Helicobacter pylori genome variability in a framework of familial transmission

<p>Abstract</p> <p>Background</p> <p><it>Helicobacter pylori </it>infection is exceptionally prevalent and is considered to be acquired primarily early in life through person-to-person transmission within the family. <it>H. pylori </it>is a genetically diverse bacterial species, which may facilitate adaptation to new hosts and persistence for decades. The present study aimed to explore the genetic diversity of clonal isolates from a mother and her three children in order to shed light on <it>H. pylori </it>transmission and host adaptation.</p> <p>Results</p> <p>Two different <it>H. pylori </it>strains and strain variants were identified in the family members by PCR-based molecular typing and sequencing of five loci. Genome diversity was further assessed for 15 isolates by comparative microarray hybridizations. The microarray consisted of 1,745 oligonucleotides representing the genes of two previously sequenced <it>H. pylori </it>strains. The microarray analysis detected a limited mean number (± standard error) of divergent genes between clonal isolates from the same and different individuals (1 ± 0.4, 0.1%, and 3 ± 0.3, 0.2%, respectively). There was considerable variability between the two different strains in the family members (147 ± 4, 8%) and for all isolates relative to the two sequenced reference strains (314 ± 16, 18%). The diversity between different strains was associated with gene functional classes related to DNA metabolism and the cell envelope.</p> <p>Conclusion</p> <p>The present data from clonal <it>H. pylori </it>isolates of family members do not support that transmission and host adaptation are associated with substantial sequence diversity in the bacterial genome. However, important phenotypic modifications may be determined by additional genetic mechanisms, such as phase-variation. Our findings can aid further exploration of <it>H. pylori </it>genetic diversity and adaptation.</p

Aspects of Helicobacter pylori transmission

The bacterium Helicobacter pylori infects the gastric mucosa of about half of the world's population. The infection causes gastritis and contributes to the development of peptic ulcer disease and gastric cancer. H. pylori infection is associated with low socioeconomic status, is typically acquired in early childhood and once established can persist throughout life unless treated. Person-to-person transmission appears to predominate and the family stands out as the primary framework for transmission In this thesis, an initial cross-sectional study aimed to disentangle the independent contributions of H. pylori infections in family members to the risk for the infection in 11to 13-year old index children from Stockholm schools. H. pylori infections in mothers and in siblings, but not in fathers, were notable risk factors for infection in the index children. Furthermore, birth of the index child in a country with high H. pylori prevalence was an independent risk factor for infection. In addition to the initial standard analysis, a weighted logistic regression method was applied to accommodate additional non-randomly sampled cases. This exemplified how appropriate analysis of epidemiological data from complex sampling schemes can improve precision and maintain validity, while enabling a more complete investigation of risk factors already identified. A subset of the infected family members underwent gastroscopy and contributed gastric biopsies from which H. pylori was isolated and typed by molecular methods. The same bacterial strains were frequently detected among siblings and between mothers and offspring. No strain concordance was detected between fathers and offspring, but parents sometimes harbored the same strains. The bacterial isolates were also examined with regard to the presence or absence of the cag pathogenicity island (PAI), a bacterial virulence factor. In a comparison with serological data, serology was supported as a suitable method to determine cag PAI status of H. pylori infections in clinical and epidemiological studies. Moreover, clonal and non-clonal bacterial isolates from members of a family were analyzed in more detail, which included microarray-based genome comparisons. Non-clonal H. pylori isolates exhibited extensive genetic variability, where certain characteristics could be discerned. However, transmission and host adaptation did not appear to be associated with substantial sequence diversity in the bacterial genome. The present data support a predominantly mother-child and sib-sib transmission of H. pylori, consistent with an important role of intimate contact in the transmission. Furthermore, methodological and microbiological aspects that could aid future research are described. In summary, the findings of this thesis and the discussions thereof shed some light on the characteristics and mechanisms of transmission and persistence of H. pylori infection

Determining the Genomic Locations of Repetitive DNA Sequences with a Whole-Genome Microarray: IS6110 in Mycobacterium tuberculosis

The mycobacterial insertion sequence IS6110 has been exploited extensively as a clonal marker in molecular epidemiologic studies of tuberculosis. In addition, it has been hypothesized that this element is an important driving force behind genotypic variability that may have phenotypic consequences. We present here a novel, DNA microarray-based methodology, designated SiteMapping, that simultaneously maps the locations and orientations of multiple copies of IS6110 within the genome. To investigate the sensitivity, accuracy, and limitations of the technique, it was applied to eight Mycobacterium tuberculosis strains for which complete or partial IS6110 insertion site information had been determined previously. SiteMapping correctly located 64% (38 of 59) of the IS6110 copies predicted by restriction fragment length polymorphism analysis. The technique is highly specific; 97% of the predicted insertion sites were true insertions. Eight previously unknown insertions were identified and confirmed by PCR or sequencing. The performance could be improved by modifications in the experimental protocol and in the approach to data analysis. SiteMapping has general applicability and demonstrates an expansion in the applications of microarrays that complements conventional approaches in the study of genome architecture

Concordance of Helicobacter pylori Strains within Families

Helicobacter pylori infection is typically acquired in early childhood, and a predominantly intrafamilial transmission has been postulated. To what extent family members share the same strains is poorly documented. Our aim was to explore patterns of shared strains within families by using molecular typing. Family members of H. pylori-infected 10- to 12-year-old index children identified in a school survey were invited to undergo gastroscopy. Bacterial isolates were typed with random amplified polymorphic DNA and PCR-restriction fragment length polymorphism of the genes ureA-B, glmM, or flaA. The presence or absence of the cag pathogenicity island, a bacterial virulence factor, was determined by PCR. GelCompar II software, supplemented with visual inspection, was used in the cluster analysis. In 39 families, 104 individuals contributed 208 bacterial isolates from the antrum and corpus. A large proportion, 29 of 36 (81%) of the offspring in a sibship, harbored the same strain as at least one sibling. Mother-offspring strain concordance was detected in 10 of 18 (56%) of the families. Of 17 investigated father-offspring relations in eight families, none were strain concordant. Spouses were infected with the same strains in 5 of 23 (22%) of the couples. Different strains in the antrum and corpus were found in 8 of 104 (8%) of the subjects. Our family-based fingerprinting study demonstrates a high proportion of shared strains among siblings. Transmission between spouses seems to be appreciable. The data support mother-child and sib-sib transmission as the primary transmission pathways of H. pylori