Changing Priorities in Vaccinology: Antibiotic Resistance Moving to the Top

Abstract

Antimicrobial resistance (AMR) is currently the most alarming issue for human health. AMR already causes 700,000 deaths/year. It is estimated that 10 million deaths due to AMR will occur every year after 2050. This equals the number of people dying of cancer every year in present times. International institutions such as G20, World Bank, World Health Organization (WHO), UN General Assembly, European Union, and the UK and USA governments are calling for new antibiotics. To underline this emergency, a list of antibiotic-resistant "priority pathogens" has been published by WHO. It contains 12 families of bacteria that represent the greatest danger for human health. Resistance to multiple antibiotics is particularly relevant for the Gram-negative bacteria present in the list. The ability of these bacteria to develop mechanisms to resist treatment could be transmitted with genetic material, allowing other bacteria to become drug resistant. Although the search for new antimicrobial drugs remains a top priority, the pipeline for new antibiotics is not promising, and alternative solutions are needed. A possible answer to AMR is vaccination. In fact, while antibiotic resistance emerges rapidly, vaccines can lead to a much longer lasting control of infections. New technologies, such as the high-throughput cloning of human B cells from convalescent or vaccinated people, allow for finding new protective antigens (Ags) that could not be identified with conventional technologies. Antibodies produced by convalescent B cell clones can be screened for their ability to bind, block, and kill bacteria, using novel high-throughput microscopy platforms that rapidly capture digital images, or by conventional technologies such as bactericidal, opsono-phagocytosis and FACS assays. Selected antibodies expressed by recombinant DNA techniques can be used for passive immunization in animal models and tested for protection. Antibodies providing the best protection can be employed to identify new Ags and then used for generating highly specific recombinant Fab fragments. Co-crystallization of Ags bound to Fab fragments will allow us to determine the structure and characteristics of new Ags. This structure-based Ag design will bring to a new generation of vaccines able to target previously elusive infections, thereby offering an effective solution to the problem of AMR.

Keywords: antibiotic resistance; human immunology; public health; reverse vaccinology; vaccination.

Figure 1

Time to detection of resistance of human pathogens to antimicrobials (in red) and to vaccines (in green). Black X symbols indicate insurgence of resistance, with lines starting at product introduction (yellow stars; except for smallpox vaccination that began much earlier; with modifications from Ref. (14) with the permission of the publisher).

Figure 2

Interplay of B cell technology and structural biology in vaccine design, as shown with the Reverse Vaccinology 2.0 approach (from 35). Flow path representation of how the analysis of the human B cell repertoire leads to the identification of protective Abs from vaccinated or infected subjects. From upper left: Single B cell sorting and culturing enables a direct screening and selection of naturally produced Abs with desired functionality, and the recovery of the corresponding Ig gene sequences. This approach allows us to interrogate single-sorted B cells through direct screening of Ab functionality. From the recovered Ig sequences, we can produce the Abs of interest as recombinant proteins, and fine-tune their properties. The structural characterization of recombinant monoclonal Abs bound to their target antigen (Ag) leads to a detailed definition of the protective epitope. The right inset shows the co-crystal structure of an Ag–Ab (Fab) complex, identifying a protective epitope (red). Engineering of the protective epitope can lead to the design of a novel optimized immunogen. For example, we can mount the epitope in an oriented multi-copy array on a nanoparticle that will act as carrier and increase an epitope-focused immune response (“structure-based Ag design”). The new Ag can be developed with the best formulation or delivery system to then be tested in humans (from Ref. (30) with permission of the publisher).