Sequencing of metagenomics sample and E. coli isolates

Antimicrobial Resistance (AMR) poses a significant global threat to public health, animal health, and environmental health. Bacteria have rapidly evolved techniques to outsmart and escape current antibiotic treatments rendering antibiotics ineffective. Non-considered and irrational use of antibiotics in each sector accelerates the development of AMR in bacteria.

For that very reason, the Directorate General of Livestock and Animal Health Services, Ministry of Agriculture (DGLAHS-MoA) has been making efforts to prevent and control the risk of AMR in the livestock and animal health sectors in Indonesia. DGLAHS-MoA subscribes to the five strategic objectives of the Global Action Plan on AMR namely to increase awareness and understanding of AMR, strengthen surveillance and research, improve infection control, optimize the prudent and responsible use of antimicrobials, and expand the availability of sustainable resources for treatment.

The FAO Emergency Centre for Transboundary Animal Diseases (ECTAD) funded by the United States Agency for International Development (USAID) commit to support Indonesian government activities to control development of AMR in the poultry industry in Indonesia under the Emerging Pandemic Threats 2 (EPT-2). This project supports the DGLAHS to establish AMR surveillance systems, including implementation of National AMR Surveillance in healthy animals, piloting AMR surveillance in diseased animals, and inclusion of molecular AMR diagnostics in DGLAHS’ AMR control programmes.

Recently, FAO piloted the use of new rapid Nanopore MinION sequencing technology at the National Animal Products Quality Control and Certification Laboratory (BPMSPH). FAO provided a high specification laptop computer, two MinION AMR gene sequencing devices and the required laboratory reagents to implement the Nanopore project at BPMSPH. The MinION is a new pocket-sized, portable sequencing device that generates long sequence reads by passing DNA/RNA through protein pores. Sample preparation can be done in as little as 10-60 minutes and the output analyzed with a laptop in real-time, using cloud-based analytics software. With the use of MinION, hundreds of pathogens as well as markers of antimicrobial resistance can be identified.

The application of MinION technology has potential to impact infection control and antimicrobial stewardship in human, animal, and environmental health. Thus, it can be one of the tools used to help Indonesia in detection, response, and control of AMR. BPMSPH will collect and analyze poultry slaughterhouse effluent and river water collected near slaughterhouse wastewater outfall points in the Greater Jakarta area. Long sequencing reads generated by the Nanopore MinION will be used to identify which bacterial species are carrying AMR genes and Mobile Genetic Elements (MGEs). In addition, general and extended-spectrum beta-lactamase (ESBLs) producing Escherichia coli will be isolated from the collected samples and DNA sequencing conducted to map the resistance mechanisms of these bacteria and their correlation with other resistance mechanisms.

FAO procured and handed over 1000 Sensititre plates to the Director of Veterinary Public Health on 23rd October 2019, for use at the BPMSPH laboratory, along with the media required for the implementation of 2019 National AMR Surveillance by the DGLAHS. The Sensititre system offers rapid access to the most up-to-date antimicrobials in a complete solution, generating reliable minimum inhibitory concentration results, and providing confidence when time is critical. With the use of the Sensititre system, lack of standardization and in some cases the need for laborious laboratory preparation of drugs and agar plates generating variability between labs, can be eliminated.