scholarly journals Bakteriofag spesifik Escherichia coli yang diisolasi dari berbagai sumber air di Bogor Tengah, Kota Bogor sebagai antibiotika alternatif

2021 ◽  
Vol 25 (2) ◽  
pp. 183
Author(s):  
Arga Darmawan Wally ◽  
Eko S. Pribadi ◽  
Surachmi Setyaningsih
Keyword(s):  
Escherichia Coli ◽  
Gold Standard ◽  
E Coli

Penelitian ini bertujuan untuk melakukan isolasi faga spesifik Escherichia coli pada beberapa titik contoh air di Bogor Tengah Kota Bogor dan menyimpannya. Penelitian dilakukan di Kota Bogor pada bulan Maret dan April 2020. Pengkayaan faga dilakukan dua kali sebagai metode baku (gold standard) mengisolasi faga. Uji plak dilakukan untuk mengukuhkan adanya faga di dalam contoh air yang diperiksa menggunakan filtrat yang diperoleh dari metode pengkayaan faga. Hasil yang diperoleh dalam Penelitian ini adalah isolat E. coli yang diisolasi dalam semua contoh air dan faga yang hanya diperoleh satu contoh air, yakni air celupan daging Pasar Merdeka Kota Bogor. kandungan faga dalam contoh air sebesar 9,1 x 108 PFU/ml. Kadar faga tersebut dinilai cukup tinggi yang berpotensi digunakan pada terapi terhadap infeksi bakteri yang disebabkan oleh E. coli.

scholarly journals SENSITIVITAS DAN SPESIFISITAS MEDIA KROMOGENIK SEBAGAI DETEKSI DINI ESCHERICHIA COLI DAN KLEBSIELLA PNEUMONIAE PENGHASIL EXTENDED SPECTRUM ΒETA LACTAMASE (ESBL) DARI SPESIMEN URIN PASIEN DI RSUD DR. SOETOMO SURABAYA

2018 ◽  
Vol 2 (1) ◽  
pp. 45
Author(s):  
Cut Asmaul Husna
Keyword(s):  
Escherichia Coli ◽  
Klebsiella Pneumoniae ◽  
Gold Standard ◽  
Blood Agar ◽  
E Coli ◽  
Extended Spectrum

Infeksi nosokomial yang disebabkan oleh bakteri resisten antibiotik termasuk bakteri penghasil ESBL telah banyak dilaporkan di seluruh dunia. Enzim ESBL paling banyak dihasilkan oleh Enterobacteriaceae, terutama Escherichia coli dan Klebsiella pneumoniae. Medium kromogenik merupakan suatu medium generasi baru sebagai metode kultur secara cepat yang menggabungkan antara deteksi presumtif ESBL dengan identifikasi organisme, yang dapat dijadikan sebagai salah satu skrining. Tujuan penelitian ini adalah untuk menganalisis sensitivitas dan spesifisitas medium kromogenik sebagai deteksi dini Escherichia coli dan Klebsiella pneumoniae penghasil ESBL dari spesimen urin. Penelitian merupakan uji validitas diagnostik. Terdapat 343 spesimen urin yang berasal dari ruangan anak, penyakit dalam dan bedah, semua urin diinokulasikan ke medium kromogenik, disamping pemeriksaan rutin dengan Mac Conkey Agar (MCA) dan Blood Agar (BA). Hasil yang tumbuh pada medium kromogenik diidentifikasi sebanyak 98 sampel berdasarkan warna koloni, 41 sampel menghasilkan koloni berwarna merah dan 28 sampel koloni berwarna hijau, sisanya tumbuh dengan koloni yang tidak berwarna. Terdapat 146 sampel yang tumbuh pada MCA dan BA yang selanjutnya diidentifikasi ddengan Phoenix sebagai gold standard, 32 sampel E. coli dan 18 sampel K. pneumoniae dengan ESBL. Hasil ini dibandingkan untuk menilai sensitivitas dan spesifisitas. Analisis data menggunakan Mc Nemar dan uji Kappa, dengan hasil (P>0,05) yang menunjukkan tidak terdapat perbedaan yang signifikan  antara medium kromogenik dengan Phoenix dalam identifikasi E. coli dan K. pneumoniae penghasil ESBL. Didapatkan sensitivitas, spesifisitas, PPV masing-masing untuk E. coli adalah 96,9%, 80% dan 91,2%; 100% untuk K. pneumoniae. Hasil deteksi dan identifikasi E. coli dan K. pneumonia penghasil ESBL yang dibandingkan dengan Phoenix menunjukkan perbedaan P>α dengan sensitivitas 98%, spesifisitas  85% dan PPV 94,2%. Kesimpulan penelitian ini menunjukkan bahwa medium kromogenik dapat digunakan sebagai deteksi dini dan identifikasi E. coli dan K. pneumonia sebagai penghasil ESBL pada spesimen urin. Penggunaan medium kromogenik dalam identifikasi E. coli dan K. pneumoniae secara langsung pada spesimen urin menunjukkan sensitivitas dan spesifisitas lebih tinggi pada K. pneumonia dibandingkan  E. coli penghasil ESBL.

scholarly journals Unacceptably High Error Rates in Vitek 2 Testing of Cefepime Susceptibility in Extended-Spectrum-β-Lactamase-Producing Escherichia coli

2014 ◽  
Vol 58 (7) ◽  
pp. 3757-3761 ◽  
Author(s):  
Nathaniel J. Rhodes ◽  
Chad L. Richardson ◽  
Ryan Heraty ◽  
Jiajun Liu ◽  
Michael Malczynski ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Gold Standard ◽  
Treatment Decisions ◽  
Error Rates ◽  
Predictive Values ◽  
Content Type ◽  
E Coli ◽  
Vitek 2 ◽  
Sensitivity Specificity ◽  
Susceptibility Breakpoint

ABSTRACTWhile a lack of concordance is known between gold standard MIC determinations and Vitek 2, the magnitude of the discrepancy and its impact on treatment decisions for extended-spectrum-β-lactamase (ESBL)-producingEscherichia coliare not. Clinical isolates of ESBL-producingE. coliwere collected from blood, tissue, and body fluid samples from January 2003 to July 2009. Resistance genotypes were identified by PCR. Primary analyses evaluated the discordance between Vitek 2 and gold standard methods using cefepime susceptibility breakpoint cutoff values of 8, 4, and 2 μg/ml. The discrepancies in MICs between the methods were classified per convention as very major, major, and minor errors. Sensitivity, specificity, and positive and negative predictive values for susceptibility classifications were calculated. A total of 304 isolates were identified; 59% (179) of the isolates carriedblaCTX-M, 47% (143) carriedblaTEM, and 4% (12) carriedblaSHV. At a breakpoint MIC of 8 μg/ml, Vitek 2 produced a categorical agreement of 66.8% and exhibited very major, major, and minor error rates of 23% (20/87 isolates), 5.1% (8/157 isolates), and 24% (73/304), respectively. The sensitivity, specificity, and positive and negative predictive values for a susceptibility breakpoint of 8 μg/ml were 94.9%, 61.2%, 72.3%, and 91.8%, respectively. The sensitivity, specificity, and positive and negative predictive values for a susceptibility breakpoint of 2 μg/ml were 83.8%, 65.3%, 41%, and 93.3%, respectively. Vitek 2 results in unacceptably high error rates for cefepime compared to those of agar dilution for ESBL-producingE. coli. Clinicians should be wary of making treatment decisions on the basis of Vitek 2 susceptibility results for ESBL-producingE. coli.

scholarly journals Identifying of protein complexes and functional modules in E.coli PPI networks

2020 ◽  
Author(s):  
Ping Kong ◽  
Wei Liu
Keyword(s):  
Escherichia Coli ◽  
Gold Standard ◽  
Clustering Algorithm ◽  
Protein Complexes ◽  
Binary Interaction ◽  
Functional Modules ◽  
Ppi Network ◽  
E Coli ◽  
Ppi Networks ◽  
Topological Modules

Abstract Background: Escherichia coli has been at the center of microbial research for decades, making it a standard microorganism for studying molecular mechanism. Molecular complexes, operons and functional modules are important molecular functional domains of Escherichia coli. Most previous studies focused on the detection of E. coli protein complexes based on the experimental methods. While the research of prediction of protein complexes in E. coli based on large-scale proteomic data, especially the functional modules of E. coli are relatively few. Identifying protein complexes and functional modules of E. coli is crucial to reveal principles of cellular organizations, processes and functions. Results: In this study, the protein complexes and functional modules of two high-quality binary interaction datasets of E. coli are predicted by an efficient edge clustering algorithm (ELPA) for complex biological network, respectively. According to the gold standard protein complexes and function annotations provided by EcoCyc dataset, the experimental results show that most topological modules predicted in the two datasets match very well with the real protein complexes, cellular processes and biological functions. By analyzing the corresponding complexes and functional modules shows that all predicted protein complexes are fully covered by one or more functional modules. Furthermore, we compared the results of ELPA with a famous node clustering algorithm (MCL) on the same PPI network of E. coli , and found that ELPA outperforms MCL in terms of matching with gold standard complexes. Conclusions: As a consequence, we surmise that topological modules of PPI network detected by ELPA fits well with real protein complexes and functional units. In most predicted topological modules, the protein complexes and corresponding functional modules are highly overlapping. ELPA is an effective tool to predict protein complexes and functional modules in PPI networks of E. coli.

Sites of Adsorption of the Bacteriophages T3 and T5 on the Wall of Escherichia Coli B.

1967 ◽  
Vol 25 ◽  
pp. 96-97
Author(s):  
Manfred E. Bayer
Keyword(s):  
Escherichia Coli ◽  
Cell Wall ◽  
Electron Microscope ◽  
Uranyl Acetate ◽  
E Coli ◽  
Receptor Sites ◽  
Rigid Cell Wall ◽  
Host Cell Surface ◽  
Bacterial Viruses ◽  
Escherichia Coli B

Bacterial viruses adsorb specifically to receptors on the host cell surface. Although the chemical composition of some of the cell wall receptors for bacteriophages of the T-series has been described and the number of receptor sites has been estimated to be 150 to 300 per E. coli cell, the localization of the sites on the bacterial wall has been unknown.When logarithmically growing cells of E. coli are transferred into a medium containing 20% sucrose, the cells plasmolize: the protoplast shrinks and becomes separated from the somewhat rigid cell wall. When these cells are fixed in 8% Formaldehyde, post-fixed in OsO4/uranyl acetate, embedded in Vestopal W, then cut in an ultramicrotome and observed with the electron microscope, the separation of protoplast and wall becomes clearly visible, (Fig. 1, 2). At a number of locations however, the protoplasmic membrane adheres to the wall even under the considerable pull of the shrinking protoplast. Thus numerous connecting bridges are maintained between protoplast and cell wall. Estimations of the total number of such wall/membrane associations yield a number of about 300 per cell.

The Influence of Glycosylation on the Catalytic and Fibrinolytic Properties of Pro-Urokinase

1992 ◽  
Vol 68 (05) ◽  
pp. 539-544 ◽  
Author(s):  
Catherine Lenich ◽  
Ralph Pannell ◽  
Jack Henkin ◽  
Victor Gurewich
Keyword(s):  
Escherichia Coli ◽  
Mammalian Cell ◽  
Human Gene ◽  
Culture Media ◽  
Mammalian Cell Culture ◽  
Glycosylation Site ◽  
Clot Lysis ◽  
Cell Culture Media ◽  
E Coli ◽  
The Uk

SummaryWe previously found that human pro-UK expressed in Escherichia coli is more active in fibrinolysis than recombinant human pro-UK obtained from mammalian cell culture media. To determine whether this difference is related to the lack of glycosylation of the E. coli product, we compared the activity of E. coli-derived pro-UK [(-)pro-UK] with that of a glycosylated pro-UK [(+)pro-UK] and of a mutant of pro-UK missing the glycosylation site at Asn-302 [(-) (302) pro-UK]. The latter two pro-UKs were obtained by expression of the human gene in a mammalian cell. The nonglycosylated pro-UKs were activated by plasmin more efficiently (≈2-fold) and were more active in clot lysis (1.5-fold) than the (+)pro-UK. Similarly, the nonglycosylated two-chain derivatives (UKs) were more active against plasminogen and were more rapidly inactivated by plasma inhibitors than the (+)UK.These findings indicate that glycosylation at Asn-302 influences the activity of pro-UK/UK and could be the major factor responsible for the enhanced activity of E. coli-derived pro-UK.

Usefulness of a Multiplex PCR for Detection of Diarrheagenic Escherichia coli in a Diagnostic Microbiology Laboratory Setting

2016 ◽  
Vol 1 (2) ◽  
pp. 38-42 ◽  
Author(s):  
Khairun Nessa ◽  
Dilruba Ahmed ◽  
Johirul Islam ◽  
FM Lutful Kabir ◽  
M Anowar Hossain
Keyword(s):  
Escherichia Coli ◽  
Multiplex Pcr ◽  
Clinical Laboratory ◽  
Proteinase K ◽  
Microbiology Laboratory ◽  
Pcr Assay ◽  
E Coli ◽  
Diarrheagenic Escherichia Coli ◽  
Multiplex Pcr Assay ◽  
Diagnostic Microbiology

A multiplex PCR assay was evaluated for diagnosis of diarrheagenic Escherichia coli in stool samples of patients with diarrhoea submitted to a diagnostic microbiology laboratory. Two procedures of DNA template preparationproteinase K buffer method and the boiling method were evaluated to examine isolates of E. coli from 150 selected diarrhoeal cases. By proteinase K buffer method, 119 strains (79.3%) of E. coli were characterized to various categories by their genes that included 55.5% enteroaggregative E. coli (EAEC), 18.5% enterotoxigenic E. coli (ETEC), 1.7% enteropathogenic E. coli (EPEC), and 0.8% Shiga toxin-producing E. coli (STEC). Although boiling method was less time consuming (<24 hrs) and less costly (<8.0 US $/ per test) but was less efficient in typing E. coli compared to proteinase K method (41.3% vs. 79.3% ; p<0.001). The sensitivity and specificity of boiling method compared to proteinase K method was 48.7% and 87.1% while the positive and negative predictive value was 93.5% and 30.7%, respectively. The majority of pathogenic E. coli were detected in children (78.0%) under five years age with 53.3% under one year, and 68.7% of the children were male. Children under 5 years age were frequently infected with EAEC (71.6%) compared to ETEC (24.3%), EPEC (2.7%) and STEC (1.4%). The multiplex PCR assay could be effectively used as a rapid diagnostic tool for characterization of diarrheagenic E. coli using a single reaction tube in the clinical laboratory setting.Bangladesh J Med Microbiol 2007; 01 (02): 38-42

Antagonistic activity of Bacillus subtilis strains isolated from various sources

2018 ◽  
Vol 8 (2) ◽  
pp. 354-364
Author(s):  
A. N. Irkitova ◽  
A. V. Grebenshchikova ◽  
A. V. Matsyura
Keyword(s):  
Escherichia Coli ◽  
Bacillus Subtilis ◽  
Wild Strain ◽  
Fish Farming ◽  
Antagonistic Activity ◽  
Antagonistic Effect ◽  
E Coli ◽  
Long Period ◽  
Test Culture ◽  
Agar Media

<p>An important link in solving the problem of healthy food is the intensification of the livestock, poultry and fish farming, which is possible only in the adoption and rigorous implementation of the concept of rational feeding of animals. In the implementation of this concept required is the application of probiotic preparations. Currently, there is an increased interest in spore probiotics. In many ways, this can be explained by the fact that they use no vegetative forms of the bacilli and their spores. This property provides spore probiotics a number of advantages: they are not whimsical, easily could be selected, cultivated, and dried. Moreover, they are resistant to various factors and could remain viable during a long period. One of the most famous spore microorganisms, which are widely used in agriculture, is <em>Bacillus subtilis</em>. Among the requirements imposed to probiotic microorganisms is mandatory – antagonistic activity to pathogenic and conditional-pathogenic microflora. The article presents the results of the analysis of antagonistic activity of collection strains of <em>B. subtilis</em>, and strains isolated from commercial preparations. We studied the antagonistic activity on agar and liquid nutrient medias to trigger different antagonism mechanisms of <em>B. subtilis</em>. On agar media, we applied three diffusion methods: perpendicular bands, agar blocks, agar wells. We also applied the method of co-incubating the test culture (<em>Escherichia coli</em>) and the antagonist (or its supernatant) in the nutrient broth. Our results demonstrated that all our explored strains of <em>B. subtilis</em> have antimicrobial activity against a wild strain of <em>E. coli</em>, but to varying degrees. We identified strains of <em>B. subtilis</em> with the highest antagonistic effect that can be recommended for inclusion in microbial preparations for agriculture.</p><p><em><br /></em><em></em></p>

NGHIÊN CỨU KHẢ NĂNG BẤT HOẠT ESCHERICHIA COLI TRONG NƯỚC BẰNG TIA CỰC TÍM VỚI SỰ HỖ TRỢ CỦA THIẾT BỊ TẠO MÀNG CHẤT LỎNG

2020 ◽  
Vol 129 (4B) ◽  
Author(s):  
Đặng Thị Thanh Lộc ◽  
Lê Văn Tuấn
Keyword(s):  
Escherichia Coli ◽  
E Coli

Công nghệ khử trùng nước không tạo ra các sản phẩm phụ độc hại ngày càng thu hút nhiều quan tâm nghiên cứu trong những năm gần đây. Nghiên cứu này trình bày kết quả khử trùng Escherichia coli trong nước bằng tia UV kết hợp với thiết bị tạo màng chất lỏng (LFFA). Sự nhạy cảm của vi khuẩn với sự khử trùng bằng UV hoặc UV/LFFA được xác định tại các điều kiện khác nhau của liều UV, tốc độ sục khí và mật độ ban đầu của vi khuẩn. Kết quả nghiên cứu cho thấy khử trùng bằng tia UV kết hợp với LFFA mang lại hiệu quả khử trùng cao hơn so với UV thông thường. Cụ thể, sự kết hợp của UV (liều UV = 20,83 mJ/cm2 và nhiệt độ phòng) và LFFA (tốc độ sục khí = 1,5 L/phút) đã bất hoạt hoàn toàn 5,4 log E. coli trong vòng 60 phút. Trong khi tại cùng một liều UV tương tự, khử trùng bằng tia UV chỉ giảm được 4,3 log vi khuẩn sau 75 phút. Nghiên cứu này hứa hẹn một khả năng áp dụng phương pháp hiệu quả để tăng cường hoạt tính diệt khuẩn của tia UV, nhằm giải quyết các mối quan tâm gần đây trong khử trùng nước.

Антимікробна резистентність провідних збудників інфекцій сечових шляхів у Києві (Україна)

2017 ◽  
Vol 1 (2) ◽  
pp. 48-60
Author(s):  
A.G. Salmanov ◽  
A.V. Rudenko
Keyword(s):  
Escherichia Coli ◽  
Pseudomonas Aeruginosa ◽  
Klebsiella Pneumoniae ◽  
Staphylococcus Epidermidis ◽  
Klebsiella Oxytoca ◽  
Enterobacter Aerogenes ◽  
Enterobacter Cloacae ◽  
Proteus Vulgaris ◽  
Providencia Rettgeri ◽  
E Coli

Мета роботи — вивчити резистентність до антибіотиків бактеріальних збудників інфекцій сечових шляхів (ІСШ), виділених у пацієнтів урологічного стаціонару в м. Києві. Матеріали і методи. Досліджено 1612 штамів бактерій, виділених із сечі хворих з ІСШ (цистит, уретрит, пієлонефрит), госпіталізованих в урологічне відділення ДУ «Інститут урології НАМН України» у м. Києві протягом 2016 р. Серед пацієнтів переважали жінки — 1201 (74,5 %). Вік хворих становив від 17 до 74 років. Для збору даних використано медичну документацію лікарні. Мікробіологічні дослідження виконано у лабораторії мікробіології ДУ «Інститут урології НАМН України». Аналізували результати культурального дослідження зразків сечі, зібраних за наявності клінічних ознак ІСШ. Дослідження клінічного матеріалу та інтерпретацію отриманих результатів проводили загальноприйнятими методами. Вивчено чутливість уропатогенів до 31 антибіотика дискодифузійним методом відповідно до рекомендацій Інституту клінічних та лабораторних стандартів США (Clinical and Laboratory Standards Institute (CLSI)). Результати та обговорення. Аналіз мікробного спектра сечі виявив домінування серед уропатогенів штамів Escherichia coli (32,0 %), Enterococcus faecalis (19,5 %), Klebsiella pneumoniae (10,9 %), Staphylococcus epidermidis (8,9 %), S. haemolyticus (6,5 %) та Pseudomonas aeruginosa (6,4 %). Частка Enterococcus faecium, Enterobacter aerogenes і Streptococcus viridans становила відповідно 2,5, 2,2 і 1,6 %, Enterobacter cloacae, Klebsiella oxytoca, Acinetobacter baumannii, Proteus vulgaris та Providencia rettgeri — менше 1,0 %. У більшості випадків (69,7 %) мікроорганізми виділено у монокультурі, у решті випадків — у мікробних асоціа- ціях. Високу резистентність до тестованих антибіотиків виявили штами E. aerogenes (45,1 %), E. cloacae (45,7 %), E. faecium (40,9 %), E. faecalis (40,7 %), E. coli (39,9 %), P. aeruginosa (34,0 %), K. pneumoniae (28,6 %). Найбільш активними до уропатогенів були іміпенем (E. coli — 87,6 %, P. aeruginosa — 75,7 %, E. cloacae — 67,3 %, E. aerogenes — 72,6 %, K. pneumoniae — 93,2 %), меропенем (E. coli — 89,1 %, P. aeruginosa — 76,7 %, K. pneumoniae — 82,6 %), лефлоцин (E. coli — 74,5 %, ентерококи — 78,7 %, P. aeruginosa — 76,7 %, E. cloacae — 73,9 %, E. aerogenes — 80,4 %, K. pneumoniae — 83,5 %), амоксицилін/клавуланат (ентерококи — 84,6 %), фурагін (ентерококи — 82,6 %), цефоперазон (K. pneumoniae — 89,2 %, P. aeruginosa — 73,8 %), цефтріаксон (K. pneumoniae — 80,1 %). Висновки. Антибіотикорезистентність збудників ІСШ — важлива терапевтична проблема. Найбільшою активністю до уропатогенів характеризуються іміпенем, меропенем, лефлоцин, амоксицилін/ клавуланат, фурагін, цефоперазон, цефтріаксон, які можна розглядати як препарат вибору для призначення стартової терапії ІСШ. Необхідно здійснювати постійний моніторинг за резистентністю до дії антибіотиків. Політику використання антибіотиків у кожному стаціонарі слід визначати залежно від локальних даних щодо резистентності до протимікробних препаратів.

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