Phenotypic and genotypic characterization of Stenotrophomonas maltophilia isolates from patients with cystic fibrosis: Genome diversity, biofilm formation, and virulence

<p>Abstract</p> <p>Background</p> <p><it>Stenotrophomonas maltophilia </it>is emerging as one of the most frequently found bacteria in cystic fibrosis (CF) patients. In the present study, phenotypic and genotypic traits of a set of 98 isolates of <it>S. maltophilia </it>obtained from clinical (CF and non-CF patients) and environmental sources were comparatively evaluated.</p> <p>Results</p> <p><it>S. maltophilia </it>exhibited a high level of genomic diversity in both CF and non-CF group, thus possibly allowing this bacterium to expand its pathogenic potentials. Strains sharing the same pulsotype infected different patients, thus likely indicating the occurrence of clonal spread or acquisition by a common source. CF isolates differed greatly in some phenotypic traits among each other and also when compared with non-CF isolates, demonstrating increased mean generation time and susceptibility to oxidative stress, but reduced ability in forming biofilm. Furthermore, in CF isolates flagella- and type IV pili-based motilities were critical for biofilm development, although not required for its initiation. Sequential isogenic strains isolated from the same CF patient displayed heterogeneity in biofilm and other phenotypic traits during the course of chronic infection. CF and non-CF isolates showed comparable virulence in a mouse model of lung infection.</p> <p>Conclusions</p> <p>Overall, the phenotypic differences observed between CF and non-CF isolates may imply different selective conditions and persistence (adaptation) mechanisms in a hostile and heterogeneous environment such as CF lung. Molecular elucidation of these mechanisms will be essential to better understand the selective adaptation in CF airways in order to design improved strategies useful to counteract and eradicate <it>S. maltophilia </it>infection.</p

Transitions at CpG Dinucleotides, Geographic Clustering of TP53 Mutations and Food Availability Patterns in Colorectal Cancer

Colorectal cancer is mainly attributed to diet, but the role exerted by foods remains unclear because involved factors are extremely complex. Geography substantially impacts on foods. Correlations between international variation in colorectal cancer-associated mutation patterns and food availabilities could highlight the influence of foods on colorectal mutagenesis. mutations from 12 countries/geographic areas. For food availabilities, we relied on data extracted from the Food Balance Sheets of the Food and Agriculture Organization of the United Nations. Dendrograms for mutation sites, mutation types and food patterns were constructed through Ward's hierarchical clustering algorithm and their stability was assessed evaluating silhouette values. Feature selection used entropy-based measures for similarity between clusterings, combined with principal component analysis by exhaustive and heuristic approaches. hotspots. Pearson's correlation scores, computed between the principal components of the datamatrices for mutation types, food availability and mutation sites, demonstrated statistically significant correlations between transitions at CpGs and both mutation sites and availabilities of meat, milk, sweeteners and animal fats, the energy-dense foods at the basis of “Western” diets. This is best explainable by differential exposure to nitrosative DNA damage due to foods that promote metabolic stress and chronic inflammation

Viral Manipulation of the Host Epigenome as a Driver of Virus-Induced Oncogenesis

Tumorigenesis due to viral infection accounts for a high fraction of the total global cancer burden (15–20%) of all human cancers. A comprehensive understanding of the mechanisms by which viral infection leads to tumor development is extremely important. One of the main mechanisms by which viruses induce host cell proliferation programs is through controlling the host’s epigenetic machinery. In this review, we dissect the epigenetic pathways through which oncogenic viruses can integrate their genome into host cell chromosomes and lead to tumor progression. In addition, we highlight the potential use of drugs based on histone modifiers in reducing the global impact of cancer development due to viral infection

Myroides odoratimimus Forms Structurally Complex and Inherently Antibiotic-Resistant Biofilm in a Wound-Like in vitro Model

Myroides odoratimimus is an aerobic, non-fermenting Gram-negative multidrug-resistant bacterium widely distributed in nature that rarely causes infections in immunocompromised patients. We recently described in a diabetic patient a case of recurrent calcaneal ulcer infection caused by a M. odoratimimus strain showing potential for biofilm formation. For the first time, we therefore evaluated the ability of M. odoratimimus to form biofilm under different pH values and glucose concentrations using an in vitro “skin-like” model, and its susceptibility to levofloxacin, meropenem, and tigecycline. The expression of some antibiotic-resistance related genes was also monitored by RT-PCR during planktonic-to-biofilm transition. Our results indicated that M. odoratimimus can produce relevant amounts of biofilm biomass, in a time-dependent manner, especially at acidic pH and regardless of glucose concentration tested. The comparative analysis of MIC and MBC values between planktonic and sessile cells showed that resistance to antibiotics increased during the planktonic-to-biofilm transition. Viable cell count indicated that none of the tested antibiotics were able to completely eradicate preformed biofilms, although meropenem and levofloxacin were the most active causing a significant, dose-independent, reduction of biofilm's viability, as also confirmed by microscopic analysis. RT-PCR showed that antibiotic-resistance related gyrA and acrB genes are over-expressed during the transition from planktonic to sessile (biofilm) lifestyle. Overall, our findings showed that M. odoratimimus can form relevant amounts of inherently antibiotic-resistant biofilm under conditions relevant to wound site, therefore suggesting a role in the pathogenesis of chronic ulcer infections

Myroides odoratimimus forms structurally complex and inherently antibiotic-resistant biofilm in a wound-like in vitro model

Myroides odoratimimus is an aerobic, non-fermenting Gram-negative multidrug-resistant bacterium widely distributed in nature that rarely causes infections in immunocompromised patients. We recently described in a diabetic patient a case of recurrent calcaneal ulcer infection caused by a M. odoratimimus strain showing potential for biofilm formation. For the first time, we therefore evaluated the ability of M. odoratimimus to form biofilm under different pH values and glucose concentrations using an in vitro “skin-like” model, and its susceptibility to levofloxacin, meropenem, and tigecycline. The expression of some antibiotic-resistance related genes was also monitored by RT-PCR during planktonic-to-biofilm transition. Our results indicated that M. odoratimimus can produce relevant amounts of biofilm biomass, in a time-dependent manner, especially at acidic pH and regardless of glucose concentration tested. The comparative analysis of MIC and MBC values between planktonic and sessile cells showed that resistance to antibiotics increased during the planktonic-to-biofilm transition. Viable cell count indicated that none of the tested antibiotics were able to completely eradicate preformed biofilms, although meropenem and levofloxacin were the most active causing a significant, dose-independent, reduction of biofilm's viability, as also confirmed by microscopic analysis. RT-PCR showed that antibiotic-resistance related gyrA and acrB genes are over-expressed during the transition from planktonic to sessile (biofilm) lifestyle. Overall, our findings showed that M. odoratimimus can form relevant amounts of inherently antibiotic-resistant biofilm under conditions relevant to wound site, therefore suggesting a role in the pathogenesis of chronic ulcer infections

Evolutionarily-Related Helicobacter pylori Genotypes and Gastric Intraepithelial Neoplasia in a High-Risk Area of Northern Italy

Helicobacter pylori (Hp) is the major recognized risk factor for non-cardia gastric cancer (GC), but only a fraction of infected subjects develop GC, thus GC risk might reflect other genetic/environmental cofactors and/or differences in virulence among infectious Hp strains. Focusing on a high GC risk area of Northern Italy (Cremona, Lombardy) and using archived paraffin-embedded biopsies, we investigated the associations between the Hp vacA and cagA genotype variants and gastric intraepithelial neoplasia (GIN, 33 cases) versus non-neoplastic gastroduodenal lesions (NNGDLs, 37 cases). The glmM gene and the cagA and vacA (s and m) genotypes were determined by polymerase chain reaction (PCR) and sequencing. Hp was confirmed in 37/37 (100%) NNGDLs and detected in 9/33 GINs (27%), consistently with the well-known Hp loss in GC. CagA was detected in 4/9 Hp-positive GINs and in 29/37 NNGDLs. The vacA s1a and m1 subtypes were more common in GINs than in NNGDLs (6/7 vs. 12/34, p=0.014, for s1a; 7/7 vs. 18/34, p=0.020 for m1), with significant vacA s genotype-specific variance. The GIN-associated vacA s1a sequences clustered together, suggesting that aggressive Hp strains from a unique founder contribute to GC in the high-risk area studied

The analysis of variation of mtDNA hypervariable region 1 suggests that Eastern and Western Pygmies diverged before the Bantu expansion

The Eastern Pygmies from Zaire and Western Pygmies from Cameroon, Congo, and the Central African Republic represent the two principal groups of African Pygmies. In the "recent divergence" hypothesis in which Western Pygmies are thought to be the result of hybridization between the ancestors of Eastern Pygmies and Bantu farmers who penetrated the equatorial belt and came into contact with Pygmies around 2-3 kiloyears ago. On the basis of recent archaeological research in the tropical rain forest, we propose a "pre-Bantu divergence" hypothesis, which posits the separation between the ancestors of Eastern and Western Pygmies earlier than 18 kiloyears ago. In order to test the two hypotheses, we analyzed the variation of the hypervariable region I of the mitochondrial DNA in the Mbenzele, Western Pygmies of the Central African Republic, and compared our results with those of previous mtDNA and Y chromosome studies. Distribution, sequence variation, and age of haplogroups along with genetic distances among populations, estimates of divergence times, and simulations based on the coalescent approach were found to be congruent with the pre-Bantu divergence but failed to support the recent divergence hypothesis

Brief communication: mtDNA variation in North Cameroon: Lack of Asian lineages and implications for back migration from Asia to sub-Saharan Africa

The hypervariable region-1 and four nucleotide positions (10400, 10873, 12308, and 12705) of the coding region of mitochondrial DNA (mtDNA) were analyzed in 441 individuals belonging to eight populations (Daba, Fali, Fulbe, Mandara, Uldeme, Podokwo, Tali, and Tupuri) from North Cameroon and four populations (Bakaka, Bassa, Bamileke, and Ewondo) from South Cameroon. All mtDNAs were assigned to five haplogroups: three sub-Saharan (L1, L2, and L3), one northern African (U6), and one European (U5). Our results contrast with the observed high frequencies of a Y-chromosome haplogroup of probable Asian origin (R1*-M173) in North Cameroon. As a first step toward a better understanding of the evident discrepancy between mtDNA and Y-chromosome data, we propose two contrasting scenarios. The first one, here termed "migration and asymmetric admixture," implies a back migration from Asia to North Cameroon of a population group carrying the haplotype R1*-M173 at high frequency, and an admixture process restricted to migrant males. The second scenario, on the other hand, temed "divergent drift," implies that modern populations of North Cameroon originated from a small population group which migrated from Asia to Africa and in which, through genetic drift, Y-chromosome haplotype R1*-M173 became predominant, whereas the Asian mtDNA haplogroups were lost