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.

Dairy farmers' knowledge, attitudes, and practices regarding the brucellosis surveillance and control program in Bogor, Indonesia.

Background and Aim: Brucellosis is an infectious and zoonotic disease that affects people's health and the economy in most countries. Brucellosis is still prevalent in several Indonesian regions. This study aimed to analyze the correlation between the characteristics, knowledge, attitudes, and practices (KAP) of dairy farmers in Bogor District in supporting brucellosis control and surveillance programs. Materials and Methods: The study was cross-sectional. Data were collected through interviews with 151 dairy farmers in Bogor Regency, West Java, Indonesia. The outcome is brucellosis surveillance and control practice among dairy farmers, and the variables include individual characteristics, knowledge, and attitudes toward brucellosis surveillance and control. Descriptive analysis and path analysis were used in statistical analysis. Results: The majority of farmers' knowledge, attitudes and practices were moderate, with the percentages 67.55%, 60.92%, and 41.72% respectively. Formal education, training, and dairy rising length are variables that have a direct and significant impact on knowledge level. Knowledge is the variable that influences the overall level of attitude. Age, knowledge, and attitude are factors that influence the practice of brucellosis surveillance and control. Conclusion: Although the practice level of brucellosis surveillance and control for dairy farmers in Bogor Regency is moderate, efforts to improve it are still required. The basic effort is critical for increasing farmers' knowledge.

Estimation of the probability risks of African swine fever outbreaks using the maximum entropy method in North Sumatra Province, Indonesia.

Background and Aim: African swine fever (ASF) is an infectious disease and a major viral pig disease that threatens pork production in several locations globally. The mortality rate of ASF in domestic pigs is very high, causing a decrease in pig populations and significant economic losses for farmers. Environmental or ecological risk factors are the most important associated with the spread of the ASF virus. Environmental (or ecological) niche models are commonly used to estimate the probability of an event using the maximum entropy (Maxent) method. This study aimed to estimate the probability risk of future ASF outbreaks in North Sumatra, Indonesia. Materials and Methods: Secondary data from the National Animal Health System Database (iSIKHNAS), including data on the ASF outbreaks of 2019-2020 in North Sumatra, Indonesia, were used in this study. The first analysis performed involved the identification of environmental risk factors using multiple regression analysis. The second analysis performed was the estimation of probability risk for future ASF outbreaks in North Sumatra, Indonesia, using the Maxent method. Data processing was performed using Microsoft Excel, ArcGIS version 10.5 software (ESRI, California, United States), Maxent version 3.4.4 software, and Rstudio (http://www.r-project.org/). Results: The Maxent method was found to be highly accurate with a statistically significant area under the curve value of 0.860. The greatest contributing environmental factor identified by the model was the harbor, which contributed 57%. The range of high probability risk of future ASF outbreaks was found to be 0.723-0.84. Conclusion: The estimation of the highest probability risk of future ASF outbreaks in North Sumatra, Indonesia, was 0.723-0.84. The most contributing environmental factor identified using the Maxent method was harbors, at 57%. This methodology can be used to carry out subsequent ASF analyses and contribute to developing prevention and control strategies in this area.

An investigation of heavy metals in edible bird's nest from Indonesia using inductively coupled plasma mass spectrometry.

Background and Aim: In 2020, Indonesia, which has the highest global production of edible bird's nest (EBNs), exported up to 1312.5 tons of this product at a value of USD 540.4 million. Recently, food safety aspects related to EBNs, including contamination with heavy metals, have become a serious concern. However, data on the presence and concentration of heavy metals in EBNs in Indonesia are not yet available. This study aimed to determine and compare the presence and concentrations of arsenic (As), mercury (Hg), lead (Pb), cadmium (Cd), and tin (Sn) in EBNs originating from several primary Indonesian islands. The study also analyzed the effect of washing on the heavy metal content in EBNs. Materials and Methods: A study on 44 swiftlet farmhouses (SFHs) was conducted to determine the concentrations of heavy metals in EBNs. The number of samples from the SFHs was allocated proportionally to the main EBN-producing islands in Indonesia, that is, Kalimantan, Sumatera, Sulawesi, and Java (22, 13, 7, and 2, respectively). The concentrations of the above five elements in the samples before washing (raw-unclean EBNs) and after washing (raw-clean EBNs) were determined by inductively coupled plasma mass spectrometry. Washing was conducted according to the general procedures at an EBN processing plant. Results: The raw-unclean EBNs from the four islands contained As, Pb, Cd, and Sn at varying concentrations. However, Hg was not detected in the raw-unclean EBN samples from Sulawesi. The raw-unclean EBNs from Kalimantan had lower concentrations of Pb and Cd compared with the other islands. The concentrations of As, Pb, Cd, and Sn in the EBNs decreased significantly after washing with clean water. Conclusion: Heavy metals (As, Hg, Pb, Cd, and Sn) were detected at a low level in most of the raw-unclean EBNs originating from the main Indonesian island where they were produced. The concentrations of all the heavy metals reviewed in the raw-unclean EBNs samples decreased significantly after washing.

Nationally and locally-initiated One Health approach in controlling rabies in West Kalimantan, Indonesia.

Background and Aim: Rabies is one of the prioritized zoonoses in Indonesia and West Kalimantan is one of the rabies-endemic provinces in the country. This study aimed to evaluate a locally-initiated One Health approach to implement rabies prevention and control programs in Pontianak City and Sanggau District (through a bottom-up approach), and the central government initiated a program in Ketapang District (through a top-down approach). Materials and Methods: Data were collected using three focused group discussions involving public health and animal health/veterinary sectors from each district or city. This study collected data from the rabies control program in West Kalimantan from 2014 to 2020. Results: The evaluation results of the rabies prevention and control program in Pontianak City and Sanggau District that used the local initiative approach were considered effective in reducing the number of rabies cases in these areas, and they overcame the challenges, for example, limited resources, in this area. Pontianak City and Sanggau District initiatives' approach was a bottom-up policy. Thus, this program had better sustainability than the One Health approach in the Ketapang District, which used a top-down implementation. The approach in Ketapang District was also considered adequate to reduce the number of rabies cases in the area. However, the reshuffle of animal health officers and health workers in 2020, which was not followed by training on One Health for the new officers, became a challenge in implementing One Health in Ketapang District. Conclusion: National and local initiatives' One Health approach implemented by Ketapang District, Sanggau District, and Pontianak City involved multiple sectors and was considered effective in preventing and controlling rabies in these areas. However, the sustainability of this program in the Ketapang District requires commitment and support from the local government.

Viral-derived DNA invasion and individual variation in an Indonesian population of large flying fox Pteropus vampyrus.

Here, we performed next-generation sequencing (NGS) on six large flying foxes (Pteropus vampyrus) collected in Indonesia. Seventy-five virus species in the liver tissue of each specimen were listed. Viral homologous sequences in the bat genome were identified from the listed viruses. This finding provides collateral evidence of viral endogenization into the host genome. We found that two of the six specimens bore partial sequences that were homologous to the plant pathogens Geminiviridae and Luteoviridae. These sequences were absent in the P. vampyrus chromosomal sequences. Hence, plant viral homologous sequences were localized to the hepatocytes as extrachromosomal DNA fragments. Therefore, this suggests that the bat is a potential carrier or vector of plant viruses. The present investigation on wild animals offered novel perspectives on viral invasion, variation, and host interaction.

Identification and differentiation of Campylobacter isolated from chicken meat using real-time polymerase chain reaction and high resolution melting analysis of hipO and glyA genes.

BACKGROUND AND AIM: Campylobacter species have been recognized as the most frequently identified bacterial cause of human gastroenteritis. The aims of this study were to identify Campylobacter jejuni and Campylobacter coli species isolated from chicken meat and to analyze the differences in the melting curve patterns of both species. MATERIALS AND METHODS: A total of 105 chicken meat samples collected from slaughterhouses and retailers in six provinces in Indonesia were examined for the isolation and identification of Campylobacter spp. A total of 56 positive isolates of Campylobacter spp. were analyzed using the quantitative real-time polymerase chain reaction and high resolution melting method. RESULTS: The prevalence of Campylobacter spp. in chicken meat was found to be 61.9%. Regarding the identification, 23 isolates (41.07%) were C. jejuni, 22 (39.29%) were C. coli, six (10.71%) were a mix between C. jejuni and C. coli, and five isolates (8.93%) were Campylobacter spp. All the C. jejuni and C. coli isolates produced varied melting curve patterns. CONCLUSION: The high prevalence of C. jejuni and C. coli in chicken meat in Indonesia indicates a high risk of the incidence of campylobacteriosis in humans.

Isolation of Pteropine orthoreovirus from Pteropus vampyrus in Garut, Indonesia.

Flying foxes belonging to the genus Pteropus are known to be reservoirs of zoonotic viruses. In this study, we describe the isolation of Pteropine orthoreovirus (PRV) from rectal swab samples of Pteropus vampyrus in Indonesia. PRV is an emerging zoonotic respiratory virus that can be transmitted from bats to humans. Rectal swabs (n = 91) were screened by PCR for PRV and 10 (11%) were positive. Phylogenetic analysis based on nucleotide sequences indicated that the S2, S3, S4, M3, L2, and L3 segments of one isolate (Garut-69) were closely related to previously isolated strains in Indonesia. The remaining gene segments showed both similarity and genetic divergence with other PRV strains, suggesting that re-assortment events had occurred. This is the first report of PRV infection to P. vampyrus in West Java, Indonesia.

Nighttime behavioral study of flying foxes on the southern coast of West Java, Indonesia.

Flying foxes are important in the maintenance of forests and diversity. However, knowledge of their behavioral ecology, especially of movement and foraging patterns, which are essential for conservation and management of their populations, are not well known. Therefore, movement behavior of two individuals of Pteropus vampyrus were examined using an Argos telemetry system, and foraging pattern of Pteropus spp. was directly observed, at West Java province, Indonesia in October 2017. The maximum distance between the location at which bats were released and their furthest roost, recorded via satellite telemetry, was approximately 100 km. This reflects the long-distance flight ability of P. vampyrus. Daytime roosting sites and nighttime foraging places consisted of several types of habitats, such as intact forests, agricultural lands, and residential areas. This evidence indicated that there was habitat overlap between humans and bats in West Java province. According to direct observation of the behaviors of flying foxes at two locations within residential areas, various activities such as wing spreading, excretion, fighting, aggressive calls, movement, hanging relax, and hanging alert were found. The number of bat-visits to the trees varied among night hours, and had a positive correlation with the number of fruit dropping. The data obtained in this study have improved our understanding of nighttime behavior and habitat utilization of P. vampyrus, that can be used to support landscape management, species conservation, and disease prevention in regions of Southeast Asia.

Potential risk of viral transmission from flying foxes to domestic animals and humans on the southern coast of West Java, Indonesia.

Flying foxes have been considered to be involved in the transmission of serious infectious diseases to humans. Using questionnaires, we aimed to determine the direct and/or indirect contacts of flying foxes in an Indonesian nature conservation area with domestic animals and humans living in the surrounding area. We surveyed 150 residents of 10 villages in West Java. Villages were classified into 3 groups: inside and/or within 1 km from the outer border of the conservation area and 1-5 km or 5-10 km away from the reserve's outer border. Data were collected by direct interview using a structured questionnaire consisting of the respondent characteristics (age, sex and occupation); histories of contacts between flying foxes and humans, dogs and other domestic animals; and knowledge about infectious diseases, mainly rabies, in flying foxes. We found that flying foxes from the nature conservation area often enter residential areas at night to look for food, especially during the fruit season. In these residential areas, flying foxes had direct contacts with humans and a few contacts with domestic animals, especially dogs. People who encounter flying foxes seldom used personal protective equipment, such as leather gloves, goggles and caps. The residents living around the conservation area mostly had poor knowledge about flying foxes and disease transmission. This situation shows that the population in this region is at a quite high risk for contracting infectious diseases from flying foxes.

Daytime behavior of Pteropus vampyrus in a natural habitat: the driver of viral transmission.

Flying foxes, the genus Pteropus, are considered viral reservoirs. Their colonial nature and long flight capability enhance their ability to spread viruses quickly. To understand how the viral transmission occurs between flying foxes and other animals, we investigated daytime behavior of the large flying fox (Pteropus vampyrus) in the Leuweung Sancang conservation area, Indonesia, by using instantaneous scan sampling and all-occurrence focal sampling. The data were obtained from 0700 to 1700 hr, during May 11-25, 2016. Almost half of the flying foxes (46.9 ± 10.6% of all recorded bats) were awake and showed various levels of activity during daytime. The potential behaviors driving disease transmission, such as self-grooming, mating/courtship and aggression, peaked in the early morning. Males were more active and spent more time on sexual activities than females. There was no significant difference in time spent for negative social behaviors between sexes. Positive social behaviors, especially maternal cares, were performed only by females. Sexual activities and negative/positive social behaviors enable fluid exchange between bats and thus facilitate intraspecies transmission. Conflicts for living space between the flying foxes and the ebony leaf monkey (Trachypithecus auratus) were observed, and this caused daily roosting shifts of flying foxes. The ecological interactions between bats and other wildlife increase the risk of interspecies infection. This study provides the details of the flying fox's behavior and its interaction with other wildlife in South-East Asia that may help explain how pathogen spillover occurs in the wild.

Corrigendum: Determinants of Vaccination Coverage and Consequences for Rabies Control in Bali, Indonesia.

[This corrects the article on p. 123 in vol. 3, PMID: 28119919.].

Determinants of Vaccination Coverage and Consequences for Rabies Control in Bali, Indonesia.

Maintaining high vaccination coverage is key to successful rabies control, but mass dog vaccination can be challenging and population turnover erodes coverage. Declines in rabies incidence following successive island-wide vaccination campaigns in Bali suggest that prospects for controlling and ultimately eliminating rabies are good. Rabies, however, has continued to circulate at low levels. In the push to eliminate rabies from Bali, high coverage needs to be maintained across all areas of the island. We carried out door-to-door (DTD) questionnaire surveys (n = 10,352 dog-owning households) and photographic mark-recapture surveys (536 line transects, 2,597 observations of free-roaming dogs) in 2011-2012 to estimate dog population sizes and assess rabies vaccination coverage and dog demographic characteristics in Bali, Indonesia. The median number of dogs per subvillage unit (banjar) was 43 (range 0-307) for owned dogs estimated from the DTD survey and 17 (range 0-83) for unconfined dogs (including both owned and unowned) from transects. Vaccination coverage of owned dogs was significantly higher in adults (91.4%) compared to juveniles (<1 year, 43.9%), likely due to insufficient targeting of pups and from puppies born subsequent to vaccination campaigns. Juveniles had a 10-70 times greater risk of not being vaccinated in urban, suburban, and rural areas [combined odds ratios (ORs): 9.9-71.1, 95% CI: 8.6-96.0]. Free-roaming owned dogs were also 2-3 times more likely to be not vaccinated compared to those confined (combined Ors: 1.9-3.6, 95% CI: 1.4-5.4), with more dogs being confined in urban (71.2%) than in suburban (16.1%) and rural areas (8.0%). Vaccination coverage estimates from transects were also much lower (30.9%) than household surveys (83.6%), possibly due to loss of collars used to identify the vaccination status of free-roaming dogs, but these unconfined dogs may also include dogs that were unowned or more difficult to vaccinate. Overall, coverage levels were high in the owned dog population, but for future campaigns in Bali to have the highest chance of eliminating rabies, concerted effort should be made to vaccinate free-roaming dogs particularly in suburban and rural areas, with advertising to ensure that owners vaccinate pups. Long-lasting, cheap, and quick methods are needed to mark vaccinated animals and reassure communities of the reach of vaccination campaigns.