapped gas saturation measured in WAG_G experiments starting at mobile water saturation is higher than that measured in WAG_G experiments starting at connate water, even though the initial gas saturation in the second experiments is much higher. The 2-phase experiments included both oil-gas and water-gas systems in order to investigate whether trapped gas was affected by the type of gas (methane or CO2) or by the displacing phase (water or oil). The results of the 2-phase experiments showed that: 1- Sgt is much higher in 2-phase compared to 3-phase experiments, 2- The water-gas experiments showed that trapped CO2 is higher than trapped methane at high Sgi with the trapped CO2 being as high as 50%, 3- Oil-gas experiments showed that trapped methane is higher than trapped CO2 and 4- Trapped CO2 by water is higher than trapped CO2 by oil, however, trapped CH4 was similar and independent of the displacing phase. The comprehensive dataset presented in this paper is rarely available in the literature and is vital for validating the predictions of gas injection and storage models available in commercial simulators. The results of this study demonstrated that Sgt obtained in 2-phase flow experiments is not applicable to 3-phase flow conditions. The study also shows that capillary trapped gas in CCS projects is much higher than trapped gas in CO2 EOR projects. Finally, CO2 WAG projects can be designed to optimize CO2 utilization factor when starting with gas injection or optimize CO2 sequestration when starting with water injection.
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Valavanides, Marios, Nikolaos Karadimitriou, and Holger Steeb. "Flow Dependent Relative Permeability Scaling for Steady-State Two-Phase Flow in Porous Media: Laboratory Validation on a Microfluidic Network." In 2022 SPWLA 63rd Annual Symposium. Society of Petrophysicists and Well Log Analysts, 2022. http://dx.doi.org/10.30632/spwla-2022-0054.
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Conventionally, the relative permeabilities of two immiscible fluid phases flowing in porous media are considered and expressed as functions of saturation. Yet, this has been put into challenge by theoretical, numerical and laboratory studies of flow in artificial pore network models and real porous media. These works have revealed a significant dependency of the relative permeabilities on the flow rates, especially when the flow regime is capillary to capillary-viscous dominated, and part of the disconnected non-wetting phase (NWP) remains mobile. These studies suggest that relative permeability models should include the functional dependence on flow intensities. However, revealing the explicit form of such dependence remains a persistent problem. Just recently, a general form of dependence was inferred, based on extensive simulations with the DeProF model for steady-state two-phase flows in pore networks. The simulations revealed a systematic dependence of the relative permeabilities on the local flow rate intensities. This dependence can be described analytically by a universal scaling functional form of the actual independent variables of the process, namely, the capillary number, Ca, and the flow rate ratio, r. The proposed scaling comprises a kernel function accounting for the transition between capillarity- and viscositydominated flow phenomena. In a follow-up systematic laboratory study SCAL measurements provided a preliminary proof-of-concept on the applicability of the model and validated its specificity. In the laboratory study presented here, we examine the applicability of the basic flow-rate dependent relative permeability scaling model in immiscible two-phase flows in an artificial two-dimensional microfluidic network, across different flow regimes. In particular, we assess the applicability of the flowdependent relative permeability scaling model in a microfluidic pore-network and we correlate the form of the associated kernel function with the interstitial structure of the flow across different flow regimes. The scope is to assess the applicability and/or universality of the aforementioned scaling function and to examine the forensic character of the kernel function, i.e. the potential for revealing the interstitial flow structure. The proposed scaling opens new possibilities in improving SCAL protocols and other important applications, e.g. characterization of systems and flow conditions, rock typing, assessment of end-effects during R/SCAL, as well as the development of more efficient field-scale simulators.
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Cossu, M., L. van Bon, M. Rossato, L. Beretta, and TRDJ Radstake. "AB0177 Increased levels of the inflammatory proteins CXCL10, CXCL11, TNFR2 and YLK-40 typify the earliest phase of systemic sclerosis (SSC)." In Annual European Congress of Rheumatology, 14–17 June, 2017. BMJ Publishing Group Ltd and European League Against Rheumatism, 2017. http://dx.doi.org/10.1136/annrheumdis-2017-eular.5295.
Full textReports on the topic "Phage typing"
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Wagner, John T., and Z. E. Schwarzbein. Enhanced Vehicle and Event Typing Software. Phase 1. Fort Belvoir, VA: Defense Technical Information Center, December 1993. http://dx.doi.org/10.21236/ada284862.
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Yogev, David, Ricardo Rosenbusch, Sharon Levisohn, and Eitan Rapoport. Molecular Pathogenesis of Mycoplasma bovis and Mycoplasma agalactiae and its Application in Diagnosis and Control. United States Department of Agriculture, April 2000. http://dx.doi.org/10.32747/2000.7573073.bard.
Full textAbstract:
Mycoplasma bovis and M. agalactiae are two phylogenetically related mycoplasmas which cause economically significant diseases in their respective bovine or small ruminant hosts. These organisms cause persistent asymptomatic infections that can result in severe outbreaks upon introduction of carrier animals into susceptible herds. Little is known about the mechanisms underlying mycoplasma-host interaction, variation in virulence, or of the factors enabling avoidance of the host immune system. In recent years it has become apparent that the ability of pathogenic microorganisms to rapidly alter surface antigenic structures and to fine tune their antigenicity, a phenomena called antigenic variation, is one of the most effective strategies used to escape immune destruction and to establish chronic infections. Our discovery of a novel genetic system, mediating antigenic variation in M. bovis (vsp) as well as in M. agalactiae (avg) served as a starting point for our proposal which included the following objectives: (i) Molecular and functional characterization of the variable surface lipoproteins (Vsp) system of M. bovis and comparison with the Vsp-counterpart in M. agalactiae (ii) Determination of the role of Vsp proteins in the survival of M. bovis when confronted by host defense factors, (iii) Assessment of Vsp-based genetic and antigenic typing of M. bovis and M. agalactiae for epidemiology of infection and (iv) Improvement of diagnostic tests for M. bovis and M. agalactiae based on the vsp-and vsp-analogous systems. We have carried out an extensive molecular characterization of the vsp system and unravelled the precise molecular mechanism responsible for the generation of surface antigenic variation in M. bovis. Our data clearly demonstrated that the two pathogenic mycoplasma species possess large gene families encoding variable lipoprotein antigens that apparently play an important role in immune evasion and in pathogen-host interaction during infection. Phase variable production of these antigens was found to be mediated by a novel molecular mechanism utilizing double site-specific DNA inversions via an intermediate vsp configuration. Studies in model systems indicate that phase variation of VspA is relevant in interaction between M. bovis and macrophages or monocytes, a crucial stage in pathogenesis. Using an ELISA test with captured VspA as an antigen, phase variation was shown to occur in vivo and under field conditions. Genomic rearrangements in the avg gene family of M. agalactiae were shown to occur in vivo and may well have a role in evasion of host defences and establishment of chronic infection. An epidemiological study indicated that patterns of vsp-related antigenic variation diverge rapidly in an M. bovis infected herd. Marked divergence was also found with avg-based genomic typing of M. agalactiae in chronically infected sheep. However, avg-genomic fingerprints were found to be relatively homogeneous in different animals during acute stages of an outbreak of Contagious Agalactiae, and differ between unrelated outbreaks. These data support the concept of vsp-based genomic typing but indicate the necessity for further refinement of the methodology. The molecular knowledge on these surface antigens and their encoding genes provides the basis for generating specific recombinant tools and serological methods for serodiagnosis and epidemiological purposes. Utilization of these methods in the field may allow differentiating acutely infected herds from chronic herds and disease-free herds. In addition the highly immunogenic nature of these lipoproteins may facilitate the design of protective vaccine against mycoplasma infections.