Inference from the analysis of genetic structure of Helicobacter pylori strains isolates from two paediatric patients with recurrent infection

Mixed (multiple-genotype) Helicobacter pylori infections in Bulgarian patients

The aim of the study was to evaluate the frequency and characteristics of mixed (multiple-genotype) Helicobacter pylori infections (MGIs) in 155 Bulgarian symptomatic patients (21 children and 134 adults). MGIs were common (36.1%), including double-strain (34.8%) and triple-strain infections (1.3%). None of the 8 ulcer patients harbored multiple subtypes. We detected 18 multiple allelic combinations, of which the most frequent subtypes (17.4%) were vacA s1as2 and vacA s1cs2. The 2 patients with triple-strain infections had vacA s1bs1cs2i1i2/iceA1A2 and vacA s1as1cs2 subtypes. They were both adult men with chronic gastritis and both were examined in 2022. The prevalence of MGIs (51.7%) was 2-fold higher in 2020 to 2022 than in 2015 to 2019 (26.3%). Putative factors for the increase may be the patient's characteristics and COVID-19 pandemic-associated factors. MGI rates corresponded to the high infection seroprevalence (72.4% in 2011) in Bulgaria. The evolution and clinical importance of mixed H. pylori infections merit extensive evaluation.

Recombination in Bacterial Genomes: Evolutionary Trends

Bacterial organisms have undergone homologous recombination (HR) and horizontal gene transfer (HGT) multiple times during their history. These processes could increase fitness to new environments, cause specialization, the emergence of new species, and changes in virulence. Therefore, comprehensive knowledge of the impact and intensity of genetic exchanges and the location of recombination hotspots on the genome is necessary for understanding the dynamics of adaptation to various conditions. To this end, we aimed to characterize the functional impact and genomic context of computationally detected recombination events by analyzing genomic studies of any bacterial species, for which events have been detected in the last 30 years. Genomic loci where the transfer of DNA was detected pertained to mobile genetic elements (MGEs) housing genes that code for proteins engaged in distinct cellular processes, such as secretion systems, toxins, infection effectors, biosynthesis enzymes, etc. We found that all inferences fall into three main lifestyle categories, namely, ecological diversification, pathogenesis, and symbiosis. The latter primarily exhibits ancestral events, thus, possibly indicating that adaptation appears to be governed by similar recombination-dependent mechanisms.

High prevalence of Helicobacter pylori mixed infections identified by multilocus sequence typing in Ningbo, China

This study used multilocus sequence typing (MLST) to investigate the prevalence of Helicobacter pylori (H. pylori) mixed infections and H. pylori mixed infections involving unrelated strains; and determined the phylogeographic groups of H. pylori recovered from patients in Ningbo, China. A total of 156 H. pylori isolates were obtained from a convenience sample of 33 patients with culture-positive H. pylori infection. MLST was used to classify 150 H. pylori clinical isolates and 12 methodological control strains (6 clinical isolates and 6 strains of American Type Culture Collection H. pylori) into 43 and 12 sequence types (STs), respectively. In this study, 246 new alleles and 53 new STs were identified by MLST. The prevalence of mixed infections was 41% (11/27). The prevalence of H. pylori mixed infections involving unrelated strains was 46% (5/11) and the prevalence of H. pylori mixed infections involving completely unrelated strains (strains with all 7 housekeeping genes different) was 36% (4/11). A phylogenetic tree was created to determine the evolutionary relationships between different strains. The STs in this study were clustered within the hspEAsia subgroup (98%) and hpEurope group (2%). H. pylori mixed infections were common in Ningbo, China. The H. pylori isolates belonging to the hpEurope group were recovered from three different biopsy samples in a native Chinese patient. Most of H. pylori strains colonizing the antrum, corpus, and duodenum bulb were homologous.

Regulatory B cells (Bregs) in Helicobacter pylori chronic infection

BACKGROUND

Helicobacter pylori (H. pylori) infection is linked with a wide variety of diseases and was reported in more than half of the world's population. Chronic H. pylori infection and its final clinical outcome depend mainly on the bacterial virulence factors and its ability to manipulate and adapt to human immune responses. Bregs blood levels have been correlated with increased bacterial load and infection chronicity, especially Gram-negative bacterial infection. This study aimed to identify prevalence and virulence factors of chronic H. pylori infection among symptomatic Egyptian patients and to examine its possible correlation to levels of regulatory B cells (Bregs) in blood.

MATERIALS AND METHODS

Gastric biopsies and blood samples from each of 113 adult patients, who underwent upper endoscopy, were examined for the detection of H. pylori by culture and PCR methods. Conventional PCR was used to determine various virulent genes prevalence and association to clinical outcome. Flow cytometry was used to evaluate Bregs levels.

RESULTS

Helicobacter pylori prevalence was 49.1% (55/112). Regarding virulence genes incidence, flaA gene was detected in 73% (40/55), vir B11 in 56.4% (31/55), hopZ1 in 34.5% (19/55), hopZ2 in 89% (49/55), babA2 in 52.7% (29/55), dupA jhp917 in 61.8% (34/55), vacA m1/m2 in 70.9% (39/55), and vacA s1/s2 in 69% (38/55) strains. Bregs levels were significantly lower in H. pylori-infected patients (p = 0.013), while total leukocyte count (TLC) showed no significant differences.

CONCLUSION

Helicobacter pylori infection prevalence was almost 49%, and the infection was found to be related to inflammatory conditions as gastritis and ulcers rather than malignant transformations. Also, we found that CD24⁺ CD38⁺ B cells were downregulated in H. pylori-infected patients.

Analysis of Genetic Relatedness between Gastric and Oral Helicobacter pylori in Patients with Early Gastric Cancer Using Multilocus Sequence Typing

The oral cavity is the second most colonized site of Helicobacter pylori after the stomach. This study aimed to compare the genetic relatedness between gastric and oral H. pylori in Japanese patients with early gastric cancer through multilocus sequence typing (MLST) analysis using eight housekeeping genes. Gastric biopsy specimens and oral samples were collected from 21 patients with a fecal antigen test positive for H. pylori. The number of H. pylori allelic profiles ranged from zero to eight since the yield of DNA was small even when the nested PCR was performed. MLST analysis revealed that only one patient had a matching oral and gastric H. pylori genotype, suggesting that different genotypes of H. pylori inhabit the oral cavity and gastric mucosa. The phylogenetic analysis showed that oral H. pylori in six patients was similar to gastric H. pylori, implying that the two strains are related but not of the same origin, and those strains may be infected on separate occasions. It is necessary to establish a culture method for oral H. pylori to elucidate whether the oral cavity acts as the source of gastric infection, as our analysis was based on a limited number of allele sequences.

Genomic population structure of Helicobacter pylori Shanghai isolates and identification of genomic features uniquely linked with pathogenicity

Severe Helicobacter pylori-linked gastric disorders are especially prevalent in the East Asia region. The ability of H. pylori to cause different clinical outcomes is thought to be associated with unique sets of its genetic features. However, only few genetic features have been definitively linked to specific gastrointestinal pathologies. Genome heterogeneity of clinical H. pylori strains from patients with four different gastric disorders was studied to explore the population structure and molecular genomic features and their association with pathogenicity. Population analysis showed that 92.9% of the Shanghai H. pylori isolates were clustered in the East Asia group. Among 2,866 genes detected in all genomes, 1,146 genes formed the core genome, whereas 209 unique genes were detected in individual disease groups. The unique genes of peptic ulcer and gastric cancer groups represented the inorganic ion transport and metabolism function gene clusters. Sixteen virulence genes were detected with statistically different detection rates among the four disease groups. Furthermore, 127 clustered regularly interspaced short palindromic repeats were found with significantly different rates in the four disease groups. A total of 337 putative genomic islands were identified, and three genomic islands were individually found in more than 10% of strains. The genomic islands included several metabolism-associated genes and many genes with unknown function. In total, 88 sequence types were detected among the 112 Shanghai H. pylori isolates. Our study provides an essential milestone in the mapping of specific genomic features and their functions to identify factors needed to induce specific gastric disorders in H. pylori.

Antimicrobial resistance and virulence in Helicobacter pylori: Genomic insights

Microbes evolve rapidly by modifying their genome through mutations or acquisition of genetic elements. Antimicrobial resistance in Helicobacter pylori is increasingly prevalent in India. However, limited information is available about the genome of resistant H. pylori isolated from India. Our pan- and core-genome based analyses of 54 Indian H. pylori strains revealed plasticity of its genome. H. pylori is highly heterogenous both in terms of the genomic content and DNA sequence homology of ARGs and virulence factors. We observed that the H. pylori strains are clustered according to their geographical locations. The presence of point mutations in the ARGs and absence of acquired genetic elements linked with ARGs suggest target modifications are the primary mechanism of its antibiotic resistance. The findings of the present study would help in better understanding the emergence of drug-resistant H. pylori and controlling gastric disorders by advancing clinical guidance on selected treatment regimens.

Prevalence of Helicobacter pylori among residents and their environments in the Nara prefecture, Japan

BACKGROUND

Chronic infection with Helicobacter pylori, specifically cagA-positive strains, is associated with gastric cancer. Thus, measures to prevent H. pylori infection are required. This study was conducted to clarify the prevalence of H. pylori in the community to identify the infection source and comprehensively assess the risk of H. pylori infection.

METHODS

We collected 90 human faecal samples and 73 environmental samples (water, vegetable, and animal faecal samples) from the residents in an area with a high incidence of gastric cancer in Japan. Polymerase chain reaction assay was performed to detect the glmM housekeeping gene and the cagA virulence gene of H. pylori. A questionnaire survey was conducted, and the responses were analyzed statistically.

RESULTS

The glmM gene was detected in 18 of 90 (20%) faecal samples obtained from residents; among them, the cagA gene was detected in 33.3% (6/18), and in all who had undergone eradication therapy. H. pylori was not detected in environmental samples. However, contact with dogs (OR 3.89, 95% CI 1.15-13.15, P < 0.05) was associated with higher odds for glmM gene positivity in the questionnaire survey.

CONCLUSIONS

The prevalence of H. pylori and cagA-positive strains among the residents was low. However, the study results suggest a correlation between recurrent infection and cagA-positive H. pylori strains. Although H. pylori genes were not detected in living environments, an association between contact with dogs and a glmM positive status was revealed. Further investigations targeting community-dwelling healthy people and their living environments would be required for H. pylori infection control.

Risk factors for recurrence of Helicobacter pylori infection after successful eradication in Chinese children: A prospective, nested case-control study

BACKGROUND

Limited research has been published on the recurrence of Helicobacter pylori infection and risk factors in Chinese children. Our study aimed to identify risk factors for Helicobacter pylori infection recurrence after successful eradication in children.

MATERIALS AND METHODS

A prospective, nested case-control study was performed. A cohort of 230 children with successful eradication of Helicobacter pylori in Baoding (China) was selected from January 2018 to February 2019. A standardized questionnaire was used to obtain socioeconomic details. Eradication regimens and Helicobacter pylori antibiotic susceptibility testing results were also recorded. Interleukin-1β level, interferon-γ level, and genetic susceptibility (IFNGR1 and PTPRZ1 gene polymorphisms) were analyzed. All children were followed for 1 year.

RESULTS

Among 218 (94.8%) children who were successfully followed, 41 children (18.8%) had a Helicobacter pylori infection recurrence. The recurrence rate was higher in children ≤10 years old than >10 years old (22.8% vs 7.1%, P = .01). There was no significant difference between the recurrence group and the non-recurrence group in terms of types of therapy and antibiotic sensitivity (P > .05). Multivariable regression results indicated that residence in urban areas, higher household income, and having lunch at home were significantly protective against recurrence (OR 0.155, 0.408, and 0.351 respectively), whereas Helicobacter pylori infection in family members increased the risk of recurrence (OR 2.283). The levels of IL-1β and IFN-γ exhibited no significant difference between the recurrence group and the non-recurrence group. The allele frequency of G in the IFNGR1-56 site, A in the IFNGR1-600 site, and T in the IFNGR1-565 site was significantly higher in the recurrence group when compared to the non-recurrence group (P < .05).

CONCLUSIONS

The Helicobacter pylori infection recurrence rate is high in children in Baoding region and is closely correlated to socioeconomic factors. The IFNGR1 gene polymorphism may be an independent risk factor for Helicobacter pylori infection recurrence.