Background According to recent estimates 80% of Latvian population is infected with Helicobacter pylori thus their susceptibility to numerous gastric tract diseases is increased. The 1st line H. pylori eradication therapy includes treatment with clarithromycin in combination with amoxicillin or metronidazole and a proton pump inhibitor. However, potential adverse events caused by such therapies to microbiome are insufficiently studied. Objective This study aimed to evaluate the long‐term effect of H. pylori eradication on human gastrointestinal tract (GIT) microbiome. Methods The assessment of H pylori eradication impact on GIT microbiome was done by analyzing 120 samples acquired from 60 subjects. Each individual was prescribed the following 10‐day eradication regimen: Esomeprazolum 40 mg, Clarithromycinum 500 mg, and Amoxicillinum 1000 mg, BID. Samples from each individual were collected before starting H pylori eradication therapy, and 2 years after the completion of the therapy in OC‐Sensor (Eiken Chemical Co.) sample collection containers and stored at −86°C. Prior to DNA extraction, the samples were lyophilized, and total DNA was extracted using FastDNA Spin Kit for Soil. 16S V3 rRNA gene sequencing was done employing Ion Torrent PGM, and the obtained raw sequences were analyzed using vsearch and R (phyloseq, cluster packages). Results Alpha diversity measurements—observed OTUs, Chao1 and Shannon index did not differ significantly between the pre‐ and post‐eradication states (two‐tailed paired t test: P = .95; P = .71, P = .24, respectively). Unweighted and weighted UniFrac distances of beta diversity analysis indicated a non‐specific pattern of sample clustering. Enterotype shift was observed for the majority of individuals comparing pre‐ and post‐eradication study groups. Association analysis revealed that certain bacterial genera significantly correlated with age (eg, Dialister, Paraprevotella, Bifidobacterium), individual (eg, Thermotunica, Streptomyces, Faecalibacterium), and history of respiratory and/or allergic diseases (eg, Colinsella, Faecalibacterium). Redundancy analysis confirmed that the individual was a significant determinant of the subject's microbial community composition (ANOVA, 999 perm., P = .001) with the further lower impact of subject‐specific medical history (eg, medication used as prescribed: P = .005, history of cardiovascular diseases: P = .005, history of respiratory, and/or allergic diseases: P = .015) and physiological (eg, age: P = .005, gender: P = .02) parameters. In the post‐eradication study group, number of influential genera (n = 260) was increased compared to the pre‐eradication study group (n = 209). Conclusion Modest global differences at the community level exist between individuals before and after the eradication therapy; however, the microbiome structure is more related to the subject‐specific parameters rather than by the eradication therapy itself.

The spread of extended-spectrum beta-lactamases (ESBLs) in nosocomial and community-acquired enterobacteria is an important challenge for clinicians due to the limited therapeutic options for infections that are caused by these organisms. The epidemiology of these infections is complex and combines the expansion of mobile genetic elements with clonal spread. Insufficient empirical therapy for serious infections caused by these organisms is independently associated with increased mortality. Here, we developed an ESBL coding gene panel, evaluated the abundance and prevalence of ESBLs encoding genes in patients undergoing H. pylori eradication therapy, and summarized the effect of eradication therapy on gut microbiome functional profiles. To assess the repertoire of known beta lactamase (BL) genes, we divided them in clusters according to their evolutionary relation, designed primers for amplification of cluster marker regions and assessed efficiency of this amplification panel on 120 fecal samples acquired from 60 patients undergoing H. pylori eradication therapy. In addition, fecal samples from additional 30 patients were used to validate the detection efficiency of designed ESBL panel. The presence for majority of targeted clusters was confirmed by NGS of amplification products. Metagenomic sequencing revealed that the abundance of ESBL genes within the pool of microorganisms was very low. The global relative abundances of the ESBL-coding gene clusters did not differ significantly across the treatment states. However, at the level of each cluster, classical ESBL producers, such as Klebsiella sp. for blaOXY (p = 0.0076), Acinetobacter sp. for blaADC (p = 0.02297), and others, differed significantly with a tendency to decrease compared to the pre- and post-eradication states. Only 13 clusters were common among all three datasets, suggesting a patient-specific prevalence profile of ESBL-coding genes. The number of AMR genes detected in the post-eradication state was higher than that in the pre-eradication state, which at least partly might be attributed to the therapy. This study demonstrated that the ESBL screening panel was efficient for targeting ESBL-coding gene clusters from bacterial DNA and that minor differences exist in the abundance and prevalence of ESBL-coding gene levels before and after eradication therapy.

The spread of extended-spectrum beta-lactamases (ESBLs) in nosocomial and community-acquired enterobacteria is an important challenge for clinicians due to the limited therapeutic options for infections that are caused by these organisms. Here, we developed a panel of ESBL coding genes, evaluated the abundance and prevalence of ESBL encoding genes in patients undergoing H. pylori eradication therapy, and summarized the effects of eradication therapy on functional profiles of the gut microbiome. To assess the repertoire of known beta lactamase (BL) genes, they were divided into clusters according to their evolutionary relation. Primers were designed for amplification of cluster marker regions, and the efficiency of this amplification panel was assessed in 120 fecal samples acquired from 60 patients undergoing H. pylori eradication therapy. In addition, fecal samples from an additional 30 patients were used to validate the detection efficiency of the developed ESBL panel. The presence for majority of targeted clusters was confirmed by NGS of amplification products. Metagenomic sequencing revealed that the abundance of ESBL genes within the pool of microorganisms was very low. The global relative abundances of the ESBL-coding gene clusters did not differ significantly among treatment states. However, at the level of each cluster, classical ESBL producers such as Klebsiella sp. for blaOXY (p = 0.0076), Acinetobacter sp. for blaADC (p = 0.02297) and others, differed significantly with a tendency to decrease compared to the pre- and post-eradication states. Only 13 clusters were common across all three datasets, suggesting a patient-specific distribution profile of ESBL-coding genes. The number of AMR genes detected in the post-eradication state was higher than that in the pre-eradication state, which could be attributed, at least in part, to the therapy. This study demonstrated that the ESBL screening panel was effective in targeting ESBL-coding gene clusters from bacterial DNA and that minor differences exist in the abundance and prevalence of ESBL-coding gene levels before and after eradication therapy.

Lung cancer is the leading cause of cancer-related mortality worldwide. Early diagnosis of lung cancer is hampered by the absence of specific symptoms and the lack of a widely recognised cost-effective screening programme. Acquisition of a tumour tissue sample for morphological and molecular genetic examination is of paramount importance for cancer diagnosis. We describe diagnostic challenges for early-stage lung cancer and their possible current solutions. Liquid biopsy is a relatively new technology that was developed for evaluation of tumour-related circulating genetic material. Recent achievements in data processing provide more opportunities for wider implementation of Next Generation Sequencing (NGS) in clinical practice. This article summarises available data on the current and future role of liquid biopsy in the management of lung cancer. We also present an ongoing Latvian lung cancer study that focuses on integration of liquid biopsy with comprehensive clinical data utilising advantages of information technologies.