The Helicobacter pylori Genome Project : insights into H. pylori population structure from analysis of a worldwide collection of complete genomes

Helicobacter pylori, a dominant member of the gastric microbiota, shares co-evolutionary history with humans. This has led to the development of genetically distinct H. pylori subpopulations associated with the geographic origin of the host and with differential gastric disease risk. Here, we provide insights into H. pylori population structure as a part of the Helicobacter pylori Genome Project (HpGP), a multi-disciplinary initiative aimed at elucidating H. pylori pathogenesis and identifying new therapeutic targets. We collected 1011 well-characterized clinical strains from 50 countries and generated high-quality genome sequences. We analysed core genome diversity and population structure of the HpGP dataset and 255 worldwide reference genomes to outline the ancestral contribution to Eurasian, African, and American populations. We found evidence of substantial contribution of population hpNorthAsia and subpopulation hspUral in Northern European H. pylori. The genomes of H. pylori isolated from northern and southern Indigenous Americans differed in that bacteria isolated in northern Indigenous communities were more similar to North Asian H. pylori while the southern had higher relatedness to hpEastAsia. Notably, we also found a highly clonal yet geographically dispersed North American subpopulation, which is negative for the cag pathogenicity island, and present in 7% of sequenced US genomes. We expect the HpGP dataset and the corresponding strains to become a major asset for H. pylori genomics

SARS-CoV-2 infection in asymptomatic healthcare workers at a clinic in Chile.

Asymptomatic SARS-CoV-2 infection of healthcare workers (HCWs) has been reported as a key player in the nosocomial spreading of COVID-19. Early detection of infected HCWs can prevent spreading of the virus in hospitals among HCWs and patients. We conducted a cross-sectional study to determine the asymptomatic infection of HCWs in a private clinic in the city of Santiago, Chile. Our study was conducted during a period of 5 weeks at the peak of transmission of SARS-CoV-2 in Chile. Nasopharyngeal samples were obtained from 413 HCWs and tested for the presence of SARS-CoV-2 using RT-qPCR. We found that a 3.14% of HCWs were positive for the presence of SARS-CoV-2 (14/413). Out of these, 7/14 were completely asymptomatic and did not develop symptoms within 3 weeks of testing. Sequencing of viral genomes showed the predominance of the GR clade; however, sequence comparison demonstrated numerous genetic differences among them suggesting community infection as the main focus of transmission among HCWs. Our study demonstrates that the protocols applied to protect HCWs and patients have been effective as no infection clusters due to asymptomatic carriers were found in the clinic. Together, these data suggest that infection with SARS-CoV-2 among HCWs of this health center is not nosocomial

Chilean Gastric Cancer Task Force: a study protocol to obtain a clinical and molecular classification of a cohort of gastric cancer patients

Gastric cancer (GC) is the world’s second-leading cause of neoplastic mortality. Genetic alterations, response to treatments, and mortality rates are highly heterogeneous across different regions. Within Latin America, GC is the leading cause of cancer death in Chile, affecting 17.6 per 100,000 people and causing >3000 deaths/y. Clinical outcomes and response to “one size fits all” therapies are highly heterogeneous and thus a better stratification of patients may aid cancer treatment and response. The Gastric Cancer Task Force is a Chilean collaborative, noninterventional study that seeks to stratify gastric adenocarcinomas using clinical outcomes and genomic, epigenomic, and protein alterations in a cohort of 200 patients. Tumor samples from the Pathology Department and the Cancer Center at UC-Christus healthcare network, Pontificia Universidad Católica de Chile will be analyzed using a panel of 143 known cancer genes (Oncomine Comprehensive Assay) at the Center of Excellence in Precision Medicine in Santiago, Chile. In addition, promoter methylation for selected genes will be performed along with tissue microarray for clinically relevant proteins (e.g., PD-L1, Erb-2, VEGFR2, among others) and Helicobacter pylori and Epstein–Barr virus status. Obtained data will be correlated to 120 clinical parameters retrieve from medical records, including general patient information, cancer history, laboratory studies, comorbidity index, chemotherapy, targeted therapies, efficacy, and follow-up. The development of a clinically meaningful classification that encompasses comprehensive clinical and molecular parameters may improve patient treatment, predict clinical outcomes, aid patient selection/stratification for clinical trials and may offer insights into future preventive and/or therapeutic strategies in patients from Latin America region. Trial registration: ClinicalTrials.gov Identifier: NCT03158571, Registered on May 18, 2017