Acoustic reporter genes for noninvasive imaging of microorganisms in mammalian hosts

• Published in: Nature (London) 2018-01, Vol.553 (7686), p.86-90
• Main Authors: Bourdeau, Raymond W., Lee-Gosselin, Audrey, Lakshmanan, Anupama, Farhadi, Arash, Kumar, Sripriya Ravindra, Nety, Suchita P., Shapiro, Mikhail G.
• Format: Article
• Language: English
• Subjects: 14/5; 14/63; 42/44; 59/5; 631/1647/1511; 631/1647/245/1859; 631/61/338/469; 631/61/338/552; 64/60; 82/80; 9/10; Acoustics; Bacteria; Chemical compounds; Diagnostic imaging; Diagnostic systems; Drug development; E coli; Escherichia coli; Gases; Gene clusters; Gene expression; Genes; Genetic aspects; Genetic engineering; Humanities and Social Sciences; Imaging; In vivo methods and tests; letter; Light scattering; Mammals; Methods; Microbiomes; Microorganisms; multidisciplinary; Multiplexing; Photosynthesis; Proteins; Salmonella; Science; Spatial discrimination; Tumors; Ultrasonic imaging; Ultrasound; Vesicles
• ISSN: 0028-0836; 1476-4687
• DOI: 10.1038/nature25021

Heterologous expression of engineered gas vesicles allows noninvasive, deep-tissue ultrasound visualization of engineered bacteria in vivo in mouse tumour models and in the gastrointestinal tract. The sound of inner microbes Currently available techniques for noninvasive imaging of the microbes that live within mammalian hosts are limited by low tissue penetration or are expensive. Mikhail Shapiro and colleagues constructed a reporter gene cluster containing genes that encode gas vesicles used by photosynthetic bacteria to regulate buoyancy. As these vesicles produce sound waves, other bacterial strains engineered with the reporter gene cluster and expressing these vesicles can be detected with ultrasound imaging. The researchers show that this approach can be used for noninvasive, deep in vivo imaging of bacterial colonization in the gastrointestinal tract and of tumours. Further technical development is needed to harness the advantages of ultrasound imaging over the use of fluorescent reporter genes for noninvasive, inexpensive in vivo imaging of gene expression with high resolution and deep tissue penetration. The mammalian microbiome has many important roles in health and disease 1 , 2 , and genetic engineering is enabling the development of microbial therapeutics and diagnostics 3 , 4 , 5 , 6 , 7 . A key determinant of the activity of both natural and engineered microorganisms in vivo is their location within the host organism 8 , 9 . However, existing methods for imaging cellular location and function, primarily based on optical reporter genes, have limited deep tissue performance owing to light scattering or require radioactive tracers 10 , 11 , 12 . Here we introduce acoustic reporter genes, which are genetic constructs that allow bacterial gene expression to be visualized in vivo using ultrasound, a widely available inexpensive technique with deep tissue penetration and high spatial resolution 13 , 14 , 15 . These constructs are based on gas vesicles, a unique class of gas-filled protein nanostructures that are expressed primarily in water-dwelling photosynthetic organisms as a means to regulate buoyancy 16 , 17 . Heterologous expression of engineered gene clusters encoding gas vesicles allows Escherichia coli and Salmonella typhimurium to be imaged noninvasively at volumetric densities below 0.01% with a resolution of less than 100 μm. We demonstrate the imaging of engineered cells in vivo in proof-of-concept models of gastrointestinal and tumour