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[ABSTRAK
Latar belakang: Metode PCR rutin untuk mendeteksi mutasi pada thalassemia α seperti PCR multi kompleks dan restriction fragment length polymorphism (RFLP) membutuhkan proses yang lama dan reagen yang banyak serta biaya yang besar. Saat ini telah dikembangkan metode baru yaitu tes strip (α-globin strip assay), yang dapat mendeteksi 21 macam mutasi gen globin -α secara simultan dalam satu paket reaksi dan hanya membutuhkan DNA dalam jumlah sedikit. Tujuan : Mengetahui nilai sensitivitas dan spesifisitas metode α-globin strip assay dalam mendeteksi mutasi thalassemia-α. Metode penelitian: Penelitian merupakan uji diagnostik yang dilakukan dengan metode belah lintang yang membandingkan pemeriksaan α -globin strip assay dan PCR rutin dalam mendeteksi mutasi gen pada thalassemia α. Pada tahap I disertakan 17 pasien yang berobat ke pusat thalassemia di RSCM dan Lembaga Biomolekular Eijkman Jakarta pada bulan Oktober 2014 sampai Maret 2015, kemudian tahap II disertakan 18 anggota keluarga inti subjek pada tahap I. Pada semua subjek dilakukan pemeriksaan hematologi termasuk indeks eritrosit, morfologi darah tepi, analisis Hb, PCR rutin dan α -globin strip assay. Hasil penelitian dan pembahasan: Ditemukan tujuh jenis mutasi yang terdiri dari: 1) delesi 1 gen 3,7kb; 2) non delesi Cd59; 3) non delesi HbCS; 4) delesi 2 gen SEA; 5) mutasi campuran 3,7kb/Cd59 ; 6) mutasi campuran Cd59/HbCS; 7) mutasi campuran SEA/HbCS. Metode α-globin strip assay memiliki nilai sensitivitas dan spesifisitas sebesar 100%. Kesimpulan : Metode α-globin strip assay akurat mendeteksi mutasi thalassemia-α dengan tingkat sensitivitas dan spesifisitas sebesar 100%.

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ABSTRACT
Background : Routine PCR methods in detecting mutations that occur in α thalassemia such as multi-complex single tube PCR and PCR restriction fragment length polymorphism (RFLP) require a lengthy process and utilize large amount of reagents and are costly. α-globin strip assay is a new method in detecting α thalassemia related mutations that is able to detect 21 types of globin-α mutations simultaneously in a single reaction and requires only small amount of DNA. Objective: To determine the sensitivity and specificity of α-globin strip assay compared to routine PCR in detecting α thalassemia associated mutations. Methods: A cross sectional diagnostic study was performed comparing α-globin strip assay and routine PCR in detecting mutations related to α thalassemia. Phase I of the study includes 17 patients treated for α thalassemia at RSCM and Biomolecular Eijkman Institute between October 2014 and March 2015, phase II includes 18 close relatives of patients recruited in phase I. All subjects underwent hematological examination including erythrocyte indices, peripheral blood morphology, Hb analysis, routine PCR and α ?globin strip assay. Results: Seven kind of mutations were identified including 1) deletion of one gene 3,7 kb; 2) non-deletion of CD59; 3) non deletion of HbCS; 4) deletion of two genes SEA; 5) mixed mutation of 3,7kb/CD59; 6) mixed mutation of CD59/HbCS; 7) mixed mutation of SEA/HbCS. α-globin strip assay has sensitivity and specificity of 100%. Conclusion: α ?globin strip assay accurately detect mutations in α thalassemia with 100% sensitivity and specificity., Background : Routine PCR methods in detecting mutations that occur in α thalassemia such as multi-complex single tube PCR and PCR restriction fragment length polymorphism (RFLP) require a lengthy process and utilize large amount of reagents and are costly. α-globin strip assay is a new method in detecting α thalassemia related mutations that is able to detect 21 types of globin-α mutations simultaneously in a single reaction and requires only small amount of DNA. Objective: To determine the sensitivity and specificity of α-globin strip assay compared to routine PCR in detecting α thalassemia associated mutations. Methods: A cross sectional diagnostic study was performed comparing α-globin strip assay and routine PCR in detecting mutations related to α thalassemia. Phase I of the study includes 17 patients treated for α thalassemia at RSCM and Biomolecular Eijkman Institute between October 2014 and March 2015, phase II includes 18 close relatives of patients recruited in phase I. All subjects underwent hematological examination including erythrocyte indices, peripheral blood morphology, Hb analysis, routine PCR and α –globin strip assay. Results: Seven kind of mutations were identified including 1) deletion of one gene 3,7 kb; 2) non-deletion of CD59; 3) non deletion of HbCS; 4) deletion of two genes SEA; 5) mixed mutation of 3,7kb/CD59; 6) mixed mutation of CD59/HbCS; 7) mixed mutation of SEA/HbCS. α-globin strip assay has sensitivity and specificity of 100%. Conclusion: α –globin strip assay accurately detect mutations in α thalassemia with 100% sensitivity and specificity.]

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Latar Belakang: Tuberkulosis (TB) merupakan masalah kesehatan utama di dunia, khususnya di Indonesia. Tuberkulosis umumnya menyerang paru (TB paru), namun bisa juga menyerang organ lain (TB ekstraparu), seperti kolitis TB. Diagnosis kolitis TB menjadi tantangan karena klinis dan hasil pemeriksaannya menyerupai penyakit lain, seperti inflammatory bowel disease (IBD). Studi ini bertujuan untuk mengetahui proporsi hasil PCR-TB feses pada pasien teduga kolitis TB dan uji diagnosis pemeriksaan PCR-TB feses jika dibandingkan dengan hasil kolonoskopi, histopatologi, dan evaluasi klinis. Metode: Dilakukan studi uji diagnostik pada 60 subjek terduga kolitis TB di RSCM yang menjalani pemeriksaan kolonoskopi pada bulan Februari-April 2019. Ekstraksi DNA dari feses dilakukan dengan menggunakan QIAamp® Fast Stool DNA Mini Kit dan PCR dilakukan dengan kit artus® M. tuberculosis RG dengan target gen 16s rRNA. Hasil pemeriksaan PCR-TB feses dibandingkan dengan hasil kolonoskopi, histopatologi, dan evaluasi klinis. Hasil: Terdapat 60 subjek terduga kolitis TB yang disertakan dan dianalisis dalam penelitian ini. Diperoleh 26 (43,3%) hasil PCR-TB feses positif, yang terdiri atas 7/8 subjek kolitis TB dan 19/52 subjek bukan kolitis TB. Dari hasil penelitian ini, didapatkan nilai diagnostik PCR-TB feses dibandingkan hasil kolonoskopi, histopatologi, dan evaluasi klinis memiliki sensitivitas 87,5%, spesifisitas 63,5%, NPP 26,9%, dan NPN 97,1%. Simpulan: Pemeriksaan PCR-TB feses memiliki sensitivitas baik namun spesifisitas yang rendah untuk diagnosis kolitis TB sehingga lebih baik sebagai pemeriksaan penyaring untuk kolitis TB. ......Background: Tuberculosis (TB) is a major health problem in the world, particularly in Indonesia. Tuberculosis commonly affects lung (pulmonary TB), but it can also affect other organs (extrapulmonary TB), such as TB colitis. The diagnosis of TB colitis has become a challenge because the clinical manifestation and its tests result can mimic other diseases, such as inflammatory bowel disease (IBD). This study was aimed to find the proportion of stool TB-PCR result in patients which suspected with TB colitis and the diagnostic value of stool TB-PCR if compared to colonoscopy, histopathology, and clinical evaluation. Methods: Diagnostic study was done in 60 subjects suspected for TB colitis in RSCM which underwent colonoscopy and histopathology examination in February-April 2019. The DNA extraction from the stool was done by using QIAamp® Fast Stool DNA Mini Kit and TB-PCR was done with artus® M. tuberculosis RG PCR kit which targeting 16s rRNA gene. The result of stool TB-PCR then was compared to the result of colonoscopy, histopathology, and clinical evaluation. Results: There were 60 subjects suspected with TB colitis recruited and analyzed in this study. There were 26 (43,3%) positive stool TB, consist of 7/8 subjects with TB colitis and 19/52 subjects with non-TB colitis. From this study, the diagnostic value of stool TB-PCR that was compared to combination of colonoscopy, histopathology, and clinical evaluation were: sensitivity 87,5%, specificity 63,5%, positive predictive value (PPV) 26,9% and negative predictive value (NPV) 97,1%. Conclusion: Stool TB-PCR has good sensitivity but low specificity for diagnosing TB colitis. Therefore, stool TB-PCR is better utilized for TB colitis screening.

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Buku ini berisi tentang gambaran uji coba PCR multipleks yang dikembangkan oleh peneliti di Badan Penelitian dan Pengembangan Kesehatan untuk identifikasi penyebab difteri secara cepat dan akurat. Hal ini penting disampaikan karena sampai dengan saat ini pemeriksaan laboratorium masih menjadi salah satu kendala dalam penatalaksanaan kasus dan pengendalian KLB difteri, khususnya di Indonesia. Jarangnya kasus difteri berimplikasi pada terbatasnya laboratorium klinik yang siap melakukan pemeriksaan sampel secara rutin. Selain itu, lamanya mendapatkan hasil pemeriksaan menggunakan metode konvensional sebagai gold standard seringkali menjadi kendala di lapangan. Oleh karena itu, buku ini mencoba menyajikan beberapa keunggulan dari pemeriksaan laboratorium difteri menggunakan teknik PCR multipleks dibandingkan dengan metode lain. Inti dari buku ini disajikan pada Bab IV dan V tentang hasil penelitian dan pembahasan. Sebagai tambahan, konsep umum atau tinjauan pustaka disajikan pada Bab II untuk memudahkan para pembaca memahami apa yang disampaikan pada Bab IV dan V.

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Latar Belakang. Coronavirus Disease-19 (COVID-19) sampai sekarang masih menjadi ancaman kesehatan global. Baku emas diagnosis COVID-19 adalah pemeriksaan RT-PCR dari sampel usap nasofaring. Pengambilan sampel dengan cara ini memiliki kekurangan seperti rasa tidak nyaman pada pasien, risiko perdarahan, dan risiko paparan pada tenaga medis. Saliva merupakan salah satu alternatif sampel yang bisa digunakan untuk tujuan ini. Tujuan. Mengetahui sensitivitas, spesifisitas, nilai duga positif, nilai duga negatif, dan akurasi RTPCR saliva. Metode. Penelitian potong lintang pasien dewasa suspek COVID-19 pada April-Juni 2021 di instalasi gawat darurat rumah sakit Siloam Lippo Village. Pasien yang memenuhi syarat dan menyatakan setuju dilakukan pemeriksaan RT-PCR dari sampel usap nasofaring dan saliva. RTPCR dikerjakan dengan menilai gen N dan gen ORF1AB menggunakan alat Rotorgen QPlex-5Plus dengan batas positif CT Value < 40. Hasil. Sebanyak 126 pasien suspek COVID-19 yang eligible ikut penelitian selama periode studi. Enam pasien menolak mengikuti penelitian. Analisis akhir dikerjakan pada 120 pasien dengan proporsi laki-laki 42,5% dan median usia 50 tahun. Hasil RT-PCR positif ditemukan pada 69 (57,5%) sampel saliva dan 75 (62,5%) sampel usap nasofaring. Sensitivitas uji RT-PCR COVID19 dari sampel saliva adalah 86,67% (95% CI 76,84- 93,42), spesifisitasnya 91,11% (95% CI 78,78- 97,52). Nilai NDP yang didapat adalah 94,20% (95% CI 86,39-97,65) dan nilai NDN yang didapat 80,39% (95% CI 69,57-88,03). Akurasi yang didapat adalah 88,33% (95% CI 81,2093,47). Rerata CT value RT-PCR dari sampel saliva lebih tinggi dibandingkan sampel nasofaring, baik pada gen N (mean saliva 26,22 vs nasofaring 22,18; p= 0,01) maupun ORF1AB (mean saliva 26,39 vs nasofaring 23,24; p= 0,01). Simpulan. Saliva yang diambil dengan metode drooling merupakan sampel yang akurat untuk pemeriksaan RT-PCR COVID-19. ......Background. Coronavirus Disease-19 (COVID-19) is still a global health problem. Diagnostic gold standard for COVID-19 is RT-PCR of the nasopharyngeal swab specimen. However, this method has several issues such as patient’s discomfort, risk of bleeding, and risk of exposure to examiner. Saliva is a viable alternative sample for this examination. Aim. To find out the sensitivity, specificity, positive predictive value, negative predictive value, and accuracy of saliva RT-PCR. Method. Crossectional study in adult patient with suspect ofCOVID-19 during April-June 2021 in emergency unit Lippo Village Hospital. Eligible and agreed patient are examined with RT-PCR from nasopharyngeal swab and saliva. RT-PCR was done by targeting gene N and ORF1AB using Rotorgen QPlex-5-Plus with CT value cut off 40. Result. A total of 126 suspected COVID-19 cases were admitted to ER during study period. Six patients were disagree to join. Final analysis was carried out on 120 patients (42.5% male, media age 60). Positive RT-PCR was found in 69 (57.5%) saliva specimens and 75 (62.5%) nasopharyngeal specimens. Sensitivity of saliva specimens was 86.67% (95% CI 76.84- 93.42), with specificity of 91.11% (95% CI 78.78-97.52). NDP of saliva was 94.20% (95% CI 86.39-97.65) with NDN of 80.39% (95% CI 69.57-88.03). Saliva’s accuracy was 88.33% (95% CI 81.20-93.47). Mean CT value of saliva specimens was higher than nasopharyngeal specimens in both gene N (mean saliva 26.22 vs nasopharyngeal 22.18; p= 0.01) and ORF1AB (mean saliva 26.39 vs nasopharyngeal 23.24; p= 0.01). Conclusion. Saliva collected with drooling method is an accurate sample for COVID-19 RT-PCR.

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ABSTRACT
Vibrio cholera, Vibrio parahaemolyticus and Vibrio vulnificus are opportunistic pathogens causing disease in weak shrimp and possible food poisoning in shrimp consumers. In this study, three pairs of primers were designed to amplify the target DNA fragments of three Vibrio spp. and together with one pair for internal amplification control. The PCR condition was optimized to detect three Vibrio spp. in one reaction tube. The specificity and sensitivity of the reaction were evaluated. The results showed that this technique can detect V. cholera, V. parahaemolyticus and V. vulnificus in the same reaction tube with high specificity. Sensitivity is moderate, 0.5 ng-10 pg. In the future, this technique can be used to detect these bacteria in shrimp. It is potentially useful for shrimp farmers and shrimp consumers.

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Methisilin Resistant Staphylococcus aureus MRSA adalah bakteri S.aureus yang resisten terhadap penisilin dan antibiotik golongan beta-laktam lainnya. Bakteri ini sering menyebabkan berbagai infeksi termasuk infeksi yang serius dengan mortalitas yang tinggi. Infeksi MRSA tidak hanya terbatas pada lingkungan rumah sakit saja, melainkan sudah menyebar ke komunitas. Metode pemeriksaan yang cepat untuk mendeteksi MRSA pada pasien diperlukan agar klinisi dapat segera menangani dengan baik. Metode biakan membutuhkan waktu hingga lebih dari 1 hari, sedangkan pemeriksaan PCR dapat memberikan hasil yang lebih cepat. Pemeriksaan PCR bertujuan untuk mencari gen mecA yang telah diketahui sebelumnya, berperan dalam mekanisme resistensi MRSA. Namun sekarang telah diketahui adanya MRSA dengan gen mecA negatif karena adanya peran gen lain yang juga dapat berperan yaitu mecC dan blaZ. Sehingga diperlukan pemeriksaan PCR yang dapat mendeteksi ketiga gen tersebut. Penelitian ini bertujuan untuk mendapatkan uji skrining dan konfirmasi untuk deteksi MRSA. Optimasi multipleks PCR diawali dengan optimasi unipleks masing-masing gen mecA, mecC, dan blaZ. Uji coba telah dilakukan terhadap 30 isolat MRSA dan 30 isolat MSSA. Dari 30 isolat MRSA yang diuji diperoleh hasil hanya didapatkan perbedaan pada 3 isolat MRSA sedangkan pada isolat MSSA, unipleks dan multipleks PCR memperlihatkan hasil yang sama. Perbedaan yang tampak kemungkinan diakibatkan oleh bias PCR. Berdasarkan uji diagnostik diperoleh sensitivitas tertinggi tampak pada unipleks PCR mecA sensitivitas 95,83 sehingga dapat digunakan sebagai skrining, sedangkan spesifisitas tertinggi tampak pada multipleks PCR spesifisitas 100 sehingga dapat digunakan sebagai konfirmasi. Diperlukan uji lanjutan untuk konfirmasi peran blaZ pada MRSA. ...... Methicillin Resistant Staphylococcus aureus MRSA is S.aureus that resistant to penicillin and other beta lactam antibiotics. This bacteria often cause serious infection with high mortality. Methicillin Resistant Staphylococcus aureus infection is not only found in hospital, but it also spreads into community. Rapid detection of MRSA is needed to help clinicians in giving accurate treatment. The result obtained by culture method takes more than one day, while PCR result can be read in the same day. The common purpose of PCR assay is to detect mecA gene that known to be responsible for the occurance of resistant in MRSA isolates. Nowadays, there are some MRSA with negative mecA. In that case, mecC and blaZ may play an important role in resistant mechanism in MRSA. Therefore, new PCR method that can detect all of the three genes is needed. The purpose of this study is to develop method for screening and confirming MRSA. First, we conduct uniplex PCR for each gene mecA, mecC, and blaZ, followed by multiplex PCR. Furthermore, assay was performed to detect those genes from 30 MRSA and 30 MSSA isolates. All MSSA gave the same result of uniplex and multiplex PCR. From 30 MRSA isolates, three isolates showed discrepancies between uniplex and multiplex PCR result. It may be due to PCR bias. Uniplex PCR mecA can be used as a screening test since its high sensititivity sensitivity 95,83 , whereas multiplex PCR mecA, mecC, and blaZ may be used as a confirmation test due to its high specificity 100 . Another test is needed to confirm the detection of blaZ gene in MRSA isolates.

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Diare karena rotavirus adalah masalah kesehatan masyarakat di seluruh dunia. Rotavirus grup A yang menyerang manusia adalah penyebab terbesar dari penyakit gastroenteritis akut pada anak - anak baik di negara maju maupun negara berkembang. Rotavirus saat ini menjadi subjek penelitian dan ujicoba untuk pencarian vaksin yang efektif dan aman. Penelitian dilakukan untuk menentukan prevalensi rotavirus grup A di daerah Makassar selama bulan Oktober 2005 sampai Oktober 2006. Sampel feses dengan gejala diare dikumpulkan dari pasien pediatri sebanyak 326 sampel. Sampel kemudian diuji dengan metode ELISA dan menunjukkan 26,07% positif terinfeksi rotavirus grup A. Sampel positif tersebut kemudian dianalisis lebih lanjut dengan metode RT dan nested PCR menunjukkan bahwa prevalensi terbesar dari galur rotavirus grup A di daerah Makassar adalah serotipe G4G9P[8] sebanyak 36,55 (n = 31).

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Rotavirus diarrhea is a public health problem throughout the world. Group A human rotaviruses are a major cause of acute gastroenteritis in young children in both developing and developed countries. Rotaviruses are at present the subject of intense vaccine research and trials worldwide to find an effective and safety vaccine. The study was conducted to determine the prevalence of group A rotavirus in Makassar on October 2005 until October 2006. Three hundred twenty six stool samples were collected from pediatric patient with diarrhea symptoms. The samples were tested by ELISA method and resulted as 26,07% positive of group A rotavirus. The ELISA positive samples were then analyzed by RT and nested PCR method, subsequently, and result showed that the major prevalence of group A rotavirus in Makassar that is 36,55% (n = 31) were G4G9P[8] serotype.