Judul: Whole Genome Sequencing of Antibiotic-resistant Salmonella Isolates from Kampung Chicken and Broiler Carcasses
Abstrak: Daging ayam yang merupakan komoditi dengan tingkat konsumsi tertinggi di Indonesia namun mengandung potensi bahaya kontaminasi Salmonella penyebab Salmonelosis yang berkaitan erat dengan higienitas penanganan dan pengolahan karkas ayam. Konsumsi daging ayam di Indonesia cenderung terus meningkat akan tetapi beberapa tahun terakhir kecenderungan resistansi terhadap beberapa jenis antibiotik (multiresistan) pada Salmonella spp. yang diisolasi dari bahan pangan semakin meningkat. Hal ini diduga akibat penggunaan antibiotik yang tidak tepat dan berulang sehingga berdampak pada pengobatan infeksi yang semakin sulit. Saat ini, data yang berkaitan dengan tingkat resistansi antibiotik di Indonesia masih minim, terutama data terhadap isolat lokal. Keberadaan informasi mengenai tingkat resistansi antibiotik ini dapat menjadi dasar penting dalam penentuan kebijakan. Penelitian bertujuan mengidentifikasi profil resistansi antibiotik isolat Salmonella spp. asal karkas ayam kampung dan asal karkas ayam broiler secara fenotipik, menganalisis sekuensing genom total isolat Salmonella spp. asal karkas ayam yang memiliki karakteristik resistansi tertentu dan mengidentifikasi hasil sekuensing genom total isolat Salmonella spp. terhadap profil genotipe penyandi resistansi antimikroba, faktor virulensi, gen plasmid terkait serta identifikasi Salmonella pathogenicity island. Penelitian dilakukan dengan menguji sifat resistansi antibiotik 25 isolat Salmonella spp. menggunakan metode KirbyBauer Disc Diffusion Test terhadap 8 jenis antibiotik. Sebanyak 3 isolat dengan karakter paling multiresistan kemudian diisolasi DNAnya dan disekuensing genom total menggunakan GridION (Teknologi Oxford Nanopore). Assembly genom total isolat hingga analisis genom total dilakukan pada platform Galaxy. Sebanyak 52% isolat Salmonella spp. asal karkas ayam (2/8 asal ayam kampung dan 11/17 asal karkas ayam broiler) memiliki sifat resistansi terhadap minimal 1 jenis antibiotik uji. Isolat BCID6.4 asal karkas ayam broiler memiliki sifat resistansi terhadap antibiotik uji tertinggi dibandingkan semua isolat uji dengan pola resistansi TE-OT-AMP-NA-CIP-E. Sekuensing genom total dilakukan pada isolat BCID6.2, BCID6.4 dan KCID6.5 menghasilkan genom lengkap dengan ukuran sekitar 4,80Mbp. Sebanyak 33 gen penyandi resistansi antibiotik, 104 faktor virulensi dan 8 jenis Salmonella Pathogenicity Island ditemukan pada genom total ketiga isolat uji. Plasmid kecil ditemukan pada sekuen genom isolat BCID6.4 tetapi tidak ditemukan gen penyandi resistansi antimikroba dan faktor virulensi. Hasil serotyping secara in silico menunjukkan ketiga isolat merupakan Salmonella enterica serovar Kentucky., Chicken meat is a commodity with the highest consumption level in Indonesia but contains a potential danger of Salmonella contamination which causes salmonellosis that might be closely related to the hygiene of handling and processing of the chicken carcasses. Consumption of chicken meat in Indonesia tends to increase every year, but in recent years there has been an increase in resistant Salmonella spp. isolated from food that also tends to be resistant to several types of antibiotics (multi-resistant). This is thought to be due to the inappropriate and repeated use of antibiotics thus could increase the difficulty of the infection treatment. Currently, data relating to the level of antibiotic resistance in Indonesia's predominantly local-based data is minimal. Whereas, information on the level of antibiotic resistance could be an important basis in determining related policy. The study aimed to determine the antibiotic resistance profiles of Salmonella spp. isolates from Kampung chicken carcasses and broiler carcasses phenotypically, analyze the total genome sequencing of Salmonella spp. isolates. from chicken carcasses that have certain resistance characteristics
Keyword: antibiotik resistansi, basis data, isolat lokal, Salmonella, sekuensing nanopore

Judul: Identifikasi Sifat Resistensi Antibiotik dan Deteksi Gen Penyandinya pada Salmonella spp. Asal Karkas Ayam Kampung
Abstrak: Daging ayam kampung sudah banyak dikonsumsi di Indonesia seperti halnya ayam ras. Namun, pemeliharaan secara ekstensif memungkinkan paparan bakteri yang bersifat multidrug-resistant (MDR) pada ayam kampung, termasuk melalui transfer gen horizontal. Penelitian ini bertujuan menghubungkan sifat resisten dengan keberadaan gen penyandi resistensi antibiotik pada Salmonella spp. yang diisolasi dari karkas ayam kampung. Identifikasi sifat resisten dilakukan dengan metode difusi cakram Kirby-Bauer dan deteksi gen resistensi antibiotik pada tujuh belas isolat Salmonella spp. dilakukan dengan PCR. Semua (17 dari 17) isolat Salmonella sensitif terhadap ampisilin dan kloramfenikol. Salmonella spp. paling resisten terhadap eritromisin (82,4%; 14 dari 17), sementara penurunan sensitivitas (sifat intermediet) banyak terjadi pada oksitetrasiklin (82,4%; 14 dari 17) dan siprofloksasin (53,0%; 9 dari 17). Salmonella Typhimurium menunjukkan pola resistensi terhadap lebih banyak golongan antibiotik dibandingkan dengan S. Weltevreden dan S. Newport. Gen blaTEM, tetG, cmlA, dan gyrA terdeteksi pada semua (17 dari 17) isolat Salmonella spp. Sifat resisten dan keberadaan gen penyandi resistensi antibiotik tidak selalu berhubungan satu sama lain. Penelitian ini dapat memberikan informasi yang bermanfaat mengenai penyebaran fenotipe dan genotipe resistensi antibiotik pada Salmonella spp. dari ayam kampung., Kampung chicken meats have been widely consumed in Indonesia as well as broiler chicken. However, the extensive rearing allowed exposure of multidrug-resistant (MDR) bacteria to kampung chicken, including through horizontal gene transfer. This study aimed to correlate resistance phenotype with the presence of genes-encoding antibiotics resistance in Salmonella spp. isolated from kampung chicken carcasses. Identification of resistance phenotype was carried out by Kirby-Bauer disc diffusion method, while detection of antibiotics resistance genes in seventeen isolates of Salmonella spp. was carried out by PCR. All (17 of 17) isolates of Salmonella were susceptible to ampicillin and chloramphenicol. Salmonella spp. was most resistant to erythromycin (82.4%; 14 of 17), while the decreased susceptibility (intermediate category) most occurred in oxytetracycline (82.4%; 14 of 17) and ciprofloxacin (53.0%; 9 of 17). Salmonella Typhimurium showed a resistance pattern to more antibiotic groups than S. Weltevreden and S. Newport. The blaTEM, tetG, cmlA, and gyrA genes were present in all (17 of 17) isolates of Salmonella spp. Resistance phenotype and the presence of genes-encoding antibiotics resistance were not always related to each other. This study could provide beneficial information regarding the distribution of antibiotics resistance phenotype and genotype in Salmonella spp. from kampung chicken.
Keyword: antibiotic, kampung chicken, multidrug-resistant, PCR, Salmonella

Judul: Hamiltonian formulation for linear waves motion in two layers fluid
Abstrak: The surface wave could be considered as a wave that separates two fluids, namely water and air. Based on this assumption, it is introduced the interfacial wave, a wave between two layers of fluid with different density. The formulation of interfacial waves motion begins with deriving the base equation of irrotational ideal fluid. Furthermore, according to irrotational fluid assumption, the base equation can be stated in velocity potential. In this derivation, the fluids domain is assumed to be restricted by rigid lid boundary conditions, both at the upper and lower limit. Therefore, the interfacial waves motion can be explained in a hamiltonian formulation. In the hamiltonian formulation, total energy is defined as the sum of kinetic and potential energy. The hamiltonian system is obtained from reduction of kinetic energy by using the Dirichlet Neumann Operator. The resulted kinetic energy equation is nonlinear. Therefore, this form is linearized by first part of the Taylor expansion. This linearization gives a dispersion relation of linear wave. Based on this dispersion relation, the phase speed of the linear wave depends on the density ratio of the two layers fluid.
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