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Volume 70 (2021): Issue 3 (September 2021)

Volume 70 (2021): Issue 2 (June 2021)

Volume 70 (2021): Issue 1 (March 2021)

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Volume 69 (2020): Issue 3 (September 2020)

Volume 69 (2020): Issue 2 (June 2020)

Volume 69 (2020): Issue 1 (March 2020)

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Volume 68 (2019): Issue 3 (September 2019)

Volume 68 (2019): Issue 2 (June 2019)

Volume 68 (2019): Issue 1 (March 2019)

Volume 67 (2018): Issue 4 (December 2018)

Volume 67 (2018): Issue 3 (September 2018)

Volume 67 (2018): Issue 2 (June 2018)

Volume 67 (2018): Issue 1 (January 2018)

Volume 66 (2017): Issue 4 (December 2017)

Volume 66 (2017): Issue 3 (September 2017)

Volume 66 (2017): Issue 2 (June 2017)

Volume 66 (2017): Issue 1 (March 2017)

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Volume 65 (2016): Issue 3 (August 2016)

Volume 65 (2016): Issue 2 (June 2016)

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Journal Details
Format
Journal
eISSN
2544-4646
First Published
04 Mar 1952
Publication timeframe
4 times per year
Languages
English

Search

Volume 67 (2018): Issue 1 (January 2018)

Journal Details
Format
Journal
eISSN
2544-4646
First Published
04 Mar 1952
Publication timeframe
4 times per year
Languages
English

Search

32 Articles

original-paper

Open Access

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

Published Online: 21 Feb 2022
Page range: 81 - 88

Abstract

Abstract

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 IFA were found as 100% for seronegative, 100% for acute primary infection, 22.2% for late primary infection, 92.1% for past infection. The rates of agreement between immunoblotting and IFA were found as 80.8% for seronegative, 68.8% for acute primary infection, 55.6% for late primary infection, 86.6% for past infection. The sensitivity of immunoblotting for anti-VCA IgM was identical with ELISA, and higher for anti-VCA IgG, anti-EBNA IgG, anti-EA antibodies, while the specificity of immunoblotting for these antibodies were found to be lower. The sensitivity and specificity of Real-time PCR for detection of viremia in acute primary infection were found as 56.25% (9/16) and 97.89% (139/142), respectively. The diagnostic methods should be chosen by evaluating the demographic characteristics of patients and laboratory conditions together.

Keywords

  • ELISA
  • Epstein-Barr virus
  • immunoblotting
  • Indirect Fluorescence Assay (IFA)
  • Real-time PCR
Open Access

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

Published Online: 21 Feb 2022
Page range: 11 - 18

Abstract

Abstract

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 followed by qPCR of the ureC gene of H. pylori was carried out. We evaluated the presence of H. pylori, in 103 females and 40 males, mean (± SD) age of 56.5 ± 14.18. The sensitivity of RUT to detect the infection was 67.0% (95% C.I.: 57.2 – 75.8) and specificity was 92.3% (95% C.I.: 76.5 – 99.1). Histology by Giemsa stain, commonly used as a reference for H. pylori detection, showed a sensitivity of 98.6% (95% C.I.: 92.5 – 100.0) and a specificity of 89.7% (95% C.I.: 72.7 – 97.8). In contrast, detection of H. pylori infection in stools by nested-qPCR showed a sensitivity of 100% (95% C.I.: 94.9 – 100.0) and a specificity of 83.9% (95% C.I.: 66.3 – 94.6). Our test, based in nested-qPCR is a better diagnostic alternative than conventional RUT, and is similar to histology by Giemsa stain in the detection of H. pylori, by which the test could be used for non-invasive diagnosis in clinical practice.

Keywords

  • molecular diagnostics
  • nested-qPCR
  • stools
Open Access

Detection of Acinetobacter spp. in Blood Cultures by an Improved Fluorescent in Situ Hybridization Assay

Published Online: 21 Feb 2022
Page range: 3 - 10

Abstract

Abstract

Fluorescent in situ hybridization (FISH) allows rapid detection of microorganisms. We aimed (i) to evaluate the sensitivity and specificity of FISH for the detection of Acinetobacter spp. in blood culture specimens and (ii) to test the simultaneous application of two genus-specific probes labeled with the same fluorochrome to increase the fluorescent signal intensity and improve the detection of Acinetobacter spp. Three hundred and twenty blood culture specimens were tested via both the conventional laboratory methods and FISH to detect Acinetobacter spp. The specimens were examined separately with each genus-specific probe Aci and ACA, and also using a mixture of the both probes Aci and ACA. In all examinations, probe EUB338 was used accompanied by Aci and ACA. The specificity of FISH was 100% (97.5% confidence interval [CI] = 98.7% – 100%). The sensitivity of FISH by the use of probe Aci was 96.4% (95% CI = 81.7% – 99.9%), whereas, the sensitivity of this technique by the use of probe ACA as well as by the combination of both probes Aci and ACA was 100% (97.5% CI = 87.7% – 100%). Moreover, simultaneous hybridization by probes Aci and ACA increased the fluorescent signal of Acinetobacter spp. cells to 3+ in 13 specimens. In conclusion, FISH, particularly using a combination of Aci and ACA, is a highly accurate method for the detection of Acinetobacter spp. in blood cultures. Furthermore, simultaneous hybridization by the both probes Aci and ACA can increase the fluorescent signal intensity of Acinetobacter spp. cells in some blood culture specimens and facilitate the detection of these microorganisms.

Keywords

  • bacteremia
  • blood culture
  • FISH
  • simultaneous hybridization
Open Access

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

Published Online: 21 Feb 2022
Page range: 19 - 26

Abstract

Abstract

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 32.1% of the 28 isolates analyzed, respectively. Surprisingly, reduced lengths of cry4B gene segments were detected in 28.6% of B. thuringiensis samples. The presence of cry10 or cyt1 was not detected in any of the 28 samples of B. thuringiensis, despite the high sensitivity of the assays used. The results show that B. thuringiensis samples from the Colombian Caribbean have atypical characteristics compared to those of Latin America and elsewhere in the world, which is consistent with the idea that the geographic origin of B. thuringiensis samples is associated with their biological and genetic characteristics.

Keywords

  • – Colombian strains
  • genes
  • larvae
  • PCR methods
  • biological test
Open Access

High-Throughput Sequencing Analysis of Endophytic Bacteria Diversity in Fruits of White and Red Pitayas from Three Different Origins

Published Online: 21 Feb 2022
Page range: 27 - 35

Abstract

Abstract

Pitaya contains various types of polyphenols, flavonoid and vitamins which are beneficial for health and it is among the most important commercial tropical fruits worldwide. Endophytic bacteria might be beneficial for plant growth and yield. However, bacterial diversity in pitaya is poorly characterized. In this study, fruits of white and red pitayas from three different origins (Thailand, Vietnam and China) were chosen for endophytic bacteria diversity investigation by using Illumina HiSeq second-generation high-throughput sequencing technology. Large number of endophytic bacteria were detected and 22 phyla, 56 classes, 81 orders, 122 families and 159 genera were identified. Endophytic bacteria diversity was uneven among pitaya fruits from different origins and bacteria structure was different between white pitaya group and red pitaya group. Phylum Bacteroidetes, classes Bacteroidia and Coriobacteriia, orders Bacteroidales and Coriobacteriales, families Prevotellaceae, Bacteroidaceae, Ruminococcaceae, Paraprevotellaceae, Rikenellaceae, Alcaligenaceae and Coriobacteriaceae, genera Prevotella, Bacteroides, Roseburia, Faecalibacterium and Sutterella were statistically significant different species (P < 0.05) between white and red pitayas. These findings might be useful for growth improvement, fruit preservation and processing of different pitaya species from different origins.

Keywords

  • endophytic bacteria diversity
  • high-throughput sequencing
  • pitaya from three different origins
Open Access

Natural Attenuation Potential of Polychlorinated Biphenyl-Polluted Marine Sediments

Published Online: 21 Feb 2022
Page range: 37 - 48

Abstract

Abstract

The marine environment in Kuwait is polluted with various hazardous chemicals of industrial origin. These include petroleum hydrocarbons, halogenated compounds and heavy metals. Bioremediation with dedicated microorganisms can be effectively applied for reclamation of the polluted marine sediments. However, information on the autochthonous microbes and their ecophysiology is largely lacking. We analyzed sediments from Shuwaikh harbor to detect polychlorinated biphenyls (PCBs) and total 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 showed the presence of members of the Proteobacteria, Spirochaetes, Firmicutes and Bacteroidetes in the analyzed sediments. However, Chloroflexi-related bacteria dominated the detected bacterial community. We also enriched a biphenyl-utilizing mixed culture using the W2 station sediment as an inoculum in chemically defined medium using biphenyl as a sole carbon and energy source. The enriched mixed culture consisted mainly of the Firmicute Paenibacillus spp. Sequences of genes encoding putative aromatic ring-hydroxylating dioxygenases were detected in sediments from most sampling stations and the enriched mixed culture. The results suggest the potential of bioremediation as a means for natural attenuation of Shuwaikh harbor sediments polluted with PCBs and TPHs.

Keywords

  • aromatic ring oxygenases
  • bacterial communities
  • bioremediation
  • Chloroflexi
  • DGGE
  • polluted marine sediments
Open Access

Isolation and Characteristics of Biotechnologically Important Antagonistic Thermophilic Bacteria from Rhizosphere of Haloxylon salicornicum

Published Online: 21 Feb 2022
Page range: 49 - 58

Abstract

Abstract

Rhizobacteria are an active part of microbial population in the rhizosphere of plants. In this study, twenty rhizobacteria were isolated from the rhizosphere of a perennial grass, Haloxylon salicornicum, found in Cholistan desert, an arid landmass near Bahawalpur Pakistan, in one set of experimental conditions. Colony characteristics, biochemical and molecular analyses of these isolates were performed. All isolates were bacilli, gram positive with off-white colonies and exhibited typical bacilli colony morphology. None of the isolates was gelatinase, urease, indole, H2S and catalase producer. Eleven isolates were amylase producers and 8 isolates were acid producers. All isolates fermented glucose, 3 fermented lactose and 19 fermented fructose. Molecular data revealed that out of twenty isolates, 14 isolates showed 91–99% identity with Brevibacillus borstelensis, 4 with Bacillus subtilis (97–98%) and 2 with Bacillus licheniformis (94–99%) through BLAST analysis. All identified bacterial isolates cladded with their respective groups in the phylogenetic tree. Many (11–15 out of 20) of the isolates were more effective in inhibiting growth of the tested bacterial strains as compared to the positive control (Ampicillin 50 μg/disc). We conclude that bacilli are the predominant form populating rhizosphere of this desert grass. Among the isolated bacteria Brevibacillus borstelensis, Bacillus subtilis and Bacillus licheniformis are the most predominant species.

Keywords

  • rhizobacteria
  • 16S rRNA for phylogenic analysis
  • rhizosphere on Cholistan desert
Open Access

A Low-Tech Bioreactor System for the Enrichment and Production of Ureolytic Microbes

Published Online: 21 Feb 2022
Page range: 59 - 65

Abstract

Abstract

Ureolysis-driven microbially induced carbonate precipitation (MICP) has recently received attention for its potential biotechnological applications. However, information on the enrichment and production of ureolytic microbes by using bioreactor systems is limited. Here, we report a low-tech down-flow hanging sponge (DHS) bioreactor system for the enrichment and production of ureolytic microbes. Using this bioreactor system and a yeast extract-based medium containing 0.17 M urea, ureolytic microbes with high potential urease activity (> 10 μmol urea hydrolyzed per min per ml of enrichment culture) were repeatedly enriched under non-sterile conditions. In addition, the ureolytic enrichment obtained in this study showed in vitro calcium carbonate precipitation. Fluorescence in situ hybridization analysis showed the existence of bacteria of the phylum Firmicutes in the bioreactor system. Our data demonstrate that this DHS bioreactor system is a useful system for the enrichment and production of ureolytic microbes for MICP applications.

Keywords

  • DHS bioreactor system
  • enrichment culture
  • microbially induced carbonate precipitation (MICP)
  • ureolytic microbes
Open Access

MALDI-TOF MS Detection of Endophytic Bacteria Associated with Great Nettle (Urtica dioica L.), Grown in Algeria

Published Online: 21 Feb 2022
Page range: 67 - 72

Abstract

Abstract

Any plant with a vascular system has a specific endophytic microflora. The identification of bacteria is essential in plant pathology. Although identification methods are effective, they are costly and time consuming. The purpose of this work is to isolate and to identify the different bacteria from the internal tissues of Urtica dioica L. and to study their diversity. This last is based on the different parts of the plant (stems, leaves and roots) and the harvest regions (Dellys and Tlamcen). The identification of bacteria is done by biochemical tests and confirmed by MALDI-TOF MS. Seven genus and eleven species were isolated from the Great Nettle. They belong to the genera Bacillus, Escherichia, Pantoea, Enterobacter, Staphylococcus, Enterococcus and Paenibacillus. The majority of these bacteria were isolated from Tlemcen which makes this region the richest in endophytic bacteria compared to that harvested from Dellys. The results show also that the leaves are the most diversified in endophytic bacteria. Bacillus pumilus-ME is the common species of the three parts of the plant harvested in both regions. From this work, it emerges that the Great Nettle can be settled by various endophytic bacteria which are differently distributed within the same plant harvested in different regions.

Keywords

  • -ME
  • diversity
  • endophytic bacteria
  • MALDI-TOF MS
  • L.
Open Access

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

Published Online: 21 Feb 2022
Page range: 73 - 79

Abstract

Abstract

Viruses including Epstein-Barr virus (EBV), JCV and BKV have been reported to be associated with some cancers. The association of these viruses with colorectal cancers remains controversial. Our objective was to investigate their infections association with adenocarcinoma and adenomatous polyps of the colon. Totally, 210 paraffin-embedded tissue specimens encompassing 70 colorectal adenocarcinoma, 70 colorectal adenomatous and 70 colorectal normal tissues were included. The total DNA was 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. Moreover, all the patients and healthy subjects were negative for BKV DNA sequences. The results suggested that EBV and JCV genomes were not detectable in the colorectal tissue of patients with colorectal cancer in our population. Hence, BKV might not be necessitated for the development of colorectal cancer. The findings merit more investigations.

Keywords

  • Epstein-Barr virus
  • adenocarcinoma
  • colorectal cancer
  • JCV
  • BKV
  • adenomatous
Open Access

Isolation of Sabin-like Polioviruses from Sewage in Poland

Published Online: 21 Feb 2022
Page range: 89 - 96

Abstract

Abstract

As a complement to the active search for cases of acute flaccid paralysis, environmental sampling was conducted from January to December 2011, to test for any putative polio revertants and recombinants in sewage. A total of 165 environmental samples were obtained and analyzed for the presence of polioviruses by use of cell culture (L20B, RD and Caco-2) followed by neutralization and reverse-transcription polymerase chain reaction. Out of the 31 CPE positive samples, 26 contained one and 5 two different serotypes, yielding a total of 36 PVs. The microneutralization test revealed the presence of 7, 10 and 19 strains belonging to poliovirus serotype 1, 2 and 3, respectively. The genomic variability of 36 poliovirus strains was examined by the restriction fragment length polymorphism assay (RFLP). By combined analyses of two distant, polymorphic segments of the viral genome, one situated in the capsid protein VP1 coding region and the other in the 3D-polymerase coding region, we screened for the putative poliovirus revertants and recombinants. All detected PVs were classified as vaccine strains on the basis of RFLP-VP1 test. None of wild-type PVs or vaccine derived polioviruses were detected. RFLP assay also revealed the presence of 11 recombinants in 3D-polymerase coding region. Nine isolates appeared to be S3/S2, one S3/S1 and S1/S2 recombinant in analyzed 3Dpol region. This study revealed, through environmental monitoring, the introduction of SL PVs into the population associated with the routine use of OPV in Poland before the April 2016. Our findings demonstrate the usefulness of environmental surveillance in the overall polio eradication program.

Keywords

  • environmental surveillance
  • oral polio vaccine (OPV)
  • poliovirus recombinants and revertants in sewage

short-communication

Open Access

Evaluation of the Carba NP Test for the Detection of Carbapenemase Activity in Bacteroides Species

Published Online: 21 Feb 2022
Page range: 97 - 101

Abstract

Abstract

We evaluated the usefulness of the Carba NP test for rapid detection of carbapenemase activity in Bacteroides spp. The minimum inhibitory concentration (MIC) for imipenem was determined with gradient test strips, and cfiA gene was investigated by polymerase chain reaction for 27 clinical Bacteroides spp. isolates. Carba NP test was performed according to recommendations of the Clinical and Laboratory Standards Institute. Among three cfiA gene harboring clinical isolates, two imipenem resistant isolates were Carba NP test positive, while the imipenem intermediate isolate was negative. Our preliminary results suggest that the Carba NP test can be useful as a rapid test to detect carbapenemases in Bacteroides species.

Keywords

  • carbapenemase
  • Carba NP
  • imipenem
Open Access

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

Published Online: 21 Feb 2022
Page range: 103 - 107

Abstract

Abstract

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 method for the rapid identification of pathogens and resistance genes from blood culture in oncologic patients

Keywords

  • bloodstream infection
  • FilmArray
  • multiplex PCR
  • oncologic patients
Open Access

Changes of Microbial Diversity During Swine Manure Treatment Process

Published Online: 21 Feb 2022
Page range: 109 - 112

Abstract

Abstract

We investigated microbial diversity in a manure storage tank (MST) storing untreated manure and an aeration tank (AT) during swine manure treatment process using the next-generation sequencing in order to find the aeration effect on microbial diversity. Proteobacteria were more abundant in the AT group than in the MST group and may include denitrifying bacteria contributing to nitrous oxide (N2O) emission or aerobic bacteria stimulated by oxygen. The opposite held true for the phyla Bacteroidetes and Firmicutes that may include anaerobic bacteria inhibited under aerobic conditions in the AT group.

Keywords

  • biological swine manure treatment
  • manure storage tanks
  • microbial communities in swine manure
  • next-generation sequencing
Open Access

Comparative Seroprevalence of Hepatitis A And E Viruses in Blood Donors from Wielkopolska Region, West-Central Poland

Published Online: 21 Feb 2022
Page range: 113 - 115

Abstract

Abstract

The objective of the present study was to investigate the seroprevalence of HAV and HEV in Polish blood donors (BDs). One hundred and ten randomly selected healthy BDs, living in Wielkopolska Region were tested for anti-HAV IgG and anti-HEV IgG with commercial assays. The seroprevalence of anti-HAV was 11.8%; anti-HEV were detected in 60.9% of BDs (p < 0.0001). Consumption of risky food was more common in anti-HEV-positive BDs (59.1% vs. 33.3%; p = 0.01). Twelve out of 20 BDs (60%) with no history of travel abroad were exposed to HEV. Wielkopolska Region, Poland should be regarded as a new HEV infection-hyperendemic area in Europe.

Keywords

  • blood donors
  • HAV
  • HEV
  • Poland
  • seroprevalence
Open Access

The Prevalence of Campylobacter spp. in Polish Poultry Meat

Published Online: 21 Feb 2022
Page range: 117 - 120

Abstract

Abstract

The prevalence, count and molecular identification of Campylobacter spp. in Polish poultry meat were analysed. 181 samples of meat from chicken (70), turkey (47), duck (54) and goose (10) were studied. Campylobacter spp. was found in 64% of meat samples. The highest prevalence of this pathogen was detected for duck meat. On average 80% of duck samples were contaminated with Campylobacter spp. The counts of Campylobacter spp. in positive samples remained under ten colony forming units per gram of product in 59% of poultry meat. C. jejuni was more frequently detected in poultry meat than C. coli.

Keywords

  • spp.
  • microbiological quality
  • poultry meat
32 Articles

original-paper

Open Access

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

Published Online: 21 Feb 2022
Page range: 81 - 88

Abstract

Abstract

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 IFA were found as 100% for seronegative, 100% for acute primary infection, 22.2% for late primary infection, 92.1% for past infection. The rates of agreement between immunoblotting and IFA were found as 80.8% for seronegative, 68.8% for acute primary infection, 55.6% for late primary infection, 86.6% for past infection. The sensitivity of immunoblotting for anti-VCA IgM was identical with ELISA, and higher for anti-VCA IgG, anti-EBNA IgG, anti-EA antibodies, while the specificity of immunoblotting for these antibodies were found to be lower. The sensitivity and specificity of Real-time PCR for detection of viremia in acute primary infection were found as 56.25% (9/16) and 97.89% (139/142), respectively. The diagnostic methods should be chosen by evaluating the demographic characteristics of patients and laboratory conditions together.

Keywords

  • ELISA
  • Epstein-Barr virus
  • immunoblotting
  • Indirect Fluorescence Assay (IFA)
  • Real-time PCR
Open Access

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

Published Online: 21 Feb 2022
Page range: 11 - 18

Abstract

Abstract

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 followed by qPCR of the ureC gene of H. pylori was carried out. We evaluated the presence of H. pylori, in 103 females and 40 males, mean (± SD) age of 56.5 ± 14.18. The sensitivity of RUT to detect the infection was 67.0% (95% C.I.: 57.2 – 75.8) and specificity was 92.3% (95% C.I.: 76.5 – 99.1). Histology by Giemsa stain, commonly used as a reference for H. pylori detection, showed a sensitivity of 98.6% (95% C.I.: 92.5 – 100.0) and a specificity of 89.7% (95% C.I.: 72.7 – 97.8). In contrast, detection of H. pylori infection in stools by nested-qPCR showed a sensitivity of 100% (95% C.I.: 94.9 – 100.0) and a specificity of 83.9% (95% C.I.: 66.3 – 94.6). Our test, based in nested-qPCR is a better diagnostic alternative than conventional RUT, and is similar to histology by Giemsa stain in the detection of H. pylori, by which the test could be used for non-invasive diagnosis in clinical practice.

Keywords

  • molecular diagnostics
  • nested-qPCR
  • stools
Open Access

Detection of Acinetobacter spp. in Blood Cultures by an Improved Fluorescent in Situ Hybridization Assay

Published Online: 21 Feb 2022
Page range: 3 - 10

Abstract

Abstract

Fluorescent in situ hybridization (FISH) allows rapid detection of microorganisms. We aimed (i) to evaluate the sensitivity and specificity of FISH for the detection of Acinetobacter spp. in blood culture specimens and (ii) to test the simultaneous application of two genus-specific probes labeled with the same fluorochrome to increase the fluorescent signal intensity and improve the detection of Acinetobacter spp. Three hundred and twenty blood culture specimens were tested via both the conventional laboratory methods and FISH to detect Acinetobacter spp. The specimens were examined separately with each genus-specific probe Aci and ACA, and also using a mixture of the both probes Aci and ACA. In all examinations, probe EUB338 was used accompanied by Aci and ACA. The specificity of FISH was 100% (97.5% confidence interval [CI] = 98.7% – 100%). The sensitivity of FISH by the use of probe Aci was 96.4% (95% CI = 81.7% – 99.9%), whereas, the sensitivity of this technique by the use of probe ACA as well as by the combination of both probes Aci and ACA was 100% (97.5% CI = 87.7% – 100%). Moreover, simultaneous hybridization by probes Aci and ACA increased the fluorescent signal of Acinetobacter spp. cells to 3+ in 13 specimens. In conclusion, FISH, particularly using a combination of Aci and ACA, is a highly accurate method for the detection of Acinetobacter spp. in blood cultures. Furthermore, simultaneous hybridization by the both probes Aci and ACA can increase the fluorescent signal intensity of Acinetobacter spp. cells in some blood culture specimens and facilitate the detection of these microorganisms.

Keywords

  • bacteremia
  • blood culture
  • FISH
  • simultaneous hybridization
Open Access

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

Published Online: 21 Feb 2022
Page range: 19 - 26

Abstract

Abstract

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 32.1% of the 28 isolates analyzed, respectively. Surprisingly, reduced lengths of cry4B gene segments were detected in 28.6% of B. thuringiensis samples. The presence of cry10 or cyt1 was not detected in any of the 28 samples of B. thuringiensis, despite the high sensitivity of the assays used. The results show that B. thuringiensis samples from the Colombian Caribbean have atypical characteristics compared to those of Latin America and elsewhere in the world, which is consistent with the idea that the geographic origin of B. thuringiensis samples is associated with their biological and genetic characteristics.

Keywords

  • – Colombian strains
  • genes
  • larvae
  • PCR methods
  • biological test
Open Access

High-Throughput Sequencing Analysis of Endophytic Bacteria Diversity in Fruits of White and Red Pitayas from Three Different Origins

Published Online: 21 Feb 2022
Page range: 27 - 35

Abstract

Abstract

Pitaya contains various types of polyphenols, flavonoid and vitamins which are beneficial for health and it is among the most important commercial tropical fruits worldwide. Endophytic bacteria might be beneficial for plant growth and yield. However, bacterial diversity in pitaya is poorly characterized. In this study, fruits of white and red pitayas from three different origins (Thailand, Vietnam and China) were chosen for endophytic bacteria diversity investigation by using Illumina HiSeq second-generation high-throughput sequencing technology. Large number of endophytic bacteria were detected and 22 phyla, 56 classes, 81 orders, 122 families and 159 genera were identified. Endophytic bacteria diversity was uneven among pitaya fruits from different origins and bacteria structure was different between white pitaya group and red pitaya group. Phylum Bacteroidetes, classes Bacteroidia and Coriobacteriia, orders Bacteroidales and Coriobacteriales, families Prevotellaceae, Bacteroidaceae, Ruminococcaceae, Paraprevotellaceae, Rikenellaceae, Alcaligenaceae and Coriobacteriaceae, genera Prevotella, Bacteroides, Roseburia, Faecalibacterium and Sutterella were statistically significant different species (P < 0.05) between white and red pitayas. These findings might be useful for growth improvement, fruit preservation and processing of different pitaya species from different origins.

Keywords

  • endophytic bacteria diversity
  • high-throughput sequencing
  • pitaya from three different origins
Open Access

Natural Attenuation Potential of Polychlorinated Biphenyl-Polluted Marine Sediments

Published Online: 21 Feb 2022
Page range: 37 - 48

Abstract

Abstract

The marine environment in Kuwait is polluted with various hazardous chemicals of industrial origin. These include petroleum hydrocarbons, halogenated compounds and heavy metals. Bioremediation with dedicated microorganisms can be effectively applied for reclamation of the polluted marine sediments. However, information on the autochthonous microbes and their ecophysiology is largely lacking. We analyzed sediments from Shuwaikh harbor to detect polychlorinated biphenyls (PCBs) and total 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 showed the presence of members of the Proteobacteria, Spirochaetes, Firmicutes and Bacteroidetes in the analyzed sediments. However, Chloroflexi-related bacteria dominated the detected bacterial community. We also enriched a biphenyl-utilizing mixed culture using the W2 station sediment as an inoculum in chemically defined medium using biphenyl as a sole carbon and energy source. The enriched mixed culture consisted mainly of the Firmicute Paenibacillus spp. Sequences of genes encoding putative aromatic ring-hydroxylating dioxygenases were detected in sediments from most sampling stations and the enriched mixed culture. The results suggest the potential of bioremediation as a means for natural attenuation of Shuwaikh harbor sediments polluted with PCBs and TPHs.

Keywords

  • aromatic ring oxygenases
  • bacterial communities
  • bioremediation
  • Chloroflexi
  • DGGE
  • polluted marine sediments
Open Access

Isolation and Characteristics of Biotechnologically Important Antagonistic Thermophilic Bacteria from Rhizosphere of Haloxylon salicornicum

Published Online: 21 Feb 2022
Page range: 49 - 58

Abstract

Abstract

Rhizobacteria are an active part of microbial population in the rhizosphere of plants. In this study, twenty rhizobacteria were isolated from the rhizosphere of a perennial grass, Haloxylon salicornicum, found in Cholistan desert, an arid landmass near Bahawalpur Pakistan, in one set of experimental conditions. Colony characteristics, biochemical and molecular analyses of these isolates were performed. All isolates were bacilli, gram positive with off-white colonies and exhibited typical bacilli colony morphology. None of the isolates was gelatinase, urease, indole, H2S and catalase producer. Eleven isolates were amylase producers and 8 isolates were acid producers. All isolates fermented glucose, 3 fermented lactose and 19 fermented fructose. Molecular data revealed that out of twenty isolates, 14 isolates showed 91–99% identity with Brevibacillus borstelensis, 4 with Bacillus subtilis (97–98%) and 2 with Bacillus licheniformis (94–99%) through BLAST analysis. All identified bacterial isolates cladded with their respective groups in the phylogenetic tree. Many (11–15 out of 20) of the isolates were more effective in inhibiting growth of the tested bacterial strains as compared to the positive control (Ampicillin 50 μg/disc). We conclude that bacilli are the predominant form populating rhizosphere of this desert grass. Among the isolated bacteria Brevibacillus borstelensis, Bacillus subtilis and Bacillus licheniformis are the most predominant species.

Keywords

  • rhizobacteria
  • 16S rRNA for phylogenic analysis
  • rhizosphere on Cholistan desert
Open Access

A Low-Tech Bioreactor System for the Enrichment and Production of Ureolytic Microbes

Published Online: 21 Feb 2022
Page range: 59 - 65

Abstract

Abstract

Ureolysis-driven microbially induced carbonate precipitation (MICP) has recently received attention for its potential biotechnological applications. However, information on the enrichment and production of ureolytic microbes by using bioreactor systems is limited. Here, we report a low-tech down-flow hanging sponge (DHS) bioreactor system for the enrichment and production of ureolytic microbes. Using this bioreactor system and a yeast extract-based medium containing 0.17 M urea, ureolytic microbes with high potential urease activity (> 10 μmol urea hydrolyzed per min per ml of enrichment culture) were repeatedly enriched under non-sterile conditions. In addition, the ureolytic enrichment obtained in this study showed in vitro calcium carbonate precipitation. Fluorescence in situ hybridization analysis showed the existence of bacteria of the phylum Firmicutes in the bioreactor system. Our data demonstrate that this DHS bioreactor system is a useful system for the enrichment and production of ureolytic microbes for MICP applications.

Keywords

  • DHS bioreactor system
  • enrichment culture
  • microbially induced carbonate precipitation (MICP)
  • ureolytic microbes
Open Access

MALDI-TOF MS Detection of Endophytic Bacteria Associated with Great Nettle (Urtica dioica L.), Grown in Algeria

Published Online: 21 Feb 2022
Page range: 67 - 72

Abstract

Abstract

Any plant with a vascular system has a specific endophytic microflora. The identification of bacteria is essential in plant pathology. Although identification methods are effective, they are costly and time consuming. The purpose of this work is to isolate and to identify the different bacteria from the internal tissues of Urtica dioica L. and to study their diversity. This last is based on the different parts of the plant (stems, leaves and roots) and the harvest regions (Dellys and Tlamcen). The identification of bacteria is done by biochemical tests and confirmed by MALDI-TOF MS. Seven genus and eleven species were isolated from the Great Nettle. They belong to the genera Bacillus, Escherichia, Pantoea, Enterobacter, Staphylococcus, Enterococcus and Paenibacillus. The majority of these bacteria were isolated from Tlemcen which makes this region the richest in endophytic bacteria compared to that harvested from Dellys. The results show also that the leaves are the most diversified in endophytic bacteria. Bacillus pumilus-ME is the common species of the three parts of the plant harvested in both regions. From this work, it emerges that the Great Nettle can be settled by various endophytic bacteria which are differently distributed within the same plant harvested in different regions.

Keywords

  • -ME
  • diversity
  • endophytic bacteria
  • MALDI-TOF MS
  • L.
Open Access

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

Published Online: 21 Feb 2022
Page range: 73 - 79

Abstract

Abstract

Viruses including Epstein-Barr virus (EBV), JCV and BKV have been reported to be associated with some cancers. The association of these viruses with colorectal cancers remains controversial. Our objective was to investigate their infections association with adenocarcinoma and adenomatous polyps of the colon. Totally, 210 paraffin-embedded tissue specimens encompassing 70 colorectal adenocarcinoma, 70 colorectal adenomatous and 70 colorectal normal tissues were included. The total DNA was 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. Moreover, all the patients and healthy subjects were negative for BKV DNA sequences. The results suggested that EBV and JCV genomes were not detectable in the colorectal tissue of patients with colorectal cancer in our population. Hence, BKV might not be necessitated for the development of colorectal cancer. The findings merit more investigations.

Keywords

  • Epstein-Barr virus
  • adenocarcinoma
  • colorectal cancer
  • JCV
  • BKV
  • adenomatous
Open Access

Isolation of Sabin-like Polioviruses from Sewage in Poland

Published Online: 21 Feb 2022
Page range: 89 - 96

Abstract

Abstract

As a complement to the active search for cases of acute flaccid paralysis, environmental sampling was conducted from January to December 2011, to test for any putative polio revertants and recombinants in sewage. A total of 165 environmental samples were obtained and analyzed for the presence of polioviruses by use of cell culture (L20B, RD and Caco-2) followed by neutralization and reverse-transcription polymerase chain reaction. Out of the 31 CPE positive samples, 26 contained one and 5 two different serotypes, yielding a total of 36 PVs. The microneutralization test revealed the presence of 7, 10 and 19 strains belonging to poliovirus serotype 1, 2 and 3, respectively. The genomic variability of 36 poliovirus strains was examined by the restriction fragment length polymorphism assay (RFLP). By combined analyses of two distant, polymorphic segments of the viral genome, one situated in the capsid protein VP1 coding region and the other in the 3D-polymerase coding region, we screened for the putative poliovirus revertants and recombinants. All detected PVs were classified as vaccine strains on the basis of RFLP-VP1 test. None of wild-type PVs or vaccine derived polioviruses were detected. RFLP assay also revealed the presence of 11 recombinants in 3D-polymerase coding region. Nine isolates appeared to be S3/S2, one S3/S1 and S1/S2 recombinant in analyzed 3Dpol region. This study revealed, through environmental monitoring, the introduction of SL PVs into the population associated with the routine use of OPV in Poland before the April 2016. Our findings demonstrate the usefulness of environmental surveillance in the overall polio eradication program.

Keywords

  • environmental surveillance
  • oral polio vaccine (OPV)
  • poliovirus recombinants and revertants in sewage

short-communication

Open Access

Evaluation of the Carba NP Test for the Detection of Carbapenemase Activity in Bacteroides Species

Published Online: 21 Feb 2022
Page range: 97 - 101

Abstract

Abstract

We evaluated the usefulness of the Carba NP test for rapid detection of carbapenemase activity in Bacteroides spp. The minimum inhibitory concentration (MIC) for imipenem was determined with gradient test strips, and cfiA gene was investigated by polymerase chain reaction for 27 clinical Bacteroides spp. isolates. Carba NP test was performed according to recommendations of the Clinical and Laboratory Standards Institute. Among three cfiA gene harboring clinical isolates, two imipenem resistant isolates were Carba NP test positive, while the imipenem intermediate isolate was negative. Our preliminary results suggest that the Carba NP test can be useful as a rapid test to detect carbapenemases in Bacteroides species.

Keywords

  • carbapenemase
  • Carba NP
  • imipenem
Open Access

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

Published Online: 21 Feb 2022
Page range: 103 - 107

Abstract

Abstract

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 method for the rapid identification of pathogens and resistance genes from blood culture in oncologic patients

Keywords

  • bloodstream infection
  • FilmArray
  • multiplex PCR
  • oncologic patients
Open Access

Changes of Microbial Diversity During Swine Manure Treatment Process

Published Online: 21 Feb 2022
Page range: 109 - 112

Abstract

Abstract

We investigated microbial diversity in a manure storage tank (MST) storing untreated manure and an aeration tank (AT) during swine manure treatment process using the next-generation sequencing in order to find the aeration effect on microbial diversity. Proteobacteria were more abundant in the AT group than in the MST group and may include denitrifying bacteria contributing to nitrous oxide (N2O) emission or aerobic bacteria stimulated by oxygen. The opposite held true for the phyla Bacteroidetes and Firmicutes that may include anaerobic bacteria inhibited under aerobic conditions in the AT group.

Keywords

  • biological swine manure treatment
  • manure storage tanks
  • microbial communities in swine manure
  • next-generation sequencing
Open Access

Comparative Seroprevalence of Hepatitis A And E Viruses in Blood Donors from Wielkopolska Region, West-Central Poland

Published Online: 21 Feb 2022
Page range: 113 - 115

Abstract

Abstract

The objective of the present study was to investigate the seroprevalence of HAV and HEV in Polish blood donors (BDs). One hundred and ten randomly selected healthy BDs, living in Wielkopolska Region were tested for anti-HAV IgG and anti-HEV IgG with commercial assays. The seroprevalence of anti-HAV was 11.8%; anti-HEV were detected in 60.9% of BDs (p < 0.0001). Consumption of risky food was more common in anti-HEV-positive BDs (59.1% vs. 33.3%; p = 0.01). Twelve out of 20 BDs (60%) with no history of travel abroad were exposed to HEV. Wielkopolska Region, Poland should be regarded as a new HEV infection-hyperendemic area in Europe.

Keywords

  • blood donors
  • HAV
  • HEV
  • Poland
  • seroprevalence
Open Access

The Prevalence of Campylobacter spp. in Polish Poultry Meat

Published Online: 21 Feb 2022
Page range: 117 - 120

Abstract

Abstract

The prevalence, count and molecular identification of Campylobacter spp. in Polish poultry meat were analysed. 181 samples of meat from chicken (70), turkey (47), duck (54) and goose (10) were studied. Campylobacter spp. was found in 64% of meat samples. The highest prevalence of this pathogen was detected for duck meat. On average 80% of duck samples were contaminated with Campylobacter spp. The counts of Campylobacter spp. in positive samples remained under ten colony forming units per gram of product in 59% of poultry meat. C. jejuni was more frequently detected in poultry meat than C. coli.

Keywords

  • spp.
  • microbiological quality
  • poultry meat

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