ERIC and RAPD PCR-based DNA fingerprinting techniques application for microbial source tracking (MST) at Al-Madinah Al-Munwwarah, KSA

Diab, Atef M.; Al-Turk, Idriss

doi:10.1016/s1658-3655(12)60036-3

Cited by 3 publications

(3 citation statements)

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“…Several molecular techniques exist to identity M. tuberculosis such as variable-number tandem repeats of different families of genetic elements that are called mycobacterial interspersed repetitive units and polymerase chain reaction-based spoligotyping. [ 89 90 ] In another study Marais et al . in South Africa by spoligotyping that they performed for drug susceptibility testing on 391 isolates; 12.5% were resistant to isoniazid, and 20% were resistant to both isoniazid and rifampin.…”

Section: Discussionmentioning

confidence: 99%

Prevalence of Mycobacterium tuberculosis LAM family in the worldwide population: A systematic review and meta-analysis

Ramazanzadeh

Rouhi

Shakib

2015

International Journal of Mycobacteriology

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Background: Transmission of Mycobacterium tuberculosis ( M. tuberculosis ) can occur in different ways. Furthermore, drug resistant in M. tuberculosis family is a major problem that creates obstacles in treatment and control of tuberculosis (TB) in the world. One of the most prevalent families of M. tuberculosis is Haarlem, and it is associated with drug resistant. Our objectives of this study were to determine the prevalence and occurrence rate of M. tuberculosis Haarlem family multi-drug resistant (MDR) in the worldwide using meta-analysis based on a systematic review that performed on published articles. Materials and Methods: Data sources of this study were 78 original articles (2002-2012) that were published in the literatures in several databases including PubMed, Science Direct, Google Scholar, Biological abstracts, ISI web of knowledge and IranMedex. The articles were systematically reviewed for prevalence and rate of MDR. Data were analyzed using meta-analysis and random effects models with the software package Meta R, Version 2.13 ( P < 0.10). Results: Final analysis included 28601 persons in 78 articles. The highest and lowest occurrence rate of Haarlem family in M. tuberculosis was in Hungary in 2006 (66.20%) with negative MDR-TB and in China in 2010 (0.8%), respectively. From 2002 to 2012, the lowest rate of prevalence was in 2010, and the highest prevalence rate was in 2012. Also 1.076% were positive for MDR and 9.22% were negative (confidence interval: 95%).0020. Conclusion: Many articles and studies are performed in this field globally, and we only chose some of them. Further studies are needed to be done in this field. Our study showed that M. tuberculosis Haarlem family is prevalent in European countries. According to the presence of MDR that was seen in our results, effective control programs are needed to control the spread of drug-resistant strains, especially Haarlem family.

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Section: Discussionmentioning

confidence: 99%

Prevalence of Mycobacterium tuberculosis LAM family in the worldwide population: A systematic review and meta-analysis

Ramazanzadeh

Rouhi

Shakib

2015

International Journal of Mycobacteriology

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“…In this study, the method of RAPD-PCR belonging to the most universal genetic typing techniques was used. The RAPD-PCR method was successfully used for the identification and differentiation of many species of Gram-positive and Gram-negative bacteria and fungi (Alvarez-Perez et al 2009 ; Bogiel and Gospodarek 2010 ; Chiang et al 2014 ; Diab and Al-Turk 2011 ; Stefańska et al 2008 ; Zeinali et al 2015 ). However, in the available scientific literature, information on its use in the occupational environment is rather scarce.…”

Section: Discussionmentioning

confidence: 99%

Monitoring of bacterial pathogens at workplaces in power plant using biochemical and molecular methods

Ławniczek-Wałczyk

Gołofit-Szymczak

Cyprowski

et al. 2017

Int Arch Occup Environ Health

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PurposeThe aim of this study was to characterize the ways of spreading of the most common bacterial species isolated from workers as well as from the air and raw materials at the workplaces in power plant utilizing biomass sources. To monitor microbial transmission and identify the source of contamination in the working environment, a combination of molecular and biochemical methods was applied.MethodsThe study was carried out at workplaces in power plant utilizes biomass as a main fuel source. At each of the studied workplaces, bioaerosol particles were collected on sterile Teflon filters using personal conical inhalable samplers (CIS), and biomass samples (straw pellets and briquettes, corn briquettes, sunflower pellets and wood chips) were directly taken from their storage places. Simultaneously with that, the swab samples from the hands of ten workers and their used respiratory masks (of FFP2 class) were also collected after the work shift to evaluate individual workers’ microbial contamination. In all collected samples, total bacterial concentrations were assessed and the most common microbial isolates were identified to the species level using both biochemical (API tests) and molecular polymerase chain reaction (PCR), followed by random amplification of polymorphic DNA (RAPD) typing methods.ResultsThe mean concentrations of culturable bacteria in the air and in biomass samples at the studied workplaces were high, i.e. 1.2 × 106cfu/m3 and 3.8 × 104cfu/g, respectively. The number of bacteria in the swab and mask samples also reached a high level of 1.4 × 104 cfu/ml and 1.9 × 103 cfu/cm2, respectively. Among the most frequently isolated microorganisms from all types of samples were Gram-positive bacteria of the genus Bacillus and Staphylococcus xylosus. 37 bacterial strains belonging to the genus Bacillus (B. licheniformis 8, B. pumilus 15 and B. subtilis 4) and Staphylococcus (10) were genotyped by the RAPD-PCR method. Based on RAPD-PCR analyses, the genomic similarity among 19 Bacillus strains isolated from biomass, air, protective mask and hand samples as well as 6 S. xylosus strains isolated from air, mask and hand samples exceeded 80%.ConclusionThis study demonstrated that biomass is the primary source of bacteria at power plant workplaces. These results also revealed that biomass-associated bacteria can be easily transferred to workers’ hands and mask during their routine activities. To improve health protection at the workplaces, adequate training courses on hand hygiene and how to use and remove respiratory masks correctly for workers should be introduced as a key element of the prevention strategy. From the occupational point of view, the PCR-based methods seem to be an efficient tool for a fast and precise typing of bacterial strains isolated from different sources in the occupational environment. Such methods may help to implement appropriate prophylactic procedures and minimize transmission of infectious agents at workplaces.

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“…However, this typing method is commonly used as it is rapid, cost-effective and can classify E. coli into different clonal groups for the purpose of epidemiological studies (Cherifi et al, 1991;Gillings and Holley, 1997;Meacham et al, 2003;Ranjbar et al, 2017;Ugorski and Chmielewski, 2000;Wilson and Sharp, 2006). Several studies have recommended the usage of ERIC-PCR for E. coli strains obtained from different sources due to it is power of differentiation (Dhanashree and Shrikara, 2012 ;Diab and Al-urk, 2011;Maryam, 2016) In addition, several other PCR based typing methods have been developed based on the repeated DNA sequence elements distributed throughout the genome. These include randomly amplified polymorphic DNA and restriction fragment length polymorphism (Jonas et al, 2003).…”

Section: Enterobacterial Repetitive Intergenic Consensus (Eric)mentioning

confidence: 99%

Studies on avian pathogenic Escherichia coli in commercial broiler chicken in South East Queensland

Awawdeh¹,

Turni²,

Henning³

et al.

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Avian pathogenic Escherichia coli (APEC) is the causative agent of avian colibacillosis, a localised or systemic infection resulting in clinical diseases such as colisepticemia, chronic respiratory disease and swollen-head syndrome. Globally, avian colibacillosis is the leading cause of morbidity and mortality in poultry, and it has been associated with massive economic losses and welfare problems.This organism is of public health significance as APEC is communicable to humans. The diagnosis of avian colibacillosis relies on clinical signs, typical pathological lesions and culture of E. coli from affected tissue(s). Antimicrobial therapy is often used both for treatment and control. Previous overseas studies have characterised APEC and identified virulence genes (VGs) that can be used as molecular markers for the identification of APEC. Little is known about APEC in broiler chickens in Australia.The aim of this thesis was to gain a better understanding of the epidemiology of APEC in Australian broiler flocks and how factors including presence of VGs and phylogenetic group can improve the identification of this pathotype in Australia. Firstly, three faecal DNA extraction methods were evaluated. Faeces were collected from healthy chickens and chickens with colibacillosis from commercial broiler farms in South East Queensland (SEQ). The extracted DNA was screened by a pentaplex-PCR for five APEC-associated VGs (iroN, iutA, iss, hlyF and ompT). DNA extracted from E. coli isolates cultured from the cloaca and organs of the birds were screened using the same PCR.Repeated bead beating plus column elution was the preferred DNA extraction method, as it yielded good PCR quality and adequate quantity DNA. However, identifying APEC by direct detection of the five VGs from the faecal material was not feasible as all of these genes were also detected in all of the birds. However, the VGs were more commonly detected in E. coli isolates cultured from birds with colibacillosis.A cross-sectional study was performed to estimate APEC farm-level prevalence in healthy broiler chickens in SEQ and to identify potential risk factors associated with the carriage of APEC. At the farm-level, all of the 40 farms sampled were positive for APEC, that is at least one bird per farm carried APEC, while the within-farm prevalence was 63% (95% Confidence Interval: 55.8, 70.2).Higher APEC within-farm bird-level prevalence was significantly associated with the usage of well water as a source of drinking water, failure to disinfect the water line after each flock, farm visitors not showering before entering the shed, distances greater than 20 metres between the car park and the poultry shed and the presence of wild birds within 50 metres of the shed. Chlorinating the drinking water combined with automatic water filtration reduced within-farm bird-level APEC prevalence. Page | 3Therefore, based on the results concluded from the multivariable model, improving biosecurity and water treatments might reduce APEC prevalence, decrease the risk of co...

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ERIC and RAPD PCR-based DNA fingerprinting techniques application for microbial source tracking (MST) at Al-Madinah Al-Munwwarah, KSA

Cited by 3 publications

References 25 publications

Prevalence of Mycobacterium tuberculosis LAM family in the worldwide population: A systematic review and meta-analysis

Prevalence of Mycobacterium tuberculosis LAM family in the worldwide population: A systematic review and meta-analysis

Monitoring of bacterial pathogens at workplaces in power plant using biochemical and molecular methods

Studies on avian pathogenic Escherichia coli in commercial broiler chicken in South East Queensland

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