Genetic and phenotypic characterization of a Pseudomonas aeruginosa population with high frequency of genomic islands.

Various genomic islands, PAPI-1, PAPI-2, PAGI-1, PAGI-2, PAGI-3, and PAGI-4, and the element pKLC102 have been characterized in different P. aeruginosa strains from diverse habitats and geographical locations. Chromosomal DNA macroarray of 100 P. aeruginosa strains isolated from 85 unrelated patients hospitalized in an intensive care unit was created to assess the occurrence of these genomic islands (GEIs). The macroarray was then hybridized with labeled probes derived from each genomic island. In addition, PFGE patterns with SpeI, frequency of virulence genes, and antimicrobial resistance patterns of the strains were studied. Our results showed that almost all P. aeruginosa strains presented up to eight virulence genes. By SpeI macrorestriction fragment analysis we were able to identify 49 restriction patterns; 35 patterns correspond to single strains and the remaining 14 to strains subgroup (a-n). Most of the strains showed variation in number or composition of GEIs and a specific antimicrobial pattern indicating that each strain was an unrelated isolate. In terms of the number of genomic islands per strain, 7 GEIs were found in 34% of the strains, 6 in 18%, 5 in 12%, 4 in 14%, 3 in 10%, 2 in 7%, and 1 in 4%; only one isolate did not present any GEI. The genomic islands PAPI-1 and PAPI-2 and the element pKLC102 were the most frequently detected. The analysis of the location of each GEI in the chromosome of two strains show that the islands PAGI-3, PAPI-1, PAPI-2 and pKLC102 are present in the insertion site previously reported, but that PAGI-2 and PAGI-4 are inserted in another chromosome place in a site not characterized yet. In conclusion our data show that P. aeruginosa strains exhibited an epidemic population structure with horizontal transfer of DNA resulting in a high frequency of GEIs.

Helicobacter pylori genotyping from American indigenous groups shows novel Amerindian vacA and cagA alleles and Asian, African and European admixture.

It is valuable to extend genotyping studies of Helicobacter pylori to strains from indigenous communities across the world to better define adaption, evolution, and associated diseases. We aimed to genetically characterize both human individuals and their infecting H. pylori from indigenous communities of Mexico, and to compare them with those from other human groups. We studied individuals from three indigenous groups, Tarahumaras from the North, Huichols from the West and Nahuas from the center of Mexico. Volunteers were sampled at their community site, DNA was isolated from white blood cells and mtDNA, Y-chromosome, and STR alleles were studied. H. pylori was cultured from gastric juice, and DNA extracted for genotyping of virulence and housekeeping genes. We found Amerindian mtDNA haplogroups (A, B, C, and D), Y-chromosome DYS19T, and Amerindian STRs alleles frequent in the three groups, confirming Amerindian ancestry in these Mexican groups. Concerning H.pylori cagA phylogenetic analyses, although most isolates were of the Western type, a new Amerindian cluster neither Western nor Asian, was formed by some indigenous Mexican, Colombian, Peruvian and Venezuelan isolates. Similarly, vacA phylogenetic analyses showed the existence of a novel Amerindian type in isolates from Alaska, Mexico and Colombia. With hspA strains from Mexico and other American groups clustered within the three major groups, Asian, African or European. Genotyping of housekeeping genes confirmed that Mexican strains formed a novel Asian-related Amerindian group together with strains from remote Amazon Aborigines. This study shows that Mexican indigenous people with Amerindian markers are colonized with H. pylori showing admixture of Asian, European and African strains in genes known to interact with the gastric mucosa. We present evidence of novel Amerindian cagA and vacA alleles in indigenous groups of North and South America.

Genotipos vacA de Helicobacter pylori en una población venezolana / Helicobacter pylori vac A genotypes in a Venezuelan population

La infección por Helicobacter pylori está  asociada con gastritis, úlcera gastroduodenal, linfoma tipo Maltoma, y es considerado un importante factor de riesgo para el desarrollo de cáncer gástrico. El objetivo de este estudio fue caracterizar los genotipos vacA de cepas de  H. pylori provenientes de biopsias gástricas de una población venezolana. Se evaluaron 128 pacientes con indicación de endoscopia, por enfermedad de las vías digestivas superiores. Se obtuvieron biopsias gástricas de cada uno de ellos para la amplificación de glm y tipificación de las formas alélicas  de vacA, empleando la reacción en cadena de la polimerasa. Los resultados demostraron que 82 (64%) de las muestras fueron positivas para la amplificación de glm. De estos, 51 (62%) de las cepas tenían el genotipo vacA, forma alélica S1 (17 s1a, 29 s1b, 5 s1a+s1b, 10 fueron no tipificables) y 21 (26%) tenían el subtipo S2. El análisis de la región media de vacA reveló que 42 (51%) fueron vac A m1, 26 (32%) m2 y 14 (17%) no tipificaron para m1  o m2. Los resultados de la presente investigación demostraron una alta frecuencia de infección por  H  pylori  genotipo vac A variante alèlica s1/ m1.

Helicobacter pylori infection is associated with gastritis, gastroduodenal ulcer, and Maltoma type lymphoma, and is also considered an important risk factor for the development of gastric cancer. The purpose of this study was to characterize vacA genotypes of H. pylori strains from gastric biopsies from a Venezuelan population. One hundred and  twenty eight patients who required endoscopy due to disease of the upper digestive system were evaluated. A gastric biopsy was taken from each of them for glm amplification and typing of the allelic vacA  forms, using the polymerase chain reaction assay. Results showed that 82 (64%) of the samples were positive for glm amplification. Of these, 51 (62%) of the strains had the vacA genotype, S1 allelic form (17 sla, 29 slb, 5 sla+slb, 10 were not typable) and 21 (26%) had the S2 subtype. The analysis of the vacA mid region revealed that 42 (51%) were vacA m1, 26 (32%) m2, and 14 did not type for m1 or m2. The results of this investigation showed a high frequency of H. pylori vacA genotype infections, s1/m1 allelic variants.

Lewis antigen expression by Helicobacter pylori strains colonizing different regions of the stomach of individual patients.

The diversity in the expression of Lewis antigens (Le) of 226 single colonies of Helicobacter pylori isolated from four regions of the stomach of eight adults is shown. Le(y) was expressed more in strains colonizing antrum than in strains colonizing fundus, whereas Le(x) was more common in fundus strains. cagA(+) strains were more associated with Le-negative strains.

Characterization of mtDNA haplogroups in 14 Mexican indigenous populations.

In this descriptive study we investigated the genetic structure of 513 Mexican indigenous subjects grouped in 14 populations (Mixteca-Alta, Mixteca-Baja, Otomi, Purépecha, Tzeltal, Tarahumara, Huichol, Nahua-Atocpan, Nahua-Xochimilco, Nahua-Zitlala, Nahua-Chilacachapa, Nahua-Ixhuatlancillo, Nahua-Necoxtla, and Nahua-Coyolillo) based on mtDNA haplogroups. These communities are geographically and culturally isolated; parents and grandparents were born in the community. Our data show that 98.6% of the mtDNA was distributed in haplogroups A1, A2, B1, B2, C1, C2, D1, and D2. Haplotype X6 was present in the Tarahumara (1/53) and Huichol (3/15), and haplotype L was present in the Nahua-Coyolillo (3/38). The first two principal components accounted for 95.9% of the total variation in the sample. The mtDNA haplogroup frequencies in the Purépecha and Zitlala were intermediate to cluster 1 (Otomi, Nahua-Ixhuatlancillo, Nahua-Xochimilco, Mixteca-Baja, and Tzeltal) and cluster 2 (Nahua-Necoxtla, Nahua-Atocpan, and Nahua-Chilacachapa). The Huichol, Tarahumara, Mixteca-Alta, and Nahua-Coyolillo were separated from the rest of the populations. According to these findings, the distribution of mtDNA haplogroups found in Mexican indigenous groups is similar to other Amerindian haplogroups, except for the African haplogroup found in one population.

Genetic analysis of Helicobacter pylori strain populations colonizing the stomach at different times postinfection.

Genetic diversity of the human gastric pathogen Helicobacter pylori in an individual host has been observed; whether this diversity represents diversification of a founding strain or a mixed infection with distinct strain populations is not clear. To examine this issue, we analyzed multiple single-colony isolates from two to four separate stomach biopsies of eight adult and four pediatric patients from a high-incidence Mexican population. Eleven of the 12 patients contained isolates with identical random amplified polymorphic DNA, amplified fragment length polymorphism, and vacA allele molecular footprints, whereas a single adult patient had two distinct profiles. Comparative genomic hybridization using whole-genome microarrays (array CGH) revealed variation in 24 to 67 genes in isolates from patients with similar molecular footprints. The one patient with distinct profiles contained two strain populations differing at 113 gene loci, including the cag pathogenicity island virulence genes. The two strain populations in this single host had different spatial distributions in the stomach and exhibited very limited genetic exchange. The total genetic divergence and pairwise genetic divergence between isolates from adults and isolates from children were not statistically different. We also analyzed isolates obtained 15 and 90 days after experimental infection of humans and found no evidence of genetic divergence, indicating that transmission to a new host does not induce rapid genetic changes in the bacterial population in the human stomach. Our data suggest that humans are infected with a population of closely related strains that vary at a small number of gene loci, that this population of strains may already be present when an infection is acquired, and that even during superinfection genetic exchange among distinct strains is rare.

Evolution of the Helicobacter pylori vacuolating cytotoxin in a human stomach.

We describe two subclones of Helicobacter pylori, isolated contemporaneously from a human stomach, which differ markedly in the vacuolating cytotoxin gene, vacA, but whose near identity in sequences outside this locus implies a very recent common origin. The differences are consistent with homologous recombination with DNA from another strain and result in a changed vacA midregion and, importantly, in changed toxicity.

Production of cytotoxins and enterotoxins by strains of Shigella and Salmonella isolated from children with bloody diarrhea

The role of toxins in the pathogenesis of bloody diarrhea caused by Shigella and Salmonella isolated from children with bloody diarhea was studied for production of toxins active on cells in culture and in rat intestinal loops. Humman epithelial cellls from colon carcinoma (HT-29), Chinese hamster ovary cells (CHO) and kidney fibroblast from rhesus monkey (Vero) were used to detect cytotoxins. On HT-29 almost 50 percent of the Shigella and about 20 percent of the Salmonella strain caused rounding of cells; on CHO over 50 percent Salmonella and 20 percent of Shigella strains caused elongation of cells, some strains caused also rounding of these cells whereas on Vero over 60 percent of Salmonella and 40 percent of Shigella strains caused rounding of cells. Cytotoxicity on Vero and CHO cells was strongly inhibited with cholera toxin antiserum, whereas that on HT-29 was inhibited with C. difficile toxin B antiserum. Cytotonic activity on CHO cells and rounding on Vero cells seem to be suitable models to detect toxins cross-reacting with cholera toxin. Both species, Shigella and Salmonella, produce cytotoxins and enterotoxins which could play a role in intestinal disease