Genomes of Helicobacter pylori from native Peruvians suggest admixture of ancestral and modern lineages and reveal a western type cag-pathogenicity island

BACKGROUND: Helicobacter pylori is presumed to be co-evolved with its human host and is a highly diverse gastric pathogen at genetic levels. Ancient origins of H. pylori in the New World are still debatable. It is not clear how different waves of human migrations in South America contributed to the evolution of strain diversity of H. pylori. The objective of our 'phylogeographic' study was to gain fresh insights into these issues through mapping genetic origins of H. pylori of native Peruvians (of Amerindian ancestry) and their genomic comparison with isolates from Spain, and Japan. RESULTS: For this purpose, we attempted to dissect genetic identity of strains by fluorescent amplified fragment length polymorphism (FAFLP) analysis, multilocus sequence typing (MLST) of the 7 housekeeping genes (atpA, efp, ureI, ppa, mutY, trpC, yphC) and the sequence analyses of the babB adhesin and oipA genes. The whole cag pathogenicity-island (cagPAI) from these strains was analyzed using PCR and the geographic type of cagA phosphorylation motif EPIYA was determined by gene sequencing. We observed that while European genotype (hp-Europe) predominates in native Peruvian strains, approximately 20% of these strains represent a sub-population with an Amerindian ancestry (hsp-Amerind). All of these strains however, irrespective of their ancestral affiliation harbored a complete, 'western' type cagPAI and the motifs surrounding it. This indicates a possible acquisition of cagPAI by the hsp-Amerind strains from the European strains, during decades of co-colonization. CONCLUSION: Our observations suggest presence of ancestral H. pylori (hsp-Amerind) in Peruvian Amerindians which possibly managed to survive and compete against the Spanish strains that arrived to the New World about 500 years ago. We suggest that this might have happened after native Peruvian H. pylori strains acquired cagPAI sequences, either by new acquisition in cag-negative strains or by recombination in cag positive Amerindian strains

Genomes of <i>Helicobacter pylori</i> from native Peruvians suggest admixture of ancestral and modern lineages and reveal a western type cag-pathogenicity island

Background: Helicobacter pylori is presumed to be co-evolved with its human host and is a highly diverse gastric pathogen at genetic levels. Ancient origins of H. pylori in the New World are still debatable. It is not clear how different waves of human migrations in South America contributed to the evolution of strain diversity of H. pylori. The objective of our 'phylogeographic' study was to gain fresh insights into these issues through mapping genetic origins of H. pylori of native Peruvians (of Amerindian ancestry) and their genomic comparison with isolates from Spain, and Japan. Results: For this purpose, we attempted to dissect genetic identity of strains by fluorescent amplified fragment length polymorphism (FAFLP) analysis, multilocus sequence typing (MLST) of the 7 housekeeping genes (atpA, efp, ureI, ppa, mutY, trpC, yphC) and the sequence analyses of the babB adhesin and oipA genes. The whole cag pathogenicity-island (cagPAI) from these strains was analyzed using PCR and the geographic type of cagA phosphorylation motif EPIYA was determined by gene sequencing. We observed that while European genotype (hp-Europe) predominates in native Peruvian strains, approximately 20% of these strains represent a sub-population with an Amerindian ancestry (hsp-Amerind). All of these strains however, irrespective of their ancestral affiliation harbored a complete, 'western' type cagPAI and the motifs surrounding it. This indicates a possible acquisition of cagPAI by the hsp-Amerind strains from the European strains, during decades of co-colonization. Conclusion: Our observations suggest presence of ancestral H. pylori (hsp-Amerind) in Peruvian Amerindians which possibly managed to survive and compete against the Spanish strains that arrived to the New World about 500 years ago. We suggest that this might have happened after native Peruvian H. pylori strains acquired cagPAI sequences, either by new acquisition in cagnegative strains or by recombination in cag positive Amerindian strains

Comparative genomics of <i>Helicobacter pylori</i> isolates recovered from ulcer disease patients in England

Background. Genomic diversity of H. pylori from many different human populations is largely unknown. We compared genomes of 65 H. pylori strains from Nottingham, England. Molecular analysis was carried out to identify rearrangements within and outside the cag-pathogenicity-island (cag PAI) and DNA sequence divergence in candidate genes. Phylogenetic analysis was carried out based on various high-resolution genotyping techniques. Results. Analyses of virulence genes (cagT, cagE, cagA, vacA, iceA, oipA and babB) revealed that H. pylori strains from England are genetically distinct from strains obtained from other countries. The toxigenic vacA s1m1 genotype was found to be less common and the plasticity region cluster was found to be disrupted in all the isolates. English isolates showed a predominance of iceA1 alleles and a functional proinflammatory oipA gene. The English H. pylori gene pool revealed several Asian/oriental features. This included the predominance of cagA – glr (cagA right junction) motif types III and II (up to 42%), presence of vacA m1c alleles and phylogenetic affinity towards East Asian / Amerindian gene pools based on fluorescent amplified fragment length polymorphism (FAFLP) analysis and glmM sequence analysis. Conclusion. Overall, our results demonstrated genetic affinities of H. pylori in England with both European and the Asian gene pools and some distinctive genetic features of virulence genes that may have evolved in this important European population

Antimicrobial activities of eugenol and cinnamaldehyde against the human gastric pathogen <i>Helicobacter pylori</i>

Background: Eradication of Helicobacter pylori is an important objective in overcoming gastric diseases. Many regimens are currently available but none of them could achieve 100% success in eradication. Eugenol and cinnamaldehyde that are commonly used in various food preparations are known to possess antimicrobial activity against a wide spectrum of bacteria. Aim: The present study was performed to assess the in vitro effects of eugenol and cinnamaldehyde against indigenous and standard H. pylori strains, their minimum inhibitory concentrations (MICs) and time course lethal effects at various pH. Methods: A total of 31 strains (29 indigenous and one standard strain of H. pylori ATCC 26695, one strain of E. coli NCIM 2089) were screened. Agar dilution method was used for the determination of drug sensitivity patterns of isolates to the commonly used antibiotics and broth dilution method for the test compounds. Results: Eugenol and cinnamaldehyde inhibited the growth of all the 30 H. pylori strains tested, at a concentration of 2 μg/ml, in the 9th and 12th hours of incubation respectively. At acidic pH, increased activity was observed for both the compounds. Furthermore, the organism did not develop any resistance towards these compounds even after 10 passages grown at sub-inhibitory concentrations. Conclusion: These results indicate that the two bioactive compounds we tested may prevent H. pylori growth in vitro, without acquiring any resistance

A preliminary study of soil analysis of Sonmiani, Gadani and Kund Malir coasts of District Lasbela, Balochistan, Pakistan

The purpose of the soil analysis is to study the beach characteristics of different coasts of Balochistan. Three sites Sonmiani, Gadani and Kund Malir were selected. The Gaddani coast is known as sandy cum rocky shore, Sonmiani as sandy cum muddy shore while Kund Malir is sandy. Three different stations were selected on each site for sampling. At each station, five different samples were collected. At all three sites, the amount of medium and fine sand showed greater amount and very fine sand depicted lesser. The results showed that soil samples collected from three coasts mostly have highest fraction of find sand and lowest portions of very fine sand. At Sonmiani the soil composition is fine sand and very fine sand as compared to Gadani where the soil is of fine sand and medium sand and at Kund Malir the soil is of fine sand along with medium sand but very fine sand also present

Protective effect of Arque-Ajeeb on acute experimental diarrhoea in rats

BACKGROUND: Diarrhoea is a major health problem for children worldwide, accounting for 5–8 million deaths each year. Arque-Ajeeb (AA) is a compound formulation of Unani medicine. It is reputed for its beneficial effects in the treatment of diarrhoea and cholera, but the claim of its efficacy is yet to be tested. Therefore the present study has been planned to investigate the real efficacy of this drug in rats. METHODS: The effect of Arque-Ajeeb was investigated for antidiarrhoeal activity against charcoal-induced gut transit, serotonin-induced diarrhoea and PGE(2)-induced small intestine enteropooling in rats. The control, standard and test groups of experimental animals were administered with normal saline (p.o.), diphenoxylate hydrochloride (5 mg/kg, p.o.) and Arque-Ajeeb (0.07 ml and 0.14 ml/kg, p.o.) respectively except the control group of PGE(2)-induced small intestine enteropooling which received only 5% ethanol in normal saline (i.p.). Charcoal (10 ml/kg, p.o.) and serotonin (600 μg/kg, i.p.) were administered after 30 min, while PGE(2 )(100 μg/kg, p.o.) was administered immediately afterwards. The distance traveled by charcoal in small intestine was measured after 15 and 30 min of charcoal administration, diarrhoea was observed every 30-min for six hour after serotonin administration and the volume of intestinal fluid was measured after 30 min of PGE(2 )administration. RESULTS: Arque-Ajeeb (0.07 ml and 0.14 ml/kg) significantly inhibited the frequency of defaecation and decreased the propulsion of charcoal meal through the gastrointestinal tract, reduced the wetness of faecal droppings in serotonin-induced diarrhoea and also reduced the PGE(2)-induced small intestine enteropooling. CONCLUSION: Arque-Ajeeb may have potential to reduce the diarrhoea in rats. Thus the drug may prove to be an alternate remedy in diarrhoea

Impacts of biological globalization in the Mediterranean: Unveiling the deep history of human-mediated gamebird dispersal

Humans have a long history of moving wildlife that over time has resulted in unprecedented biotic homogenization. It is, as a result, often unclear whether certain taxa are native to a region or naturalized, and how the history of human involvement in species dispersal has shaped present-day biodiversity. Although currently an eastern Palaearctic galliform, the black francolin (Francolinus francolinus) was known to occur in the western Mediterranean from at least the time of Pliny the Elder, if not earlier. During Medieval times and the Renaissance, the black francolin was a courtly gamebird prized not only for its flavor, but also its curative, and even aphrodisiac qualities. There is uncertainty, however, whether this important gamebird was native or introduced to the region and, if the latter, what the source of introduction into the western Mediterranean was. Here we combine historical documentation with a DNA investigation of modern birds and archival (13th–20th century) specimens from across the species’ current and historically documented range. Our study proves the black francolin was nonnative to the western Mediterranean, and we document its introduction from the east via several trade routes, some reaching as far as South Asia. This finding provides insight into the reach and scope of long-distance trade routes that serviced the demand of European aristocracy for exotic species as symbols of wealth and prestige, and helps to demonstrate the lasting impact of human-mediated long-distance species dispersal on current day biodiversity