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PubMed2004

Bordetella species are distinguished by patterns of substantial gene loss and host adaptation.

Pathogens of the bacterial genus Bordetella cause respiratory disease in humans and animals. Although virulence and host specificity vary across the genus, the genetic determinants of this diversity remain unidentified. To identify genes that may underlie key phenotypic differences between these species and clarify their evolutionary relationships, we performed a comparative analysis of genome content in 42 Bordetella strains by hybridization of genomic DNA to a microarray representing the genomes of three Bordetella species and by subtractive hybridization. Here we show that B. pertussis and B. parapertussis are predominantly differentiated from B. bronchiseptica by large, species-specific regions of difference, many of which encode or direct synthesis of surface structures, including lipopolysaccharide O antigen, which may be important determinants of host specificity. The species also exhibit sequence diversity at a number of surface protein-encoding loci, including the fimbrial major subunit gene, fim2. Gene loss, rather than gene acquisition, accompanied by the proliferation of transposons, has played a fundamental role in the evolution of the pathogenic bordetellae and may represent a conserved evolutionary mechanism among other groups of microbial pathogens.

Animals↗
PubMed2026

In-host adaptation of Staphylococcus aureus during recurrent prosthetic joint infections: a retrospective longitudinal study.

UNLABELLED: The aim of this study was to characterize the in vivo evolution of Staphylococcus aureus strains involved in recurrent prosthetic joint infections (PJIs) both phenotypically and genomically. We conducted a monocentric retrospective study in a 1,437-bed French teaching hospital between 2013 and 2021. All patients presenting a recurrent S. aureus-related PJI-defined as at least two strains isolated from distinct clinical samples more than 90 days apart-of the knee, hip, or shoulder were included. Clinical data were reviewed, and all isolates underwent phenotypic characterization, including antimicrobial susceptibility testing, growth rate determination, biofilm production assays, metabolic profiling (API 50 CH), and virulence evaluation using the Galleria mellonella infection model. Whole-genome sequencing (WGS) was performed for all strains, followed by analyses of core-genome multilocus sequence typing (cgMLST), resistome, virulome, and mobilome composition, and single-nucleotide polymorphisms (SNPs). Thirteen patients met inclusion criteria, yielding 55 S. aureus isolates. Eight patients experienced recurrent infections caused by genetically closely related strains throughout the clinical course (median: three strains per patient; range: 2-6), whereas five patients were infected by genetically distinct strains. At baseline, isolates were genetically diverse and susceptible to methicillin and rifampicin; two showed fluoroquinolone resistance due to grlA and/or gyrA mutations. In one patient (patient C), a recurrent isolate acquired an rpoB S486L mutation, conferring rifampicin resistance after rifampicin exposure. Due to the limited sample size, it is difficult to draw definitive conclusions from the phenotypic analyses. This study highlights the adaptive evolution of S. aureus during chronic PJIs and underscores the need for further research to better understand intra-host dynamics in long-standing infections. IMPORTANCE: This study conducted in a 1,437-bed French teaching hospital analyzed the genomic and phenotypic evolution of 55 Staphylococcus aureus strains recovered in recurrent PJIs from 13 patients. The first strains showed high genotypic diversity across 12 different sequence types. Among the 13 patients, only eight experienced a true recurrence with the same strain, while five were contaminated with a different strain of S. aureus, indicating a new infection. Moreover, this study underscores the complex within-host evolution of S. aureus and highlights the phenotypical and genotypical adaptation during chronic infection.

Staphylococcus aureus↗
PubMed2026

Algae-to-host horizontal gene transfer in Paramecium bursaria is associated with host adaptation during endosymbiosis.

Paramecium bursaria maintains a stable endosymbiosis with green algae, yet the evolutionary consequences of this association remain unclear. Here, we screened the host genome for algal-derived horizontally transferred genes (HTGs) using a lineage-aware workflow designed to detect horizontal gene transfer (HGT) between two defined lineages. We identified 16 candidate HTGs, including four putative newly transferred genes and 12 homologous transferred genes, most of which were functionally associated with redox homeostasis and metabolism. Five HTGs showed symbiosis-dependent expression. RNAi knockdown of GH32s and SATs reduced host proliferation, total cell area, and motility, while GH32s knockdown also reduced endosymbiont load. Duplication patterns suggest that most transfers may have occurred after the P. bursaria lineage diverged from the sampled Paramecium species but before its lineage-specific whole-genome duplication (WGD). The HTGs also showed host-associated shifts in GC content and gene length, while representative HTGs retained conserved domains and functional motifs. Together, our results support algae-to-host HGT in P. bursaria and suggest that some transferred genes may contribute to metabolic integration during endosymbiosis.

Gene Transfer, Horizontal↗
PubMed2006

Bacterial endosymbioses in Solemya (Mollusca: Bivalvia)--model systems for studies of symbiont-host adaptation.

Endosymbioses between chemosynthetic bacteria and marine invertebrates are remarkable biological adaptations to life in sulfide-rich environments. In these mutualistic associations, sulfur-oxidizing chemoautotrophic bacteria living directly within host cells both aid in the detoxification of toxic sulfide and fix carbon to support the metabolic needs of the host. Though best described for deep-sea vents and cold seeps, these symbioses are ubiquitous in shallow-water reducing environments. Indeed, considerable insight into sulfur-oxidizing endosymbioses in general comes from detailed studies of shallow-water protobranch clams in the genus Solemya. This review highlights the impressive body of work characterizing bacterial symbiosis in Solemya species, all of which are presumed to harbor endosymbionts. In particular, studies of the coastal Atlantic species Solemya velum and its larger Pacific congener Solemya reidi are the foundation for our understanding of the metabolism and physiology of marine bivalve symbioses, which are now known to occur in five families. Solemya velum, in particular, is an excellent model organism for symbiosis research. This clam can be collected easily from coastal eelgrass beds and maintained in laboratory aquaria for extended periods. In addition, the genome of the S. velum symbiont is currently being sequenced. The integration of genomic data with additional experimental analyses will help reveal the molecular basis of the symbiont-host interaction in Solemya, thereby complementing the wide array of research programs aimed at better understanding the diverse relationships between bacterial and eukaryotic cells.

Adaptation, Physiological↗
PubMed2004

Helper-dependent adenovirus vectors elicit intact innate but attenuated adaptive host immune responses in vivo.

Helper-dependent adenovirus (HD-Ad) vectors with all adenoviral genes deleted mediate very long-term expression of therapeutic transgenes in a variety of animal models of disease. These vectors are associated with reduced toxicity and improved safety relative to traditional early region 1 deletion first-generation Ad (FG-Ad) vectors. Many studies have clearly demonstrated that FG-Ad vectors induce innate and adaptive immune responses in vivo; however, a comprehensive analysis of host immune responses to HD-Ad vectors has not yet been performed. In DBA/2 mice, intravenous injection of HD-Ad vectors encoding LacZ (HD-AdLacZ) or a murine secreted alkaline phosphatase (HD-AdSEAP) induced an early expression of inflammatory cytokine and chemokine genes in the liver, including interferon-inducible protein 10, macrophage inflammatory protein 2, and tumor necrosis factor alpha, and were expressed in a pattern similar to that induced by FG-Ad vectors encoding AdSEAP. Like AdSEAP, and consistent with the pattern of cellular gene expression, HD-AdLacZ and HD-AdSEAP induced the recruitment of CD11b-positive leukocytes to the transduced liver within hours of administration. AdSEAP also induced a second phase of liver inflammation, consisting of inflammatory gene expression and CD3-positive lymphocytic infiltrates 7 days posttransduction. In contrast, beyond 24 h no infiltrates or expression of inflammatory genes was detected in the livers of mice receiving HD-AdSEAP. Despite the lack of liver inflammation at 7 days, Ad-specific cytotoxic T lymphocytes could be detected in mice receiving HD-AdSEAP. This lack of liver inflammation was not due to reduced transduction since levels of transgene expression and the amounts of vector DNA in the liver were equivalent in mice receiving HD-AdSEAP and AdSEAP. These results demonstrate that HD-Ad vectors induce intact innate but attenuated adaptive immune responses in vivo.

Adenoviridae↗
PubMed2003

Co-existence of different host-adapted forms of the Myzus persicae group (Hemiptera: Aphididae) in southern Italy.

Multivariate morphometric analysis (method of canonical variates) was used to compare 38 parthenogenetic lineages and three field collections of aphids of the Myzus persicae (Sulzer) group sampled on peach and tobacco in the Caserta region of southern Italy. Comparisons were also made with the morphology of lineages collected on peach in Lehonia, in central eastern Greece away from tobacco-growing regions, and on tobacco in Naphplion, in southern Greece. The lineages were measured after parthenogenetic rearing for one to three generations on the same host (potato) under constant conditions. As in previous work, the multivariate morphometric approach separated the aphids from peach from those feeding on tobacco. The life cycle category of the lineages was also examined. Almost all the lineages from peach in Caserta were holocyclic, yet the lineages from tobacco in the same region were unable to produce sexual morphs. The results suggest that tobacco-adapted and non-tobacco-adapted forms co-exist in the same region in southern Italy, not only because they colonize different host plants, but also because they have different life cycles. This is in complete contrast to the situation in peach-growing areas of northern Greece, and shows that the ecology and population structure of M. persicae is different in neighbouring counties of the Mediterranean area, even where climatic conditions and cultivated crops are similar.

Adaptation, Physiological↗
PubMed2002

Molecular evolution of Turnip mosaic virus: evidence of host adaptation, genetic recombination and geographical spread.

Turnip mosaic virus (TuMV), a species of the genus Potyvirus, occurs worldwide. Seventy-six isolates of TuMV were collected from around the world, mostly from Brassica and Raphanus crops, but also from several non-brassica species. Host tests grouped the isolates into one or other of two pathotypes; Brassica (B) and Brassica-Raphanus (BR). The nucleotide sequences of the first protein (P1) and coat protein (CP) genes of the isolates were determined. One-tenth of the isolates were found to have anomalous and variable phylogenetic relationships as a result of recombination. The 5'-terminal 300 nt of the P1 gene of many isolates was also variable and phylogenetically anomalous, whereas the 380 nt 3' terminus of the CP gene was mostly conserved. Trees calculated from the remaining informative parts of the two genes of the non-recombinant sequences by neighbour-joining, maximum-likelihood and maximum-parsimony methods were closely similar, and so these parts of the sequences were concatenated and trees calculated from the resulting 1150 nt. The isolates fell into four consistent groups; only the relationships of these groups with one another and with the outgroup differed. The "basal-B" cluster of eight B-pathotype isolates was most variable, was not monophyletic, and came from both brassicas and non-brassicas from southwest and central Eurasia. Closest to it, and forming a monophyletic subgroup of it in most trees, and similarly variable, was the "basal-BR" group of eight BR pathotype Eurasian isolates. The third and least variable group, the "Asian-BR" group, was of 22 BR-pathotype isolates, all from brassicas, mostly Raphanus, and all from east Asia mostly Japan. The fourth group of 36 isolates, the "world-B" group, was from all continents, most were isolated from brassicas and most were of the B-pathotype. The simplest of several possible interpretations of the trees is that TuMV originated, like its brassica hosts, in Europe and spread to the other parts of the world, and that the BR pathotype has recently evolved in east Asia.

3' Untranslated Regions↗
PubMed2006

Innate and adaptive host response during the initial phase of herpes simplex virus encephalitis in the neonatal mouse.

To study early events of neonatal herpes simplex virus (HSV) encephalitis and its sequelae, the authors induced a controlled infection in the brains of mice using HSVgH, a genetically modified Disabled Infective Single Cycle virus. Neonatal Balb/C mice were infected with various amounts of HSVgH- virus by intracerebral injection. Results showed that the survival of infected mice was dependent on the amount of virus injected. Infection with 200,000 plaque forming units (pfu) of HSVgH-, virus resulted in 0% survival, whereas 25,000 pfu resulted in 75% survival. If the mice died, 98% of the deaths occurred between 3 and 7 days after infection. Replication competent virus was recovered from 20% of mice brains infected with 25,000 pfu of HSVgH-. Neutralizing antibodies were not detected 6 weeks post infection in sera of mice, which survived infection with 25,000 pfu of HSVgH-. LacZ histochemistry and immunoperoxidase staining using anti-HSV and anti- beta-galactosidase antibodies revealed that the infection was limited to the site of injection. Tissue destruction was observed at the site of inoculation 3 days post infection using cresyl violet staining. At 3 days post infection adjacent sections showed positive cells for viral antigens and apoptotic cells in the infected area. Immunoperoxidase staining using antibodies to surface markers showed microglial activation beginning on day 1 and astrocyte proliferation beginning on day 3 post infection. B and T lymphocytes were not detected on day 1 through 7 post infection. This controlled experimental HSV infection suggests a limited non-specific early host response in the neonate to HSV encephalitis.

Animals↗
PubMed2005

Host adaptation and immune modulation are mediated by homologous recombination in Helicobacter pylori.

Rearrangement of genomic DNA via homologous recombination provides an alternative mechanism of gene regulation that is essential for successful colonization of the gastric mucosa by Helicobacter pylori. Inoculation of outbred mice with the H. pylori SS1 wild-type strain elicited a T helper (Th) 2 response and established a persistent infection. In contrast, inoculation with an isogenic H. pylori strain defective for homologous recombination elicited a Th1-mediated immune response and clearance of infection within 70 days. We, therefore, demonstrate that recombination is critical for mediating persistence of a microbial pathogen through the induction of ineffective immune responses.

Adaptation, Physiological↗
PubMed1979

The influence of host adaptation of Rous sarcoma virus on the transfecting activity of its DNA provirus.

Mammalian cells transformed with either Prague strain Rous sarcoma virus of subgroup C (XC cells) or Schmidt-Ruppin strain Rous sarcoma virus of subgroup D (RSCH cells) yielded virus upon fusion with chick cells. Virus was also rescued by transfection of DNA from these cells on to chick cells. However, virus rescue did not occur upon transfection of duck cells, and fusion with duck cells led to virus rescue only from RSCH and not from XC cells. To investigate this restriction on the duck cells the non-defective Prague strain of Rous sarcoma virus of subgroup C (PR-RSV-C) was adapted for efficient replication in duck embryo cells (daPR-RSV-C) by long-term passage in vitro. However, a second PR-RSV-C isolate, rescued from the rat XC sarcoma line (XC DNA 940 virus), failed to adapt to growth in duck cells. When transformed with daPR-RSV-C, which replicates in duck cells as well as in brown leghorn embryo (BLEF) cells, duck cells yielded DNA which transfects fresh duck cells, in contrast to DNA isolated from chicken or duck cells transformed with parental PR-RSV-C.

Animals↗
PubMed1993

Variation in the ribosomal RNA cistron among host-adapted races of an aphid (Schizaphis graminum).

The greenbug, Schizaphis graminum, is an aphid species that consists of races that can be separated based on morphology, life histories, cytogenetics, mitochondrial DNA RFLPs and virulence to plant cultivars. Variation in the greenbug rDNA multigene family was studied to determine the extent to which rDNA cistrons have diverged among and within races. A restriction map of the rDNA cistron was constructed. Probing DNA from different races with subclones from rDNA coding regions and internal spacers identified little variation. However, probing with subclones of the intergenic spacer (IGS) identified continuous length variation within and among races. Race specific patterns were identified. Within a race, almost continuous variation in total IGS length was detected and asexual lineages possessed distinct patterns useful in genetic fingerprinting studies.

Adaptation, Physiological↗
PubMed2005

Aspects of adaptive host response in periodontitis.

OBJECTIVE: To review host response in periodontitis with respect to cellular composition of lesions, T cell receptor (TCR) gene expression, cytokine profiles of T-helper (Th) cells and autoimmune components. MATERIAL AND METHODS: The studies included were confined to human material (biopsies, gingival crevicular fluid, blood from subjects with periodontitis). RESULTS AND CONCLUSIONS: In periodontitis lesions, plasma cells are the most common cell type and represent about 50% of all cells, while B cells comprise about 18%. The proportion of B cells is larger than that of T cells and Th cells occur in larger numbers than T cytotoxic cells. Polymorphonuclear cells and macrophages are found in fractions of less than 5% of all cells. Lesions in aggressive and chronic forms of periodontitis exhibit similar cellular composition. Differences in disease severity, however, may reflect increases in plasma cell and B cell densities. B cells serve as important antigen-presenting cells in periodontitis. The periodontitis lesion expresses a unique TCR gene repertoire that is different from that in blood. The role of superantigens in periodontitis is unclear. There are few studies using comparative designs and unbiased quantitative methods regarding Th-1 and Th-2 cells in periodontitis. The relative dominance of B cells and plasma cells in periodontitis lesions cannot entirely be explained by enhanced Th-2 functions but maybe because of an imbalance between Th-1 and Th-2. Autoimmune reactions are evident in periodontitis lesions. The role of auto-antibodies in the regulation of host response in periodontitis, however, needs to be clarified. Auto-reactive B cells occur in larger proportions in subjects with periodontitis than in healthy controls.

Acute Disease↗
PubMed2004

Host-adapted Cryptosporidium spp. in Canada geese (Branta canadensis).

The prevalence and distribution of Cryptosporidium spp. in the fecal droppings of the free-living waterfowl Canada geese were examined at 13 sites in Ohio and Illinois. On the basis of the analysis of the small-subunit rRNA gene by PCR, followed by restriction fragment length polymorphism analysis and DNA sequencing, 49 (23.4%) of 209 fecal specimens collected from 10 sites (76.9%) were positive for Cryptosporidium spp. The following five Cryptosporidium species and genotypes were identified: Cryptosporidium goose genotype I (in 36 specimens), Cryptosporidium goose genotype II (in 9 specimens), Cryptosporidium duck genotype (in 1 specimen), Cryptosporidium parvum (in 4 specimens), and C. hominis (in 2 specimens). Cryptosporidium goose genotype I was the most prevalent parasite and was found at all five Cryptosporidium-positive sites in Ohio and at four of five positive sites in Illinois, followed by Cryptosporidium goose genotype II, which was found at two of five positive sites in Ohio and at four of five positive sites in Illinois. Cryptosporidium goose genotype II was detected for the first time, and it is phylogenetically related to goose genotype I and the duck genotype. All three genotypes have not so far been reported in humans, and their pathogenicity in geese has not been determined. Only 10.2% of the Cryptosporidium-positive specimens had C. parvum and C. hominis. The results of this study indicate that Canada geese might only serve as accidental carriers of cryptosporidia infectious to humans and probably play a minor role in the animal-to-human transmission cycle of the pathogen.

Adaptation, Physiological↗