Phase and antigenic variation result in a heterogenic phenotype of a clonal bacterial population, in which individual cells either express the phase-variable protein(s) or not, or express one of multiple antigenic forms of the protein, respectively. This form of regulation has been identified mainly, but by no means exclusively, for a wide variety of surface structures in animal pathogens and is implicated as a virulence strategy. This review provides an overview of the many bacterial proteins and structures that are under the control of phase or antigenic variation. The context is mainly within the role of the proteins and variation for pathogenesis, which reflects the main body of literature. The occurrence of phase variation in expression of genes not readily recognizable as virulence factors is highlighted as well, to illustrate that our current knowledge is incomplete. From recent genome sequence analysis, it has become clear that phase variation may be more widespread than is currently recognized, and a brief discussion is included to show how genome sequence analysis can provide novel information, as well as its limitations. The current state of knowledge of the molecular mechanisms leading to phase variation and antigenic variation are reviewed, and the way in which these mechanisms form part of the general regulatory network of the cell is addressed. Arguments both for and against a role of phase and antigenic variation in immune evasion are presented and put into new perspective by distinguishing between a role in bacterial persistence in a host and a role in facilitating evasion of cross-immunity. Finally, examples are presented to illustrate that phase-variable gene expression should be taken into account in the development of diagnostic assays and in the interpretation of experimental results and epidemiological studies.

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Phase and Antigenic Variation in Bacteria

Coxiella burnetii is the agent of Q fever, or ``query fever,'' a zoonosis first described in Australia in 1937. Since this first description, knowledge about this pathogen and its associated infections has increased dramatically. We review here all the progress made over the last 20 years on this topic. C. burnetii is classically a strict intracellular, Gram-negative bacterium. However, a major step in the characterization of this pathogen was achieved by the establishment of its axenic culture. C. burnetii infects a wide range of animals, from arthropods to humans. The genetic determinants of virulence are now better known, thanks to the achievement of determining the genome sequences of several strains of this species and comparative genomic analyses. Q fever can be found worldwide, but the epidemiological features of this disease vary according to the geographic area considered, including situations where it is endemic or hyperendemic, and the occurrence of large epidemic outbreaks. In recent years, a major breakthrough in the understanding of the natural history of human infection with C. burnetii was the breaking of the old dichotomy between ``acute'' and ``chronic'' Q fever. The clinical presentation of C. burnetii infection depends on both the virulence of the infecting C. burnetii strain and specific risks factors in the infected patient. Moreover, no persistent infection can exist without a focus of infection. This paradigm change should allow better diagnosis and management of primary infection and long-term complications in patients with C. burnetii infection.

https://hal.archives-ouvertes.fr/hal-01496178/document

From Q Fever to Coxiella burnetii Infection: a Paradigm Change.

After repeated passages through embyronated eggs, the Nine Mile strain of Coxiella burnetii exhibits antigenic variation, a loss of virulence characteristics, and transition to a truncated lipopolysaccharide (LPS) structure. In two independently derived strains, Nine Mile phase II and RSA 514, these phenotypic changes were accompanied by a large chromosomal deletion (M. H. Vodkin and J. C. Williams, J. Gen. Microbiol. 132:2587-2594, 1986). In the work reported here, additional screening of a cosmid bank prepared from the wild-type strain was used to map the deletion termini of both mutant strains and to accumulate all the segments of DNA that comprise the two deletions. The corresponding DNAs were then sequenced and annotated. The Nine Mile phase II deletion was completely nested within the deletion of the RSA 514 strain. Basic alignment and homology studies indicated that a large group of LPS biosynthetic genes, arranged in an apparent O-antigen cluster, was deleted in both variants. Database homologies identified, in particular, mannose pathway genes and genes encoding sugar methylases and nucleotide sugar epimerase-dehydratase proteins. Candidate genes for addition of sugar units to the core oligosaccharide for synthesis of the rare sugar 6-deoxy-3-C-methylgulose (virenose) were identified in the deleted region. Repeats, redundancies, paralogous genes, and two regions with reduced G+C contents were found within the deletions.

https://iai.asm.org/content/iai/70/12/6726.full.pdf

Chromosomal DNA Deletions Explain Phenotypic Characteristics of Two Antigenic Variants, Phase II and RSA 514 (Crazy), of the Coxiella burnetii Nine Mile Strain†

Coxiella burnetii is an obligate intracellular bacterium and the etiological agent of the zoonotic disease Q fever. Acute human Q fever is characterized by flu-like symptoms that, in some cases, can result in a persistent infection that may reactivate months or years after initial exposure. Mechanisms by which this obligate parasite evades clearance by the host immune response during persistent infection are unknown. Here, we characterized the interaction of C. burnetii with dendritic cells (DC), critical components of both innate and adaptive immunity. Human DC were infected with two isogenic C. burnetii strains that differ in LPS length. Infection by the Nine Mile phase I (NMI) strain, which is fully virulent and produces full-length LPS, did not result in DC maturation. In contrast, infection by the avirulent Nine Mile phase II strain, producing a severely truncated LPS, resulted in toll-like receptor 4-independent DC maturation and ≈10-fold more IL-12 and TNF production. NMI did not actively inhibit DC maturation as NMI-infected DC subsequently matured if treated with Escherichia coli LPS or Nine Mile phase II. Furthermore, removal of LPS from NMI dramatically increased its ability to stimulate DC. We propose a model whereby LPS of virulent C. burnetii masks toll-like receptor ligands from innate immune recognition by DC, thereby allowing replication without significant maturation or inflammatory cytokine production. This immune evasion strategy may allow C. burnetii to persist in an immunocompetent host.

https://www.pnas.org/content/pnas/102/24/8722.full.pdf

Virulent Coxiella burnetii does not activate human dendritic cells: Role of lipopolysaccharide as a shielding molecule

The role of Toll-like receptors (TLRs) in the recognition of extracellular and facultative intracellular bacteria by the innate immune system has been extensively studied, but their role in the recognition of obligate intracellular organisms remains unknown. Coxiella burnetii , the agent of Q fever, is an obligate intracellular bacterium that specifically inhabits monocytes/macrophages. We showed in this study that C. burnetii LPS is involved in the uptake of virulent organisms by macrophages but not in that of avirulent variants. The uptake of virulent organisms was dependent on TLR4 because it was reduced in macrophages from TLR4 −/− mice. In addition, LPS was responsible for filamentous actin reorganization induced by virulent C. burnetii , which was prevented in TLR4 −/− macrophages. In contrast, the intracellular fate of C. burnetii was not affected in TLR4 −/− macrophages, suggesting that TLR4 does not control the maturation of C. burnetii phagosome and the microbicidal activity of macrophages. These results are consistent with in vivo experiments because the pattern of tissue infection and the clearance of C. burnetii were similar in wild-type and TLR4 −/− mice. We also showed that the number of granulomas was decreased in the liver of infected TLR4 −/− mice, and the formation of splenic granulomas was only transient. The impaired formation of granulomas was associated with decreased production of IFN-γ and TNF. Taken together, these results demonstrate that TLR4 controls early events of C. burnetii infection such as macrophage phagocytosis, granuloma formation, and cytokine production.

Lipopolysaccharide from Coxiella burnetii Is Involved in Bacterial Phagocytosis, Filamentous Actin Reorganization, and Inflammatory Responses through Toll-Like Receptor 4

During the phase variation of Coxiella burnetii, modifications in its lipopolysaccharide (LPS) component were investigated. The cloned phase I C. burnetii cells were passed serially in chicken embryo yolk sacs up to the egg passage (EP) 90. The LPSs from the cells in EPs 3, 12, 21, 40, 60, and 90 were all separated by steric exclusion chromatography into three major populations: the high, intermediate, and low molecular weight fractions, differing one from another in size and chemical composition. No noticeable shortening of the O-polysaccharide chains was observed in the LPSs isolated during the C. burnetii cultivation. However, a redistribution of the existing LPS populations has been observed due to an increasing prevalence of those cells in the whole cell population that express LPS molecules with truncated O-chains and those being of R-type. In the high and intermediate molecular weight LPS populations, virenose and dihydrohydroxystreptose are lost gradually with the progress in phase variation. This...

https://journals.sagepub.com/doi/pdf/10.1177/09680519000060050701

Phase variation of Coxiella burneti0i strain Priscilla: influence of this phenomenon on biochemical features of its lipopolysaccharide:

NMR study of virenose and dihydrohydroxystreptose isolated from Coxiella burnetii phase I lipopolysaccharide

Coxiella burnetii , the etiological agent of Q fever, is found worldwide. In humans, infection with the microbe can be asymptomatic or result in acute 1 or chronic 2 form of the disease. Some investigators suggest 3 that there are specific strains causing acute or chronic disease. Genomic DNA restriction fragment length polymorphism 4,5 and chemotype determination of lipopolysaccharides 6 (LPS) were the basis for such differentiation. However, other investigators believe 2 that occurrence of chronic disease, e.g., Q fever endocarditis, is determined by host factors rather than by properties of the pathogen. An LPS has been considered 7 to be a major determinant of virulence expression and infection of C. burnetii . It has been hypothesized that differences in both composition and structure of LPSs might also contribute to predetermination of the conditions of Q fever, but no detailed investigations have been undertaken in this respect thus far. In our studies, the LPSs isolated from Henzerling and S strains, considered to be associated with acute and chronic forms of Q fever, respectively, were analyzed for their chemical composition in considerable detail. The results are reported herein.

Peter Ftáček

Papers

Phase variation of Coxiella burneti0i strain Priscilla: influence of this phenomenon on biochemical features of its lipopolysaccharide:

NMR study of virenose and dihydrohydroxystreptose isolated from Coxiella burnetii phase I lipopolysaccharide

Structural properties of lipopolysaccharides from Coxiella burnetii strains Henzerling and S.