In a first-of-its-kind pilot project, researchers from the Food and Agriculture Organization of the United Nations, Indonesia’s Ministry of Agriculture and Arizona State University tested the novel integration of a handheld DNA sequencing device within Indonesia’s national antibiotic resistance surveillance system across six chicken slaughterhouses in the Greater Jakarta area. They collected samples from both wastewater and surrounding rivers.

The goal: to determine whether portable DNA sequencing could improve national efforts to track drug-resistant E. coli, a key indicator of antibiotic resistance.

Laboratory medicine is an essential part of the diagnostic process, supporting clinical decisions, guiding and addressing therapy. The recent COVID-19 pandemic illustrated well the key role of laboratory medicine in the diagnosis, management and prognosis of SARS-CoV-2 infected patients. Technological advances improved the laboratory diagnosis and patients’ management and others appear very promising as clustered regularly interspaced short palindromic repeats (CRISPR) or artificial intelligence (AI). This review describes the current diagnostic assays routinely used in laboratory as well as the novel technologies not in routine yet but that represent future directions and will probably dominate the laboratory in the next years. Serology is important for detecting antibodies and/or antigens of the infectious pathogens or for epidemiological purposes, while real-time PCR with its high sensitivity and specificity has a key role in pathogen detection in different biological matrices and in monitoring the therapy. Nanochip-based technologies make possible delivering a laboratory report at the patient’s bed or in settings where a laboratory-based hospital is not available. Next generation sequencing (NGS) is a massively high throughput parallel sequencing technology that allows the simultaneous sequence of billions of DNA fragments in a short time frame. This technology can be used to detect drug-associated mutations, minority species within an infected patient or for pathogen identification. CRISPR-based technology is a fast and accurate diagnostic method that can be applied to different human diseases including infectious diseases. Artificial intelligence is increasingly used in laboratory medicine. In clinical microbiology, it is used to build up diagnosis analyzing genomic information or mass spectra from isolated bacteria, for predicting antibiotic sensitivity or for processing in a short time a large number of images with meaningful results. Thus, the laboratory is becoming increasingly automated and interwoven with sophisticated software or algorithms that will increase the sensitivity and specificity of diagnoses, besides reducing time to results.

Researchers have discovered two new viruses in bats that are closely related to the deadly Nipah and Hendra viruses — pathogens that can cause severe brain inflammation and respiratory disease in humans. The viruses, as well as other new viruses, bacteria, and parasites identified from bat kidneys, were reported this week in the open-access journal PLOS Pathogens by Yun Feng of the Yunnan Institute of Endemic Disease Control and Prevention, China, and colleagues.