Vaccines and other alternative products can help minimize the need for antibiotics by preventing and controlling infectious diseases in animal populations, and are central to the future success of animal agriculture. To assess scientific advancements related to alternatives to antibiotics and provide actionable strategies to support their development, the United States Department of Agriculture, with support from the World Organisation for Animal Health, organized the second International Symposium on Alternatives to Antibiotics. It focused on six key areas: vaccines; microbial-derived products; non-nutritive phytochemicals; immune-related products; chemicals, enzymes, and innovative drugs; and regulatory pathways to enable the development and licensure of alternatives to antibiotics. This article, part of a two-part series, synthesizes and expands on the expert panel discussions regarding opportunities, challenges and needs for the development of vaccines that may reduce the need for use of antibiotics in animals; new approaches and potential solutions will be discussed in part 2 of this series. Vaccines are widely used to prevent infections in food animals. Various studies have demonstrated that their animal agricultural use can lead to significant reductions in antibiotic consumption, making them promising alternatives to antibiotics. To be widely used in food producing animals, vaccines have to be safe, effective, easy to use, and cost-effective. Many current vaccines fall short in one or more of these respects. Scientific advancements may allow many of these limitations to be overcome, but progress is funding-dependent. Research will have to be prioritized to ensure scarce public resources are dedicated to areas of potentially greatest impact first, and private investments into vaccine development constantly compete with other investment opportunities. Although vaccines have the potential to improve animal health, safeguard agricultural productivity, and reduce antibiotic consumption and resulting resistance risks, targeted research and development investments and concerted efforts by all affected are needed to realize that potential.Electronic supplementary materialThe online version of this article (10.1186/s13567-018-0560-8) contains supplementary material, which is available to authorized users.

Vaccines and other alternative products are central to the future success of animal agriculture because they can help minimize the need for antibiotics by preventing and controlling infectious diseases in animal populations. To assess scientific advancements related to alternatives to antibiotics and provide actionable strategies to support their development, the United States Department of Agriculture, with support from the World Organisation for Animal Health, organized the second International Symposium on Alternatives to Antibiotics. It focused on six key areas: vaccines; microbial-derived products; non-nutritive phytochemicals; immune-related products; chemicals, enzymes, and innovative drugs; and regulatory pathways to enable the development and licensure of alternatives to antibiotics. This article, the second part in a two-part series, highlights new approaches and potential solutions for the development of vaccines as alternatives to antibiotics in food producing animals; opportunities, challenges and needs for the development of such vaccines are discussed in the first part of this series. As discussed in part 1 of this manuscript, many current vaccines fall short of ideal vaccines in one or more respects. Promising breakthroughs to overcome these limitations include new biotechnology techniques, new oral vaccine approaches, novel adjuvants, new delivery strategies based on bacterial spores, and live recombinant vectors; they also include new vaccination strategies in-ovo, and strategies that simultaneously protect against multiple pathogens. However, translating this research into commercial vaccines that effectively reduce the need for antibiotics will require close collaboration among stakeholders, for instance through public–private partnerships. Targeted research and development investments and concerted efforts by all affected are needed to realize the potential of vaccines to improve animal health, safeguard agricultural productivity, and reduce antibiotic consumption and resulting resistance risks.

The objectives of the present study were to assess the mucosal, cellular, and humoral immune responses induced by two different infectious bronchitis virus (IBV) vaccination regimes and their efficacy against challenge by a variant IBV Q1. One-day-old broiler chicks were vaccinated with live H120 alone (group I) or in combination with CR88 (group II). The two groups were again vaccinated with CR88 at 14 days of age (doa). One group was kept as the control (group III). A significant increase in lachrymal IgA levels was observed at 4 doa and then peaked at 14 doa in the vaccinated groups. The IgA levels in group II were significantly higher than those in group I from 14 doa. Using immunohistochemistry to examine changes in the number of CD4 ؉ and CD8؉ cells in the trachea, it was found that overall patterns of CD8 ؉ cells were dominant compared to those of CD4 ؉ cells in the two vaccinated groups. CD8؉ cells were significantly higher in group II than those in group I at 21 and 28 doa. All groups were challenged oculonasally with a virulent Q1 strain at 28 doa, and their protection was assessed. The two vaccinated groups gave excellent ciliary protection against Q1, although group II's histopathology lesion scores and viral RNA loads in the trachea and kidney showed greater levels of protection than those in group I. These results suggest that greater protection is achieved from the combined vaccination of H120 and CR88 of 1-day-old chicks, followed by CR88 at 14 doa. T he prevention of infectious bronchitis (IB) in chickens isachieved through the use of live and inactivated vaccines, which provide protection against virulent field IB viruses (IBVs) in the event of an exposure. Despite these preventative measures, outbreaks of IB frequently occur in many poultry producing countries (1-3). This is probably due to the emergence of new variants of infectious bronchitis virus (1-5). For the successful protection of chickens against infection, it is essential to identify the prevalent genotypes in the region, determine the cross-protective potential of available vaccines, and optimize strategic vaccination programs.IB was first described in the United States during the 1930s and was identified in the United Kingdom in 1948. Thereafter, many IBV variants were isolated from Europe, significantly a variant called 793B that emerged in the 1990s (6). Later, IBV QX was first identified in China (7) before spreading to Europe (8). Another IBV genotype, Q1, genetically and serologically distinct from the classical IBVs, was also reported in China (9), the Middle East (10), and Europe (11). To contain this strain, an effective vaccination program is needed. However, very little is known about the cross protection induced by the commercially available vaccines or vaccination regimes against this variant Q1.An effective and long-lasting protection against IBV infection requires the activation of effector, memory cell-mediated, and humoral immune responses (HIRs) against the virus (12). A number of studies have reported the systemi...

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New variants of infectious bronchitis viruses (IBVs; Coronaviridae) continuously emerge despite routine vaccinations. Here, we report genome sequence variations of IBVs identified by random non-targeted next generation sequencing (NGS) of vaccine and field samples collected on FTA cards from commercial flocks in Mexico in 2019–2021. Paired-ended sequencing libraries prepared from rRNA-depleted RNAs were sequenced using Illumina MiSeq. IBV RNA was detected in 60.07% (n = 167) of the analyzed samples, from which 33 complete genome sequences were de novo assembled. The genomes are organized as 5'UTR-[Rep1a-Rep1b-S-3a-3b-E-M-4b-4c-5a-5b-N-6b]-3'UTR, except in eight sequences lacking non-structural protein genes (accessory genes) 4b, 4c, and 6b. Seventeen sequences have auxiliary S2' cleavage site located 153 residues downstream the canonically conserved primary furin-specific S1/S2 cleavage site. The sequences distinctly cluster into lineages GI-1 (Mass-type; n = 8), GI-3 (Holte/Iowa-97; n = 2), GI-9 (Arkansas-like; n = 8), GI-13 (793B; n = 14), and GI-17 (California variant; CAV; n = 1), with regional distribution in Mexico; this is the first report of the presence of 793B- and CAV-like strains in the country. Various point mutations, substitutions, insertions and deletions are present in the S1 hypervariable regions (HVRs I-III) across all 5 lineages, including in residues 38, 43, 56, 63, 66, and 69 that are critical in viral attachment to respiratory tract tissues. Nine intra-/inter-lineage recombination events are present in the S proteins of three Mass-type sequences, two each of Holte/Iowa-97 and Ark-like sequence, and one each of 793B-like and CAV-like sequences. This study demonstrates the feasibility of FTA cards as an attractive, adoptable low-cost sampling option for untargeted discovery of avian viral agents in field-collected clinical samples. Collectively, our data points to co-circulation of multiple distinct IBVs in Mexican commercial flocks, underscoring the need for active surveillance and a review of IBV vaccines currently used in Mexico and the larger Latin America region.