In vivo evolution of an emerging zoonotic bacterial pathogen in an immunocompromised human host

Chemical Synthesis and Antigenic Evaluation of Oligosaccharides of Bordetella hinzii O-Antigen Containing Unique Amidated 2,3-Diacetamido-2,3-dideoxy-alduronic Acids

Bordetella hinzii is a zoonotic pathogen, which can cause brain abscess, pneumonia, bacteremia, and urinary tract infection. Vaccines are economical and effective means for combating infectious diseases. Herein, we present the first total synthesis of the highly functionalized mono- and oligosaccharides of B. hinzii O-antigen for vaccine development. The rare 2,3-diacetamidopyranoses were generated from 3-O-acetyl-2-nitroglycals via an organocatalyzed one-pot relay glycosylation method. The postglycosylation oxidation strategy was used to overcome the poor reactivity of 2,3-diacetamido-aldouronic acid building blocks in glycosylation reactions. Direct amidation of alduronic acid with NH3 in the late stage reduced the protecting group operation and increased the synthetic efficiency. Di-tert-butylsilylidene-directed α-galactosylation method was used to construct challenging 1,2-cis-glycosidic bond. Six oligosaccharides of B. hinzii O-antigen were obtained and further conjugated to human serum albumin for antigenicity evaluation (the sera antibodies were obtained from vaccinated mouse via inactivated B. hinzii). The terminal tetrasaccharide of B. hinzii O-antigen has been identified as a potential glycol-epitope and might be useful for vaccine development against B. hinzii.

Transcriptional diversification in a human-adapting zoonotic pathogen drives niche-specific evolution

Bacterial pathogens can undergo striking adaptive evolutionary change in the context of infection, driven by selection forces associated with host defenses and antibiotic treatment. In this work, we analyze the transcriptional landscape associated with adaptation in an emerging zoonotic pathogen, Bordetella hinzii, as it evolved during a 45-month infection in an IL12Rβ1-deficient immunocompromised host. We find evidence of multiple niche-specific modifications in the intravascular and gastrointestinal compartments, involving the superoxide dismutase system, glutamate and ectoine metabolism, chaperone-mediated protein folding, pilus organization, and peptide transport. Individual blood lineages displayed modifications in glutathione, phenylacetate, and 3-phenylpropionate metabolism, iron cluster assembly, and electron transport, whereas individual gastrointestinal lineages demonstrated changes relating to gluconeogenesis, de novo pyrimidine synthesis, and transport of peptides and phosphate ions. Down regulation of the flagellar operon with corresponding loss of flagellar structures occurred in multiple lineages, suggesting an evolutionary tradeoff between motility and host immune evasion. Finally, methylome analysis demonstrates alteration of global genome methylation associated with loss of a Type III methyltransferase. Our findings reveal striking plasticity in how pathogen transcriptomes explore functional space as they evolve in the context of host infection, and demonstrate that such analysis may uncover phenotypic adaptations not apparent from genomic analysis alone.

The impacts of animal agriculture on One Health-Bacterial zoonosis, antimicrobial resistance, and beyond

The industrialization of animal agriculture has undoubtedly contributed to the improvement of human well-being by increasing the efficiency of food animal production. At the same time, it has also drastically impacted the natural environment and human society. The One Health initiative emphasizes the interdependency of the health of ecosystems, animals, and humans. In this paper, we discuss some of the most profound consequences of animal agriculture practices from a One Health perspective. More specifically, we focus on impacts to host-microbe interactions by elaborating on how modern animal agriculture affects zoonotic infections, specifically those of bacterial origin, and the concomitant emergence of antimicrobial resistance (AMR). A key question underlying these deeply interconnected issues is how to better prevent, monitor, and manage infections in animal agriculture. To address this, we outline approaches to mitigate the impacts of agricultural bacterial zoonoses and AMR, including the development of novel treatments as well as non-drug approaches comprising integrated surveillance programs and policy and education regarding agricultural practices and antimicrobial stewardship. Finally, we touch upon additional major environmental and health factors impacted by animal agriculture within the One Health context, including animal welfare, food security, food safety, and climate change. Charting how these issues are interwoven to comprise the complex web of animal agriculture's broad impacts on One Health will allow for the development of concerted, multidisciplinary interventions which are truly necessary to tackle these issues from a One Health perspective.

Incomplete immunity in a natural animal-microbiota interaction selects for higher pathogen virulence

Incomplete immunity in recovered hosts is predicted to favor more virulent pathogens upon re-infection in the population.1 The microbiota colonizing animals can generate a similarly long-lasting, partial immune response, allowing for infection but dampened disease severity.2 We tracked the evolutionary trajectories of a widespread pathogen (Pseudomonas aeruginosa), experimentally passaged through populations of nematodes immune-primed by a natural microbiota member (P. berkeleyensis). This bacterium can induce genes regulated by a mitogen-activated protein kinase (MAPK) signaling pathway effective at conferring protection against pathogen-induced death despite infection.3 Across host populations, this incomplete immunity selected for pathogens more than twice as likely to kill as those evolved in non-primed (i.e., naive) or immune-compromised (mutants with a knockout of the MAPK ortholog) control populations. Despite the higher virulence, pathogen molecular evolution in immune-primed hosts was slow and constrained. In comparison, evolving pathogens in immune-compromised hosts were characterized by substantial genomic differentiation and attenuated virulence. These findings directly attribute the incomplete host immunity induced from microbiota as a significant force shaping the virulence and evolutionary dynamics of novel infectious diseases.

Within-Host Evolution of Bacterial Pathogens in Acute and Chronic Infection

Bacterial pathogens undergo remarkable adaptive change in response to the selective forces they encounter during host colonization and infection. Studies performed over the past few decades have demonstrated that many general evolutionary processes can be discerned during the course of host adaptation, including genetic diversification of lineages, clonal succession events, convergent evolution, and balanced fitness trade-offs. In some cases, elevated mutation rates resulting from mismatch repair or proofreading deficiencies accelerate evolution, and active mobile genetic elements or phages may facilitate genome plasticity. The host immune response provides another critical component of the fitness landscapes guiding adaptation, and selection operating on pathogens at this level may lead to immune evasion and the establishment of chronic infection. This review summarizes recent advances in this field, with a special focus on different forms of bacterial genome plasticity in the context of infection, and considers clinical consequences of adaptive changes for the host.

Investigating and combatting the key drivers of viral zoonoses in Africa: an analysis of eight epidemics

Investigating the interplay of factors that result in a viral zoonotic outbreak is difficult, though it is increasingly important. As anthropogenic influences shift the delicate balance of ecosystems, new zoonoses emerge in humans. Sub-Saharan Africa is a notable hotspot for zoonotic disease due to abundant competent mammalian reservoir hosts. Furthermore, poverty, corruption, and an overreliance on natural resources play considerable roles in depleting biological resources, exacerbating the population's susceptibility. Unsurprisingly, viral zoonoses have emerged in Africa, including HIV/AIDS, Ebola, Avian influenza, Lassa fever, Zika, and Monkeypox. These diseases are among the principal causes of death in endemic areas. Though typically distinct in their manifestations, viral zoonoses are connected by underlying, definitive factors. This review summarises vital findings on viral zoonoses in Africa using nine notable case studies as a benchmark for future studies. We discuss the importance of ecological recuperation and protection as a central strategy to control zoonotic diseases. Emphasis was made on moderating key drivers of zoonotic diseases to forestall future pandemics. This is in conjunction with attempts to redirect efforts from reactive to pre-emptive through a multidisciplinary "one health" approach.

The role of oxidative stress in genome destabilization and adaptive evolution of bacteria

The review is devoted to bacterial genome destabilization by oxidative stress. The article discusses the main groups of substances causing such stress. Stress regulons involved in destabilization of genetic material and mechanisms enhancing mutagenesis, bacterial genome rearrangements, and horizontal gene transfer, induced by oxidative damage to cell components are also considered. Based on the analysis of publications, it can be claimed that rapid development of new food substrates and ecological niches by microorganisms occurs due to acceleration of genetic changes induced by oxidative stress, mediated by several stress regulons (SOS, RpoS and RpoE) and under selective pressure. The authors conclude that non-lethal oxidative stress is probably-one of the fundamental processes that guide evolution of prokaryotes and a powerful universal trigger for adaptive destabilization of bacterial genome under changing environmental conditions.

The Notable Achievements and the Prospects of Bacterial Pathogen Genomics

Throughout the entirety of human history, bacterial pathogens have played an important role and even shaped the fate of civilizations. The application of genomics within the last 27 years has radically changed the way we understand the biology and evolution of these pathogens. In this review, we discuss how the short- (Illumina) and long-read (PacBio, Oxford Nanopore) sequencing technologies have shaped the discipline of bacterial pathogen genomics, in terms of fundamental research (i.e., evolution of pathogenicity), forensics, food safety, and routine clinical microbiology. We have mined and discuss some of the most prominent data/bioinformatics resources such as NCBI pathogens, PATRIC, and Pathogenwatch. Based on this mining, we present some of the most popular sequencing technologies, hybrid approaches, assemblers, and annotation pipelines. A small number of bacterial pathogens are of very high importance, and we also present the wealth of the genomic data for these species (i.e., which ones they are, the number of antimicrobial resistance genes per genome, the number of virulence factors). Finally, we discuss how this discipline will probably be transformed in the near future, especially by transitioning into metagenome-assembled genomes (MAGs), thanks to long-read sequencing.