Phylogeny of Vibrio cholerae Isolates from Patients with Cholera Disease in Babylon Province

2019 ◽  
Vol 10 (04) ◽  
pp. 701-707
Author(s):  
Ilham Abbas Bunyan ◽  
Hussein T. Abdulabbas ◽  
Lamees A. Abdul-Lateef
Keyword(s):  
Vibrio Cholerae ◽  
High Rate ◽  
Clinical Samples ◽  
Chain Reaction ◽  
Biochemical Tests ◽  
Diagnostic Kits ◽  
Stool Samples ◽  
Polymerase Chain ◽  
El Tor ◽  
Issr Pcr

In the present study, a total of 35 stool samples were collected in the Central Health Laboratory of Babylon Province from patients presenting invasive cholera disease. The period of collection was from November 2017 to December 2018. Identification of Vibrio cholerae species was carried out by conventional methods, biochemical tests, diagnostic kits and then confirmed by PCR-based assay targeting the ompW gene. The results of this study reported that O1 serogroups were the predominant serogroup among all clinical samples with a high rate of 94.3% (N = 33), while only two isolates of non-O1/non-O139 (NAG) (5.7%) were documented as a causative agent to cholera or cholera-like disease. The phylogenetic relationship among all 35 studied strains elucidated by using polymerase chain reaction (PCR)-based fingerprinting assay (ISSR-PCR). The results of this assay showed grouping of Inaba strains into different clusters indicating that these strains were genetically diverse. Furthermore, V. cholerae El Tor O1 Ogawa strain (OG1) was closely related to strains of Inaba serotype. In contrast, NAG strains (NAG1 and NAG2) were not genetically similar to any of Inaba or Ogawa strains indicating different clone origin.

scholarly journals Detection of SARS-CoV2 in Clinical Samples: Target-specific Analysis of Qualitative Reverse Transcription–Polymerase Chain Reaction(RT-PCR) Diagnostic Kits

IJID Regions ◽  
2021 ◽  
Author(s):  
Ambica Rangaiah ◽  
Sathyanarayan Muthur Shankar ◽  
Shantala Gowdara Basawarajappa ◽  
Pritik A Shah ◽  
Aditya Chandrashekar ◽  
...  
Keyword(s):  
Polymerase Chain Reaction ◽  
Reverse Transcription ◽  
Clinical Samples ◽  
Rt Pcr ◽  
Chain Reaction ◽  
Diagnostic Kits ◽  
Specific Analysis ◽  
Polymerase Chain

scholarly journals Influence of Some Physicochemical Stresses on the Survival of Vibrio cholerae O1 at Non-Culturable State

1970 ◽  
Vol 24 (2) ◽  
pp. 133-136 ◽  
Author(s):  
M Mahfuzul Haque ◽  
Sirajul Islam Khan ◽  
Chowdhury Rafiqul Ahsan
Keyword(s):  
Polymerase Chain Reaction ◽  
Vibrio Cholerae ◽  
Toxin Gene ◽  
Chain Reaction ◽  
Pcr Assay ◽  
Nonculturable State ◽  
Vibrio Cholerae O1 ◽  
Polymerase Chain ◽  
Specific Fragment ◽  
El Tor

Survival study of toxigenic Vibrio cholerae O1 Classical Inaba and El Tor Ogawa biotypes was carried out in artificial microcosm without any nutrients under stressed physiochemical conditions. The organisms were found to undergo viable but non-culturable (VBNC) state, which was detected by polymerase chain reaction (PCR) technique using primers that flank a specific fragment of the cholera toxin gene (ctx). The findings of the study showed that about 89% of samples gave positive result although the organisms were in nonculturable state. Depending upon the conditions the Classical biotype of vibrios had undergone non-culturable state within 2-15 days and 55-92 days were subjected to PCR assay after 45 and 120 days of incubation respectively. A similar tend was also observed in case of El Tor biotype. With non-culturable cell only 5 of 18 microcosms (of both Classical and El Tor biotypes) at pH 4.5 showed no viability. Since the PCR assay demonstrated positive results after 90 (in case of El Tor biotype) and 120 days (in case of Classical biotype), the total survival time thus ranges over 3 and 4 months. Thus PCR has an important advantage over the techniques those are used in routine laboratories for the identification of pathogenic organisms. Keywords: Physicochemical stresses, Survivality, Vibrio cholerae, Artificial microcosms, Polymerase chain reaction (PCR), Non-culturable state, Viable but non-culturable (VBNC)DOI: http://dx.doi.org/10.3329/bjm.v24i2.1258 Bangladesh J Microbiol, Volume 24, Number 2, December 2007, pp 133-136

scholarly journals Conventional and molecular detection of vibrio cholerae isolated from environmental water with the prevalence of antibiotic resistance mechanisms.

2019 ◽  
Vol 10 (3) ◽  
Author(s):  
Suad A Al-Hilu ◽  
Ali M Al-Mohana ◽  
Zainab Jaber
Keyword(s):  
Polymerase Chain Reaction ◽  
Vibrio Cholerae ◽  
Molecular Detection ◽  
Public Health Problem ◽  
Environmental Water ◽  
Selective Medium ◽  
Chain Reaction ◽  
Biochemical Tests ◽  
Vibrio Cholera ◽  
Polymerase Chain

Environmental water is an important source for Vibrio cholerae, which is autochthonous to the aquatic environment, monitoring this bacterium in water is important for control of cholera. Vibrio cholerae represents an enormous public health problem around the world, especially in developing countries. One hundred samples were collected and selected. The samples were filtered and transferred to slants containing 2ml of alkaline peptone water, then subcultured on selective medium Thiosulphate Citrate Bile Salt Sucrose agar. All presumptive isolates were confirmed by using a series of biochemical tests including Oxidase test, Simmon Citrate test, DNase test, Indole test, Klingler Iron Agar (KIA) test, MacConkey agar test and motility. Confirmed Vibrio cholera strains were then screening for slide agglutination test by using commercially antisera polyvalent and monovalent O1 and O139 for determining strain serotype. The DNA extracted from pure culture and Polymerase Chain Reaction assay was used for molecular detection of Vibrio cholerae, a specific primer which designed according to ctxA gene sequences. This primer was detection and amplifying 241 base pairs of the ctxA gene. The resistance to antibiotics by Vibrio cholerae was determining by using thirteen standardized disc diffusion including Amikacin, Ceftriaxone, Ceftazidime, Gentamycin, Tetracycline, Streptomycin, Tobramycin, Cephotaxime, Nalidixic Acid, Norfloxacin, Cephalothin, Rifampicin, Cefixime. From one hundred water samples were detected, fifty-six samples were motile and positive for biochemical tests. Fifteen isolates confirmed as Vibrio cholera by Polymerase Chain Reaction (PCR) assay with primers de­signed for ctxA and 241bp band was observed. These fifteen isolates showed agglutination with polyvalent and monovalent O1 antisera, and two strains represented Ogawa from other strains that showed Inaba. The fifteen isolates exhibited an identical response to each antibiotic examined. They showed sensitive to all antibiotics except Amikacin, Streptomycin, Cefixime, Norfloxacin, Cephalothin. the aim of this study was determined the accurate method for detection of Vibrio cholerae in environmental water. In the current study, we found that the molecular method using Polymerase Chain Reaction performance using the ctxA gene-specific primers for detection of Vibrio cholerae was faster and accurate and specific.

scholarly journals Detection of Mixed Populations ofClostridium difficilefrom Symptomatic Patients Using Capillary-Based Polymerase Chain Reaction Ribotyping

2013 ◽  
Vol 34 (9) ◽  
pp. 961-966 ◽  
Author(s):  
Adam A. Behroozian ◽  
Jeffrey P. Chludzinski ◽  
Eugene S. Lo ◽  
Sarah A. Ewing ◽  
Sheila Waslawski ◽  
...  
Keyword(s):  
Polymerase Chain Reaction ◽  
Stool Sample ◽  
Diagnostic Testing ◽  
High Rate ◽  
Simultaneous Occurrence ◽  
Chain Reaction ◽  
Pcr Ribotyping ◽  
Sample Range ◽  
Stool Samples ◽  
Polymerase Chain

Objective.To investigate the simultaneous occurrence of more than 1Clostridium difficileribotype in patients' stool samples at the time of diagnostic testing.Methods.Stool samples submitted for diagnostic testing for the presence of toxigenicC. difficilewere obtained for 102 unique patients. A total of 95 single colonies ofC. difficileper stool sample were isolated on selective media, subcultured alongside negative (uninoculated) controls, and polymerase chain reaction (PCR) ribotyped using capillary gel electrophoresis.Results.Capillary-based PCR ribotyping was successful for 9,335C. difficileisolates, yielding a median of 93 characterized isolates per stool sample (range, 69-95). More than 1 C.difficileribotype was present in 16 of 102 (16%)C. difficileinfection (CDI) cases; 2 of the 16 mixtures were composed of at least 3 ribotypes, while the remaining 14 were composed of at least 2.Conclusions.Deep sampling of patient stool samples coupled with capillary-based PCR ribotyping identified a high rate of mixed CDI cases compared with previous estimates. Studies seeking to quantify the clinical significance of particular C.difficileribotypes should account for mixed cases of disease.

scholarly journals Bacteriological and molecular study of Pseudomonas aeruginosa strains isolated from different clinical cases in Erbil and Kurkuk

2018 ◽  
Vol 41 (2) ◽  
pp. 124-130
Author(s):  
Asif Hasan Abdul Razzaq
Keyword(s):  
Molecular Weight ◽  
Polymerase Chain Reaction ◽  
Virulence Genes ◽  
Antibiotic Sensitivity ◽  
Molecular Study ◽  
Clinical Samples ◽  
Chain Reaction ◽  
Biochemical Tests ◽  
Antibiotic Sensitivity Test ◽  
Polymerase Chain

     This study included isolates of bacteria from 125 clinical samples in Erbil and Kirkuk Hospital including (burns, wounds, urine and sputum); 38 isolates were identified as P. aeruginosa after conducting microscopic and biochemical tests. The results of antibiotic sensitivity test showed that all isolates of P. aeruginosa  were different in resistance to Pipracillin, Erythromycin with rate of (100%) and to the Nalidixic acid (94.73%) while the lowest resistant antibiotics were to Co-trimoxazole, Ceftazidime and Ciprofloxacin, which amounted to (26.31%, 23.68 and 21.05%) respectively. For molecular diagnosis of P. aeruginosa some virulence genes the alg D and exo A were amplified through Polymerase Chain Reaction technique. The results showed that in 38 isolates cases only 22 (57.9%) were positive for algD gene by amplification of 520 bp band. While in urinary tract infection; 6 samples (60%) had alg D gene, and 8 (57.14%) isolates had alg D gene in wounds samples; also 7(70%) isolates from burns had that gene, while the sputum samples showed only one with alg D gene which was the lowest ratio; but in amplification of exo A, the results showed the presence of only one isolate from burns with molecular weight 396 bp with no appearance in others. 

scholarly journals Polymerase Chain Reaction: An Innovative Tool in Periodontal Diagnosis

2013 ◽  
Vol 4 (1) ◽  
pp. 60-66
Author(s):  
Suvarna H Patil ◽  
Kishore G Bhat ◽  
Paresh S Lotlekar ◽  
Laxmi V Hombal
Keyword(s):  
Polymerase Chain Reaction ◽  
Bacterial Species ◽  
Antibiotic Sensitivity ◽  
Periodontal Pathogen ◽  
Current Status ◽  
Clinical Samples ◽  
Chain Reaction ◽  
Biochemical Tests ◽  
Innovative Tool ◽  
Polymerase Chain

ABSTRACT Bacterial species colonizing the surfaces of the human oral cavity play an important role in oral health and disease and thus an accurate means of identification is crucial. Traditionally, identification has been based on microscopy, biochemical tests, immunofluorescence staining and antibiotic sensitivity. However, these tests are labor-intensive and costly, providing sometimes inconsistent results that make identification rather tentative. Recently, molecular DNA-based techniques have been used to identify bacteria directly from clinical samples. Development of a microbiological diagnostic kit using this technology therefore requires the ability to extract the bacterial DNA from the plaque sample and amplify the specific DNA sequence of the target periodontal pathogen. Polymerase chain reaction has emerged as the most powerful tool for the amplification of the genes and their RNA transcripts. The focus of this review is to describe the current status of the DNA-based method PCR which has become a standard diagnostic and research tool in dentistry. How to cite this article Patil SH, Bhat KG, Lotlekar PS, Hombal LV. Polymerase Chain Reaction: An Innovative Tool in Periodontal Diagnosis. World J Dent 2013;4(1):60-66.

Using a Polymerase Chain Reaction as a Complementary Test to Improve the Detection of Dermatophyte Fungus in Nails

2014 ◽  
Vol 104 (3) ◽  
pp. 233-237 ◽  
Author(s):  
María José Iglesias Sánchez ◽  
Ana María Pérez Pico ◽  
Félix Marcos Tejedor ◽  
María Jesús Iglesias Sánchez ◽  
Raquel Mayordomo Acevedo
Keyword(s):  
Polymerase Chain Reaction ◽  
Dna Sequences ◽  
Classical Method ◽  
Clinical Manifestations ◽  
Culture Method ◽  
Clinical Samples ◽  
Chain Reaction ◽  
Nested Polymerase Chain Reaction ◽  
Traditional Procedure ◽  
Polymerase Chain

Background Dermatomycoses are a group of pathologic abnormalities frequently seen in clinical practice, and their prevalence has increased in recent decades. Diagnostic confirmation of mycotic infection in nails is essential because there are several pathologic conditions with similar clinical manifestations. The classical method for confirming the presence of fungus in nail is microbiological culture and the identification of morphological structures by microscopy. Methods We devised a nested polymerase chain reaction (PCR) that amplifies specific DNA sequences of dermatophyte fungus that is notably faster than the 3 to 4 weeks that the traditional procedure takes. We compared this new technique and the conventional plate culture method in 225 nail samples. The results were subjected to statistical analysis. Results We found concordance in 78.2% of the samples analyzed by the two methods and increased sensitivity when simultaneously using the two methods to analyze clinical samples. Now we can confirm the presence of dermatophyte fungus in most of the positive samples in just 24 hours, and we have to wait for the result of culture only in negative PCR cases. Conclusions Although this PCR cannot, at present, substitute for the traditional culture method in the detection of dermatophyte infection of the nails, it can be used as a complementary technique because its main advantage lies in the significant reduction of time used for diagnosis, in addition to higher sensitivity.

scholarly journals Seasonal Differences in Cyclospora cayetanensis Prevalence in Colombian Indigenous People

2021 ◽  
Vol 9 (3) ◽  
pp. 627
Author(s):  
Hagen Frickmann ◽  
Juliane Alker ◽  
Jessica Hansen ◽  
Juan Carlos Dib ◽  
Andrés Aristizabal ◽  
...  
Keyword(s):  
Indigenous People ◽  
Rainy Season ◽  
Gastrointestinal Symptoms ◽  
Dry Season ◽  
Seasonal Effects ◽  
Chain Reaction ◽  
Resource Limited Settings ◽  
Resource Limited ◽  
Stool Samples ◽  
Polymerase Chain

Fecal-orally transmitted cyclosporiasis is frequent in remote resource-limited settings in Central and South America with poor hygiene conditions. In this study, we aimed at assessing seasonal effects on the epidemiology of colonization or infection with C. cayetanensis in Colombian indigenous people living under very restricted conditions. In the rainy season between July and November and in the dry season between January and April, stool samples from indigenous people with and without gastrointestinal symptoms were collected and screened for C. cayetanensis applying in-house real-time polymerase chain reaction (PCR). In the rainy season and in the dry season, positive PCR results were observed for 11.8% (16/136) and 5.1% (15/292), respectively, with cycle threshold (Ct) values of 30.6 (±3.4) and 34.4 (±1.6), respectively. Despite higher parasite loads in the rainy season, fewer individuals (2/16, 12.5%) reported gastrointestinal symptoms compared to the dry season (6/15, 40%). In conclusion, considerable prevalence of C. cayetanensis in Colombian indigenous people persists in the dry season. Low proportions of gastrointestinal symptoms along with higher parasite loads make colonization likely rather than infection.

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