Whole genome sequencing analysis on antibiotic-resistant Escherichia coli isolated from pig farms in Banten Province, Indonesia.

IMPORTANCE: The emergence and rapid increase in the incidence of multidrug-resistant (MDR) bacteria in pig farms has become a serious concern and reduced the choice of effective antibiotics. OBJECTIVE: This study analyzed the phylogenetics and diversity of antibiotic resistance genes (ARGs) and molecularly identified the source of ARGs in antibiotic-resistant Escherichia coli isolated from pig farms in Banten Province, Indonesia. METHODS: Forty-four antibiotic-resistant E. coli isolates from fecal samples from 44 pig farms in Banten Province, Indonesia, were used as samples. The samples were categorized into 14 clusters. Sequencing was performed using the Oxford Nanopore Technologies MinION platform, with barcoding before sequencing with Nanopore Rapid sequencing gDNA-barcoding (SQK-RBK110.96) according to manufacturing procedures. ARG detection was conducted using ResFinder, and the plasmid replicon was determined using PlasmidFinder. RESULTS: Three phylogenetic leaves of E. coli were identified in the pig farming cluster in Banten Province. The E. coli isolates exhibited potential resistance to nine classes of antibiotics. Fifty-one ARGs were identified across all isolates, with each cluster carrying a minimum of 10 ARGs. The ant(3'')-Ia and qnrS1 genes were present in all isolates. ARGs in the E. coli pig farming cluster originated mainly from plasmids, accounting for an average of 89.4%. CONCLUSIONS AND RELEVANCE: The elevated potential for MDR events, coupled with the dominance of ARGs originating from plasmids, increases the risk of ARG spread among bacterial populations in animals, humans, and the environment.

Detection of tetracycline resistance genes and their diversity in Escherichia coli isolated from pig farm waste in Banten province, Indonesia.

Background and Aim: Livestock waste in the form of feces and liquid represents an important reservoir of antibiotic resistance genes (ARGs). Because many ARGs can be horizontally transferred to other pathogens, livestock waste plays an essential role in the emergence and transmission of various ARGs in the environment. Therefore, this study aimed to detect and assess the diversity of tet genes in Escherichia coli isolated from pig farm waste in Banten province, Indonesia. Materials and Methods: Solid waste (feces) and wastewater were collected from 44 pig farms in Banten province. The isolation and identification of E. coli referred to the Global Tricycle Surveillance extended-spectrum beta-lactamase E. coli World Health Organization (2021) guidelines. tet genes were detected using quantitative real-time polymerase chain reaction after dividing pig farms in the province into four clusters based on their adjacent areas and characteristics. Results: tetA, tetB, tetC, tetM, tetO, and tetX were detected in solid waste and wastewater from pig farms, whereas tetE was not detected in either sample type. tetX (100%) and tetO (75%) were the most dominant genes in solid waste, whereas wastewater samples were dominated by tetA, tetM, tetO, and tetX (prevalence of 50% each). Furthermore, eight tet gene patterns were found in pig farm waste (prevalence of 12.5% each). Conclusion: The results showed a high prevalence of tetO and tetX in solid waste and wastewater from pig farms in Banten province. This significant prevalence and diversity indicated the transmission of tet genes from pigs to the environment, posing a serious threat to public health.

Distribution analysis of tetracycline resistance genes in Escherichia coli isolated from floor surface and effluent of pig slaughterhouses in Banten Province, Indonesia.

Background and Aim: Slaughterhouses and their effluents could serve as a "hotspot" for the occurrence and distribution of antibiotic-resistant bacteria in the environment. This study aimed to understand the distribution of tetracycline resistance genes in Escherichia coli isolated from the floor surface and effluent samples of pig slaughterhouses in Banten Province, Indonesia. Materials and Methods: Ten samples, each from floor surface swabs and effluents, were collected from 10 pig slaughterhouses in Banten Province. Escherichia coli strains were isolated and identified by referring to the protocol of the Global Tricycle Surveillance extended-spectrum beta-lactamase E. coli from the WHO (2021). Quantitative real-time polymerase chain reaction (qPCR) was used to detect the tet genes. Results: The tetA, tetB, tetC, tetM, tetO, and tetX genes were distributed in the isolates from the floor surface samples, and the tetA, tetC, tetE, tetM, tetO, and tetX genes were distributed in the isolates from the effluent samples. The tetO gene (60%) was the most dominant gene in the isolates from floor surface samples, while the tetA gene was the dominant one in the isolates from the effluent samples (50%). The tetA + tetO gene combination was the dominant pattern (15%) in the E. coli isolates. Conclusion: The high prevalence and diversity of the tet genes in floor surface and effluent samples from pig slaughterhouses in Banten Province indicated that the transmission of the tet genes had occurred from pigs to the environment; thus, this situation should be considered a serious threat to public health.

Antimicrobial susceptibility test and antimicrobial resistance gene detection of extracellular enzyme bacteria isolated from tilapia (Oreochromis niloticus) for probiotic candidates.

Background and Aim: Antimicrobial resistance (AMR) is a global problem that can increase mortality and morbidity rates and adversely affect health. Therefore, AMR control must be carried out in various sectors, including the fisheries sector, using probiotics. Bacteria can become resistant to antibiotics, including bacteria used for probiotics. This study aimed to isolate bacteria as potential producers of extracellular enzymes, phenotypic characterization, and antibiotic-resistant gene patterns. Materials and Methods: In this study, 459 bacterial isolates were isolated from the stomach of tilapia in Indonesia. Tilapia was obtained from Sukabumi, Ciamis, Serang, Banjarnegara, Jayapura, Sorong, Manokwari Selatan, Takalar, Lampung, Batam, and Mandiangin. Enzymatic bacteria were identified. An antimicrobial susceptibility test was conducted by agar disk diffusion, and genotypic detection of encoding genes was performed using a molecular method. Results: This study obtained 137 isolates (29.84%) that can produce extracellular enzymes. The highest number of E-sensitive isolates was found, including 130 isolates (94.89%). Six isolates (6/137) can produce four enzymes (amylase, protease, cellulose, and lipase), and they were sensitive to antibiotics. A total of 99 isolates can produce extracellular enzymes, and they were sensitive to antibiotics. Such isolates serve as a consortium of probiotic candidates. The isolates that are resistant to oxytetracycline (OT), erythromycin (E), tetracycline (TE), and enrofloxacin (ENR) included 15 isolates (10.95%), seven isolates (5.11%), three isolates (2.19%), and one isolate (0.73%), respectively. In addition, four isolates (2.92%) were detected as multidrug-resistant. The tet(A) gene obtained the highest result of detection of resistance genes in isolates that were intermediate and resistant to TE and OT. Isolates that serve as ENR intermediates have a high qnr(S) resistance gene. Conclusion: The data in this study provide the latest update that bacteria can serve as a consortium of potential probiotics with antibiotic-resistant genes for the treatment of fish. Bacteria that are intermediate to antibiotics may contain resistance genes. The results of this study will improve the policy of probiotic standards in Indonesia.

Chicken Enterococcus faecalis-induced immunoglobulin Y as a prophylactic and therapeutic agent against streptococcosis in red tilapia (Oreochromis hybrid).

Background and Aim: Streptococcosis is a common bacterial disease in red tilapia, in which Enterococcus faecalis infection has not been widely reported. This study aimed to evaluate the efficacy of pellets that contain chicken E. faecalis-induced immunoglobulin Y (IgY) to treat and prevent streptococcosis in red tilapia. Materials and Methods: We conducted a 28-day study for immunoprophylaxis and immunotherapy, each using four groups with two replications: Healthy control fish (KS), non-IgY pellets (PA and TA), pellets with 25% egg yolk containing E. faecalis-induced IgY (PB and TB), and pellets with 50% egg yolk containing E. faecalis-induced IgY(PC and TC). Indirect enzyme-linked immunosorbent assay was performed on prototype pellets produced with an IgY suspension at 1.63 mg/mL as the standard optical density curve. For the immunoprophylaxis study, pellets of 3% of the average body weight of the experimental fish (0.50 g per fish per day) were given daily until day 14 before the challenge test with E. faecalis (2.1 × 109 Colony-forming unit/mL peroral) on day 15. The data from the observation period on days 15-28 were analyzed. For the immunotherapy study, pellets of 3% of the average body weight (0.50 g per fish per day) were given daily for 21 days (days 8-28) 7 day spost-infection. The data from the immunotherapy study were collected during the observation period on days 8-28. Statistical analysis was performed on non-specific immune variables: Total leukocytes, monocytes, lymphocytes, neutrophils, phagocytic activity, and macrophage capacity; and the semi-quantitative distribution of melanomacrophage centers (MMCs) in the lymphoid organs, such as spleen and liver. Photomacrographic data were analyzed descriptively and qualitatively by comparing the healing process and clinical signs found between experiments in the immunotherapy study. Results: The pellet with 50% egg yolk with an IgY at 2.43 mg/g pellet, 3% of body weight once daily, was the best formula on experimental fish. The administration of this formulation can also increase non-specific immunity and the distribution of MMCs in the spleen and liver with a survival rate of 55% for 14 days of challenge period in the immunoprophylaxis study and 70% for 21 days of therapy period in the immunotherapy study. Conclusion: Immunoglobulin Y can be a prophylactic and therapeutic agent against streptococcal infections caused E. faecalis in red tilapia with an optimum dosage of 2.43 mg/g pellet.

Antibiotic resistance gene-free probiont administration to tilapia for growth performance and Streptococcus agalactiae resistance.

Background and Aim: The rapid development of aquaculture as a major food sector is accompanied by challenges, including diseases that affect tilapia farming worldwide. One such infectious disease caused by Streptococcus agalactiae poses a serious threat to tilapia populations. Probiotics have emerged as a potentially safe preventive measure against S. agalactiae infection. However, antimicrobial resistance from antibiotic-resistant bacteria remains a concern because it can lead to the spread of resistant bacteria and serve as a reservoir of antibiotic-resistant genes in fishes and the surrounding environment. This study aimed to identify candidate probiotic bacteria capable of promoting tilapia growth, providing resistance to S. agalactiae infection, devoid of potential pathogenicity, and free from antibiotic resistance genes. Subsequently, the performance of these probiotic candidates in tilapia was evaluated. Materials and Methods: Lactococcus garvieae, Priestia megaterium, Bacterium spp., Bacillus megaterium, Bacillus subtilis, and Bacillus pumilus were examined to assess their antibacterial properties, hemolytic patterns, and antibiotic resistance genes. We used the specific primers tetA, tetB, tetD, tetE, tetO, tetQ, ermB, and qnrS that were used for antibiotic resistance gene detection. In vivo probiotic efficacy was evaluated by administering probiotic candidates in tilapia feed at a concentration of 1 × 106 colonies/mL/50 g of feed over a 60-day maintenance period. Resistance to S. agalactiae infection was observed for 14 days after the challenge test. Results: Lactococcus garvieae, P. megaterium, and Bacterium spp. were identified as promising probiotic candidates among the bacterial isolates. On the other hand, B. megaterium, B. subtilis, and B. pumilus carried resistance genes and exhibited a ß hemolytic pattern, rendering them unsuitable as probiotic candidates. The selected probiotic candidates (L. garvieae, P. megaterium, and Bacterium spp.) demonstrated the potential to enhance tilapia growth, exhibited no pathogenic tendencies, and were free from antibiotic resistance genes. Supplementation with L. garvieae and Bacterium spp. enhanced tilapia resistance to S. agalactiae infection, whereas P. megaterium supplementation showed an insignificant survival rate compared with controls after the challenge test period. Conclusion: Probiotics, particularly L. garvieae, P. megaterium, and Bacterium spp., enhance growth and resistance against S. agalactiae infection, without harboring antibiotic resistance genes. Selecting probiotic candidates based on antibiotic resistance genes is essential to ensure the safety of fish, the environment, and human health.

A sequential toggle cell-SELEX DNA aptamer for targeting Staphylococcus aureus, Streptococcus agalactiae, and Escherichia coli bacteria.

BACKGROUND: Mastitis is an inflammation of the mammary glands caused by a microbial infection. The common bacteria causing this infection in dairy farms are Staphylococcus aureus, Streptococcus agalactiae, and Escherichia coli. The aptamer is a new biosensor platform for detecting pathogens; however, its use for simultaneous detection of S. aureus, S. agalactiae, and E. coli bacteria has not been reported. This study's objective is to isolate and characterize polyclonal DNA aptamer with broad reactivity to the mastitis bacteria S. aureus, S. agalactiae, and E. coli using a sequential toggle cell-SELEX. METHODS AND RESULTS: The DNA aptamer pool from SELEX 15 was inserted into the pGEM-T easy plasmid. Furthermore, the transformant clones were selected by PCR colony, plasmid isolation, and sequencing. Six DNA aptamers, consisting of S15K3, S15K4, S15K6, S15K13, S15K15, and S15K20 with a constant region and the right size of 81 bp were derived from the sequencing analysis. The secondary structure of the DNA was predicted using Mfold software. The DNA was analyzed with binding characteristics, including binding capacity and affinity (Kd), using qPCR. The results indicated aptamer S15K15 has the highest binding ability into S. agalactiae, while S15K13 performed binding capacity most to E. coli EPEC 4, and S15K3 has the highest capacity of binding to S. aureus BPA-12. CONCLUSION: Aptamer S15K3 has the best binding characteristics on all three bacterial targets.

Screening and purification of NanB sialidase from Pasteurella multocida with activity in hydrolyzing sialic acid Neu5Acα(2-6)Gal and Neu5Acα(2-3)Gal.

Study on sialidases as antiviral agents has been widely performed, but many types of sialidase have not been tested for their antiviral activity. Pasteurella multocida NanB sialidase is one such sialidase that has never been isolated for further research. In this study, the activity of NanB sialidase was investigated in silico by docking the NanB sialidase of Pasteurella multocida to the Neu5Acα(2-6)Gal and Neu5Acα(2-3)Gal ligands. Additionally, some local isolates of Pasteurella multocida, which had the NanB gene were screened, and the proteins were isolated for further testing regarding their activity in hydrolyzing Neu5Acα(2-6)Gal and Neu5Acα(2-3)Gal. Silico studies showed that the NanB sialidase possesses an exceptional affinity towards forming a protein-ligand complex with Neu5Acα(2-6)Gal and Neu5Acα(2-3)Gal. NanB sialidase of Pasteurella multocida B018 at 0.129 U/mL and 0.258 U/mL doses can hydrolyze Neu5Acα(2-6)Gal and Neu5Acα(2-3)Gal better than other doses. In addition, those doses can inhibit effectively H9N2 viral binding to red blood cells. This study suggested that the NanB sialidase of Pasteurella multocida B018 has a potent antiviral activity because can hydrolyze sialic acid on red blood cells surface and inhibit the H9N2 viral binding to the cells.

An assessment of knowledge and attitude toward antibiotic misuse by small-scale broiler farmers in Bogor, West Java, Indonesia.

Background and Aim: Antibiotics are often overused and misused by broiler farmers. Moreover, this practice may lead to antibiotic resistance. Antibiotics may be used for various purposes such as therapy, prophylaxis, flushing, and growth promoters. The study aimed to examine the association of knowledge and attitudes with antibiotics used by broiler farmers. Materials and Methods: The study design was cross-sectional. The data were obtained from interviewing 132 farmers' households in Bogor District, West Java, Indonesia. The outcome variable was antibiotic use, whereas the independent variables included knowledge and attitude toward antibiotic resistance. The statistical analysis used a t-test and correlation test. Results: A total of 78% of broilers farmers use antibiotics, and most of the farmers used antibiotics for flushing and prophylaxis. Furthermore, antibiotic use was associated with broiler farmers' knowledge and attitudes toward antibiotic resistance. However, there is no significant correlation between the duration of antibiotics use and their knowledge and attitude. Conclusion: The use of antibiotics in broilers is still high in Bogor, and most of the used antibiotics belong to the Medically Important Antimicrobial category. In general, the use of antibiotics in broilers is influenced by knowledge.

First Molecular Detection of Coxiella burnetii in Beef Cattle in West Java, Indonesia.

Coxiella burnetii is a bacterial pathogen that causes Q fever, which is widespread worldwide. Livestock such as cattle, goats, and sheep are the main sources of C. burnetii infection. C. burnetii infection causes abortion in livestock, resulting in economic damage. Q fever is a zoonotic disease and a potential public health hazard. To date, little is known about C. burnetii infection in livestock in Indonesia. The objective of this study was to screen the genome of C. burnetii bacteria in beef cattle in West Java, Indonesia. Organ tissue samples were collected from cattle slaughtered in slaughterhouses in West Java. C. burnetii genome was detected in cattle samples obtained from three sampling areas using nested PCR, targeting the com1 gene of C. burnetii. Sequencing analysis of the 16S rRNA gene revealed that the amplicons showed 99.9% nucleotide identity to the C. burnetii strains: Heizberg, 1843, 2574, 701CbB1, and 14160-001. Our results indicate that C. burnetii infection occurs in Indonesian beef cattle and highlight the risk of exposure to C. burnetii infection in humans.

Experimental infection of Enterococcus faecalis in red tilapia (Oreochromis hybrid) revealed low pathogenicity to cause streptococcosis.

Background: Streptococcosis, as a bacterial disease with broad tropism in fish and one of the causes of septicemia. Enterococcus faecalis is one of the causative agents of streptococcosis that can be isolated in tilapia. Aim: This study was undertaken to complete the reporting gap on the pathogenicity profile and clinical symptoms of E. faecalis bacterial infection in red tilapia (Oreochromis hybrid). The study is expected to provide enriching information regarding recognizable clinical signs in the field that can lead to the diagnosis of streptococcosis caused by E. faecalis, especially in the Indonesian aquaculture environment. Methods: The method used in this artificial infection study using red tilapia, which were divided into two types of route groups infection, namely intraperitoneal (IP) and peroral (PO) with bacterial concentrations given for each route of infection to be 2.1 × 108 CFU ml-1; 2.1 × 107 CFU ml-1; and 2.1 × 106 CFU ml-1. One group was given brain heart infusion broth media sterile as a non-infectious control. Clinical symptoms, changes in swimming habits and consuming feed, external and internal organ lesion, and leukocytes profile changes were observed during the observation period along 14 days to evaluate the infectious effect of each treated fish group. The lethal dose 50 (LD50) was estimated with the Spearman-Kärber method. The evaluation of the leukocyte profile was performed to find leukocytosis as the clinical sign of infection. Results: The results showed variations in clinical symptoms inflicted on fish through death or the moribund stage. The highest mortality occurred in the treatment group of 2.1 × 108 CFU ml-1 with the PO route. The bacterial concentration of 2.1 × 107 CFU ml-1 given either as PO or IP can cause mild infection symptoms but did not cause mortality. The LD50 of the PO and IP route was obtained at 1.99 × 108 CFU ml-1 and 0.79 × 108 CFU ml-1, respectively. The total leukocytes in the infected fish group increased significantly (p < 0.05) by twofold when compared with the non-infectious group. The bacteria's discovery on the blood smear examination was taken from fresh dead fish or moribund fish in the treatment group of 2.1 × 108 CFU ml-1, for both PO and IP. Conclusion: Enterococcus faecalis with low pathogenicity can lead to septicemia, characterized by a total increase in leukocytes, bacteria's discovery on the blood smear examination, and various clinical symptoms systemically found in the treated fish.

Isolation and detection of antibiotics resistance genes of Escherichia coli from broiler farms in Sukabumi, Indonesia.

OBJECTIVE: This study aimed to isolate and identify Escherichia coli from broiler samples from Sukabumi, Indonesia. Also, antibiogram studies of the isolated bacteria were carried out considering the detection of the antibiotic resistance genes. MATERIALS AND METHODS: Cloaca swabs (n = 45) were collected from broilers in Sukabumi, Indonesia. Isolation and identification of E. coli were carried out according to standard bacteriological techniques and biochemical tests, followed by confirmation of the polymerase chain reaction targeting the uspA gene. Antibiotic sensitivity test, using several antibiotics [tetracycline (TE), oxytetracycline (OT), ampicillin (AMP), gentamicin (CN), nalidixic acid (NA), ciprofloxacin (CIP), enrofloxacin (ENR), chloramphenicol, and erythromycin] was carried out following the Kirby-Bauer disk diffusion method. Detection of antibiotic resistance coding genes was carried out by PCR using specific oligonucleotide primers. Statistical analysis was carried out with one-way analysis of variance. RESULTS: The results showed that 55.6% (25/45) of the samples were associated with the presence of E. coli. Antibiotic sensitivity test showed that the E. coli isolates were resistant to TE (88%; 22/25), OT (88%; 22/25), AMP (100%; 25/25), CN (64%; 16/25), NA (100%; 22/25), CIP (88%; 22/25), ENR (72%; 18/25), chloramphenicol (0%; 0/25), and erythromycin (92%; 23/25). On the other hand, the antibiotic resistance coding genes were tetA (86.4%; 19/22), blaTEM (100%; 25/25), aac(3)-IV (0%; 0/16), gyrA (100%; 25/25), and ermB (13%; 3/23). It was found that chloramphenicol is markedly different from other antibiotic treatment groups. CONCLUSION: Escherichia coli was successfully isolated from cloacal swabs of broiler in Sukabumi, Indonesia. The bacteria were resistant to TE, OT, AMP, CN, NA, CIP, ENR, and erythromycin. Chloramphenicol was more sensitive and effective than other antibiotics in inhibiting the growth of E. coli. The antibiotic resistance genes detected were tetA, blaTEM, gyrA, and ermB.

Development of lateral flow assay based on anti-IBDV IgY for the rapid detection of Gumboro disease in poultry.

The poultry industry faces serious problems against infectious diseases, including Gumboro, which is caused by contagious bursal disease virus (IBDV). IBDV infects the bursa of Fabricius (BF), a lymphoid organ for controlling the B-cell maturation. Thus, it can trigger the secondary infection's vulnerability, leading to the high mortality and morbidity of the chicken. Moreover, managing the Gumboro post-outbreaks also requires considerable time and costs. Besides vaccination programs, the early detection of IBDV is vital as an outbreak control strategy. The most popular diagnostic tool is a lateral flow immunoassay or a rapid test that meets ASSURED (Affordable, Sensitive, Specific, User-friendly, Rapid and Robust, Equipment-free, and Deliverable to end-users) criteria. In this study, the lateral flow immunoassay was successfully developed based on anti-IBDV IgY as the bio receptor. Anti-IBDV IgY was successfully isolated from Isa Brown's egg yolk. The detection system showed an acceptable affinity against the inactivated IBDV sample (1.5 × 103 TCID50). In addition, it did not react with avian influenza and Newcastle disease viruses, demonstrating a good specificity of the test.

Phylogenetic group determination and plasmid virulence gene profiles of colistin-resistant Escherichia coli originated from the broiler meat supply chain in Bogor, Indonesia.

BACKGROUND AND AIM: Pathogenic Escherichia coli contamination along the broiler meat supply chain is a serious public health concern. This bacterial infection with multidrug-resistant can lead to treatment failure. Several studies have revealed that avian pathogenic E. coli (APEC) and human extraintestinal pathogenic E. coli (ExPEC) showed a close genetic relationship and may share virulence genes. This study aimed to determine the phylogenetic group and virulence gene profiles in colistin-resistant E. coli obtained from the broiler meat supply chain in Bogor, West Java, Indonesia. MATERIALS AND METHODS: Fifty-eight archive isolates originated from the cloacal swab, litter, drinking water, inside plucker swab, fresh meat at small scale poultry slaughterhouses, and traditional markets were used in this study. All the isolates were characterized by a polymerase chain reaction to determine the phylogenetic group (A, B1, B2, or D) and virulence gene profiles with APEC marker genes (iutA, hlyF, iss, iroN, and ompT). RESULTS: Phylogenetic grouping revealed that the isolates belong to A group (34.48%), D group (34.48%), B1 group (17.24%), and B2 group (13.79%). The virulence gene prevalence was as follows: iutA (36%), hlyF (21%), ompT (21%), iroN (10%), and iss (9%). The B2 group presented with more virulence genes combinations. iroN, hlyF, and ompT genes were positively associated with the B2 group (p≤0.05). CONCLUSION: Our results highlight the role of colistin-resistant E. coli originated from the broiler meat supply chain as a potential reservoir for human ExPEC virulence genes.

Risk assessment on rabies entry through hunting dog movement with semi-quantitative approach to Sumatera Island, Indonesia.

OBJECTIVE: The objective of this study was to assess the risk of rabies entry through the movement of hunting dog from Garut District to Sumatera Island with a semi-quantitative approach. MATERIALS AND METHODS: Rabies entry assessment used the standard risk analysis according to the World Organization for Animal Health, with a semi-quantitative approach referring to Australian Biosecurity. Risk estimation calculation used Microsoft Excel and probabilities were estimated using Monte Carlo stochastic simulation modeling with @Risk (Palisade Corporation). RESULTS: Risk estimation were considered as "very low" with a 0.02 (90%; 0.01-0.03) probability. The probability of undetected rabies-infected dog during Veterinary Certificate issuance [node probability (NP4)] was considered as the highest, with "moderate" likelihood and 0.63 (90%; 0.51-0.75) of probability value. The number of dog movement to Sumatera reached 27,000 heads per year which 5,050 heads of them come from Garut District. There were 2 of 100 dogs from Garut District entered to Sumatera possibly infected by rabies. The five highest parameters most determinant of the risk were dog vaccination before transported (0.66), dog obtained from other District (0.41), vaccination program (0.32), serologically test (0.27), and history of vaccination (0.23). CONCLUSION: Risk estimation from assessing on rabies entry to Sumatera through hunting dogs movement from Garut District was considered "very low." Risk mitigation is focused on the highest parameters that contribute the most to risk based on the results of the sensitivity analysis. Semi-quantitative likelihood evaluations can consider the volume of dog traffic which is an important issue in risk analysis which is not easy to get with a simpler qualitative approach.

Detection of multi-drug resistant (MDR) Escherichia coli and tet gene prevalence at a pig farm in Kupang , Indonesia.

OBJECTIVE: The purpose of this study was to detect the incidence of multi-drug resistant (MDR) and the spread of tet genes that encode tetracycline (TE) resistance in E. coli in pig farms in the city of Kupang, Indonesia. MATERIALS AND METHODS: Samples of pig feces have been obtained from 96 pig farms in Kupang city, Indonesia. Escherichia coli bacteria were isolated and identified morphologically and biochemically, and finally confirmed by the API test. The disk diffusion method has been used to observe the antibiotic sensitivity effects and has been followed by observing resistant genes encoding TE resistance using the multiplex polymerase chain reaction (m-PCR) method to detect the presence of tet genes such as tet (A), tet (B), tet (C), tet (D), and tet (E), respectively. RESULTS: A total of 82 (85.4%) of E. coli isolates have been found in all pig feces samples obtained from 96 pig farms in Kupang city. This study has shown a high level of antibiotic resistance dominated by erythromycin (85.4%) and cephalothin (58.5%) and followed by several other antibiotics with a percentage below 34.1%. The prevalence of MDR E. coli was 57.3% by showing 39 different patterns. The most common pattern was showed by the Cephalothin-Colistin-Erythromycin pattern. The resistance of E. coli to TE appears to be related to the presence of tet (A) and tet (E) genes. CONCLUSION: This study has encouraged the need for public awareness (farmers) of the wise use of antibiotics in preventing the spread of resistant bacteria that can cause health problems in animals and humans.

Molecular analysis of hemagglutinin-1 fragment of avian influenza H5N1 viruses isolated from chicken farms in Indonesia from 2008 to 2010.

Highly pathogenic avian influenza virus of subtype H5N1 (AIV-H5N1) has been circulating in Indonesia since 2003. To understand the genetic diversity of these viruses, and to predict vaccine efficacy, the hemaglutinin-1 (HA-1) fragment of viruses isolated from chicken farms in Indonesia from 2008 to 2010 was sequenced and analyzed. The effects of these molecular changes were investigated in challenge experiments and HI assays of homologous and heterologous strains. Molecular analysis showed that these AIV-H5N1 isolates had evolved into three distinct sub-lineages from an ancestor circulating since 2003. Although no significant positive selection of residues was detected, 12 negatively selected sites were identified (p<0.05). Moreover, four sites showed evidence of significant episodic diversifying selection. The findings indicated complete protectivity and high HI titers with homologous strains, compared with protectivity ranging from 40 to 100% and lower HI titers with heterologous strains resulting from polymorphisms at antigenic sites. Our findings provide valuable insight into the molecular evolution of AIV and have important implications for vaccine efficacy and future vaccination strategies.

Silent spread of highly pathogenic Avian Influenza H5N1 virus amongst vaccinated commercial layers.

The aim of this study was to determine whether a single vaccination of commercial layer type chickens with an inactivated vaccine containing highly pathogenic avian influenza virus strain H5N1 A/chicken/Legok/2003, carried out on the farm, was sufficient to protect against infection with the homologous virus strain. A transmission experiment was carried out with pairs of chicken of which one was inoculated with H5N1 virus and the other contact-exposed. Results showed that the majority of the vaccinated birds developed haemagglutination inhibition (HI) titres below 4log2. No clinical signs were observed in the vaccinated birds and virus shedding was limited. However, nearly all vaccinated birds showed a four-fold or higher increase of HI titres after challenge or contact-exposure, which is an indication of infection. This implies that virus transmission most likely has occurred. This study showed that a single vaccination applied under field conditions induced clinical protection, but was insufficient to induce protection against virus transmission, suggesting that silent spread of virus in vaccinated commercial flocks may occur.

Persistent occurrence of a single Streptococcus equi subsp. zooepidemicus clone in the pig and monkey population in Indonesia.

In the present study 41 mucoid growing Streptococcus equi subsp. zooepidemicus strains (37 strains isolated from healthy two from diseased pigs, two strains isolated from healthy monkeys) appeared to be phenotypically and genotypically identical to mucoid growing S. equi subsp. zooepidemicus strains isolated from a previously described outbreak among the pig and monkey population on the island of Bali, Indonesia. These findings indicate that the mucoid growing S. equi subsp. zooepidemicus clone was still present in the pig and monkey population in Indonesia.