scholarly journals Development of a DNA microarray assay for rapid detection of fifteen bacterial pathogens in pneumonia

2020 ◽  
Author(s):  
Xiuqing Ma ◽  
Yanqin Li ◽  
Yuan Liang ◽  
Yang Liu ◽  
Ling Yu ◽  
...  
Keyword(s):  
Dna Microarray ◽  
Legionella Pneumophila ◽  
Burkholderia Cepacia ◽  
Pathogenic Bacteria ◽  
Chlamydia Pneumoniae ◽  
Bacterial Pathogens ◽  
Positive Control ◽  
Negative Control ◽  
Clinical Isolates ◽  
Microarray Assay

Abstract Background: Rapid identification of pathogenic bacteria is important for appropriate antimicrobial therapy of pneumonia, but traditional bacteria culture is time-consuming and laborious. The aim of this study was to develop and evaluate a DNA microarray assay for the simultaneously detection of fifteen bacteria species directly from respiratory tract specimens in patients with pneumonia. These species included Streptococcus pneumoniae, Staphylococcus aureus, Haemophilus influenzae, Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, Acinetobacter baumannii, Mycoplasma pneumoniae, Enterococcus faecalis, Enterococcus faecium, Enterobacter cloacae, Stenotrophomonas maltophilia, Burkholderia cepacia, Legionella pneumophila and Chlamydia pneumoniae. The 16S rDNA and specific genes of each pathogen were chosen as the amplification target, amplified with multiplex polymerase chain reaction (PCR), and hybridized to the oligonucleotide probes on the microarray. Results: The DNA microarray can reach a detection limit of 10 3 copies/μL. Nineteen standard strains, 119 positive control clinical isolates and 4 negative control clinical isolates were correctly detected with our microarray. Meanwhile, bacterial pathogens were accurately identified when two or three bacterial targets were mixed together. Furthermore, the results of 99.4% (156/157) clinical specimens were the same to that from the conventional assay. Conclusions: we developed a DNA microarray that could simultaneously detect various bacterial pathogens in pneumonia. The method described here has the potential to provide considerable labor and time savings due to its ability to screen for 15 bacterial pathogens simultaneously.

scholarly journals Development of a DNA microarray assay for rapid detection of fifteen bacterial pathogens in pneumonia

2020 ◽  
Author(s):  
Xiuqing Ma ◽  
Yanqin Li ◽  
Yuan Liang ◽  
Yang Liu ◽  
Ling Yu ◽  
...  
Keyword(s):  
Dna Microarray ◽  
Legionella Pneumophila ◽  
Burkholderia Cepacia ◽  
Pathogenic Bacteria ◽  
Chlamydia Pneumoniae ◽  
Bacterial Pathogens ◽  
Bacterial Species ◽  
Simultaneous Detection ◽  
Clinical Isolates ◽  
Microarray Assay

Abstract Background: The rapid identification of pathogenic bacteria is important for determining an appropriate antimicrobial therapy for pneumonia, but traditional bacterial culture is time-consuming and labourious. The aim of this study was to develop and evaluate a DNA microarray assay for the simultaneous detection of fifteen bacterial species directly from respiratory tract specimens in patients with pneumonia. These species included Streptococcus pneumoniae, Staphylococcus aureus, Haemophilus influenzae, Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, Acinetobacter baumannii, Mycoplasma pneumoniae, Enterococcus faecalis, Enterococcus faecium, Enterobacter cloacae, Stenotrophomonas maltophilia, Burkholderia cepacia, Legionella pneumophila and Chlamydia pneumoniae. The 16S rDNA genes and other specific genes of each pathogen were chosen as the amplification targets, amplified via multiplex polymerase chain reaction (PCR), and hybridized to oligonucleotide probes in a microarray.Results: The DNA microarray detection limit was 103 copies/μL. Nineteen standard strains and 119 clinical isolates were correctly detected with our microarray, and 3 nontarget species from 4 clinical isolates were not detected. Additionally, bacterial pathogens were accurately identified when two or three bacterial targets were mixed together. Furthermore, the results for 99.4% (156/157) of clinical specimens were the same as those from a conventional assay.Conclusions: We developed a DNA microarray that could simultaneously detect various bacterial pathogens in pneumonia. The method described here has the potential to provide considerable labour and time savings due to its ability to screen for 15 bacterial pathogens simultaneously.

scholarly journals Development of a DNA microarray assay for rapid detection of fifteen bacterial pathogens in pneumonia

2020 ◽  
Author(s):  
Xiuqing Ma ◽  
Yanqin Li ◽  
Yuan Liang ◽  
Yang Liu ◽  
Ling Yu ◽  
...  
Keyword(s):  
Dna Microarray ◽  
Legionella Pneumophila ◽  
Burkholderia Cepacia ◽  
Pathogenic Bacteria ◽  
Chlamydia Pneumoniae ◽  
Bacterial Pathogens ◽  
Rapid Identification ◽  
Clinical Isolates ◽  
Microarray Assay ◽  
Bacteria Culture

Abstract Background: Rapid identification of pathogenic bacteria is important for appropriate antimicrobial therapy of pneumonia, but traditional bacteria culture is time-consuming and laborious. The aim of this study was to develop and evaluate a DNA microarray assay for the simultaneously detection of fifteen bacteria species directly from respiratory tract specimens in patients with pneumonia. These species included Streptococcus pneumoniae, Staphylococcus aureus, Haemophilus influenzae, Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, Acinetobacter baumannii, Mycoplasma pneumoniae, Enterococcus faecalis, Enterococcus faecium, Enterobacter cloacae, Stenotrophomonas maltophilia, Burkholderia cepacia, Legionella pneumophila and Chlamydia pneumoniae. The 16S rDNA and specific genes of each pathogen were chosen as the amplification target, amplified with multiplex polymerase chain reaction (PCR), and hybridized to the oligonucleotide probes on the microarray. Results: The DNA microarray can reach a detection limit of 10 3 copies/μL. Nineteen standard strains and 119 clinical isolates were correctly detected with our microarray and 3 non-target species from 4 clinical isolates were not detected. Meanwhile, bacterial pathogens were accurately identified when two or three bacterial targets were mixed together. Furthermore, the results of 99.4% (156/157) clinical specimens were the same to that from the conventional assay. Conclusions: we developed a DNA microarray that could simultaneously detect various bacterial pathogens in pneumonia. The method described here has the potential to provide considerable labor and time savings due to its ability to screen for 15 bacterial pathogens simultaneously.

scholarly journals AKTIVITAS ANTIBAKTERI EKSTRAK ETANOL BIJI KAPULAGA JAWA (Amomum compactum Soland. ex Maton) TERHADAP Streptococcus pyogenes

EKOLOGIA ◽  
2020 ◽  
Vol 20 (1) ◽  
pp. 31-39
Author(s):  
Oom Komala ◽  
. Ismanto ◽  
Muhammad Alan Maulana
Keyword(s):  
Antibacterial Activity ◽  
Streptococcus Pyogenes ◽  
Pathogenic Bacteria ◽  
Inhibition Zone ◽  
Positive Control ◽  
Negative Control ◽  
Diffusion Method ◽  
Dilution Method ◽  
Natural Treatment ◽  
Amomum Compactum

Streptococcus pyogenes is one of the pathogenic bacteria that causes pharyngitis. Natural treatment to overcome these problems is to use cardamom seeds. The purpose of this study was to test the antibacterial activity, determine the concentration of inhibitory zone and phytochemical compounds from  ethanol 96% extract of Java cardamom seeds (Amomum compactum Soland. Ex Maton) against Streptococcus pyogenes. The method is used   solid dilution and paper disc diffusion method. The solid dilution method is used for the Minimum Inhibitory Concentration (MIC) test with a concentration of 1.25%, 2.5%, 5% and 7.5% while the paper diffusion method is used for the Inhibition zone Diameter (IZD)  using five treatments namely three concentrations of ethanol 96% extract of Java cardamom seeds (7.5%, 10% and 12%), one positive control of amoxicillin 0.01 mg/mL and one negative control of sterile distilled water. IZD data were  analyzed using ANOVA with a confidence level of 95% and α = 0.05 and Duncan's further tests to determine differences between treatments. The results showed that the MIC  was at a concentration of 7.5% while for the IZD test which had the highest activity there was a concentration of 12% with an average inhibition diameter of 12.03 ± 0.14 mm. In addition, ethanol 96% extract of Java cardamom seeds contain alkaloids, flavonoids, terpenoids and tannins which function in antibacterial activity.

scholarly journals Green Coffea robusta (Coffea canephora) from Lampung province effect toward free radicals in chickens infected with Salmonella enteritidis bacteria

2021 ◽  
Vol 11 (1) ◽  
pp. 61-69
Author(s):  
Dahliatul Qosimah ◽  
Djalal Rosyidi ◽  
Lilik E. Radiati ◽  
Indah A. Amri ◽  
Dodik Prasetyo ◽  
...  
Keyword(s):  
Salmonella Enteritidis ◽  
Pathogenic Bacteria ◽  
Negative Control Group ◽  
Coffea Canephora ◽  
Positive Control ◽  
Negative Control ◽  
The Body ◽  
Control Group ◽  
High Dose ◽  
Treatment Groups

Background: Foodborne diseases are caused by acquired pathogenic bacteria such as Salmonella enteritidis. It causes an intestinal imbalance and the microbial toxins found in the gastrointestinal tract induce symptoms such as diarrhea. Coffee contains active ingredients such as antioxidants and is used as an anti-inflammatory agent by reducing pro-inflammatory cytokine levels in the body. Aim: The purpose of this study was to determine the interaction between Lampung’s robusta coffee and tissue damage in chickens infected by S. enteritidis. Methods: This study used first-day-old Isa brown layer chickens (n = 60), which were divided into five treatment groups. The negative control group consisted of healthy and normal chickens, whereas the positive control group consisted of chickens infected with S. enteritidis bacteria at a concentration of 108 CFU/ml. Groups T1, T2, and T3 were given coffee extract with doses of 500 mg/kg BW (low dose), 1,000 mg/kg BW (moderate dose), and 1,500 mg/kg BW (high dose), respectively, and then infected with S. enteritidis bacteria at a concentration of 108 CFU/ml. The coffee extract and bacteria were given orally via a feeding tube at a volume of 0.5 ml per chick. The extract was given for 14 days (from day 3 to day 16), and the bacteria were given on days 16 and 17. On day 18, the chickens were necropsied. The malondialdehyde (MDA) level was analyzed using one-way analysis of variance test with the GLM procedure (<0.05), while the tissue histopath was analyzed using a descriptive qualitative study to examine the ileal damage Results: The results showed that the MDA levels (nmol/l) decreased in treatment groups T1, T2, and T3 compared to the positive control. On the contrary, we found improvements in the ileum histopathology of group T1 and T2 in the form of normal and regular intestinal epithelium arrangement of the ileum, long intestinal villi, and decreased total leukocytes. Conclusion: Green coffee robusta has the potential to increase antioxidants and reduce inflammation in the small intestine of chickens infected with S. enteritidis.

Setting Time of Calcium Hydroxide from Indonesian Limestone Paste with Various Solvent Vehicle for Intracanal Medicament

2021 ◽  
Vol 1044 ◽  
pp. 165-170
Author(s):  
Atia Nurul Sidiqa ◽  
Fadhilah Hanif ◽  
Myrna Nurlatifah Zakaria ◽  
Ira Artilia ◽  
Arief Cahyanto
Keyword(s):  
Calcium Hydroxide ◽  
Root Canal ◽  
Pathogenic Bacteria ◽  
Setting Time ◽  
Antimicrobial Effect ◽  
High Viscosity ◽  
Positive Control ◽  
Negative Control ◽  
Ion Dissociation ◽  
Group 2

Calcium hydroxide (Ca(OH)2 has been recently synthesized from natural Indonesian limestone to be used as an intracanal medicament for root canal infection. Ca(OH)2 is applied into the infected root canal in a non-setting paste form to release calcium and hydroxyl ions which elevates the pH and provide an antimicrobial effect to pathogenic bacteria. To form an injectable paste, Ca(OH)2 powder has to be mixed with a proper solvent to produce optimal consistency, ion dissociation, and maintain its property as a non-set material. Solvent is an important factor affecting ion dissociation and preserving its non-setting paste condition. The aim of this study is to synthesize Ca(OH)2 powder from Indonesian limestone, and evaluate the setting time of Ca(OH)2 paste from mixture of Ca(OH)2 powder synthesized from Indonesian limestone (limestone Ca(OH)2) with various solvent, to evaluate which solvent serve best to prevent the Ca(OH)2 paste from setting, to form an ideal paste be used as an intracanal medicament. This study consists of 5 groups (n=5); commercially Ca(OH)2 paste (Calcipex II) as positive control, Ca(OH)2 powder (Merck) + distilled water as negative control, limestone Ca(OH)2 powder + natrium carboxy methylcellulose (Na CMC) as group 1, limestone Ca(OH)2 powder + propylene glycol (PG) as group 2, and limestone Ca(OH)2 powder + polyethylene glycol (PEG) as group 3. Setting time evaluation was measured according to ISO 9917 by vicat needle in 37°C to mimic the physiological body condition. Results were analyzed by One Way Anova test and Post Hoc Tukey test. The result of this study showed that the setting time of Ca(OH)2 paste mixed with Na CMC solvent was 1:04 hours, PG 72:15 hours, and PEG did not harden until 7 days of observation. PEG is a hygroscopic high viscosity solvent, resulting in low and steady molecule interaction, thus prolonged its setting time. From this study it can be concluded that PEG inhibit Ca(OH)2 setting reaction up to 7 days and might be used as solvent for Ca(OH)2 paste as intracanal medicament.

scholarly journals Comparative Studies on Effectiveness of Branded and Unbranded Disinfectants on E. coli and Staphylococcus Species

2019 ◽  
pp. 1-8
Author(s):  
N. P. Akani ◽  
J. O. Williams ◽  
A. U. Nnamdi
Keyword(s):  
Staphylococcus Aureus ◽  
Positive Control ◽  
Negative Control ◽  
Clinical Isolates ◽  
Zone Of Inhibition ◽  
E Coli ◽  
Antimicrobial Potential ◽  
Zones Of Inhibition ◽  
June July ◽  
And Staphylococcus Aureus

Aims: To compare the antimicrobial potential of branded and unbranded disinfectants on clinical bacterial isolates. Study Design: The agar-well diffusion and micro broth dilution were adopted for the study. Ten disinfectants of which five were branded (industrial prepared) and five unbranded (indigenous prepared) were used against E. coli and Staphylococcus aureus. Place and Duration of Study: Department of Microbiology, Rivers State University. the study was for a period of two months (June-July, 2018). Methodology: Faecal samples were collected from the University Medical centre and were analyzed in the Microbiology Laboratory for the isolation of Escherichia coli and Staphylococcus aureus using standard microbiological method. The antimicrobial potential of both branded and unbranded disinfectants on the clinical isolates were evaluated using the micro dilution technique and the well in agar technique. Results: The result in this study showed that both branded and unbranded disinfectants were effective on the E. coli and Staphylococcus isolates. However, the unbranded were only effective at high concentrations. E. coli had zone of inhibition ranging from 0 to 22 mm when tested with the unbranded disinfectant, while 0 to 17 mm was recorded for Staphylococcus aureus. The zones of inhibition of the branded disinfectant on E. coli ranged from 0 to 27 mm, while zone diameter of Staphylococcus aureus ranged from 0 to 25 mm. Among the unbranded disinfectants, Lysol produced the highest zone of inhibition While among the branded disinfectants, Savlon produced the highest zone of inhibition. The positive control was effective against all tested organisms with zones of inhibition ranging from 9-28 mm. On the other hand, as expected, the negative control (sterile distilled water) did not show any zone of inhibition. Conclusion: The study showed that branded disinfectants were more effective on the clinical isolates than the unbranded disinfectants.

scholarly journals Development of a DNA microarray assay for rapid detection of fifteen bacterial pathogens in pneumonia

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Xiuqing Ma ◽  
Yanqin Li ◽  
Yuan Liang ◽  
Yang Liu ◽  
Ling Yu ◽  
...  
Keyword(s):  
Dna Microarray ◽  
Rapid Detection ◽  
Bacterial Pathogens ◽  
Microarray Assay

scholarly journals Tenebrio molitor and Zophobas morio Full-Fat Meals in Broiler Chicken Diets: Effects on Nutrients Digestibility, Digestive Enzyme Activities, and Cecal Microbiome

Animals ◽  
2019 ◽  
Vol 9 (12) ◽  
pp. 1128 ◽  
Author(s):  
Abdelbasset Benzertiha ◽  
Bartosz Kierończyk ◽  
Mateusz Rawski ◽  
Agata Józefiak ◽  
Krzysztof Kozłowski ◽  
...  
Keyword(s):  
Clostridium Perfringens ◽  
Broiler Chickens ◽  
Pathogenic Bacteria ◽  
Digestive Enzyme ◽  
Tenebrio Molitor ◽  
Positive Control ◽  
Negative Control ◽  
Broiler Chicks ◽  
Ileal Digestibility ◽  
Dietary Treatments

This study was conducted to investigate the effect of insect full-fat meals added in relatively small amounts to a complete diet on the coefficients of apparent ileal digestibility, short-chain fatty acid (SCFA) concentrations, bacterial enzymes, and the microbiota community in the cecal digesta of broiler chickens. In total, 600 one-day-old female Ross 308 broiler chicks were randomly assigned to six dietary treatments with 10 replicate pens/treatment and 10 birds/pen. The groups consisted of a negative control (NC) with no additives; a positive control (PC; salinomycin 60 ppm), and supplementation with 0.2% or 0.3% Tenebrio molitor or Zophobas morio full-fat meals. Z. morio (0.2%) addition increased the activities of α- and β-glucosidase and α-galactosidase. Dietary insects significantly decreased the cecal counts of the Bacteroides–Prevotella cluster in comparison to those in the NC and PC. Whereas, Clostridium perfringens counts were increased in the broiler chickens subjected to the 0.3% Z. morio treatment. In conclusion, small amounts of full-fat insect meals added to broiler diets were capable of reducing the abundance of potentially pathogenic bacteria, such as the Bacteroides–Prevotella cluster and Clostridium perfringens. In addition, this supplementation was able to stimulate the GIT microbiome to produce enzymes, especially glycolytic enzymes.

scholarly journals Application of Bacillus probiotic to prevent Aeromonas hydrophilla infection in Clarias sp.

2015 ◽  
Vol 13 (2) ◽  
pp. 105 ◽  
Author(s):  
Mohammad Faizal Ulkhaq ◽  
, Widanarni ◽  
Angela Mariana Kusumastuti
Keyword(s):  
Aeromonas Hydrophila ◽  
Pathogenic Bacteria ◽  
Clarias Gariepinus ◽  
Positive Control ◽  
Negative Control ◽  
Probiotic Bacteria ◽  
African Catfish ◽  
Control Application

<p class="BasicParagraph" align="center"><strong>ABSTRACT</strong></p><p class="BasicParagraph" align="center"><strong> </strong></p><p class="Pa2">The aim of this study was to test the effectiveness of a probiotic <em>Bacillus </em>for the prevention of motile aeromonad septicemia (MAS) disease caused by <em>Aeromonas hydrophila </em>in African catfish (<em>Clarias gariepinus</em>). The study consisted of the inhibition testing of <em>A. hydrophila </em>by <em>Bacillus </em>(<em>in vitro</em>) and the application of probiotic in African catfish (<em>in vivo</em>). The <em>in vivo </em>test, consisted of five treatments such as the addition of probiotic <em>Bacillus </em>P4I1 RifR, <em>Bacillus </em>P4I2 RifR, <em>Bacillus </em>P4I1 RifR + <em>Bacillus </em>P4I2 RifR (Kom), positive control (K+; only added with <em>A. hydrophila</em>) and negative control (K-; without probiotic nor <em>A. hydrophila </em>addition). African catfish (13.35±2.80 g) was maintained in 15 aquariums (40 L in volume) with 30 fishes each for 30 days. Probiotic bacteria was applied in water once a day, whereas pathogenic bacteria <em>A. hydrophila </em>RifR (103 cfu/mL) were added once in earlier treatment (except for the negative control). The result showed that the optimal concentration of <em>Bacillus </em>to inhibit <em>A. hydrophila </em>on <em>in vitro </em>test was 104 cfu/mL. <em>In vivo </em>test showed that the addition of probiotic in media of cultivation could reduce the number of <em>A. hydrophila</em>, improve immune response, and also increase the survival of African catfish compared to positive control. Application of probiotic P4I1 RifR showed the highest survival (92.23%) of all treatments.</p><p class="Default"> </p>Keywords: <em>Bacillus</em>, <em>Clarias gariepinus</em>, <em>motile aeromonad septicemia</em>, probiotic<br /><p class="BasicParagraph"> </p><p class="BasicParagraph"> </p><p class="BasicParagraph" align="center"><strong>ABSTRAK</strong></p><p class="BasicParagraph"> </p><p class="Pa2">Penelitian ini bertujuan untuk menguji efektivitas probiotik <em>Bacillus </em>dalam pencegahan penyakit <em>motile aeromonad septicaemia </em>(MAS) yang disebabkan oleh <em>Aeromonas hydrophila </em>pada ikan lele dumbo (<em>Clarias gariepinus</em>). Penelitian terdiri atas pengujian penghambatan bakteri probiotik <em>Bacillus </em>terhadap <em>A. hydrophila </em>secara <em>in vitro</em>, dilanjutkan dengan aplikasi pada budidaya ikan lele dumbo (<em>in vivo</em>). Pada uji <em>in vivo</em>, penelitian terdiri atas lima perlakuan yaitu budidaya ikan lele dumbo dengan penambahan probiotik <em>Bacillus </em>P4I1 RifR, <em>Bacillus </em>P4I2 RifR, kombinasi probiotik <em>Bacillus </em>P4I1 RifR + <em>Bacillus </em>P4I2 RifR (Kom), kontrol positif (K+; hanya ditambahkan <em>A. hydrophila</em>) dan kontrol negatif (K-; tanpa pemberian probiotik dan <em>A. hydrophila</em>). Ikan lele dumbo (13,35±2,80 g) dipelihara pada akuarium volume 40 L dengan kepadatan 30 ekor/akuarium selama 30 hari. Bakteri probiotik ditambahkan pada media pemeliharaan ikan setiap hari, sedangkan bakteri patogen <em>A. hydrophila </em>RifR (103 cfu/ mL) diberikan sekali pada awal pemeliharaan (kecuali pada kontrol negatif). Hasil penelitian menunjukkan bahwa konsentrasi terbaik pada penghambatan <em>in vitro </em>adalah dengan penambahan <em>Bacillus </em>104 cfu/mL. Hasil uji <em>in vivo </em>menunjukkan perlakuan penambahan probiotik pada media budidaya efektif dapat menekan jumlah bakteri <em>A. hydrophila</em>, memperbaiki respons imun, dan meningkatkan kelangsungan hidup ikan lele dumbo dibanding kontrol positif. Perlakuan probiotik P4I1 RifR memberikan hasil terbaik dengan tingkat kelangsungan hidup tertinggi yaitu 92,23%.</p><p class="Default"> </p><p>Kata kunci: <em>Bacillus</em>, <em>Clarias gariepinus</em>, <em>motile aeromonad septicemia</em>, probiotik</p><br class="BasicParagraph" /><p> </p>

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