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"ABSTRACTBackground: early detection of H. pylori is essential to prevent the development of infections into gastric malignancies. The coccoid form of H. pylori is difficult to detect either by culture or histopathology; however, it can be detected using molecular methods, such as real-time PCR. The study was expected to provide new information on the development of H. pylori detection. Methods: a cross-sectional study was conducted at the Gastrointestinal Endoscopy Center of Cipto Mangunkusumo Hospital between October 2016 and August 2017. The sampling method used was consecutive sampling. Biopsy from gastric antrum and corpus were performed in 64 patients. We collected 2 specimens from each site to be examined using real-time PCR and histopathology. Initially, we conducted real-time PCR optimization followed by application of clinical samples from gastric biopsy. Data analysis using McNemars χ2 and Kappa tests. Results: the real-time PCR showed 25% positivity, while the positive proportion of histopathological examination was 14%. Real-time PCR has a sensitivity and specificity 88.9% dan 85.5%, respectively. The McNemars x2 test showed that there is significantly different (p=0.039) between the two tests; kappa value (p=0.561). Conclusion: the real-time PCR examination is more sensitive than histopathology. This technique can improve diagnosis by 11% compared to histopathological examination."

"ABSTRAKHelicobacter pylori diperkirakan menginfeksi lebih dari setengah populasi orang dewasa. Deteksi dini H.pylori sangat diperlukan untuk mencegah berkembangnya infeksi menjadi keganasan lambung. Bentuk coccoid dari H. pylori sulit dideteksi dengan kultur dan histopatologi, namun dapat terdeteksi dengan metode molekuler seperti real-time PCR. Salah satu gen yang dapat digunakan sebagai gen target real-time PCR yaitu 16S rRNA, yang diketahui spesifik dan juga digunakan untuk menganalisis kekerabatan antar strain. Analisis ini bermanfaat untuk melihat penyebaran infeksi H.pylori di dunia. Penelitian ini merupakan penelitian eksperimental laboratorium. Metode pengambilan sampel yang digunakan yaitu, metode consecutive sampling. Biopsi diambil dari 2 antrum dan 2 korpus pada 42 penderita dispepsia untuk pemeriksaan real-time PCR dan histopatologi. Optimasi kondisi real-time PCR meliputi uji volume cetakan DNA, sensitifitas dan spesifisitas teknik, kemudian dilanjutkan aplikasi pada sampel klinis dari biopsi lambung. Delapan dari 11 sampel yang positif dilakukan sekuensing dan analisis filogenetik. Hasil optimasi diperoleh suhu annealing 64?C, konsentrasi primer 0,8 ?M dan konsentrasi probe 0,6 ?M. Ambang batas deteksi real-time PCR untuk mendeteksi jumlah DNA minimal H.pylori yaitu 46 bakteri. Spesifisitas uji reaksi silang real-time PCR ini tidak menunjukkan adanya reaksi silang dengan mikroorganisme lain. Proporsi positif hasil pemeriksaan real-time PCR sebesar 26,2 , sedangkan histopatologi sebesar 11,9 . Pemeriksaan real-time PCR mampu meningkatkan diagnosis sebesar 14,3 dibandingkan pemeriksaan histopatologi. Hasil sekuensing dan analisis filogenetik menunjukkan bahwa strain H.pylori dari sampel memiliki kekerabatan dengan strain Taiwan, India, dan Australia. Kata kunci : H.pylori, histopatologi, real-time PCR, analisis filogenetik

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ABSTRACTHelicobacter pylori infection is estimated infect almost half of the adult population in the world. Early detection of H.pylori is needed to prevent the development of infections into gastric malignancies. The coccoid form of H. pylori is difficult to detect using culture and histopathology but it can be detected by molecular methods such as real time PCR. One of the genes that can be used as a real time PCR target gene is 16S rRNA, which is known to be specific and also used to analyze closely related strain. This analysis were useful to showed the spread of H.pylori infection in the world.This study is an experimental laboratory. The sampling method used is the consecutive sampling method. Biopsy was taken from 2 antrum and 2 corpus in 42 patients with dyspepsia for real time PCR and histopathology examination. Optimization real time PCR conditions include DNA template volume testing, sensitivity and specificity of the technique, followed by application of clinical samples from gastric biopsy. Eight of the 11 positive samples were sequenced and analyzed for phylogenetics pattern. The optimization result obtained annealing temperature 64 C, primer concentration was 0,8 M and probe concentration was 0,6 M. Limit detection of the DNA was 46 bacteria. The specificity of the PCR 39 s real time indicate that there was no cross reaction with other microorganisms. The positive proportion of PCR real time examination was 26.2 , while histopathology was 11.9 . A real time PCR examination was able to improve the diagnosis by 14,3 compared to histopathology examination. Sequencing and phylogenetic analysis results showed that our strain were closely related to Taiwan, India and Australia strains. Keywords H.pylori, histopathology, real time PCR, phylogenetic analysis"

"ABSTRAKHelicobacter pylori (H. pylori) infection causes various abnormalities in the stomach. Only particular strain can cause severe problems in the stomach. CagA is a microbial virulent factor which is associated with more severe stomach problems, such as: peptic ulcer and stomach cancer. We would like to know the prevalence of CagA in Balinese population, and the association of H. Pylori CagA status with the severity of endoscopic appearance in dyspepsia patients.Method: Study design being used was analytic cross sectional study, involving 71 dyspepsia patients who underwent upper gastrointestinal endoscopic examination in Surya Husada Hospital and Balimed Hospital in June-December 2013. Sample was chosen in consecutive manner. Later, polymerase chain reaction (PCR) examinations of the stomach mucous biopsy tissue to determine H. pylori infection status and CagA status were performed. Further, Chi square test was used to identify the difference in proportion of H. pylori and CagA between mild and severe endoscopic appearance.Results: In this study, we found that the prevalence of H. pylori infection was 22.5% using PCR examination. Prevalence of CagA positive in H. pylori positive was 62.5%. There was significant association between status of H. Pylori infection and severity of endoscopic appearance (p = 0.038; OR= 2.67; 95% CI = 1.18-6.05). Status of CagA in H. pylori infected patients was not associated with the severity of endoscopic appearance. Additionally, there was significant association between patients’ age and severity of endoscopic appearance.Conclusion: The prevalence of CagA in H. pylori positive was 62.5%. H. pylori infection was associated with severity of endoscopic appearance and CagA status in H. pylori infected patients was not associated with severity of endoscopic appearance."

"Dyspepsia is one of numerous general complaints, which is commonly encountered by doctors of various disciplines. In daily practice, the complaint is not only limited for gastroenterologists. Knowledge on pathophysiology of dyspepsia have been developing continuously since a scientific investigation has been started in 1980s, which considers Helicobacter pylori as one of key factor in managing dyspepsia, either it is associated with ulcer or non-ulcer. The management of dyspepsia cannot be separated from the management of H. pylori and there is an additional new knowledge associated with definition, pathophysiology, diagnosis and treatment of both dyspepsia and H. pylori infection.

This consensus document on the management of dyspepsia and H. pylori infection in Indonesia has been developed using the evidence-based medicine principles; therefore, it can be used as a reference for doctors in dealing with dyspepsia and H. pylori infection cases in their daily practice. It is expected that with the new consensus, doctors can provide greater service to their patients who have dyspepsia and H. pylori infection."

"Dyspepsia is a common complain in clinical practice. Correlation between helicobacter pylori (H. pylori) and functional dyspepsia had been reported in many studies, but studies that analyzed the severity of dyspepsia and H. pylori were limited and the result were controversial. This study is about to know the correlation between the severity of dyspepsia and H. pylori infection. A retrospective descriptive analysis to patients with dyspepsia at Permata Bunda Hospital, Medan was done in 2010-2014. Simple random sampling was done to get 44 patient with dyspepsia, 22 are H. pylori positive and 22 patients are H. pylori negative. The severity of dyspepsia assessed with porto alegre dyspeptic symptoms questionnaire (PADYQ) scoring instrument. Univariate and bivariate analysis (Chi-square and spearman correlation) were done using SPSS version 22. Epigastric pain is teh most common symptom in dyspepsia patients. There is a correlation between ulcer type dyspepsia and H. pylori infection (p=0.030), while dysmotility type and mixed type were not correlated. The severity of epigastric pain has significant positive correlation with H. pylori (r=0.386;p=0.01), while the severity of other symptoms such as nausea, vomit, and abdominal bloating have negative correlation with H.pylori. Dyspepsia total scoring is significantly lower in H. pylori positive than in H.pylori negative (p=0.033). There is a positive correlation between the severity of nausea, vamit, and abdominal bloating and H.pylori infection, and correlation between lower dyspepsia total scoring and H.pylori pain."

"Latar Belakang: Diagnosis definitif Helicobacter pylori H.pylori hingga kini masih merupakan masalah. Biakan untuk isolasi dan identifikasi bakteri ini sulit. Uji cepat urease direkomendasikan sebagai uji diagnostik lini pertama pasien dispepsia. Tujuan: Mengembangkan komposisi medium biakan dan deteksi cepat H.pylori pada spesimen biopsi lambung pasien dispepsia. Metode: Desain penelitian merupakan studi potong lintang dan eksperimental laboratorium. Sampel diambil dengan cara consecutive sampling sebanyak 68 spesimen biopsi lambung 34 antrum, 34 korpus, masing-masing untuk biakan dan uji MIU. Sebagai pembanding digunakan histopatologi dan PCR. Mula-mula dilakukan optimasi medium biakan dan MIU konsentrasi merah fenol, pH, urea dan suhu inkubasi. Selanjutnya kondisi optimal yang diperoleh diaplikasikan pada spesimen biopsi pasien dispepsia. Hasil: Medium biakan agar darah Columbia ditambah vankomisin 5 mg / 500 mL dan darah domba 7 belum optimal, namun dapat digunakan untuk isolasi dan identifikasi. Hasil MIU modifikasi sebagai berikut: konsentrasi merah fenol 0,001 ; urea 4 ; pH medium 7; Suhu inkubasi optimal 35-370 C. Proporsi positif hasil uji MIU sebesar 35,29 12/34, biakan 32,35 11/34, PCR 32,35 11/34 dan histopatologi 20,59 7/34. Kesimpulan: Pemeriksaan MIU meningkatkan positivitas hasil pemeriksaan sebesar 14,7 bila dibandingkan dengan histopatologi.

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Background: Until now, definitive diagnostic of H.pylori is still a problem. Culture for isolation and identification of this pathogen is difficult. Rapid urease test is recommended as a first line diagnostic test.

Aim: To obtain optimal composition for culture medium and Motility Indol Urease MIU test for the detection of H. pylori in dyspeptic patient biopsy specimens.

Method: A cross sectional and experimental laboratory study was performed. Sixty eight gastric biopsy samples 34 antrum, 34 corpus were collected by consecutive sampling method for culture and MIU test. Histopathology and PCR were conducted for comparison. Initially, we performed the optimation of culture medium and MIU test phenol red and urea concentration, pH, and temperature. The optimal condition obtained was then applied to the specimens.

Result: Columbia agar supplemented with vancomycin 5 mg 500 mL and 7 sheep blood was unable to create an optimal condition, but it can be used for isolation and identification. Modified MIU was performed by this following condition phenol red 0,001 urea 4 pH 7 incubation temperature 35 37oC. Positive proportion of MIU was 35.29 12 34, culture 32.35 11 34, PCR 32,35 11 34 and histopathology 20.59 7 34.

Conclusion: MIU test was able to improve the positivity rate by 14,7 compared to histopathology."

"Latar Belakang: Diagnosis definitif Helicobacter pylori (H.pylori) hingga kini masih merupakan masalah. Biakan untuk isolasi dan identifikasi bakteri ini sulit. Uji cepat urease direkomendasikan sebagai uji diagnostik lini pertama pasien dispepsia. Tujuan: Mengembangkan komposisi medium biakan dan deteksi cepat H.pylori pada spesimen biopsi lambung pasien dispepsia. Metode: Desain penelitian merupakan studi potong lintang dan eksperimental laboratorium. Sampel diambil dengan cara consecutive sampling sebanyak 68 spesimen biopsi lambung (34 antrum, 34 korpus), masing-masing untuk biakan dan uji MIU. Sebagai pembanding digunakan histopatologi dan PCR. Mula-mula dilakukan optimasi medium biakan dan MIU (konsentrasi merah fenol, pH, urea dan suhu inkubasi). Selanjutnya kondisi optimal yang diperoleh diaplikasikan pada spesimen biopsi pasien dispepsia. Hasil: Medium biakan agar darah Columbia ditambah vankomisin 5 mg/500 mL dan darah domba 7% belum optimal, namun dapat digunakan untuk isolasi dan identifikasi. Hasil MIU modifikasi sebagai berikut: konsentrasi merah fenol 0,001%; urea 4%; pH medium 7; Suhu inkubasi optimal 35-370 C. Proporsi positif hasil uji MIU sebesar 35,29% (12/34), biakan 32,35%(11/34), PCR 32,35%(11/34) dan histopatologi 20,59% (7/34). Kesimpulan: Pemeriksaan MIU meningkatkan positivitas hasil pemeriksaan sebesar 14,7% bila dibandingkan dengan histopatologi.

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Background: Until now, definitive diagnostic of H.pylori is still a problem. Culture for isolation and identification of this pathogen is difficult. Rapid urease test is recommended as a first-line diagnostic test. Aim: to obtain optimal composition for culture medium and Motility-Indol-Urease (MIU) test for the detection of H. pylori in dyspeptic patient biopsy specimens. Method: A cross sectional and experimental laboratory study was performed. Sixty eight gastric biopsy samples (34 antrum, 34 corpus) were collected by consecutive sampling method for culture and MIU test. Histopathology and PCR were conducted for comparison. Initially, we performed the optimation of culture medium and MIU test (phenol red and urea concentration, pH, and temperature). The optimal condition obtained was then applied to the specimens. Result: Columbia agar supplemented with vancomycin 5 mg / 500 mL and 7% sheep blood was unable to create an optimal condition, but it can be used for isolation and identification. Modified MIU was performed by this following condition: phenol red 0,001%; urea 4%; pH 7; incubation temperature 35-37oC. Positive proportion of MIU was 35.29% (12/34), culture 32.35% (11/34), PCR 32,35% (11/34) and histopathology 20.59% (7/34). Conclusion: MIU test was able to improve the positivity rate by 14,7% compared to histopathology. "

"Leptospirosis merupakan penyakit akibat infeksi bakteri Leptospira spp. patogen yang umumnya terjadi di negara tropis dan subtropis serta memiliki karakteristik berupa gejala klinis yang kurang spesifik. Vektor dari penyakit tersebut adalah tikus maupun hewan peliharaan, seperti anjing dan sapi. Microscopic agglutination test (MAT) merupakan uji baku emas leptospirosis yang telah ditetapkan WHO. Akan tetapi, uji tersebut kurang sensitif di fase awal terjadinya infeksi dan memiliki prosedur yang rumit. Konfirmasi melalui metode real-time polymerase chain reaction (RT-PCR) dengan gen secY menggunakan darah utuh dan serum dapat dilakukan untuk pengembangan diagnosis leptospirosis. Tujuan dari penelitian ini adalah mendeteksi gen secY pada sampel darah utuh dan serum pada pasien terduga leptospirosis yang meliputi pasien suspek dan probable di Klaten, Jawa Tengah dengan metode RT-PCR. Selain itu, penelitian ini juga bertujuan untuk membandingkan positivity rate hasil RT-PCR sampel darah utuh dan serum dari 111 pasien terduga leptospirosis di Klaten, Jawa Tengah. Metode penelitian ini meliputi isolasi DNA, kuantifikasi DNA, amplifikasi DNA dengan RT-PCR menggunakan probe dan pewarna ROX, serta analisis hasil RT-PCR. Hasil RT-PCR menunjukkan terdeteksinya gen secY pada sampel darah utuh dan serum, dengan positivity rate darah utuh sebesar 5,41% (6/111) dan serum sebesar 18,92% (21/111), sedangkan positivity rate pada pasien suspek adalah sebesar 19,51% (16/82) dan pada pasien probable sebesar 27,59% (8/29). Dengan demikian, darah utuh dan serum dapat digunakan untuk mendeteksi leptospirosis dengan RT-PCR menggunakan gen secY dengan serum sebagai sampel yang lebih sensitif dibandingkan darah utuh. Akan tetapi, perlu dilakukan upaya untuk meningkatkan kualitas metode deteksi, berupa proses ekstraksi, optimasi primer, maupun penggunaan gen pendamping. Selain itu, hasil RT-PCR tersebut juga dapat dikonfirmasi melalui analisis sekuens sebagai analisis lanjutan.

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Leptospirosis is a disease caused by infection with pathogenic Leptospira spp. bacteria that commonly occurs in tropical and subtropical countries and has characteristics in the form of less specific clinical symptoms. The vectors of the disease are rats and domestic animals, such as dogs and cattle. Microscopic agglutination test (MAT) is the WHO gold standard test for leptospirosis. However, the test is less sensitive in the early phase of infection and has a complicated procedure. Confirmation through real-time polymerase chain reaction (RT-PCR) method with secY gene using whole blood and serum can be done for the development of leptospirosis diagnosis. The aim of this study is to detect secY gene in whole blood and serum samples of presumed leptospirosis patients including suspected and probable patients in Klaten, Central Java using RT-PCR method. In addition, this study also aimed to compare the positivity rate of RT-PCR results of whole blood and serum samples from 111 presumed leptospirosis patients in Klaten, Central Java. The method of this research includes DNA isolation, DNA quantification, DNA amplification by RT-PCR using ROX probes and dyes, and analysis of RT-PCR results. RT-PCR results showed the detection of secY gene in whole blood and serum samples, with a positivity rate in whole blood is 5.41% (6/111) and in serum is 18.92 (21/111), meanwhile the positivity rate in suspected patients is 19.51% (16/82) and in probable patients is 27.59% (8/29). Thus, whole blood and serum can be used to detect leptospirosis by RT-PCR using the secY gene with serum as the more sensitive sample than whole blood. However, efforts need to be made to improve the quality of the detection method, in the form of the extraction process, primer optimization, and the use of companion genes. In addition, the RT-PCR results can also be confirmed through sequence analysis as a follow-up analysis."

"Background: pathophysiology of functional dyspepsia remains poorly understood. Many factors such as gastric motility disorder, visceral hypersensitivity, Helicobacter pylori (Hp) infection, psychological stress and excessive gastric acid secretion play roles in this symptom. Psychological stress may promote peptic ulcer and has an effect on ulcers-associated Hp. This study aimed to determine Helicobacter pylori activity and expression of mucosal IL 6 and their association with psychological stress. Methods: a cross-sectional study was done among 40 outpatients with dyspeptic syndromes in M. Djamil General Hospital and two community health centers in Padang. The subjects were divided into two groups, with and without psychological stress, which were identified using DASS 42. Gastric biopsy specimens and peripheral blood samples were taken while performing esophagogastroduodenoscopy. Immunohistochemistry methods was used to determine the expression of IL 6 and Hp in gastric mucosa. The correlation of each variable in the group experiencing psychological stress and non stress was analyzed using Chi square test. Results: there were 40 patients with functional dyspepsia with average age of 37.58(SD 11.82) years old. The cortisol levels were significantly different between both groups (non stress vs. stress groups); moreover, morning cortisol level in psychological stress group was higher beyond normal limit. Interleukin 6 expression, as the evidence of inflammatory activity, seemed higher in non stress group than the group with psychological stress (8.25% vs. 7.25%). Helicobacter pylori activity was seemed to be increased in the stress group as characterized by higher numbers of invasion to the sub mucosa epithelium compared to the non stress group (11 vs. 7 subjects). Conclusion: psychological stress seems to have no correlation with IL-6 in gastric mucous of patients with functional dyspepsia; however, there is an evidence of increasing activity of Helicobacter pylori."

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Latar belakang: Prevalensi infeksi Helicobacter pylori pada anak di Indonesia 8%- 52%. Gejala dominan pada anak dengan infeksi H. pylori adalah refluks gastroesofageal yang mengganggu kualitas hidup (penyakit refluks gastroesofageal/PRGE), yang secara definitf di diagnosis dengan pemeriksaan esofagogastroduodenoskopi (EGD). Untuk mengetahui infeksi dilakukan uji Rapid Urease Test (RUT) pada saat bedside, namun uji ini belum diketahui akurasinya Tujuan: Mendapatkan proporsi positif RUT pada biopsi lambung dibandingkan real-time PCR. Selain itu ingin diketahui karakteristik gambaran klinis, demografi, dan hubungan faktor risiko pada anak PRGE yang menjalani prosedur EGD. Metode: Penelitian potong lintang pada 46 anak dengan PRGE di RSCM dan RS MMC. Semua subyek menjalani RUT, real-time PCR dan histopatologi. Hasil: Anak perempuan berusia lebih dari 10-18 tahun dengan tingkat pendidikan orangtua rendah mendominasi karakteristik subyek penelitian ini. Nyeri perut lebih dari 3 bulan, anemia, status nutrisi, orangtua dispepsia dan kepadatan kapling rumah pada penelitian ini tidak terbukti sebagai faktor risiko terhadap terjadinya PRGE. Namun, pola makan tidak teratur dan komsumsi makan berempah memengaruhi terjadinya gastropati pada lambung anak (p < 0,05). Proporsi positif RUT; 2,2% dan real-time PCR; 8,7%. Kesimpulan: Hasil negatif pada pemeriksaan RUT tidak menyingkirkan terjadinya infeksi H. pylori, terutama pada pasien dalam terapi proton pump inhibitor (PPI). Pemeriksaan lanjutan menggunakan real-time PCR dianjurkan untuk mendukung diagnosis ini.

 

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Background: The prevalence of detected Helicobacter pylori infection of children in Indonesia was 8%-52%. Gastroesophageal reflux was the dominant symptom and might be attributable to H. pylori infection which reduced quality of life. Current definitive diagnosis was using esophagogastroduodenoscopy (EGD). Rapid Urease Test (RUT) was used in bedside setting for H. pylori detection, however its accuracy was still unkown. Objectives: This study was done to determine the positive proportion of RUT on gastric biopsy specimens and real-time PCR. Moreover, this study explored the characteristics of clinical and demographic features, and examined the risk factors in children with GERD (gastroesophageal reflux disease) who underwent diagnostic EGD. Methods: This is a cross-sectional study on 46 children diagnosed as GERD, admitted to the RSCM and MMC Hospital. All subject underwent RUT, real-time PCR and histopathology examination. Results: Most subjects are girls, more than 10-18 years with low parental education dominated the proportion of subject included in this study. According to abdominal pain more than 3 months, anemia, nutritional status, parental dyspepsia and crowded household were not proven to be risk factors for increase of GERD. However, irregular feeding habit and consumption of spicy foods were be associated with gastropathy in child’s gastric mucosa (p < 0,05). The positive proportion of RUT was 2.2% and real-time PCR was 8.7%. Conclusion: The negative result of RUT could not rule out of H. pylori infection, especially in patients with proton pump inhibitor (PPI) therapy. Further examination using real-time PCR is needed to support the diagnosis.

 

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