Prevalence of Antimicrobial Resistance in Escherichia coli and Salmonella Species Isolates from Chickens in Live Bird Markets and Boot Swabs from Layer Farms in Timor-Leste.

The rapid emergence of antimicrobial resistance is a global concern, and high levels of resistance have been detected in chicken populations worldwide. The purpose of this study was to determine the prevalence of antimicrobial resistance in Escherichia coli and Salmonella spp. isolated from healthy chickens in Timor-Leste. Through a cross-sectional study, cloacal swabs and boot swabs were collected from 25 live bird markets and two layer farms respectively. E. coli and Salmonella spp. from these samples were tested for susceptibility to six antimicrobials using a disk diffusion test, and a subset was tested for susceptibility to 27 antimicrobials using broth-based microdilution. E. coli and Salmonella spp. isolates showed the highest resistance towards either tetracycline or ampicillin on the disk diffusion test. E. coli from layer farms (odds ratio:5.2; 95%CI 2.0-13.1) and broilers (odds ratio:18.1; 95%CI 5.3-61.2) were more likely to be multi-drug resistant than those from local chickens. Based on the broth-based microdilution test, resistance to antimicrobials in the Timor-Leste Antimicrobial Guidelines for humans were low, except for resistance to ciprofloxacin in Salmonella spp. (47.1%). Colistin resistance in E. coli was 6.6%. Although this study shows that antimicrobial resistance in chickens was generally low in Timor-Leste, there should be ongoing monitoring in commercial chickens as industry growth might be accompanied with increased antimicrobial use.

Community engagement strengthens pig disease knowledge and passive surveillance in Timor-Leste.

Smallholder pig production in Timor-Leste is culturally and economically important for most households. However, regular and ongoing disease surveillance and pig husbandry training for farmers are limited. This article describes collaborative social and diagnostic research followed by a pilot community engagement program to improve farmer and technician knowledge, skills, and working relationships. There were three phases: (1) A qualitative study in 2020 to explore the experiences and knowledge of 133 pig farmers, 6 village leaders, and 16 district veterinary technicians on pig diseases and reporting, treatment methods, and access to information or assistance. (2) A pilot community engagement program in 3 villages in 2021 with the diagnostic investigation with samples analyzed from 27 dead pigs, and (3) Evaluation of community engagement and training outcomes. Results of the qualitative study revealed limited reporting of sick or dead pigs by farmers to veterinary technicians due to a lack of trust in the veterinary diagnostic system. Most technicians lacked experience with sampling or post-mortems so diagnostic training was undertaken for the pilot disease investigation. Evaluation results showed improved knowledge, motivation, and confidence of government staff and farmers. The credibility of veterinary technicians improved and gave them more confidence to work with communities. Farmers felt supported because all aspects of pig husbandry were addressed, and they were more willing to report dead or sick pigs. The project indicates that improved passive disease surveillance can be achieved by engaging communities in smallholder pig farming in Timor-Leste. Further research and testing of the approach in other districts and countries is recommended.

Use of Field Based Loop Mediated Isothermal Amplification (LAMP) Technology for a Prevalence Survey and Proof of Freedom Survey for African Swine Fever in Timor-Leste in 2019.

African Swine Fever (ASF) has been spreading in numerous southeast Asian countries since a major incursion in mainland China in 2018. Timor-Leste confirmed an outbreak of ASF in September 2019 which resulted in high mortalities in affected pigs. Pigs in Timor-Leste are the second most common type of livestock kept by villagers and represent a traditionally important source of income and prestige for householders. In order to understand the extent of ASF infected villages in Timor-Leste a prevalence survey was designed and conducted in November-December 2019. Timor-Leste has limited laboratory facilities and access to qPCR diagnostic tests. Therefore, a loop mediated isothermal amplification (LAMP) assay was used to detect ASF positive blood samples collected during the prevalence survey. The LAMP assay was proven to be a robust, highly specific and sensitive laboratory test for ASF suitable for use in the field and where there are limited laboratory facilities. The results of the prevalence survey allowed the extent of the ASF incursion to be delineated and the introduction of a disease response strategy to limit the spread of ASF and assist in the recovery of the pig population in Timor-Leste.

Complete Genome Sequence of African Swine Fever Virus Isolated from a Domestic Pig in Timor-Leste, 2019.

Here, we report the complete genome sequence of the African swine fever virus (ASFV) isolate ASFV/Timor-Leste/2019/1, isolated from a domestic pig during the first outbreak of ASF in Timor-Leste in 2019. Using target enrichment short-read Illumina data combined with long-read Oxford Nanopore data, we assembled a full-length genome sequence of 192,237 bp.

Field Verification of an African Swine Fever Virus Loop-Mediated Isothermal Amplification (LAMP) Assay During an Outbreak in Timor-Leste.

Recent outbreaks of African swine fever virus (ASFV) have seen the movement of this virus into multiple new regions with devastating impact. Many of these outbreaks are occurring in remote, or resource-limited areas, that do not have access to molecular laboratories. Loop-mediated isothermal amplification (LAMP) is a rapid point of care test that can overcome a range of inhibitors. We outline further development of a real-time ASFV LAMP, including field verification during an outbreak in Timor-Leste. To increase field applicability, the extraction step was removed and an internal amplification control (IAC) was implemented. Assay performance was assessed in six different sample matrices and verified for a range of clinical samples. A LAMP detection limit of 400 copies/rxn was determined based on synthetic positive control spikes. A colourmetric LAMP assay was also assessed on serum samples. Comparison of the LAMP assay to a quantitative polymerase chain reaction (qPCR) was performed on clinical ASFV samples, using both serum and oral/rectal swabs, with a substantial level of agreement observed. The further verification of the ASFV LAMP assay, removal of extraction step, implementation of an IAC and the assessment of a range of sample matrix, further support the use of this assay for rapid in-field detection of ASFV.

An investigation of classical swine fever virus seroprevalence and risk factors in pigs in Timor-Leste.

Classical swine fever virus (CSFV) is a highly infectious pathogen of pigs and believed to be a major constraint to pig production in Timor-Leste. The Ministry of Agriculture and Fisheries conducts vaccination campaigns in an attempt to control clinical disease, however, there is no empirical data available concerning the seroprevalence and distribution of CSFV in Timor-Leste. To help address this knowledge deficit, a cross-sectional study to determine seroprevalence was conducted in the three districts that border Indonesia. Data on farmer- and pig-level factors were also collected to look at their impact on CSFV serological status. Overall, true CSFV seroprevalence was estimated at 34.4%. Seroprevalence estimates varied widely between and within districts, subdistricts, and villages. Older pigs and pigs that had been vaccinated for CSFV were more likely to test positive for CSFV antibody. Pigs owned by farmers that experienced the sudden death of pigs in the 12 months prior to the survey were more likely to test positive for CSFV antibody, while pigs that had been sick in the previous three months were less likely to test positive for CSFV antibody. The final multivariable model accounted for a large amount of variation in the data, however, much of this variation was explained by the random effects with less than one percent of the variation explained by the fixed effects. This work further supports the need for a collaborative approach to whole-island CSFV control between West Timor, Indonesia and Timor-Leste. Further work is needed to better understand the risk factors for CSFV serological status in order to allocate resources for control. As CSFV is now endemic in Timor-Leste research involving a combination of serology, antigen detection and in-depth investigation of suspect cases over a period of time may be required.