scholarly journals DETECTION AND SEQUENCING GENES IRON, IUTA, AND HLYF IN AVIAN PATHOGENIC ESCHERICIA COLI

2019 ◽  
pp. 229
Author(s):  
Nyoman Anandiya Ramaditya ◽  
I Nengah Kerta Besung ◽  
I Gusti Ngurah Kade Mahardika
Keyword(s):  
The Other ◽  
Marker Genes ◽  
Chain Reaction ◽  
Gene Markers ◽  
E Coli ◽  
The World ◽  
Pcr Method ◽  
Polymerase Chain ◽  
Escherichia Coli Bacteria ◽  
Pathogenic Gene

Research has been carried out to detect pathogenic gene markers of Avian Pathogenic Eschericia coli (APEC) iroN, iutA, and hlyF in Escherichia coli bacteria isolated from organs of sick chickens in Bali, and to determine phylogenetic relationships between those marker genes in Bali and in the other countries in the world. Six isolates of E. coli bacteria with codes E2, E3, E7, E8, E9, and E10 were used in this study. The isolates were isolated from domestic chicken in 2018. All genes were detected using the Polymerase Chain Reaction (PCR) method. The genes of iroN, iutA, and hlyF could be detected from all isolates. Well readable sequence of iroN, hlyF, and iutA was 659 bp, 518 bp, and 250 bp, respectively. All three genes were homogenous. Phylogical analysis shows that all pathogenic markers share same cluster with the pathogenic E. coli from all countries in the world.

scholarly journals Value of polymerase chain reaction in etiological diagnostic of infectiove endocarditis

2021 ◽  
Vol 42 (Supplement_1) ◽  
Author(s):  
E O Kotova ◽  
E A Domonova ◽  
A S Pisaryuk ◽  
O Y Silveystrova ◽  
Y L Karaulova ◽  
...  
Keyword(s):  
Polymerase Chain Reaction ◽  
Microbiological Method ◽  
Chain Reaction ◽  
E Coli ◽  
Enterococcus Spp ◽  
Acinetobacter Spp ◽  
Pcr Method ◽  
Polymerase Chain ◽  
Staphylococcus Spp ◽  
Culture Negative

Abstract Introduction Identification of a causative agent in patients with infective endocarditis (IE) is crucial for diagnostic and prescribing etiotropic therapy which defines positive outcome of a disease. High rate of a culture negative IE and inaccurate results of traditional microbiological methods raise a concern. So the methods of etiological diagnostics in IE are in need of development, particularly introduction of polymerase chain reaction (PCR) method might be helpful. Aim Modernisation of the algorithm of IE etiological diagnostic by introducing PCR Materials and methods The study included 85 cases of IE [first episode of IE (n=79), recurrence/relapse (n=6)] verified by DUKE criteria 2009, 2015, hospitalized in Moscow primary hospital from 2012 to 2017. All patient had venous blood investigated both with microbiological method and with broadrange and specific PCR. Following microorganisms' DNA were assessed by PCR: Staphylococcus spp. (MRCoNS, S. aureus and others), Streptococcus spp. (S. agalactiae, S. pyogenes and others), Enterococcus spp. (E. faecium, E. faecalis and others), Enterobacteriaceae, Klebsiella spp. (K. pneumoniae and others), E. coli, Proteus spp., A. baumanii, P. aeruginosa, Fungi (C. albicans, C. glabrata, Aspergillus spp. and others). Results Median age was 55.48 years (95% confidence interval (CI) 51.16–59.8), males 67.9%. History of cardiovascular diseases was in 54 (68.35%), diabetes mellitus in 18 (22.78%), hepatitis B and/or C in 31 (39.2%), intravenous drug dependency in 27 (34.18%), chronic kidney disease in 38 (48.1%), median Charlson comorbidity index was 5.44 (95% CI 4.52–6.37). Left-side IE was in 50 (63.29%), right-side IE – in 23 (29.12%), left-right-side IE in 6 (7.59%). Secondary IE was in 53 patients (62.3%). Embolic events were diagnosed in 27 cases (34.18%), in-hospital mortality – in 22 (27.8%). Microbiological method identified etiological agent in 55 of 85 cases (61.2%), featuring Staphylococcus aureus (n=23), Staphylococcus CoNS (n=6), Escherichia coli (n=1), Acinetobacter spp. (n=2), Streptococcus spp. (n=2), Enterococcus spp. (n=8), Klebsiella pneumoniae (n=2), Gemella haemolysans (n=2), several causative agents (n=6). Additional PCR testing identified etiology in 14 of 33 (42.2%) featuring Staphylococcus spp. (n=6), Enterococcus spp. (n=3), Streptococcus spp. (n=1), Aspergillus sp. (n=1) Pasteurella multocida (n=1), Enterococcus spp. + Staphylococcus spp. (n=1), Staphylococcus spp.+ A. baumanii + E. coli (n=1). PCR method identified 6 fals-positive results of microbilogical investigation [S. epidermidis (n=2), G. haemolysans, Acinetobacter spp., E. faecalis, K. pneumoniae], that are most probably due to preanalytical sample contamination Conclusions Introduction of PCR into the algorithm of IE etiological diagnostic increased validity of laboratory findings on 23.5%. True culture negative IE was present in 19 of 85 patients. Rate of mortality and complications in IE remains high. FUNDunding Acknowledgement Type of funding sources: Public Institution(s). Main funding source(s): Peoples' Friendship University of Russia (RUDN), Moscow, Russia

scholarly journals Molecular Detection of Plasmid-Mediated Quinolone Resistance in Ciprofloxacin-Resistant Escherichia coli from Urine of Patients attending Garki Hospital, Abuja, Nigeria

2020 ◽  
Vol 1 (4) ◽  
Author(s):  
Moses Oghenaigah Eghieye ◽  
Istifanus Haruna Nkene ◽  
Rejoice Helma Abimiku ◽  
Yakubu Boyi Ngwai ◽  
Ibrahim Yahaya ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Polymerase Chain Reaction ◽  
Urinary Tract ◽  
Molecular Detection ◽  
Quinolone Resistance ◽  
Chain Reaction ◽  
E Coli ◽  
Pcr Method ◽  
Polymerase Chain ◽  
Tract Infections

Urinary tract infections (UTIs) caused by Escherichia coli (E. coli) is common worldwide; and its successful treatment using antibiotics is limited by acquisition of resistance by the bacteria. This study investigated the occurrence of plasmid-mediated quinolone resistance (PMQR) genes in ciprofloxacin-resistant E. coli from urine of patients with suspected cases of UTIs attending Garki Hospital Abuja (GHA), Nigeria. A total of 8 confirmed ciprofloxacin-resistant E. coli was screened for carriage of PMQR genes using polymerase chain reaction (PCR) method. The occurrences of the PMQR genes detected were in the order: aac-(6′)-Ib-cr (87.5%) > qnrB (50.0%) > qnrS (37.5%) > oqxAB (12.5%) > qnrA(0.0%). qnrB and qnrS did not exist alone, but in combination with other genes; aac-(6′)-Ib-crexisted both alone and in combination with others; the most prevalent patterns of existence were aac-(6′)-Ib-cr alone and aac-(6′)-Ib-cr + qnrB + qnrS at 25.0% each. This study has shown that the ciprofloxacin-resistant E. coli harbored aac-(6′)-Ib-cr, qnrB, qnrS and oqxAB PMQR genes, with aac-(6′)-Ib-cr being the most prevalent. The genes were present either alone or in combination with one another. This has implication for the clinical application of fluoroquinolones to treat UTI in the study location and environs. 

Polymerase chain reaction and Q beta replicase amplification

1991 ◽  
Vol 37 (9) ◽  
pp. 1482-1485 ◽  
Author(s):  
P Cahill ◽  
K Foster ◽  
D E Mahan
Keyword(s):  
Polymerase Chain Reaction ◽  
Nucleic Acid ◽  
Mechanisms Of Action ◽  
The Other ◽  
Template Molecule ◽  
Chain Reaction ◽  
Signal Component ◽  
Pcr Method ◽  
Polymerase Chain ◽  
Target Sequences

Abstract The polymerase chain reaction (PCR) and Q beta replicase are two methods in which nucleic acid polymerases are used for amplification. Although these approaches share many similar problems concerning target contamination and probe specificity, they differ dramatically in their mechanisms of action and modes of application. The PCR method amplifies target sequences between two priming oligonucleotides and in essence amplifies a portion of the analyte. Q beta replicase, on the other hand, amplifies a specific template molecule hybridized to target sequences and therefore amplifies a signal component of the system. For this reason, Q beta replicase amplification has applications in areas other than for the detection of nucleic acid sequences. The requirements for application and the advantages of both PCR and Q beta replicase amplification are reviewed.

scholarly journals Antibiotic Resistance and Sewage-Associated Marker Genes in Untreated Sewage and a River Characterized During Baseflow and Stormflow

2021 ◽  
Vol 12 ◽  
Author(s):  
Warish Ahmed ◽  
Pradip Gyawali ◽  
Kerry A. Hamilton ◽  
Sayalee Joshi ◽  
David Aster ◽  
...  
Keyword(s):  
Polymerase Chain Reaction ◽  
Antibiotic Resistance ◽  
Water Samples ◽  
Quantitative Polymerase Chain Reaction ◽  
River System ◽  
Marker Genes ◽  
Chain Reaction ◽  
E Coli ◽  
Untreated Sewage ◽  
Polymerase Chain

Since sewage is a hotspot for antibiotic resistance genes (ARGs), the identification of ARGs in environmental waters impacted by sewage, and their correlation to fecal indicators, is necessary to implement management strategies. In this study, sewage treatment plant (STP) influent samples were collected and analyzed using quantitative polymerase chain reaction (qPCR) to investigate the abundance and correlations between sewage-associated markers (i.e., Bacteroides HF183, Lachnospiraceae Lachno3, crAssphage) and ARGs indicating resistance to nine antibiotics (belonging to aminoglycosides, beta-lactams, sulfonamides, macrolides, and tetracyclines). All ARGs, except blaVIM, and sewage-associated marker genes were always detected in untreated sewage, and ermF and sul1 were detected in the greatest abundances. intl1 was also highly abundant in untreated sewage samples. Significant correlations were identified between sewage-associated marker genes, ARGs and the intl1 in untreated sewage (τ = 0.488, p = 0.0125). Of the three sewage-associated marker genes, the BIO-ENV procedure identified that HF183 alone best maximized correlations to ARGs and intl1 (τ = 0.590). Additionally, grab samples were collected from peri-urban and urban sites along the Brisbane River system during base and stormflow conditions, and analyzed for Escherichia coli, ARGs, the intl1, and sewage-associated marker genes using quantitative polymerase chain reaction (qPCR). Significant correlations were identified between E. coli, ARGs, and intl1 (τ = 0.0893, p = 0.0032), as well as with sewage-associated marker genes in water samples from the Brisbane River system (τ = 0.3229, p = 0.0001). Of the sewage-associated marker genes and E. coli, the BIO-ENV procedure identified that crAssphage alone maximized correlations with ARGs and intl1 in river samples (τ = 0.4148). Significant differences in E. coli, ARGs, intl1, and sewage-associated marker genes, and by flow condition (i.e., base vs. storm), and site types (peri-urban vs. urban) combined were identified (R = 0.3668, p = 0.0001), where percent dissimilarities between the multi-factorial groups ranged between 20.8 and 11.2%. Results from this study suggest increased levels of certain ARGs and sewage-associated marker genes in stormflow river water samples compared to base flow conditions. E. coli, HF183 and crAssphage may serve as potential indicators of sewage-derived ARGs under stormflow conditions, and this merits further investigation. Data presented in this study will be valuable to water quality managers to understand the links between sewage pollution and ARGs in urban environments.

Description of a Novel Intimin Variant (Type ζ) in the Bovine O84:NM Verotoxin-Producing Escherichia coli Strain 537/89 and the Diagnostic Value of Intimin Typing

2003 ◽  
Vol 228 (4) ◽  
pp. 370-376 ◽  
Author(s):  
Joerg Jores ◽  
Karen Zehmke ◽  
Juergen Eichberg ◽  
Leonid Rumer ◽  
Lothar H. Wieler
Keyword(s):  
Escherichia Coli ◽  
Diagnostic Value ◽  
Coli Strain ◽  
Chain Reaction ◽  
E Coli ◽  
Pcr Method ◽  
Polymerase Chain ◽  
Enterocyte Effacement ◽  
Phylogenetic Lineages ◽  
Adhesion Factor

Infections with verotoxin-producing Escherichia coli (VTEC) has resulted in increasing numbers of human illnesses annually. These illnesses usually result from the ability of VTEC to cause the attaching and effacing lesions (AE lesion). The AE phenotype is encoded by the locus of enterocyte effacement (LEE) pathogenicity island. A key adhesion factor involved is the outer membrane protein intimin, encoded by the eae gene within the LEE. Intimin types α, β, γ, δ, and ε have been described previously. Each intimin represents distinct phylogenetic lineages of LEE-positive strains. A new intimin type ζ was identified in a VTEC strain of the serotype O84:NM (nonmotile) that was isolated from a calf with diarrhea. ζ intimin showed the highest similarity (88%) of its amino acid sequence to the α intimin. For diagnostic purposes, we established a polymerase chain reaction (PCR) method for diagnosis of the key virulence traits of VTEC (i.e., verotoxins and intimins). This method also distinguishes between the toxins (VT1 and VT2) and the six intimin types. By applying the PCR method, intimin ζ in strains of other VTEC serotypes O84:H2, O92:NM, O119:H25, and O150:NM was identified. Because the intimin types represent distinctive phylogenetic E. coli lineages, application of the intimin subtyping PCR offers significant benefits. These include improving diagnosis of VTEC infection and increasing the understanding of evolution of attaching and effacing VTEC and other LEE-positive bacteria.

scholarly journals Toward an International Standard for PCR-Based Detection of Foodborne Escherichia coli O157: Validation of the PCR-Based Method in a Multicenter Interlaboratory Trial

2004 ◽  
Vol 87 (4) ◽  
pp. 856-860 ◽  
Author(s):  
Amir Abdulmawjood ◽  
Michael Bülte ◽  
Stefanie Roth ◽  
Hahn Schönenbrücher ◽  
Nigel Cook ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Escherichia Coli O157 ◽  
Diagnostic Specificity ◽  
Chain Reaction ◽  
E Coli ◽  
Colony Forming Units ◽  
Interlaboratory Trial ◽  
Pure Cultures ◽  
Pcr Method ◽  
Polymerase Chain

Abstract The performance of a polymerase chain reaction (PCR) method for detection of Escherichia coli O157, previously validated on DNA extracted from pure cultures, was evaluated on spiked cattle swabs through an interlaboratory trial, including 12 participating laboratories from 11 European countries. Twelve cattle swab samples, spiked at 4 levels (0, 1–10, 10–100, and 100–1000 colony-forming units, in triplicate) with E. coli O157 were prepared centrally in the originating laboratory; the receiving laboratories performed pre-PCR treatment followed by PCR. The results were reported as positive when the correct amplicons were present after gel electrophoresis. The statistical analysis, performed on 10 sets of reported results, determined the diagnostic sensitivity to be 92.2%. The diagnostic specificity was 100%. The accordance (repeatability) was 90.0%, calculated from all positive inoculation levels. The concordance (reproducibility) was 85.0%, calculated from all positive inoculation levels. The concordance odds ratio (degree of interlaboratory variation calculated from all positive inoculation levels) was 1.58, indicating the robustness of the PCR method. Thus, the interlaboratory variation due to personnel, reagents, minor temperature or pH fluctuations and, not least, thermal cyclers, did not affect the performance of the method, which is currently being considered as part of an international PCR standard.

scholarly journals Some traits of Verotoxin-producing strains of Escherichia coli isolated from cattle

2010 ◽  
Vol 64 (5-6) ◽  
pp. 339-348
Author(s):  
Srdjan Lazic ◽  
Novica Stajkovic ◽  
Bane Dimic ◽  
Zorica Lepsanovic ◽  
Milena Krstic ◽  
...  
Keyword(s):  
Intestinal Tract ◽  
Domestic Animals ◽  
Polymerase Chain Reaction Method ◽  
Geographic Region ◽  
Phenotypic Traits ◽  
Chain Reaction ◽  
E Coli ◽  
Esherichia Coli ◽  
The World ◽  
Polymerase Chain

Verotoxin-producing Esherichia coli (VTEC) is one of six pathogenicity groups of Eschericha coli. The reservoir for VTEC is the intestinal tract of domestic animals, primarily ruminants. Investigations in our geographic region have also demonstrated that domestic animals are a significant VTEC reservoir. In spite of this, sporadic diseases in humans caused by these agents are rare, and no epidemics have been registered so far. The question is, therefore, what percentage of VTEC isolated in our region have the characteristics of enterohaemorrhagic E. coli (EHEC) which cause intestinal diseases in humans. The aim of this study was to test the isolated bovine strains for some phenotypic and genotypic traits and to determine the percent of strains that belong to EHEC. A total of 105 VTEC strains isolated from cattle were tested for the presence of verotoxin (vtx) genes by PCR (polymerase chain reaction) method. All of them possessed one or more vtx genes. In accordance with our investigations, only four (3.8%) strains, of a total of 105 VTEC strains belong to groups of EHEC. It may be concluded that the majority of strains isolated from cattle in this part of the world do not have phenotypic traits typical for EHEC. Therefore human VTEC associated diseases in Serbia are rare, despite the fact that domestic animals frequently harbor VTEC.

scholarly journals Detection of E. coli O157:H7 in Meat Using Polymerase Chain Reaction Method and Culture Method

2019 ◽  
Vol 4 (3) ◽  
pp. 102-107
Author(s):  
Mozhgan Bahadoripour ◽  
Mohammad hassan Jahandar
Keyword(s):  
Polymerase Chain Reaction ◽  
Meat Products ◽  
Culture Method ◽  
Polymerase Chain Reaction Method ◽  
World Health ◽  
Microbial Culture ◽  
Chain Reaction ◽  
E Coli ◽  
The World ◽  
Polymerase Chain

Introduction: Escherichia coli O157:H7, as a pathogenic agent, can be transmitted through the foods including meat, meat products, dairy products, vegetables and water. The World Health Organization has recommended that all countries in the world, especially developing countries, should consider the investigation of E. coli O157:H7 as a research priority. The aim of this study was to determine the frequency of E. coli O157:H7 in meat of cow, sheep, goat, and camel in Kerman province of Iran using culture and polymerase chain reaction (PCR) methods. Methods: In this study, 280 meat samples consisting of sheep (90 specimens), cow (80 specimens), goat (60 specimens) and camel (50 specimens) meats were randomly separated from carcasses from April to July 2018. After the sampling, microbial culture was performed on the samples. Then, suspected E. coli O157:H7 colonies were evaluated by PCR assay. Results: Out of the 280 samples, 73 samples (26%) were contaminated with E. coli. based on bacteriological tests, and 28 samples were identified as suspected E. coli O157:H7 serotype based on the lack of sorbitol fermentation. Subsequently, sorbitol-negative samples were tested by PCR procedure using specific primers. The results revealed that out of 28 cases, 21 cases (7.5%) were E. coli O157:H7. Conclusion: As can be deduced from the observations of this study, to detect the E. coli O157, PCR as an accurate, fast, and reliable procedure can be used along with the culture method.

scholarly journals EFFECTIVENESS OF MENIRAN (PHYLLANTHUS NIRURI LINN) AS ANTIBACTERIAL FOR RESISTANCE ANTIBIOTICS PREVENTION OF ENTEROTOXIN ESCHERICHIA COLI

2018 ◽  
Vol 7 (2) ◽  
pp. 35
Author(s):  
Sri Hidanah ◽  
Emy Koestanti Sabdoningrum ◽  
Retno Sri Wahyuni ◽  
Arini Rahmi Dewi ◽  
Erma - Safitri
Keyword(s):  
Escherichia Coli ◽  
The Body ◽  
Control Group ◽  
Anova Analysis ◽  
Chain Reaction ◽  
Isolation And Identification ◽  
Phyllanthus Niruri ◽  
E Coli ◽  
Pcr Method ◽  
Polymerase Chain

ABSTRACT               Escherichia coli (E. coli) can be isolated from the environment both inside and outside the hospes body. There were 89 serotypes in which 21% showed resistance to various antibiotics, such as E. coli enterotoxin. Alternative efforts were needed as a substitute for antibiotics, one of them through the use of medicinal plants, such as meniran (Phyllanthus niruri Linn).  Meniran plant is an immunomodulator that serves to repair the immune system of the body. The research was done through several stages: isolation and identification of  E. coli enterotoxin from several broiler farms in East Java using the polymerase chain reaction (PCR) method, E. coli resistance test against some antibiotics, making meniran extract and activation test against E. coli enterotoxin The study was divided into five treatments: T0+ (group of chickens were infected by E. coli enterotoxin), T0- (control group, not infected), T1 (infected by E. coli enterotoksin + 20% meniran extract), T2 (infected by E. coli enterotoksin + 25% extract meniran), T3 (infected by E. coli enterotoxin + 30% extract meniran). Data were analyzed by ANOVA (Analysis of Variance). The results were showed that all of  E. coli DNA isolates which tested by the PCR method was showed positive reactions at 600 bp. In the next stage, that E. coli enterotoxin are resistance to some antibiotics, such as Amoxicillin, Amphicillin, Erythromycin, Cephalosporins, Tetracycline, Cloxacillin and Gentamicin. Furthermore, 30% Phyllanthus niruri linn extract  effective as an antibacterial for the prevention of antibiotic resistance from E. coli enterotoxin. 

scholarly journals Development of a Genoserotyping Method for Salmonella Infantis Detection on the Basis of Pangenome Analysis

2020 ◽  
Vol 9 (1) ◽  
pp. 67
Author(s):  
Seung-Min Yang ◽  
Jiwon Baek ◽  
Eiseul Kim ◽  
Hyeon-Be Kim ◽  
Seyoung Ko ◽  
...  
Keyword(s):  
Public Health ◽  
Polymerase Chain Reaction ◽  
Bacterial Species ◽  
Cost Effective ◽  
The Other ◽  
Gene Marker ◽  
Diagnostic Assay ◽  
Chain Reaction ◽  
Polymerase Chain ◽  
Substantial Economic Burden

In recent years, Salmonella Infantis has become a predominant serovariant in clinical and poultry isolates, thereby imposing a substantial economic burden on both public health and the livestock industry. With the aim of coping with the steep increase in serovar Infantis prevalence, a polymerase chain reaction (PCR)-based rapid and accurate diagnostic assay was developed in this study through pangenome profiling of 60 Salmonella serovars. A gene marker, SIN_02055, was identified, which is present in the S. Infantis genome but not in the pangenome of the other serovars. Primers specific to SIN_02055 were used to accurately detect serovar Infantis, and to successfully differentiate Infantis from the other 59 serovars in real-time PCR with a R2 of 0.999 and an efficiency of 95.76%. The developed method was applied to 54 Salmonella strains belonging to eight dominant serovars, and distinguished Infantis from the other seven serovars with an accuracy of 100%. The diagnostic primer set also did not show false positive amplification with 32 strains from eight non-Salmonella bacterial species. This cost-effective and rapid method can be considered an alternative to the classic serotyping using antisera.

Sign in / Sign up

Export Citation Format

Share Document