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Short Communication

An Improve Protocol for PCR Using LM1 and LM2 Primers for Listeria monocytogenes Detection in Food Matrices

Several studies have observed that use of a conventional PCR protocol with primers LM1 and LM2 for the identification of the hlyA gene of Listeria monocytogenes generates non-specific PCR amplifications and false positives. For this reason, in this study we provide a modified PCR protocol that improves the specificity of the results obtained with LM1 and LM2 primers.

Angélica Godínez-Oviede, Gerardo M. Nava, Sofía M. Arvizu-Medrano, Montserrat Hernández-Iturriaga

Polish Journal of Microbiology , ISSUE 2, 255–257

Original Paper

Comparison of PCR, Fluorescent in Situ Hybridization and Blood Cultures for Detection of Bacteremia in Children and Adolescents During Antibiotic Therapy

carried out in standard automated systems. Subsequently, FISH (Fluorescent In-Situ Hybridization) and nested multiplex-real-time-PCR (PCR) were performed. Blood cultures, FISH and PCR yielded positive results in 18%, 39.1%, and 71.7% of samples, respectively. Significant differences were found between the results obtained through culture before and after induction of antibiotherapy: 25.5% vs. 9.7%. There was no significant difference in FISH and PCR results in relation to antibiotics. The three

TOMASZ W. ŹRÓDŁOWSKI, DANUTA JURKIEWICZ-BADACZ, AGNIESZKA SROKA-OLEKSIAK, DOMINIKA SALAMON, MAŁGORZATA BULANDA, TOMASZ GOSIEWSKI

Polish Journal of Microbiology , ISSUE 4, 479–486

Short Communication

Identification of Pathogenicity of Yersinia enterocolitica in Pig Tonsils Using the Real-Time PCR

The application of DNA-based methods enables to identify Yersinia enterocolitica carrying the ail-gene with a greater sensitivity compared to culture methods and biochemical tests used for detection of pathogenic Y. enterocolitica in animal and food samples. In this study, 100 samples of pig tonsils were examined, among which 17 were positive for the ail gene. Additionally, biochemical tests and RT-PCR showed that nine Y. enterocolitica isolates carried the ail-gene. Two Y. enterocolitica

MILENA A. STACHELSKA

Polish Journal of Microbiology , ISSUE 2, –

original-paper

Assessing the Microbial Communities in Four Different Daqus by Using PCR-DGGE, PLFA, and Biolog Analyses

rise to distinctive flavors. In the past, culture-dependent methods were the commonest approach to microbial profiling analysis. However, microorganisms identified using these methods amount to ≤ 10% of the total environmental microorganisms and do not reflect the actual microbial profile distribution within Daqu (Liu et al. 2017). Culture-independent methods such as polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) analysis are highly useful to detect the whole microbial

YUXI LING, WENYING LI, TONG TONG, ZUMING LI, QIAN LI, ZHIHUI BAI, GUIJUN WANG, JIAHAO CHEN, YUGUANG WANG

Polish Journal of Microbiology , ISSUE 1, 27–37

research-article

Improvement of long segment ribosomal PCR amplification for molecular identification of Litylenchus crenatae mccannii associated with beech leaf disease

USA where related species may exist. Molecular and morphological taxonomic identifications were conducted in our lab with the nematodes isolated from the lesions of the BLD leaves collected in Fall, 2017 from Perry, Lake County, Ohio, USA by an Ohio Department of Agriculture nursery inspector from ailing American beech trees Fagus grandifolia (Fall specimens). Their ribosomal DNA (rDNA) loci were amplified by PCR with the one primer set and an enhanced DNA polymerase system, and the resulting 3.5

L.K. Carta, S. Li

Journal of Nematology , 1–15

Short Communication

Rapid Detection of Bloodstream Pathogens in Oncologic Patients with a FilmArray Multiplex PCR Assay: a Comparison with Culture Methods

The results of the FilmArray® Blood Culture Identification Panel (BCID) (BioFire Diagnostics) and the culture with susceptibility testing of 70 positive blood cultures from oncologic patients were compared. The multiplex PCR assay (BCID) identified 81 of the 83 isolates (97.6%), covered by the panel. The panel produced results in significantly shorter time than standard identification methods, when counted from receiving positive blood cultures bottles to the final results. It is an accurate

Maria Szymankiewicz, Beata Nakonowska

Polish Journal of Microbiology , ISSUE 1, 103–107

original-paper

The Effect of Environmental Stresses on lipL32 Gene Expression in Pathogenic Leptospira spp. through Real-Time PCR

incubated at 30°C for 30 days. Leptospira interrogans serovar Icterohaemorrhagiae (RTCC2823) was used as a reference strain. The mentioned strain was from a Leptospira Reference Laboratory, Razi Vaccine and Serum Research Institute, Karaj, Iran. DNA extraction. DNA was extracted from all Leptospira isolates along with the reference strain using the Purification Kia Spin polymerase chain reaction (PCR) Kit (Kiagen, Iran). The purity of the extracted DNA was evaluated by optical absorption at 260 and 280

SONA ROSTAMPOUR YASOURI, MONIR DOUDI, MASOOD GHANE, NAFISEH SADAT NAGHAVI, ABOLHASAN REZAEI

Polish Journal of Microbiology , ISSUE 3, 301–310

short-communication

Comparison of Performance Characteristics of DxN VERIS System versus Qiagen PCR for HBV Genotype D and HCV Genotype 1b Quantification

aim is to cure the infection to achieve a sustained virological response and consequently, to prevent HCC development (Akhan et al. 2015). Additionally, viral load (VL) monitoring is important in assessing the therapeutic response, monitoring treatment success and detecting drug-resistant viruses (Singh et al. 2017). There are several commercially available HBV-HCV monitoring assays which are mainly based on real-time polymerase chain reaction (RT-PCR); but, using the most effective, the cheapest

MURAT SAYAN, AYSE ARIKAN, TAMER SANLIDAG

Polish Journal of Microbiology , ISSUE 1, 139–143

research-article

Developing a real-time PCR diagnostic method for a potential threat to chrysanthemum, Paratylenchus dianthus

. kumamotoensis are known to inhabit in many chrysanthemum growing areas (Iwahori et al., 2008) and Pratylenchus may cause chronic damage to chrysanthemum (Kobayashi, 1995). Chemical treatments including nematicides, such as fosthiazate, are popular means to control nematode damage in Okinawa, however, nematode diagnosis in a chrysanthemum field is not quick and easy. Koyama et al. (2016) reported a low cost and high-throughput approach to quantify Pratylenchus spp. with the real-time PCR method by using pre

Masanori Kawanobe, Koki Toyota, Hidehito Uchihara, Mikoto Takae

Journal of Nematology , 1–11

original-paper

Establishment and Application of a Dual TaqMan Real-Time PCR Method for Proteus Mirabilis and Proteus Vulgaris

2003 and 2008; in particular, there were 110 (3.93%) public health crises caused by Proteus species as foodborne pathogens, resulting in 3,093 individuals to have symptoms of food poisoning (Wu et al. 2018). In developed countries, researchers generally do not consider Proteus as a foodborne pathogen, and thus, they pay little attention to the identification of Proteus in food. Surprisingly, no study has reported the use of quantitative fluorescence PCR (Q-PCR) to identify P. vulgaris even though

RUI YANG, GUOYANG XU, XIAOYOU WANG, ZHICHU QING, LIZHI FU

Polish Journal of Microbiology , ISSUE 3, 293–300

Original Paper

A Comparative Study: Taxonomic Grouping of Alkaline Protease Producing Bacilli

C265, were identified as Bacillus licheniformis with 99.4% and Bacillus mojavensis 99.8% based on 16S rRNA gene sequence similarities, respectively. Interestingly, the isolates identified as Bacillus safensis were also found to be high alkaline protease producing strains. Genotypic characterizations of the isolates were also determined by using a wide range of molecular techniques (ARDRA, ITS-PCR, (GTG)5-PCR, BOX-PCR). These different techniques allowed us to differentiate the alkaliphilic isolates

Nilgun Tekin, Arzu Coleri Cihan, Basar Karaca, Cumhur Cokmus

Polish Journal of Microbiology , ISSUE 1, 39–56

research-article

PCR amplification of a long rDNA segment with one primer pair in agriculturally important nematodes

Eukaryotic nuclear ribosomal DNA (rDNA) is arranged in tandem repeat arrays in the genome. Each repeat unit consists of one copy of small subunit (SSU) 18S, internal transcribed spacers (ITS1 and ITS2), 5.8S, and large subunit (LSU) 28S rDNA, and is separated by an external transcribed spacer (EST) and an intergenic spacer (IGS) (Hillis and Dixon, 1991). The copy number of the repeats within most eukaryotic genomes is high, which provide large quantities of template DNA for PCR. In

L. K. Carta, S. Li

Journal of Nematology , 1–8

original-paper

Periodontal Status and Subgingival Biofilms in Cystic Fibrosis Adults

different microorganisms, using molecular biology tools and specific gene amplification by RT-PCR (Gołyńska et al. 2017). Microbiological analysis was performed to assess the presence and quantity of following periodontal pathogens: 1. A. actinomycetemcomitans, 2. P. gingivalis, T. forsythia, and T. denticola from the red complex, 3. F. nucleatum, P. intermedia, P. micros from the orange complex as well as Eubacterium nodatum from the complex associated with the orange one, 4. C. gingivalis from the

TAMARA PAWLACZYK-KAMIEŃSKA, RENATA ŚNIATAŁA, HALINA BATURA-GABRYEL, MARIA BORYSEWICZ-LEWICKA, SZCZEPAN COFTA

Polish Journal of Microbiology , ISSUE 3, 377–382

Original Paper

Identification of Lactobacillus delbrueckii and Streptococcus thermophilus Strains Present in Artisanal Raw Cow Milk Cheese Using Real-time PCR and Classic Plate Count Methods

The aim of this paper was to detect Lactobacillus delbrueckii and Streptococcus thermophilus using real-time quantitative PCR assay in 7-day ripening cheese produced from unpasteurised milk. Real-time quantitative PCR assays were designed to identify and enumerate the chosen species of lactic acid bacteria (LAB) in ripened cheese. The results of molecular quantification and classic bacterial enumeration showed a high level of similarity proving that DNA extraction was carried out in a proper

Milena A. Stachelska

Polish Journal of Microbiology , ISSUE 4, 491–499

original-paper

PCR-based Screening Approach: A Rapid Method to Detect the Biosynthetic Potential of Antimicrobials in Actinobacterial Strains

, bleomycin, vancomycin, and penicillins. A representative NRPS unit consists of three essential domains, such as an adenylation (A) domain, a peptidyl carrier protein (PCP), and a condensation (C) domain. New domains are continually evolving, as novel gene clusters for peptide biosynthesis are being categorized (Du et al. 2000). The PCR-based screening approach sets the stage for the discovery of novel metabolites. This method helped to meet the medical severe demand for new drug candidates and enhance

NAILA NOUREEN, MOHSIN TASSAWAR CHEEMA, SUMAIRA ANWAR, SHAHIDA HASNAIN, IMRAN SAJID

Polish Journal of Microbiology , ISSUE 2, 139–149

Short Communication

Enteroviruses Associated with Aseptic Meningitis in Poland, 2011–2014

A 4-year study (2011–2014) of patients with meningitis was performed. Out of the 686 cerebrospinal fluid samples, 465 (67.8%) were posi­tive for eneteroviruses using RT-PCR and out of 334 clinical samples, 216 (64.7%) were positive for enteroviruses using cell culture methods. The highest detection rate was observed in the summer and autumn. In total, 185 enteroviruses were identified by using neutralization test. Echovirus 6 and 30 were the most common (41.7% and 37.5% respectively

Magdalena Wieczorek, Agnieszka Figas, Arleta Krzysztoszek

Polish Journal of Microbiology , ISSUE 2, 231–235

Short Communication

Detection of Coxiella burnetii and Francisella tularensis in Tissues of Wild-living Animals and in Ticks of North-west Poland

Abstract This work presents results of the research on the occurrence of Coxiella burnetii and Francisella tularensis in the tissues of wild-living animals and ticks collected from Drawsko County, West Pomeranian Voivodeship. The real-time PCR testing for the pathogens comprised 928 samples of animal internal organs and 1551 ticks. The presence of C. burnetii was detected in 3% of wild-living animals and in 0.45–3.45% (dependent on collection areas) of ticks. The genetic sequences of F

AGATA BIELAWSKA-DRÓZD, PIOTR CIEŚLIK, DOROTA ŻAKOWSKA, PATRYCJA GŁOWACKA, BOŻENA WLIZŁO-SKOWRONEK, PRZEMYSŁAW ZIĘBA, ARKADIUSZ ZDUN

Polish Journal of Microbiology , ISSUE 4, 529–534

Original Paper

Comparison of Methods Used for the Diagnosis of Epstein-Barr Virus Infections in Children

The accurate diagnosis of Epstein-Barr virus (EBV) infections is important, as many other infectious agents or diseases can cause similar symptoms. In this study, sera of pediatric patients who were suspected to have an EBV infection, were sent to Eskisehir Osmangazi University Faculty of Medicine, Department of Clinical Microbiology, and investigated by IFA, ELISA, immunoblotting and Real-time PCR. The performances of these tests were compared with IFA. The rates of agreement between ELISA and

Nilgun Kasifoglu, Semra Oz, Ener Cagri Dinleyici, Tercan Us, Ozcan Bor, Gul Durmaz, Yurdanur Akgun

Polish Journal of Microbiology , ISSUE 1, 81–88

research-article

Molecular characterization of the Pratylenchus vulnus populations on cereals in Turkey

Vovlas, 2007). Molecular techniques as RAPD-PCR and sequencing of D2 to D3 expansion segments of the 28S rRNA was used for the identification of P. vulnus on different plant species (Subbotin et al., 2008; Bakooie et al., 2012; Lopez-Nicora et al., 2012). Moreover, real-time PCR provides sensitive identification of the species with species-specific primers using 1/128 of the DNA of one nematode (Huang and Yan, 2017). Pratylenchus vulnus (Allen and Jensen, 1951) (walnut root lesion nematode) has been

Mehmet Sait Karaca, Elif Yavuzaslanoglu, Gul Imriz, Ozlem Ates Sonmezoglu

Journal of Nematology , 1–4

Article

Mitochondrial Haplotype-based Identification of Root-knot Nematodes (Meloidogyne spp.) on Cut Foliage Crops in Florida

and (ii) evaluate the feasibility of using the mtDNA haplotype as a molecular diagnostic tool for rapid identification of large samples of RKN. A total of 200 Meloidogyne females were collected from cut foliage plant roots. Meloidogyne spp. were identified by PCR and RFLP of mitochondrial DNA. PCR and RFLP of mitochondrial DNA were effective in discriminating the Meloidogyne spp. present. Meloidogyne incognita is the most dominant RKN on cut foliage crops in Florida and must be a high target for

RICHARD BAIDOO, SOUMI JOSEPH, TESFAMARIAM M. MENGISTU, JANETE A. BRITO, ROBERT MCSORLEY, ROBERT H. STAMPS, WILLIAM T. CROW

Journal of Nematology , ISSUE 3, 193–202

Research paper

Analysis of methionine synthase (rs1805087) gene polymorphism in autism patients in Northern Iran

this study was to analyze the association of MTR A2756G gene polymorphism (rs1805087) and the risk of autism in a population in northern Iran. The prevalence of MTR A2756G polymorphism was determined in 108 children with autism and 130 controls in northern Iran. Genotypes and allele frequencies were determined in patients and controls by polymerase chain reaction‑restriction fragment length polymorphism (PCR‑RFLP). The prevalence of genotype frequencies of AA, AG and GG in autistic children were

Rosa Haghiri, Farhad Mashayekhi, Elham Bidabadi, Zivar Salehi

Acta Neurobiologiae Experimentalis , ISSUE 4, 318–323

original-paper

Yeasts Associated with Various Amazonian Native Fruits

identified and characterized genotypically and phenotypically. DNA extraction, rep-PCR, and RFLP-PCR of the 5.8S-ITS region. DNA extraction was performed as per Querol et al. (1992) with a slight modification in the use of lyticase (3.3 U · µ/l; Sigma, USA) instead of zymolase. For discrimination at the strain level, PCR of the repetitive extragenic palindromic sequences (rep-PCR) (Versalovic et al. 1991) was performed using a primer (GTG)5 (5’-GTG GTG GTG GTG GTG-3’) as described by Gori et al. (2013

CARLOS VEGAS, AMPARO I. ZAVALETA, PAMELA E. CANALES, BRAULIO ESTEVE-ZARZOSO

Polish Journal of Microbiology , ISSUE 3, 251–261

Original Paper

Molecular Characterization of the cry Gene profile of Bacillus thuringiensis Isolated from a Caribbean Region of Colombia

In order to characterize native strains of Bacillus thuringiensis of the Colombian Caribbean with toxic effect against insect vectors, 28 samples of bacteria identified as B. thuringiensis were isolated from different soils and muds around the city of Valledupar. Using a biological test, five isolates of B. thuringiensis showed toxic effect against larvae of Aedes aegypti. PCR methods were used to detect cry1, cry2, cry4B, cry10 and cyt1 genes. Cry1 and cry2 genes were detected in 35.7% and

Pedro Fragoso, Alicia Armijo, Doris Gómez, Claudio Gómez, Marco Bugueño, Gittith Sánchez, Juan Venegas

Polish Journal of Microbiology , ISSUE 1, 19–26

original-paper

Resensitization of Fluconazole-Resistant Urinary Candida spp. Isolates by Amikacin through Downregulation of Efflux Pump Genes

intervals of 0, 30, 60, 90 and 120 min, using a spectrofluorometer (Shimadzu, Japan) with excitation at 485 nm and emission at 530 nm. All results were represented as an average of three biological samples. Molecular quantification of the Candida efflux pump genes MDR1, CDR1, and CDR2 using quantitative real-time PCR. Quantitative real-time PCR was applied for two isolates C6 and C21 whose efflux pump activity was more prominently affected by amikacin using the Applied Biosystems 7500 Real-Time PCR

EVA A. EDWARD, NELLY M. MOHAMED, AZZA S. ZAKARIA

Polish Journal of Microbiology , ISSUE 1, 73–84

Short Communication

Detection of Polioviruses in Sewage Using Cell Culture and Molecular Methods

The work presented here demonstrates the utility of a two-step algorithm for environmental poliovirus surveillance based on: preselection of sewage samples tested for the presence of enteroviral genetic material-RT-PCR assay and detection of infectious viruses by cell culture technique (L20B for polioviruses and RD for polio and other non-polio enteroviruses). RD and L20B cell lines were tested to determine their sensitivity for isolation of viruses from environmental samples (sewage). Finally

Agnieszka Figas, Magdalena Wieczorek, Bogumiła Litwińska, Włodzimierz Gut

Polish Journal of Microbiology , ISSUE 4, 479–483

research-article

First report of root-knot nematode, Meloidogyne arenaria, on lavender in Turkey

. Galled roots were collected from seedlings and examined with a stereo-binocular microscope. The galls were symptoms caused by root-knot nematodes (Fig. 1). Egg masses were separately collected from roots of L. angustifolia cultivars, Raya, Hemus, Sevtopolis, Hebar and Yubileina using a small needle. For molecular identification, DNA was extracted from egg masses using the High Pure PCR Template Preparation Kit (Roche). Then, DNA samples were screened by species-specific primers belonging to the most

Tevfik Özalp, Gonca Könül, Önder Ayyıldız, Adnan Tülek, Zübeyir Devran

Journal of Nematology , 1–3

research-article

First report of the stubby-root nematode Nanidorus minor infecting Paspalum vaginatum, seashore paspalum grass in Georgia, USA

 = 5) using Extract-N-Amp™ Tissue PCR Kit (Sigma-Aldrich Co. LLC, St. Louis, MO‎; USA) following kit protocol with modifications. Individual nematodes were transferred into a sterile petri dish in 5 µL water and cut into 2 to 3 pieces using pipette tip under an inverted microscope. Subsequently, each individual nematode mix was transferred into a sterile 1.5 mL microcentrifuge tube containing 20 μL of extraction buffer with 5 µL of Tissue Preparation Solution from the kit. After careful vortexing

Ganpati B. Jagdale, Fereidoun Forghani, Katherine Martin, Abolfazl Hajihassani, Alfredo Dick Martinez-Espinoza

Journal of Nematology , 1–3

Research Article

High Mitochondrial Genome Diversity and Intricate Population Structure of Bursaphelenchus xylophilus in Kyushu, Japan

Mitogenomic diversity and genetic population structure of the pinewood nematode (PWN) Bursaphelenchus xylophilus inhabiting Kyushu, Japan were analyzed. A method for performing long PCR using single nematodes and sequencing nematode mitochondrial genomes individually is presented here. About 8 kb (∼55%) of the complete mitochondrial genome was successfully obtained from 285 individuals collected from 12 populations. The 158 single nucleotide polymorphisms detected corresponded to 30 haplotypes

Hanyong Zhang, Erika Okii, Eiji Gotoh, Susumu Shiraishi

Journal of Nematology , ISSUE 3, 281–302

Article

COVID-19 – DISEASE CAUSED BY SARS-COV-2 INFECTION – VACCINE AND NEW THERAPIES RESEARCH DEVELOPMENT

objawy kliniczne często towarzyszące COVID-19 rozpoznanie zakażenia wirusem SARS-CoV-2 bez badań laboratoryjnych nie jest możliwe. Obecnie wykorzystuje się testy molekularne (genetyczne) oraz testy serologiczne (immunologiczne). Standardową metodą diagnozowania zakażenia zalecaną przez WHO jest test reakcji łańcuchowej polimerazy z odwróconą transkrypcją RT-PCR „real-time RT-PCR”. Test jest wykonywany z wymazu nosowo gardłowego lub z próbki plwociny. W toku badania przeprowadza się amplifikację dwóch

Elżbieta Nowakowska, Sylwia Sulimiera Michalak

Postępy Mikrobiologii - Advancements of Microbiology , ISSUE 3, 227–236

Original Paper

Comparison of Microbial Communities Associated with Halophyte (Salsola stocksii) and Non-Halophyte (Triticum aestivum) Using Culture-Independent Approache

, root and shoot samples was isolated with the help of FastDNA spin kit. Through PCR, the 16S rRNA gene from four different Salsola plants and wheat plants was amplified and cloned in InsTAclone PCR cloning kit. Metagenomic analyses from rhizosphere, endosphere and phyllosphere of Salsola showed that approximately 29% bacteria were uncultured and unclassified. Proteobacteria and Actinobacteria were the most abundant phyla in Salsola and wheat. How­ever, Firmicutes, Acidobacteria, Bacteriodetes

Salma Mukhtar, Ayesha Ishaq, Sara Hassan, Samina Mehnaz, Muhammad S. Mirza, Kauser A. Malik

Polish Journal of Microbiology , ISSUE 3, 353–364

Article

MOLECULAR METHODS FOR DIAGNOSTICS OF DERMATOMYCOSES – REVIEW OF AVAILABLE TECHNIQUES AND EVALUATION OF THEIR ADVANTAGES AND DISADVANTAGES IN IMPLEMENTATION FOR IN ROUTINE USE

bardziej znanych na świecie ośrodków zajmujących się tematyką dermatofitów, tj. CBS KNAW Fungal Biodiversity Centre. Obecnie w środowisku mikrobiologów trwa dyskusja nad rozpoczęciem prac nad przygotowaniem, dedykowanej specjalnie dla laboratoriów diagnostyki mykologicznej, bazy danych sekwencji nukleotydowych oraz opisów morfologicznych gatunków sklasyfikowanych według nowych zasad taksonomicznych [23, 28]. 4. Metody bezpośredniej identyfikacji grzybów z próbek klinicznych Metody PCR do

Sebastian Gnat, Dominik Łagowski, Aneta Nowakiewicz, Mariusz Dyląg

Postępy Mikrobiologii - Advancements of Microbiology , ISSUE 4, 483–494

Original Paper

The Very Low Frequency of Epstein-Barr JC and BK Viruses DNA in Colorectal Cancer Tissues in Shiraz, Southwest Iran

extracted, then qualified samples introduced to polymerase chain reaction (PCR). The EBV, JCV and BKV genome sequences were detected using specific primers by 3 different in-house PCR assays. Out of 210 subjects, 98 cases were female and the rest were male. The mean age of the participants was 52 ± 1.64 years. EBV and JCV DNA was detected just in one (1.42%) out of seventy adenocarcinoma colorectal tissues. All adenomatous polyp and normal colorectal tissues were negative for EBV and JCV DNA sequences

Jamal Sarvari, Shahab Mahmoudvand, Neda Pirbonyeh, Akbar Safaei, Seyed Younes Hosseini

Polish Journal of Microbiology , ISSUE 1, 73–79

research-article

First report of a gastropod parasitic nematode Phasmarhabditis californica (Nematoda: Rhabditidae) in Alberta, Canada

samples were taken in triplicate and stored in 95% EtOH before molecular analysis. We found a putative Phasmarhabditis species in association with an Arion rufus slug (id verified by R. Mc Donnell, OSU), collected from the exterior grounds of a local nursery. PCR amplification and subsequent direct DNA sequencing of an ~800 bp segment of the nematode 18S ribosomal RNA gene revealed a sequence that was 100% match to the 18S rRNA sequence for P. californica (KM510210; Tandingan De Ley et al., 2014, 2016

Taylor Brophy, Dana K. Howe, Dee R. Denver, Lien T. Luong

Journal of Nematology , 1–3

Short Communication

Development and Evaluation of a Latex Agglutination Test for the Identification of Francisella tularensis Subspecies Pathogenic for Human

Francisella tularensis are highly infectious bacteria causing a zoonotic disease called tularemia. Identification of this bacterium is based on antigen detection or PCR. The paper presents a latex agglutination test (LAT) for rapid identification of clinically relevant F. tularensis subspecies. The test can be performed within three minutes with live or inactivated bacteria. The possibility to test the inactivated samples reduces the risk of laboratory acquired infection and allows performing

WALDEMAR RASTAWICKI, KAMILA FORMIŃSKA, ALEKSANDRA A. ZASADA

Polish Journal of Microbiology , ISSUE 2, 241–244

short-communication

Hand, Foot, and Mouth Disease Caused by Coxsackievirus A6: A Preliminary Report from Istanbul

. SensiFAST cDNA Synthesis Kit (Bioline, London, UK) was used to synthesize cDNA from isolated viral RNAs using random primers and the manufacturer’s instructions were followed at all steps. cDNA was purified from reverse transcription products with Zymo Research DNA Clean & Concentrator™-5 kit in accordance with the manufacturer’s instructions. Designing primers and PCR. Pan-enterovirus primers specific to the Enterovirus genus targeting 5’UTR were designed for nested-PCR on basis of previously published

AYSE N. CEYLAN, OZDEN TUREL, BILGE SUMBUL GULTEPE, ELIF INAN, AYSEL VEHAPOGLU TURKMEN, MEHMET Z. DOYMAZ

Polish Journal of Microbiology , ISSUE 2, 165–171

original-paper

Biodiversity of Bacteria Associated with Eight Pleurotus ostreatus (Fr.) P. Kumm. Strains from Poland, Japan and the USA

. Suspension in a volume of 100 μl of each fungal strain was used for DNA isolation using PowerSoil DNA Isolation Kit (MO-BIO Laboraories, Inc., USA) according to the manufacturer’s protocol. DNA was purified as described above. 16S rRNA amplification and identification. The confirmation of the bacterial nature of isolated microcolonies was carried out by determining the size of the 16S rRNA gene fragment by PCR. The reaction mixture contained isolated DNA, 2 × PCR RED Master Mix (DNA-GDANSK, Poland) kit

MARIUSZ ADAMSKI, STANISLAW J. PIETR

Polish Journal of Microbiology , ISSUE 1, 71–81

Original Paper

Natural Attenuation Potential of Polychlorinated Biphenyl-Polluted Marine Sediments

petroleum hydrocarbons (TPHs). Then we adopted both culture-dependent and culture-independent (PCR-DGGE) approaches to identify bacterial inhabitants of the polluted marine sediments from Shuwaikh harbor. The chemical analysis revealed spatial variation among the sampling stations in terms of total amount of PCBs, TPHs and the PCB congener fingerprints. Moreover, in all analyzed sediments, the medium-chlorine PCB congeners were more abundant than the low-chlorine and high-chlorine counterparts. PCR-DGGE

Sarah Aldhafiri, Huda Mahmoud, Mohammed Al-Sarawi, Wael A. Ismail

Polish Journal of Microbiology , ISSUE 1, 37–48

Original Paper

Characterization of a Highly Enriched Microbial Consortium Reductively Dechlorinating 2,3-Dichlorophenol and 2,4,6-Trichlorophenol and the Corresponding cprA Genes from River Sediment

acceptors. When acetate, formate, or pyru­vate were used as electron donors, dechlorination activity was lost. Only lactate can replace dihydrogen as an electron donor. However, the dechlorination potential was decreased after successive transfers. To reveal chlororespiring species, the microbial community structure of chlorophenol-reductive dechlorinating enrichment cultures was analyzed by PCR-denaturing gradient gel electrophoresis (DGGE) of 16S rRNA gene fragments. Eight dominant bacteria were

Wael S. El-Sayed

Polish Journal of Microbiology , ISSUE 3, 341–352

original-paper

In situ Impact of the Antagonistic Fungal Strain, Trichoderma gamsii T30 on the Plant Pathogenic Fungus, Rhizoctonia solani in Soil

DNA (Anees et al. 2010b). The plasmid DNA was then diluted making ten-fold dilution series that contained the cloned ITS regions from 102 to 109 copies of the target DNA for each PCR reaction. The curve hence generated was then used for quantification of the target DNA in the different DNA samples (Fig. S1). Quantification of R. solani by qPCR. Sand samples of 1 g were used for the extraction of genomic DNA (Edel-Harmann et al. 2004). The procedure used for the DNA extraction included chemical as

MUHAMMAD ANEES, MUHAMMAD ABID, SOBIA CHOHAN, MUHAMMAD JAMIL, NADEEM AHMED, LIXIN ZHANG, EUI SHIK RHA

Polish Journal of Microbiology , ISSUE 2, 211–216

Short Communication

Analyses of Plasmids Harbouring Quinolone Resistance Determinants in Enterobacteriaceae Members

The aim of this study was to explore the plasmid characteristics of eight clinical Enterobacteriaceae strains containing extended broad spec­trum beta-lactamases and plasmid-mediated quinolone resistance. Plasmids were transferred by conjugation or transformation and resist­ance determinants were investigated by PCR. We showed that at least one plasmid harbouring qnrB or qnrS determinant was transferred by conjugation in five isolates. QepA determinant was confirmed to be on a non

Bayri Erac, Fethiye Ferda Yilmaz, Ismail Ozturk, Sabire Sohret Aydemir, Mine Hosgor-Limoncu

Polish Journal of Microbiology , ISSUE 4, 529–532

research-article

Effects of maternal thyroid hormone deficiency on differentiation of mesenchymal stem cells in CSF-exposed neonatal Wistar rats

dark blue formazan crystals. The effective CSF dosage and survival rate of cells were evaluated. BM-MSCs were exposed to HTH-CSF and N-CSF with concentrations of 0, 5%, 7%, 10 % (v/v) for 72 h. Next, the cells were incubated with MTT (5 mg/mL in PBS, Merck, Germany) at 37°C for 3 h. The formed formazan crystals were then dissolved in dimethyl sulfoxide (DMSO) (Sigma) and absorbance was measured at 570 nm via a plate reader (Stat fax 2100, USA) (Shokohi et al., 2018). Quantitative real-time PCR

Vida Mafikandi, Nasim Hayati Roodbari, Mohammad Nabiuni, Parichehreh Yaghmaei

Acta Neurobiologiae Experimentalis , ISSUE 3, 271–276

Research Article

GENETIC DIFFERENTIATION METHODS OF MICROORGANISMS IN THE SOIL – PLANT SYSTEM

Małgorzata Łyszcz, Anna Gałązka

Postępy Mikrobiologii - Advancements of Microbiology , ISSUE 3, 341–352

Original Paper

Bacterial Communities from the Arsenic Mine in Złoty Stok, Sudety Mountains, Poland

Investigations of bacterial communities and characterization of mineralogy of the environment in the Złoty Stok As-Au deposit werecarried out. PXRD analysis revealed the presence of picropharmacolite as the most common secondary arsenic mineral in the mine. Total DNA was extracted from slime streams or slime biofilms samples to investigate the bacterial communities. PCR amplification of 16S rDNA was performed followed by subcloning of its products. Over 170 clones were analyzed by means of RFLP

Tomasz Cłapa, Dorota Narożna, Rafał Siuda, Andrzej Borkowski, Marek Selwet, Cezary J. Mądrzak, Ewa Koźlecka

Polish Journal of Microbiology , ISSUE 3, 375–381

research-article

First report of Meloidogyne naasi parasitizing turfgrass in Portugal

tip and collected in 20 μl sterilized MilliQ water and stored at −20°C (Harris et al., 1990). PCR with the species-specific primers N-ITS/R195 was performed as described in Zijlstra et al. (2004). DNA extracts from J2 of a Meloidogyne incognita (Kofoid and White, 1919) Chitwood, 1949 isolate were included as a negative control. An expected PCR product of ca. 430 bp was obtained and no amplification was detected for the M. incognita DNA. To confirm the identification, partial 28S sequences were

M. Clara Vieira dos Santos, M. Teresa M. Almeida, Sofia R. Costa

Journal of Nematology , 1–4

research-article

Description of Hirschmanniella dicksoni n. sp. (Nematoda: Pratylenchidae) from rhizosphere soil of limpograss from Florida, USA

). Nematodes were picked and transferred to a PCR tube and killed with hot (95°C) 4% formalin. The PCR tube with heat-killed nematodes was immediately placed in a thermo cycler: 95°C for 2 min, 65°C for 10 min, 75°C for 10 min, 85°C for 10 min, and 95°C for 10 min. After the tube reached room temperature, the tube was rinsed with distilled water and the content was transferred to a staining dish. Nematodes were picked out and transferred to a glass slide with cavity filled with a mixture of glycerol and

Alemayehu W. Habteweld, Faruk Akyazi, Soumi Joseph, William T. Crow, Eyualem Abebe, Tesfamariam Mekete

Journal of Nematology , 1–15

research-article

Investigating the synergic effects of valproic acid and crocin on BDNF and GDNF expression in epidermal neural crest stem cells

with the appropriate drug-containing medium. On the seventh day, total RNA was extracted from both control and treatment groups, cDNA was synthesized using the mRNA extracted from each sample, and real-time PCR was performed. Cell viability test To determine the non-toxic doses of VPA (Darou Pakhsh Pharma. Chem. Co, Iran) and crocin (Puyesh Darou Sina, Iran), an MTT assay was performed. EPI-NCSCs were seeded in 96-well plates, at a density of 5×103 cells/well, 24 h prior to treatment. Then, EPI

Zahra Baharvand, Mohammad Nabiuni, Mohammad Tahmaseb, Elaheh Amini, Sareh Pandamooz

Acta Neurobiologiae Experimentalis , ISSUE 1, 38–46

Research Article

NOCARDIA SPP. – CHARACTERISTICS, PATHOGENICITY, TREATMENT

after immunosupression therapy. Nocardia asteroides is responsible for the majority of infections in humans. Diagnostic methods include cell culture and PCR. The symptoms vary depending on the form of the illness. Cough and hemoptysis are characteristic for pulmonary nocardiosis, while abscesses are typical for the cutaneous form. When the illness spreads, the symptoms vary depending on the organ. The treatment of choice is sulfonamide.

Michał Wiciński, Mateusz Maciej Węclewicz, Bartosz Malinowski, Jarosław Żak, Elżbieta Grześk, Grzegorz Grześk, Kamil Leis

Postępy Mikrobiologii - Advancements of Microbiology , ISSUE 1, 68–75

Research Article

NON-PANDEMIC HUMAN CORONAVIRUSES – CHARACTERISTICS AND DIAGNOSTICS

, nasopharyngitis, cough, bronchiolitis, pneumonia. Infections due to HCoV occur during the whole human life, but aremost frequent in children. They can occur throughout the year, but are most common in the winter season. Treatment of HCoV infections is usually symptomatic. Diagnosis of HCoV is mainly based on molecular technics such as quantitative PCR. Serological tests are only used for epidemiological purposes.

Edyta Abramczuk, Katarzyna Pancer, Włodzimierz Gut, Bogumiła Litwińska

Postępy Mikrobiologii - Advancements of Microbiology , ISSUE 2, 205–213

Original Paper

Characterization of Rhizobial Bacteria Nodulating Astragalus corrugatus and Hippocrepis areolata in Tunisian Arid Soils

Fifty seven bacterial isolates from root nodules of two spontaneous legumes (Astragalus corrugatus and Hippocrepis areolata) growing in the arid areas of Tunisia were characterized by phenotypic features, 16S rDNA PCR-RFLP and 16S rRNA gene sequencing. Phenotypically, our results indicate that A. corrugatus and H. areolata isolates showed heterogenic responses to the different phenotypic features. All isolates were acid producers, fast growers and all of them used different compounds as sole

Mosbah Mahdhi, Nadia Houidheg, Neji Mahmoudi, Abdelhakim Msaadek, Mokhtar Rejili, Mohamed Mars

Polish Journal of Microbiology , ISSUE 3, 331–339

Research Article

First report of Pratylenchus vulnus associated with apple in Tunisia

. Microscopic observation of females and males demonstrated the occurrence of Pratylenchusd vulnus on apple trees. The ribosomal DNA D2-D3 expansion segments of the 28S rRNA and of the Pratylenchus populations were PCR amplified and sequenced. The sequences were compared with those of Pratylenchus species in the GenBank database with high similarity (99%). This comparison reconfirmed the morphological identifications. Phylogenetic studies placed those populations with P. vulnus. This is the first report of

Noura Chihani-Hammas, Lobna Hajji-Hedfi, Hajer Regaieg, Asma Larayedh, Ahmed Badiss, Yu Qing, Horrigue-Raouani Najet

Journal of Nematology , ISSUE 4, 579–586

Original Paper

Expression of the Fluoroquinolones Efflux Pump Genes acrA and mdfA in Urinary Escherichia coli Isolates

Escherichia coli is one of the most frequent causes of urinary tract infections. Efflux system overexpression is reported to contribute to E. coli resistance to several antibiotics. Our aim in this study was to investigate the relation between antibiotic resistance and the expres­sion of the efflux pump genes acrA and mdfA in E. coli by real-time reverse transcription-PCR. We tested the in vitro susceptibilities to 12 antibiotics in 28 clinical isolates of E. coli obtained from urine

Sarah M. Abdelhamid, Rania R. Abozahra

Polish Journal of Microbiology , ISSUE 1, 25–30

Original Paper

The Prevalence of Exoenzyme S Gene in Multidrug-Sensitive and Multidrug-Resistant Pseudomonas aeruginosa Clinical Strains

to evaluate, using PCR, the occurrence of exoenzyme S-coding gene (exoS) in two distinct groups of P. aeruginosa strains: 83 multidrug-sensitive (MDS) and 65 multidrug-resistant (MDR) isolates. ExoS gene was noted in 72 (48.7%) of the examined strains: 44 (53.0%) MDS and 28 (43.1%) MDR. The observed differ­ences were not statistically significant (p = 0.1505). P. aeruginosa strains virulence is rather determined by the expression regulation of the possessed genes than the difference in genes

Tomasz Bogiel, Aleksander Deptuła, Joanna Kwiecińska-Piróg, Małgorzata Prażyńska, Agnieszka Mikucka, Eugenia Gospodarek-Komkowska

Polish Journal of Microbiology , ISSUE 4, 427–431

original-paper

Impact of Hydrogen on the Transcriptome of Sinorhizobium meliloti 1021 Using RNA-sequencing Technology

synthesized using Second Strand Synthesis Enzyme Mix (New England Biolabs). It was purified using AxyPrep Mag PCR Clean-up (Axygen) and treated with End Prep Enzyme Mix (Axygen) to repair both ends and add dA-tails in a single reaction. Following end-repair and adaptor ligation, RNA-seq data were obtained using a HiSeq instrument (Illumina, San Diego, CA, USA). Data analysis. As the genome of S. meliloti 1021 has already been sequenced, DNA microarrays can be used to study the regulation of gene

RUIRUI LIU, LULU LI, ZHIYING LI, WEIWEI WANG

Polish Journal of Microbiology , ISSUE 1, 39–48

original-paper

A Polyclonal Spread Emerged: Characteristics of Carbapenem-Resistant Klebsiella pneumoniae Isolates from the Intensive Care Unit in a Chinese Tertiary Hospital

). The genes encoding carbapenemases were investigated by polymerase chain reaction (PCR) using a series of primers as previously reported (Queenan and Bush 2007; Nordmann et al. 2011). The amplification products were sent for DNA sequencing (Qingke Biotech, Hangzhou). Isolates genotyping. CRKP isolates in the study were genotyped by multilocus sequence typing (MLST). Seven housekeeping genes including gapA, infB, mdh, pgi, phoE, rpoB, and tonB of K. pneumoniae were amplified and sequenced based on

ZHENGZHENG WANG, FANGYOU YU, XIAOFEI SHEN, MEILAN LI

Polish Journal of Microbiology , ISSUE 3, 311–319

research-article

A loop-mediated isothermal amplification assay for the plant-parasitic nematode Aphelenchoides besseyi in rice seedlings

Cartagena and the Inter-African Phytosanitary Council also considered it of quarantine significance (OEPP/EPPO, 1992). Currently, the World Trade Organization members follow the International Standards For Phytosanitary Measures (ISPMs) for nematode isolation from symptomatic plant or suspected plant materials. In ISPM, the identification of A. besseyi is based on morphology characteristics and PCR assays (IPPC, 2016). Compared to common plant-parasitic nematodes in the same genus, such as A

Jiue-in Yang, Guan-yi Yu

Journal of Nematology , 1–11

Original Paper

Carbapenem-resistant Acinetobacter baumannii from Air and Patients of Intensive Care Units

isolates. Resistance and resistance genes were detected by drug susceptibility test and PCR. The results demonstrated that all isolates can be classified into eight PFGE types and four sequence types (ST208, ST195, ST369 and ST530). A pair of isolates from patients (TAaba004) and from the air (TAaba012) that share 100% similarity in PFGE was identified, indicating that air might be a potential and important transmission route for A. baumannii. More than 80% of the isolates were resistant to carbapenems

MEIJIE JIANG, YUNQING MU, NING LI, ZHIJUN ZHANG, SHULIN HAN

Polish Journal of Microbiology , ISSUE 3, 333–338

Original Paper

Culturable Endophytes Diversity Isolated from Paeonia ostii and the Genetic Basis for Their Bioactivity

were classed into six families and 12 genera based on ITS gene sequence. The biosynthetic potential of all the endophytes was further investigated by the detection of putative polyketide synthase (PKS) and nonribosomal peptide synthetase (NRPS) genes. The PCR screens were successful in targeting thirteen bacterial PKS, five bacterial NRPS, ten fungal PKS and nine fungal NRPS gene fragments. Bioinformatic analysis of these detected endophyte gene fragments facilitated inference of the potential

RUI-XIAN YANG, SHAO-WEN ZHANG, DONG XUE, JUN-HAO XUAN, YUAN-BO ZHANG, BIAO-BIAO PENG

Polish Journal of Microbiology , ISSUE 4, 441–454

original-paper

Antibiotic Susceptibility of Cronobacter spp. Isolated from Clinical Samples

genes (encoding TEM, SHV, and CTX-M types of β-lactamases) was performed by PCR in all Cronobacter spp. isolates examined. As positive controls, the following strains were used: Escherichia coli NCTC 13400 (blaCTX-M-15), E. coli NCTC 13351(blaTEM-3) and Klebsiella pneumoniae NCTC 13368 (blaSHV-18). Total bacterial DNA was isolated from an overnight culture of the isolates (16 h, 37°C) grown on meatpeptone agar. Two colonies were suspended in 100 μl of water and heated at 95°C for 10 min. After

ONDŘEJ HOLÝ, ABDLRHMAN ALSONOSI, IGOR HOCHEL, MAGDALÉNA RÖDEROVÁ, SIMONA ZATLOUKALOVÁ, PATRIK MLYNÁRČIK, MILAN KOLÁŘ, JANA PETRŽELOVÁ, AIYDA ALAZRAQ, DITTMAR CHMELAŘ, STEPHEN FORSYTHE

Polish Journal of Microbiology , ISSUE 1, 5–14

Research Article

First Reports, Morphological, and Molecular Characterization of Longidorus caespiticola and Longidorus poessneckensis (Nematoda: Longidoridae) from Ukraine

processed to glycerol and mounted on permanent slides and subsequently identified morphologically and molecularly. Nematode DNA was extracted from single individuals and PCR assays were conducted as previously described for D2–D3 expansion segments of 28S rRNA. Sequence alignments for D2–D3 from L. caespiticola showed 97%–99% similarity to other sequences of L. caespiticola deposited in GenBank from Belgium, Bulgaria, Czech Republic, Russia, Slovenia, and Scotland. Similarly, D2–D3 sequence alignments

SOLOMIA SUSULOVSKA, PABLO CASTILLO, ANTONIO ARCHIDONA-YUSTE

Journal of Nematology , ISSUE 4, 396–402

Original Paper

Gas Gangrene of Different Origin Associated with Clostridium perfringens Type A in Three Patients Simultaneously Hospitalized in a Single Department of Orthopedics and Traumatology in Poland

April 2015 and 20th April 2015. The three C. perfrin­gens isolates studied had identical biochemical profiles. Two isolates had identical resistance patterns, while the third presented a different profile. Using the multiplex PCR method, all isolates showed the presence of cpa gene encoding α-toxin; furthermore, the presence of the cpb2 gene encoding β2-toxin was confirmed in two isolates. Genotyping with the use of pulsed field gel electrophoresis (PFGE) indicated that the isolates

Monika Brzychczy-Włoch, Dorota Ochońska, Anna Piotrowska, Małgorzata Bulanda

Polish Journal of Microbiology , ISSUE 4, 399–406

original-paper

Dependence of Colonization of the Large Intestine by Candida on the Treatment of Crohn’s Disease

articles describing the study of anti-Candida antibodies and methods based on the fungi cultures (McKenzie et al. 1990; Standaert-Vitse et al. 2006; Standaert-Vitse et al. 2009). Hence, the primary objective of the present study was to determine if there are quantitative differences in Candida fungi (by quantitative real-time PCR (qPCR)) between pediatric patients with CD and healthy controls. Another aim of this study was to compare the quantitative differences in Candida fungi in the newly diagnosed

KINGA KOWALSKA-DUPLAGA, AGNIESZKA KRAWCZYK, AGNIESZKA SROKA-OLEKSIAK, DOMINIKA SALAMON, ANDRZEJ WĘDRYCHOWICZ, KRZYSZTOF FYDEREK, TOMASZ GOSIEWSKI

Polish Journal of Microbiology , ISSUE 1, 121–126

Research Article

FRANCISELLA TULARENSIS – REVIEW 

. mediasiatica isolated mostly in Asia and F. tularensis subsp. novicida, non-pathogenic to humans. Due to its ability to infect and variable forms of the disease, the etiological agent of tularaemia is classified by the CDC (Centers for Disease Control and Prevention, USA) as a biological warfare agent with a high danger potential (group A). The majority of data describing incidence of tularaemia in Poland is based on serological tests. However, real-time PCR method and MST analysis of F. tularensis highly

Piotr Cieślik, Józef Knap, Agata Bielawska-Drózd

Postępy Mikrobiologii - Advancements of Microbiology , ISSUE 1, 58–67

Original Paper

Molecular Study of Indigenous Bacterial Community Composition on Exposure to Soil Arsenic Concentration Gradient

Community structure of bacteria present in arsenic contaminated agricultural soil was studied with qPCR (quantitative PCR) and DGGE (Denaturing Gradient Gel Electrophoresis) as an indicator of extreme stresses. Copy number of six common bacterial taxa (Acidobacteria, Actinobacteria, α-, β- and γ-Proteobacteria, Firmicutes) was calculated using group specific primers of 16S rDNA. It revealed that soilcontaminated with low concentration of arsenic was dominated by both

Semanti Basu, Tanima Paul, Priya Yadav, Abhijit Debnath, Keka Sarkar

Polish Journal of Microbiology , ISSUE 2, 209–221

Original Paper

Emergence of High-level Gentamicin Resistance among Enterococci Clinical Isolates from Burn Patients in South-west of Iran: Vancomycin Still Working

concentration (MIC) was evaluated by agar microdilution. Vancomycin and gentamicin resistance associated genes including vanA, vanB, vanC, aac (6’)-Ie aph(2’’), aph(3’)-IIIa and ant(4’)-Ia were detected by PCR and their statistical relation with antibiotic resistance was evaluated. E. faecalis was the more prevalent strain among our local isolates and showed a higher antibiotic resistance in comparison to E. faecium. Vancomycin had a good antibacterial effect on the

MARYAM LABIBZADEH, GHOLAM ABBAS KAYDANI, MOHAMMAD SAVARI, ALIREZA EKRAMI

Polish Journal of Microbiology , ISSUE 4, 401–406

original-paper

Dengue Outbreaks in Khyber Pakhtunkhwa (KPK), Pakistan in 2017: An Integrated Disease Surveillance and Response System (IDSRS)-Based Report

using ELISA, according to the guidelines of the manufacturer (Platelia Biorad Lab, Marnes-la-Coquette, France) (Lutfullah et al. 2017). In case of positive result, the treatment had been started immediately without any delay; however, in case of the weak positive or ambiguous result of NS1 antigen, the samples were processed with a thermal cycler. PCR. To confirm the presence of dengue virus in the samples, the protocol adopted by Khan et al. (2017) was followed. Briefly, RNA was extracted and

ABDULLAH, SHER ALI, MUHAMMAD SALMAN, MISBAHUD DIN, KACHKOL KHAN, MUNIB AHMAD, FAISAL HAYAT KHAN, MUHAMMAD ARIF

Polish Journal of Microbiology , ISSUE 1, 115–119

original-paper

Performance Evaluation of Different Commercial Serological Kits for Diagnosis of Acute Hepatitis E Viral Infection

commercial serological assays and PCR assay for the detection of HEV infection was evaluated, and the possibility of misdiagnosing of this infection using serological detection alone was determined. Experimental Materials and Methods Samples. From March 2014 to March 2018, 364 serum samples were collected from Tianjin Third Central Hospital and Tianjin Medical University General Hospital. A total of 86 cases were diagnosed with acute viral hepatitis E (Kamar et al. 2014; European Association for the

QIANG ZHANG, XIAOLONG ZONG, DONGMING LI, JING LIN, LIHUA LI

Polish Journal of Microbiology , ISSUE 2, 217–222

original-paper

Characterization of Two Macrolide Resistance-Related Genes in Multidrug-Resistant Pseudomonas aeruginosa Isolates

the accumulated nucleotide length of the mapped short reads on the gene divided by the gene size (Wu et al. 2018). Screening of the macrolide-resistant gene-positive strains and cloning of the mphE and msrE genes. As mentioned above, to confirm the presence of the genes related to macrolides resistance, P. aeruginosa strains were screened by PCR, and the positive PCR products were sequenced. The primers for cloning the complete ORFs with promoter regions and a pair of flanking restriction

QING CHEN, WEI LU, DANYING ZHOU, GUOTONG ZHENG, HONGMAO LIU, CHANGRUI QIAN, WANGXIAO ZHOU, JUNWAN LU, LIYAN NI, QIYU BAO, AIFANG LI, TENG XU, HAILI XU

Polish Journal of Microbiology , ISSUE 3, 349–356

Research paper

Aberrant changes of somatostatin and neuropeptide Y in brain of a genetic rat model for epilepsy: tremor rat

(TRM)is a genetic epileptic animal model which can manifest tonic convulsions without any external stimuli. The present study aimed to investigate the distribution and expression of SST and NPY in TRM brains, including hippocampus, temporal lobe cortex and cerebellum.Our RT‑PCR data showed that up‑regulated mRNA expression of SST and NPY was discovered in TRM hippocampus and temporal lobe cortex compared with control (Wistar) rats. The peptide levels of these neuropeptides in brain areas mentioned

Xiaoxue Xu, Feng Guo, Xinze Cai, Jun Yang, Jiuhan Zhao, Dongyu Min, Qianhui Wang, Liying Hao, Jiqun Cai

Acta Neurobiologiae Experimentalis , ISSUE 3, 165–175

Original Paper

Streptococcus anginosus (milleri) Group Strains Isolated in Poland (1996–2012) and their Antibiotic Resistance Patterns

diffusion tests and E-Tests. We also performed PCR detection of resistance determinants in antibiotic resistant strains. Clonal structure of analyzed strains was evaluated with PFGE and MLVF methods. All three species are difficult to distinguish using automated diagnostic methods and the same is true for automated MIC evaluation. Our analysis revealed SAG strains are rarely isolated in Poland, predominantly from purulent infections. All isolates are very diverse on the genomic level as estimated by

Katarzyna Obszańska, Izabella Kern-Zdanowicz, Aleksandra Kozińska, Katarzyna Machura, Elżbieta Stefaniuk, Waleria Hryniewicz, Izabela Sitkiewicz

Polish Journal of Microbiology , ISSUE 1, 33–41

Original Paper

Non-invasive Diagnostic of Helicobacter pylori in Stools by Nested-qPCR

The aim of this study was to develop a non-invasive diagnostic test for the detection of Helicobacter pylori in stool samples from digestive symptomatic patients, using a new protocol of nested-qPCR. A total of 143 patients were invited to participate in the study. A gastric biopsy of each patient was collected for Rapid Urease Testing (RUT) and histology by Giemsa stain. A fecal sample for nested-qPCR analysis was also obtained. DNA was extracted from the fecal samples, and conventional PCR

María I. Taborda, Gisela Aquea, Yenny Nilo, Karla Salvatierra, Nicolás López, Sergio López, Gustavo Bresky, Juan A. Madariaga, Vittorio Zaffiri, Sergio Häberle, Giuliano Bernal

Polish Journal of Microbiology , ISSUE 1, 11–18

Original Paper

Evaluation of Modified Hodge Test as a Non-molecular Assay for Accurate Detection of KPC-producing Klebsiella pneumoniae

the capacity of MHT with two carbapenem disks for accurate detection of KPC. MHT was performed according to guidelines of CLSI to identify isolates with carbapenem resistance. In doing so, two substrates of MHT were assigned into two groups for examination: meropenem and ertapenem groups. A total of 96 non-repetitive clinical isolates of Klebsiella pneumoniae were tested. The presence of the blaKPC gene in each MHT-positive isolate was examined by PCR. A total of 54 isolates exhibited reduced

ATOSSA GHASEMNEJAD, MONIR DOUDI, NOUR AMIRMOZAFARI

Polish Journal of Microbiology , ISSUE 3, 291–295

Original Paper

Epilithic Biofilms in Lake Baikal: Screening and Diversity of PKS and NRPS Genes in the Genomes of Heterotrophic Bacteria

synthetases) genes. PKS genes were detected in 41 strains (25%) and NRPS genes in 73 (43%) strains by PCR analysis. The occurrence of PKS genes in members of the phylum Firmicutes (the genera Bacillus and Paenibacillus) was 34% and NRPS genes were found in 78%. In Proteobacteria, PKS and NRPS genes were found in 20% and 32%, and in 22% and 22% of Actinobacteria, respectively. For further analysis of PKS and NRPS genes, six Bacillus and Paenibacillus strains with antagonistic activity were selected and

ELENA SUKHANOVA, EKATERINA ZIMENS, OKSANA KALUZHNAYA, VALENTINA PARFENOVA, OLGA BELYKH

Polish Journal of Microbiology , ISSUE 4, 501–516

original-paper

Predominance of Lactobacillus plantarum Strains in Peruvian Amazonian Fruits

characteristics of the LAB are common to all strains in a species, the characteristics of interest generally are specific to a strain, and for this reason, a method of strain discrimination should be applied (Kingston et al. 2010). The method most widely used for strain discrimination in LAB has been PCR amplification using the primers M13 (Andrighetto et al. 2001) or GTG5 (Gevers et al. 2001). The main focus of the present study was the isolation of LAB from Peruvian Amazonian fruits and their identification

JOHANNA SÁNCHEZ, CARLOS VEGAS, AMPARO IRIS ZAVALETA, BRAULIO ESTEVE-ZARZOSO

Polish Journal of Microbiology , ISSUE 1, 127–137

Original Paper

The Heavy-Metal Resistance Determinant of Newly Isolated Bacterium from a Nickel-Contaminated Soil in Southwest Slovakia

. Finally, the results from RT-PCR analysis showed that MR-CH-I2-nccA gene was significantly induced only by the addition of nickel.

MATEJ REMENÁR, ANNA KAMLÁROVÁ, JANA HARICHOVÁ, MARCEL ZÁMOCKÝ, PETER FERIANC

Polish Journal of Microbiology , ISSUE 2, 191–201

original-paper

Analysis of the Amino Acid Sequence Variation of the 67–72p Protein and the Structural Pili Proteins of Corynebacterium diphtheriae for their Suitability as Potential Vaccine Antigens

Columbia agar with 5% sheep blood (BioMerieux) for 24 h at 37°C under aerobic conditions. Genomic DNA was isolated using a Wizard Genomic DNA Purification Kit (Promega) according to the Gram-positive bacteria procedure provided by the manufacturer. Polymerase Chain Reaction (PCR). The oligonucleotide primers for amplification of the genes coding 67–72p protein and structural pili proteins (SpaC, SpaI, SapD) were designed based on the nucleotide sequence of the C. diphtheriae NCTC 13129 whole genome

KLAUDIA BRODZIK, KATARZYNA KRYSZTOPA-GRZYBOWSKA, MACIEJ POLAK, JAKUB LACH, DOMINIK STRAPAGIEL, ALEKSANDRA ANNA ZASADA

Polish Journal of Microbiology , ISSUE 2, 233–246

research-paper

miRNA-223-3p and let-7b-3p as potential blood biomarkers associated with the ischemic penumbra in rats

were used, including three penumbra brain tissue samples, three sham samples from the corresponding area of the rat brain, three blood samples from ischemic rats and three blood samples from sham rats. Detection of miRNA expression with qRT-PCR According to the results of the miRNA profiling analysis, the expression level of selected miRNAs in all the pMCAO- and sham-treated rats was further confirmed by quantitative real-time polymerase chain reaction (qRT-PCR). One microgram of total RNA was

Shenghua Li, Lan Chen, Xia Zhou, Jinpin Li, Jingli Liu

Acta Neurobiologiae Experimentalis , ISSUE 2, 205–216

original-paper

Evidence for Infections by the Same Strain of Beta 2-toxigenic Clostridium perfringens Type A Acquired in One Hospital Ward

- amoxicillin/clavulanic acid, CRO - ceftriaxone, CTX - cefotaxime, DOR - doripenem, ETP - ertapenem, IMP - imipenem, MEM - meropenem, MXF - moxifloxacin, TEC - teicoplanin, VA - vancomycin, E - erythromycin, DA - clindamycin, TE - tetracycline, C - chloramphenicol, M - metronidazole, RD - rifampicin, MIC - Minimal Inhibitory Concentration, S/R - susceptibility, R - resistant, S - susceptible PCR multiplex. To isolate DNA, the Genomic Mini Set (A&A Biotechnology) was used according to the manufacturer’s

DOMINIKA SALAMON, DOROTA OCHOŃSKA, ILONA WOJAK, EWA MIKOŁAJCZYK, MAŁGORZATA BULANDA, MONIKA BRZYCHCZY-WŁOCH

Polish Journal of Microbiology , ISSUE 3, 323–329

original-paper

Isolation and Identification of Chlamydia abortus from Aborted Ewes in Sulaimani Province, Northern Iraq

usually spreads into a new flock by the introduction of infected animals. The disease usually causes a small number of abortions in the first year. In the next year, the rate may increase to infect around 30% of the ewes (Longbottom and Coulter 2003). Etiologic diagnosis of ovine chlamydiosis depends on bacteriological testing on embryonated chicken eggs and chlamydial DNA amplification by polymerase chain reaction (PCR) (Sachse et al. 2009, Szymanska-Czerwinska et al. 2013). Infections of C. abortus

EMAN DHAHIR ARIF, NAHLA MUHAMMAD SAEED, SHWAN KAMAL RACHID

Polish Journal of Microbiology , ISSUE 1, 65–71

original-paper

Molecular Identification and Prevalence of Entamoeba histolytica, Entamoeba dispar and Entamoeba moshkovskii in Erbil City, Northern Iraq

likely inflated as a result of false positives caused by the morphologically indistinguishable, nonpathogenic E. dispar/moshkovskii, and/or polymorphic nuclear leukocytes and macrophages with similar morphology in the stool samples (Walsh 1986; Tanyuksel and Petri 2003). New methods have been developed that are better in distinguishing between the pathogenic E. histolytica and nonpathogenic amoebae in the stool sample. Emerging molecular-based techniques, such as polymerase chain reaction (PCR), have

SHLER AKRAM FAQE MAHMOOD, HAWRI MUSTAFA BAKR

Polish Journal of Microbiology , ISSUE 3, 263–272

Original Paper

Molecular Characterization of Shiga Toxin-Producing Escherichia coli Strains Isolated in Poland

distribution of various virulence determinants among STEC strains isolated in Poland from different sources. A total of 71 Shiga toxin-producing E. coli strains isolated from human, cattle and food over the years 1996–2010 were characterized by microarray and PCR detection of virulence genes. As stx1a subtype was present in all of the tested Shiga toxin 1 producing E. coli strains, a greater diversity of subtypes was found in the gene stx2, which occurred in five subtypes: stx2a, stx2b, stx2c, stx2d

Aleksandra Januszkiewicz, Waldemar Rastawicki

Polish Journal of Microbiology , ISSUE 3, 261–269

Original Paper

Genetic Characterization of a Novel Composite Transposon Carrying armA and aac(6)-Ib Genes in an Escherichia coli Isolate from Egypt

the frequency of 16S-RMTase among third generation cephalosporin-resistant clinical isolates in Egypt. One hundred and twenty three cephalosporin resistant Gram-negative clinical isolates were screened for aminoglycosides resistance by the Kirby Bauer disk diffusion method and tested for possible production of 16S-RMTase. PCR testing and sequencing were used to confirm the presence of 16S-RMTase and the associated antimicrobial resist­ance determinants, as well as the genetic region

Mona T. Kashef, Omneya M. Helmy

Polish Journal of Microbiology , ISSUE 2, 163–169

short-communication

Evaluation of a Salmonella Strain Isolated from Honeybee Gut as a Potential Live Oral Vaccine Against Lethal Infection of Salmonella Typhimurium

Salmonella species from the biochemical tests were further subjected to polymerase chain reaction (PCR) by amplifying the 16S rRNA gene and further sequencing of the amplicons. The DNA extraction was performed using Genomic Isolate II DNA extraction kit (Bio line, London, UK) by following the instructions provided in the user manual for cultured cells. The NANODROP 8000 spectrophotometer (Thermo Scientific, USA) was used for the quantification of the DNA concentration in the samples. For the

HASSAN ZAFAR, SAJJAD UR RAHMAN, SULTAN ALI, MUHAMMAD TARIQ JAVED

Polish Journal of Microbiology , ISSUE 2, 173–183

research-article

A COI DNA barcoding survey of Pratylenchus species in the Great Plains Region of North America

Interference Contrast and a Leica DC300 video camera. Each nematode was assigned a unique Nematode Identification number (NID). The NID number links images, measurements and DNA of each individual nematode specimen. Usually five individual specimens from each sample were mounted, measured, and photographed in this manner. Images were archived in the database system of the Nematology Laboratory at the University of Nebraska-Lincoln. For PCR amplification, image-vouchered specimens were removed from

Mehmet Ozbayrak, Tim Todd, Timothy Harris, Rebecca Higgins, Kirsten Powers, Peter Mullin, Lisa Sutton, Thomas Powers

Journal of Nematology , 1–21

research-article

Intracerebroventricular streptozotocin induces behavioral impairments and increases short-term C3 gene expression in the hippocampus of Wistar rats

, respectively (phase 2, Fig. 1). Fig. 1. Representative flowchart of experimental groups and main methodologies used in this study, including behavioral tasks and real-time quantitative reverse transcription PCR (qRT-PCR). Animals that received the drug are represented by STZ group and those whose did not, by control group. Besides that, phase 1 and phase 2 represents short (one month after surgery) and long (four months after surgery) term exposures. The experiments were carried out in accordance with

Gabrielle Pfutzenreuter, Kenny Nieradka, Márcia Regina Pincerati, Ilton Santos da Silva

Acta Neurobiologiae Experimentalis , ISSUE 2, 160–169

Article

First Report of the Spiral Nematode Rotylenchus incultus (Nematoda: Hoplolaimidae) from Cultivated Olive in Tunisia, with Additional Molecular Data on Rotylenchus eximius

shovel from the upper 50 cm of soil from arbitrarily chosen olive trees. Nematodes were extracted from 500 cm3 of soil by centrifugal flotation method (Coolen, 1979). Specimens were heat killed by adding hot 4% formaldehyde solution and processed to pure glycerin using the De Grisse’s (1969) method. Measurements were done using a drawing tube attached to a Zeiss III compound microscope. Nematode DNA was extracted from single individuals and PCR assays were conducted as described by Castillo et

ILHEM GUESMI-MZOUGHI, ANTONIO ARCHIDONA-YUSTE, CAROLINA CANTALAPIEDRA-NAVARRETE, HAJER REGAIEG, NAJET HORRIGUE-RAOUANI, JUAN E. PALOMARES-RIUS, PABLO CASTILLO

Journal of Nematology , ISSUE 3, 136–138

Research paper

BDNF expression in cat striate cortex is regulated by binocular pattern deprivation

months (2BD, 4BD, 6BD), and late onset BD for 2 months upon 2 months of normal vision (2N2BD), as animal models of congenital and delayed onset cataract. During normal cortical development the BDNF transcript levels, measured by quantitative RT-PCR, remained stable. Higher BDNF mRNA levels were found in central area 17 of 2BD and 6BD animals compared to age-matched controls. In central area 17, the high BDNF mRNA levels at the end of the BD period may activate a mechanism by which plastic processes

Karolina Laskowska-Macios, Lutgarde Arckens, Małgorzata Kossut, Kalina Burnat

Acta Neurobiologiae Experimentalis , ISSUE 3, 199–204

original-paper

In Vitro and In Vivo Activity of Zabofloxacin and Other Fluoroquinolones Against MRSA Isolates from A University Hospital in Egypt

by culturing the bacteria on Muller-Hinton agar (Oxoid) at 37°C for 18 h following serial dilution. The anti bio tic was considered as bactericidal at a concentration, which decreased the control count by 3 log CFU/ml (99.9%) at specified time intervals. The procedure was performed in triplicates and a graph of the log CFU/ml was then plotted against time with calculation of standard deviation. Quinolone resistance-determining region (QRDR) sequence analysis. PCR was used to amplify the QRDRs of

NELLY M. MOHAMED, AZZA S. ZAKARIA, EVA A. EDWARD, AMANY ABDEL-BARY

Polish Journal of Microbiology , ISSUE 1, 59–69

Research Article

First Report of Stubby-Root Nematode, Paratrichodorus minor, on Onion in Georgia, U.S.A

of females (n = 20) included: body length 671.1 (570.1–785.3) µm; body width 32.5 (27.8–37.0) µm; onchiostyle 32.5 (31.1–34.8) µm; anterior end to esophagus-intestinal valve 117.6 (101.2–128.5) µm; a 21.5 (15.3–28.1) µm; b 5.2 (4.9–6.3) µm; V 52.9% (48.1–55.4%) µm; and vagina length 8.7 (7.8–10.7) µm. To confirm the identity of P. minor, DNA was extracted from single females (n = 3) using Extract-N-Amp™ Tissue PCR Kit (Sigma-Alredich Inc., St. Louis, MO). The partial 18S rRNA, the D2-D3 expansion

Abolfazl Hajihassani, Negin Hamidi, Bhabesh Dutta, Chris Tyson

Journal of Nematology , ISSUE 3, 453–455

research-article

First report of Meloidogyne javanica on Ginger and Turmeric in the United States

Abolfazl Hajihassani, Weimin Ye, Brooke B. Hampton

Journal of Nematology , 1–3

Original Paper

Trends of Bloodstream Infections in a University Greek Hospital during a Three-Year Period: Incidence of Multidrug-Resistant Bacteria and Seasonality in Gram-negative Predominance

. Antibiotic susceptibility testing was performed by the disk diffusion method and E-test. Resistance genes (mecA in staphylococci; vanA/vanB/vanC in enterococci; blaKPC/blaVIM/blaNDM in Klebsiella spp.) were detected by PCR. In total, 4607 (9.7%) blood cultures were positive from 47451 sets sent to Department of Microbiology, represent­ing 1732 BSIs. Gram-negative bacteria (52.3%) were the most commonly isolated, followed by Gram-positive (39.5%), fungi (6.6%) and anaerobes bacteria (1.8%). The

Fevronia Kolonitsiou, Matthaios Papadimitriou-Olivgeris, Anastasia Spiliopoulou, Vasiliki Stamouli, Vasileios Papakostas, Eleni Apostolopoulou, Christos Panagiotopoulos, Markos Marangos, Evangelos D. Anastassiou, Myrto Christofidou, Iris Spiliopoulou

Polish Journal of Microbiology , ISSUE 2, 171–180

Research Article

First Report of Cactodera estonica in Canada

consistent with those of C. estonica, for which the elongated cyst and short hyaline in J2 are characteristic for the species. Ribosomal DNA of the ITS, 18S, and D2/D3 of 28S regions were PCR amplified from cysts and J2s using primers 18S (5′-TTGATTACGTCCCTGCCCTTT-3′) and 26S (5′-TTTCACTCGCCGTTACTAAGG-3′) (Vrain et al., 1992), D2A (5′-ACAAGTACCGTGAGGGAAAGT-3′) (Nunn, 1992) and D3B (5′-GACCCGTCTTGAAACACGGA-3′) (De Ley et al., 1999), and sequenced. The sequences of the ITS and D2/D3 regions of 1,480 and

QING YU, FENGCHENG SUN

Journal of Nematology , ISSUE 4, 403–403

Report

First Report of the Spiral Nematode Helicotylenchus microlobus Infecting Soybean in North Dakota

identified as Helicotylenchus microlobus according to morphological and morphometric characteristics (Subbotin et al., 2015). DNA was extracted from single nematodes (n = 8) using the Proteinase K method (Kumari and Subbotin, 2012). The internal transcribed spacer (ITS) region of rDNA was amplified with the primers rDNA2/rDNA1.58S (Cherry et al., 1997). The PCR products were then purified and sequenced. The consensus ITS rDNA sequence (accession no. KY271078, 822 bp) that was

GUIPING YAN, ADDISON PLAISANCE, DANQIONG HUANG, ZAFAR A. HANDOO

Journal of Nematology , ISSUE 1, 1–1

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