scholarly journals Antibacterial Effects of Octenidine Dihydrochloride, and Benzalkanium Chloride on Acinetobacter Baumannii Strains Isolated from Clinical Samples and Determination of Genetic Diversity of Isolates by RAPD-PCR Method

2021 ◽  
Author(s):  
Azar Dokht Khosravi ◽  
Effat Abasi Montazeri ◽  
Seyedeh Roya Maki
Keyword(s):  
Genetic Diversity ◽  
Acinetobacter Baumannii ◽  
Clinical Samples ◽  
Biochemical Tests ◽  
Typing Method ◽  
Conventional Culture ◽  
Rapd Pcr ◽  
Octenidine Dihydrochloride ◽  
Pcr Method

Abstract Due to the emergence of antibiotic resistance in Acinetobacter baumannii which is one of the important causes of nosocomial infections, many problems have been raised in the successful treatment of patients with the subsequent mortality. So, the present study was performed to evaluate the antibacterial effect of Actinidine dehydrochloride, Actinisept, and Benzalkanium chloride against Acinetobacter baumannii strains isolated from clinical samples and to determine the genetic diversity of strains by RAPD-PCR. A total of 119 non-duplicate, suspected Acinetobacter baumannii isolates were collected and confirmed by conventional culture and biochemical tests and PCR technique. Susceptibility of the isolates to antibiotics was evaluated by standard Antibiotic susceptibility testing (AST). For antiseptics Octenidine dihydrochloride (OCT), Actinisept, and Benzalkonium chloride (BZK), Minimal inhibitory concentration (MIC) was assessed. The prevalence of Qac E and Qac delta E genes related to antiseptics was estimated by PCR. Finally, genetic diversity of strains was determined by RAPD-PCR. All 119 suspected isolates were confirmed as Acinetobacter baumannii using conventional tests and PCR. The isolates were mostly originated from blood samples. In AST, the lowest resistance was seen for ciprofloxacin and gentamicin. The MIC values were reported as OCT (15.26 µg) and BZK (640 µg). The antiseptic genes of qacE and qac ΔE1 were found to be present in 56 (47.05%) and 59 (49.57%) of isolates respectively. RAPD typing method revealed great diversity among A. baumannii isolates, with 37 clusters in isolates from ICU, of which 32 isolates were single and 5 were multiple. In conclusion, considering the increase of resistance to antiseptics, it is of importance to monitor the susceptibility of A. baumannii to antiseptics and to promote antiseptic stewardship in hospitals. Furthermore, in this study great diversity among A. baumannii was observed making it difficult to properly carry out infection control policies. analysis of RAPD-PCR typing results, and we found 37 clusters, among them 32 isolates were single and 5 were multiple. So, the method generated 37 RAPD type which shows great diversity among 57 out of 62 A. baumannii isolates at 80% cutoff.

scholarly journals Determination of Genetic Diversity of Four Guppy Strains Using the Random Amplified Polymorphic DNA-PCR

2021 ◽  
pp. 1-8
Author(s):  
Riva Hafidah ◽  
Ayi Yustiati ◽  
Yuniar Mulyani ◽  
Ibnu Bangkit Bioshina Suryadi
Keyword(s):  
Genetic Diversity ◽  
Random Amplified Polymorphic Dna ◽  
Descriptive Analysis ◽  
Similarity Index ◽  
Quantitative Descriptive Analysis ◽  
Rapd Pcr ◽  
Result Show ◽  
Pcr Method ◽  
Quantitative Descriptive

This research aims to determine genetic diversity of four strains guppy, respectively are japan blue double sword (JBD), japan blue tiger double sword (JBTD), blue moscow (BM), and panda guppy (PG) with RAPD-PCR method. The obtained genetic diversity data is used as guide reference for hybridization between four strains. The research was conducted in September 2020 to April 2021 with explorative methods and in qualitative and quantitative descriptive analysis. The research was carried out in biotechnology Laboratory, Fishery and Marine Sciences Faculty and Central Laboratory,Padjadjaran University, Indonesia.Strains of JBD, JBTD, BM obtained fromCilengkrangSubdistrict, Bandung and PG strain obtained from Parung market, Bogor. Primary OPA-03 (AGTCAGCCAC) is used for standard parameters to interpret genetic diversity among four strains of guppy. Based on results, amplification with OPA-03 primary visualize 25 bands that include five polymorphic bands and 20 monomorphic bands. The phylogenetic tree result show that there are two relationship groups. The first group are JBD, JBTD, and BM with similarity index in the range of 80-89%The first group consist two sub groups of relationship. The first sub group are JBD and JBTD with similarity index of 89%. The second sub group is BM with similarity index of 80%. The second group isPG with similarity index of 65.5%.

scholarly journals Genotyping of fusA Gene from Clinical Isolates Acinetobacter baumannii in Baghdad

2018 ◽  
Vol 15 (1) ◽  
pp. 37-42
Author(s):  
Baghdad Science Journal
Keyword(s):  
Phylogenetic Tree ◽  
Acinetobacter Baumannii ◽  
Laboratory Diagnosis ◽  
Clinical Isolates ◽  
Clinical Samples ◽  
Bacterial Isolates ◽  
Coding Region ◽  
Biochemical Tests ◽  
Amplification Process ◽  
Group A

This study aims at detecting the differences in genotyping of coding region fusA gene in clinical isolates of Acinetobacter baumannii from Baghdad, Iraq. Collected two hundred clinical samples (50 samples from urine, 50 samples from wound, 50 samples from sputum and 50 samples from otitis infections). Laboratory diagnosis for bacterial isolates carried out by some biochemical tests and confirmed by using VITEK- 2 compact system. The results appeared that twenty isolates of Acinetobacter baumannii in all these samples. Genotyping study was performed of coding region fusA gene of the extracted genome of all bacterial isolates and used specific primers in achieved amplification process of this target gene. DNA sequencing of this gene and alignment of sequencing in NCBI was achieved and drew phylogenetic tree by using Geneious 9 software among locally isolates alone and then among locally isolates and high identity global isolates in GenBank. The results in phylogenetic tree of fusA gene in locally isolates showed 4 groups of isolates included more than one source of isolation. The results in phylogenetic tree of the locally and global isolates showed that are four different groups and each group included some locally isolates and global isolates except group A (AE_22, AE_26) and group E (AE_35, AE_32, AE_33) that not identity with global isolates. The nucleotides sequence of fusA gene from localized isolate (AE_35) was registered in national GenBank under accession number (LOCUS KY818057) and protein ID "ARV90995.1.

scholarly journals Determination of Isolated Salmonella Bacteria from Infected Animal Husbandry of Malayer City with using Molecular Methods

2017 ◽  
Vol 7 (1) ◽  
pp. 34
Author(s):  
Alireza Khakzad ◽  
Fatemeh Keshavarzi
Keyword(s):  
Genetic Diversity ◽  
Salmonella Enterica ◽  
Salmonella Enteritidis ◽  
Infected Animal ◽  
Animal Husbandry ◽  
Gram Negative Bacteria ◽  
Gram Negative ◽  
Sequence Elements ◽  
Pcr Method

Salmonella species are gram negative bacteria and members of Enterobacteriaceae family. It has a rod-shaped appearance; it is catalase positive, oxidase negative, non-spore. Salmonella classified into two species, Salmonella Enterica and Salmonella Bangori. Salmonella is now one of the main reasons of diarrhea and vomiting in humans in many countries and especially in industrialized. In a study in Japan 164 Salmonella digestions were collected during 2006 to 2008 which 81 digestions were Salmonella Infantis. Salmonella-specific characteristics are studied in the two phenotype and genotype methods. In this research, with using genotype methods based on PCR, genetic diversity was evaluated; this PCR includes rep-PCR based on repetitive sequence elements (method was done by the use of three primers ERIC, REP and BOX). Studied showed most isolated strains were relevant to Salmonella Enteritidis and dendorogram study showed that the bacteria were grouped in one cluster in dendrogram that all 37 strains were put in a large cluster of Salmonella’s type which is divided into two clusters: Salmonella Enterica and Bongori. The results also in this experiment reflect the efficiency of rep-PCR method by using three ERIC, REP and BOX primers.

scholarly journals TANAMAN INDIKATOR DAN TEKNIK RAPD-PCR UNTUK PENENTUAN BIOTIPE BEMISIA TABACI GENNADIUS (HEMIPTERA: ALEYRODIDAE)

2011 ◽  
Vol 8 (1) ◽  
pp. 1-7
Author(s):  
Purnama Hidayat ◽  
Noor Aidawati ◽  
Sri Hendrastuti Hidayat ◽  
Dewi Sartiami
Keyword(s):  
Genetic Diversity ◽  
Bemisia Tabaci ◽  
Virus Vector ◽  
Indicator Plant ◽  
Chilli Pepper ◽  
Genetic Types ◽  
Rapd Pcr ◽  
Major Pest ◽  
Biotype B

Indicator Plant and PCR-RAPD for Biotype Determination of Bemisia tabaci Gennadius (Hemiptera: Aleyrodidae).B. tabaci has been known world wide as a major pest and virus vector of horticulture. In Indonesia the presence of B.tabaci was reported since 1980 and its role as virus vector in tomato and chilli pepper has becoming more importantrecently. Genetic diversity of B. tabaci has been well recognized, but very little information available for diversity of B.tabaci in Indonesia. This research was conducted in Bogor, West Java from May 2004 to June 2005. The aim of thisresearch was to initiate basic information regarding genetic diversity of B. tabaci in Indonesia, particularly in Java Island.Whiteflies population collected from different crops, i.e. tomato, broccoli, chill pepper, eggplant, cucumber, soybean, andedamame, was evaluated using silverleaf-induction test, and RAPD-PCR. It was evidenced that only B. tabaci populationfrom broccoli was able to induce silverleaf. Two genetic types of B. tabaci, i.e. biotype B and non B, were identified basedon polymorphism character of DNA. Population from broccoli was belong to biotype B, whereas other populations fromtomato, chill pepper, eggplant, cucumber, soybean, and edamame were belong to biotype non B.

scholarly journals Occurrence and Determination of Antimicrobial Resistant Escherichia coli Isolates in Fish and Vegetables as Indicator Organism of Faecal Contamination in Dar es Salaam, Tanzania

2021 ◽  
Vol 2021 ◽  
pp. 1-9
Author(s):  
Francis Mwanza ◽  
Erick Vitus Gabriel Komba ◽  
Dominic Mukama Kambarage
Keyword(s):  
Escherichia Coli ◽  
Genetic Diversity ◽  
Genetic Relatedness ◽  
Diffusion Method ◽  
Urban Farming ◽  
Biochemical Tests ◽  
Typing Method ◽  
Organic Fertiliser ◽  
E Coli ◽  
Fish Samples

Escherichia coli such as E. coli O157:H7, a non-sorbitol-fermenting (NSF) E. coli, is an essential human pathogen among other common zoonotic pathogens carried by animals especially cattle. They are discharged through cattle faeces into the environment. With the increasing practice of urban farming, livestock manure is used as organic fertiliser in either fish ponds or vegetable gardens. This practice increases the risk of transmission of such pathogens to humans. This study aimed at determining the occurrence, antimicrobial resistance profiles, and genetic relatedness of E. coli isolates from manure, vegetables, and fish. Microbiological standard methods were used to isolate and identify E. coli isolates from manure, vegetable, and fish samples. Confirmed isolates on biochemical tests were tested for resistance against six antibiotics using the disc diffusion method. Enterobacterial repetitive intergenic consensus polymerase chain reaction (ERIC-PCR) typing method was used to generate fingerprints and determine the genetic relatedness of the E. coli isolates. Of 156 samples including 89 manure, 53 vegetables, and 16 fish, 36 (23.1%) samples were positive for E. coli from where a total of 48 E. coli different isolates were recovered that were subjected to antimicrobial susceptibility testing and genetic relatedness. Of these isolates, 25 (52.1%) were resistant to at least one antimicrobial agent and 12 (48.0%) showed multidrug resistance. ERIC-PCR profiles of E. coli isolates from manure, vegetables, and fish showed genetic diversity with genetic relatedness ranging from 74.5% to 100%. Nine phylogenetic clusters (I–IX) determined at 90% threshold level of genetic relatedness were identified among the isolates. This study determined the occurrence, antimicrobial resistant patterns, and genetic diversity of antimicrobial-resistant E. coli isolates from different sources. This study showed the potential of microbial health risk to humans through contamination, and hence, it is necessary to monitor and improve husbandry practices in urban farming.

scholarly journals Determination of Colistin and Tigecycline Resistance Profile of Acinetobacter Baumannii Strains from Different Clinical Samples in a Territory Hospital in Turkey

2020 ◽  
Author(s):  
Merih Şimşek ◽  
Cengiz Demir
Keyword(s):  
Intensive Care ◽  
Acinetobacter Baumannii ◽  
Intensive Care Units ◽  
Antimicrobial Agents ◽  
Empirical Treatment ◽  
Clinical Samples ◽  
Broth Microdilution ◽  
Broth Microdilution Method ◽  
Vitek 2

Objective: Acinetobacter baumannii (A. baumannii) can develop resistance to various antimicrobial agents via different mechanisms. Hence, the aim of this study was to investigate, by using different methods, the resistance profiles of A. baumannii strains isolated from different clinical specimens; from colistin and tigecycline antibiotics, and also the distribution of this resistance according to the clinical samples. Material and Methods: For this study, 1,265 clinical samples (a samples from each patient) were obtained from various clinics, between; January 2015/December 2018. Identification was conducted by VITEK® 2 compact (bioMerieux, USA) and conventional biochemical tests. Antibiotic susceptibility tests were performed by VITEK 2, and the results of colistin and tigecycline were confirmed by E test and the broth microdilution method. Results: A. baumannii strains (1,265) were most frequently isolated from tracheal aspirate, sputum and blood samples. At the same time, strains were obtained from intensive care units (70.4%) as well as other clinics (29.6%). The rates of colistin and tigecycline-resistant strains were determined using VITEK 2, E test and the broth microdilution methods as: 3.0%, 5.7%, 9.0% and 21.7%, 24.5%, 33.0%, respectively. Conclusion: The determination of appropriate antibioticis are important for empirical treatment. Colistin and tigecycline have become prominent as an important, alternative agent in the treatment of A. baumannii-related infections. The results of this study show that colistin and tigecycline resistance rates in intensive care units have been increasing gradually over the years. Monitoring of resistance patterns of nonfermentative bacteria, isolated from intensive care units, is important for the immediate initiation of appropriate empirical treatment. In-vitro studies with A. baumannii strains should also be supported by clinical trials.

scholarly journals Identification of Acinetobacter baumannii and its carbapenem-resistant gene blaOXA-23-like by multiple cross displacement amplification combined with lateral flow biosensor

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Shoukui Hu ◽  
Lina Niu ◽  
Fan Zhao ◽  
Linlin Yan ◽  
Jinqing Nong ◽  
...  
Keyword(s):  
Acinetobacter Baumannii ◽  
Limit Of Detection ◽  
Lateral Flow ◽  
Clinical Samples ◽  
Conventional Culture ◽  
Carbapenem Resistant ◽  
Multiple Cross ◽  
Pure Cultures ◽  
Amplification Technique ◽  
Sensitivity Specificity

AbstractAcinetobacter baumannii is a frequent cause of the nosocomial infections. Herein, a novel isothermal amplification technique, multiple cross displacement amplification (MCDA) is employed for detecting all A. baumannii strains and identifying the strains harboring blaOXA-23-like gene. The duplex MCDA assay, which targets the pgaD and blaOXA-23-like genes, could identify the A. baumannii isolates and differentiate these isolates harboring blaOXA-23-like gene. The disposable lateral flow biosensors (LFB) were used for analyzing the MCDA products. A total of sixty-eight isolates, include fifty-three A. baumannii strains and fifteen non-A. baumannii strains, were employed to optimize MCDA methods and determine the sensitivity, specificity and feasibility. The optimal reaction condition is found to be 63 °C within 1 h, with limit of detection at 100 fg templates per tube for pgaD and blaOXA-23-like genes in pure cultures. The specificity of this assay is 100%. Moreover, the practical application of the duplex MCDA-LFB assay was evaluated using clinical samples, and the results obtained from duplex MCDA-LFB method were consistent with conventional culture-based technique. In sum, the duplex MCDA-LFB assay appears to be a reliable, rapid and specific technique to detect all A. baumannii strains and identify these strains harboring blaOXA-23-like gene for appropriate antibiotic therapy.

Bacteriological Study of Pseudomonas aeruginosa Isolated from Tonsillitis Patients

2019 ◽  
Vol 9 (o3) ◽  
Author(s):  
Zahraa Hameed Oda Alquraishi ◽  
Israa Abdul Ameer Al-Kraety ◽  
Aqeel A. Alsadawi
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Microscopic Study ◽  
Clinical Samples ◽  
Molecular Method ◽  
Biochemical Tests ◽  
Bacteriological Study ◽  
Study Results ◽  
Pcr Method ◽  
Vitek 2 ◽  
Physiological And Biochemical

Present study included (50) clinical samples were collected from patients suffering from tonsillitis signs during the period from) November 2018 to January, 2019). All specimens were cultured for microscopic and microscopic study. Results show that from 50 patients, male was 60% and 40% were female. Several morphological, physiological and biochemical tests showed that P. aeruginosa constituted 18 isolates (36%) of these isolates. P. aeruginosa isolates were 18 isolates diagnosed by the morphological ,cultural and biochemical characters, the identification was confirmed by automated VITEK-2 compact system and molecular method for the presence of OprL. The results showed that only 12 (66.6%) isolates diagnosed as P. aeruginosa by automated VITEK-2 compact system and that was carrying OprL which are diagnosed as P. aeruginosa by P.C.R. According to the different diagnostic above, VITEK and PCR method were more sensitivity for P. aeruginosa detection among tonsillitis patients

scholarly journals Genetic characterization of Lactococcus garvieae isolated from farmed rainbow trout by random amplified polymorphic DNA-PCR in Iran

2020 ◽  
Vol 71 (1) ◽  
pp. 2023
Author(s):  
F. FADAEIFARD ◽  
M. RABIEI ◽  
M. F. SHARIFPOUR
Keyword(s):  
Rainbow Trout ◽  
Bacterial Infections ◽  
Random Amplified Polymorphic Dna ◽  
Farmed Fish ◽  
Biochemical Tests ◽  
Bacterial Cultures ◽  
Lactococcus Garvieae ◽  
Strain Pattern ◽  
Rapd Pcr ◽  
Pcr Method

Lactococcosis is one of the main bacterial infections of fish around the world. Lactococcus garvieae has been a major cause of rainbow trout losses in freshwater farming. This study aimed to genotype and determine the variability of L. garvieae isolated from infected farmed rainbow trout in Iran by the RAPD-PCR method. Bacterial samples were collected from 12 farms located in the western part of Iran and suspected to carry Lactococcus infection. Two hundred bacterial cultures containing cocci shaped bacteria were cultured in Trypticase soy agar (TSA) and blood agar mediums. All bacterial cultures were tested by conventional microbiological and biochemical tests, and PCR assay to identify L. garvieae by 16S rDNA genes. The RAPD-PCR method was used to determine the genetic pattern of all isolates. The sample strain pattern of the isolates was analyzed in the NTSYS program. According to a similarity coefficient index of 70%, all L. garvieae isolates were separated into two groups with four RAPD profile types. The highest and the lowest genetic pairwise similarity among the isolates were 98% and 54%, respectively. The results of the present study revealed that RAPD-PCR is an applicable method to describe the genetic diversity of different strains of L .garvieae among farmed fish.

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