Pangenome Analysis of Helicobacter pylori Isolates from Selected Areas of Africa Indicated Diverse Antibiotic Resistance and Virulence Genes

The challenge facing Helicobacter pylori (H. pylori) infection management in some parts of Africa is the evolution of drug-resistant species, the lack of gold standard in diagnostic methods, and the ineffectiveness of current vaccines against the bacteria. It is being established that even though clinical consequences linked to the bacteria vary geographically, there is rather a generic approach to treatment. This situation has remained problematic in the successful fight against the bacteria in parts of Africa. As a result, this study compared the genomes of selected H. pylori isolates from selected areas of Africa and evaluated their virulence and antibiotic drug resistance, those that are highly pathogenic and are associated with specific clinical outcomes and those that are less virulent and rarely associated with clinical outcomes. 146 genomes of H. pylori isolated from selected locations of Africa were sampled, and bioinformatic tools such as Abricate, CARD RGI, MLST, Prokka, Roary, Phandango, Google Sheets, and iTOLS were used to compare the isolates and their antibiotic resistance or susceptibility. Over 20 k virulence and AMR genes were observed. About 95% of the isolates were genetically diverse, 90% of the isolates harbored shell genes, and 50% harbored cloud and core genes. Some isolates did not retain the cagA and vacA genes. Clarithromycin, metronidazole, amoxicillin, and tinidazole were resistant to most AMR genes (vacA, cagA, oip, and bab). Conclusion. This study found both virulence and AMR genes in all H. pylori strains in all the selected geographies around Africa with differing quantities. MLST, Pangenome, and ORF analyses showed disparities among the isolates. This in general could imply diversities in terms of genetics, evolution, and protein production. Therefore, generic administration of antibiotics such as clarithromycin, amoxicillin, and erythromycin as treatment methods in the African subregion could be contributing to the spread of the bacterium's antibiotic resistance.

The prevalence of clarithromycin-resistant Helicobacter pylori isolates: a systematic review and meta-analysis

Background

Knowledge of global clarithromycin (CLA)-resistant rates of Helicobacter pylori (H. pylori) is crucial for decision of the most appropriate eradication therapies with good clinical outcomes. Therefore, this review and meta-analysis aimed to evaluate the global prevalence of the CLA resistance in H. pylori to provide some guidance for selecting the first-line antibiotics.

Method

A comprehensive search was performed for relevant literature until April 2021 in PubMed, Embase, and Web of Science databases. Freeman-Tukey double arcsine transformation was performed to estimate the weighted pooled prevalence of resistance.

Results

The meta-analysis included 248 articles. The prevalence of CLA-resistant H. pylori was 27.53% (95% CI [25.41-29.69]). The heterogeneity between reports was significant (I² = 97.80%, P < 0.01). The resistance rate increased from 24.28% in 2010-2017 to 32.14% in 2018-2021 (P < 0.01). Iran, with 38 articles, has the most report. Nevertheless, Switzerland, Portugal, and Israel had the highest resistance rates (67.16%, 48.11%, and 46.12%, respectively). The heterogeneity between the continents and the antimicrobial susceptibility methods also interpreted standard guidelines and breakpoints was insignificant (P > 0.05).

Conclusion

Overall CLA resistance rate was 27.53%, worldwide. The difference in CLA resistance rate among the included studies can be due to several reasons such as differences in antibiotic prescription rates in various geographic areas, use of different breakpoints or inaccurate criteria in performed studies, and the emergence of multidrug-resistant (MDR) strains.

Ninety-four thousand-case retrospective study on antibacterial drug resistance of Helicobacter pylori

BACKGROUND

The resistance rate to antibacterial drugs is the key inhibitor of Helicobacter pylori (H. pylori) eradication treatment.

AIM

To evaluate the prevalence and drug resistance of H. pylori based on big data.

METHODS

Gastric mucosal specimens were collected from naive patients undergoing upper gastrointestinal endoscopy for H. pylori culture and antimicrobial susceptibility testing (AST), including clarithromycin, levofloxacin, metronidazole and amoxicillin. Every 10 years of age was grouped as an age group. The H. pylori infection and resistance were explored based on the age group and gender.

RESULTS

The number of H. pylori-positive specimen was 94509 in 283823 gastric mucosal specimens, with an infection rate of 33.30%. The infection rate increased with age, and males had a higher infection rate than females. The average resistance rate of H. pylori to amoxicillin and metronidazole was 0.21% and 93.72%, which remained stable. The average resistance rate to clarithromycin was 23.99% with an increasing trend from 14.43% to 38.24%. The average resistance rate to levofloxacin was 30.29%, which increased from 17.07% to 39.42% and mostly stabilized after 2017. The resistance rate of H. pylori increased with age, except amoxicillin. H. pylori in females are at higher risk of resistance to metronidazole, but not to amoxicillin, regardless of the age group. Meanwhile, H. pylori in females are at higher risk of resistance to levofloxacin and clarithromycin in the 21-50 age group. The single, dual, triple and quadruple-drug resistance rate was 54.59%, 29.03%, 11.71% and 0.11%, respectively.

CONCLUSION

The resistance of H. pylori in Taizhou city is serious. Guided by the consensus report, individualized treatment based on AST is recommended.

Antibiotic resistance pattern and frequency of cagA and vacA genes in Helicobacter pylori strains isolated from patients in Tabriz city, Iran

Objective

Helicobacter pylori is one of the most common causes of gastric infections in humans. It is estimated that approximately 50% of people around the world are infected with this bacterium. This study aimed to determine the antibiotic resistance pattern, as well as the frequency of cagA and vacA genes in H. pylori isolates obtained from patients in the clinical centers in Tabriz city, Iran.

Results

The culture method detected 100 (45.25%) H. pylori isolates from 221 biopsy samples during 3 years. The results showed that 63% and 81% of the isolates were positive for cagA and vacA genes, respectively. The highest resistance of isolates was seen against metronidazole (79%) and amoxicillin (36%), respectively. Also, the isolates showed the least resistance to tetracycline (8%).

The increasing antimicrobial resistance of Helicobacter pylori in Iran: A systematic review and meta-analysis

BACKGROUND

Antimicrobial resistance of Helicobacter pylori can result in eradication failure. Metadata on the antimicrobial resistance of H pylori in Iran could help to formulate H pylori eradication strategies in Iran.

METHODS

A systematic review was performed after searching in MEDLINE, Scopus, Embase, Web of Science, and the Cochrane Library. A meta-analysis was performed, and a comparison of the rates between children and adults; time periods (1999-2010, 2011-2016, 2017-2019); and the methods used was carried out.

RESULTS

A total of 66 studies investigating 5936 H pylori isolates were analyzed. The weighted pooled resistance (WPR) rates were as follows: clarithromycin 21% (95% CI 16-26), metronidazole 62% (95% 57-67), clarithromycin in combination with metronidazole 16% (95% CI 10-23), ciprofloxacin 24% (95% CI 15-33), levofloxacin 18% (95% CI 9-30), erythromycin 29% (95% CI 12-50), furazolidone 13% (95% CI 4-27), tetracycline 8% (95% CI 5-13), and amoxicillin 15% (95% CI 9-22). During the three time periods, there was an increased resistance to amoxicillin, clarithromycin, ciprofloxacin, furazolidone, and tetracycline (P ˂ .05). Furazolidone and a clarithromycin/metronidazole combination had the higher resistance rates in children (P ˂ .05).

CONCLUSION

An increasing rate of resistance to amoxicillin, clarithromycin, ciprofloxacin, furazolidone, and tetracycline in Iranian H pylori isolates was identified. In children, the resistance to furazolidone and a combination of clarithromycin and metronidazole is higher compared to adults. As a stable, high resistance to metronidazole was found in children and adults in all Iranian provinces, we suggest that metronidazole should not be included in the Iranian H pylori eradication scheme.

The study of H. pylori putative candidate factors for single- and multi-component vaccine development

Helicobacter pylori has grown to colonize inside the stomach of nearly half of the world's population, turning into the most prevalent infections in the universe. Medical care failures noticeably confirm the need for a vaccine to hinder or deal with H. pylori. This review is planned to discuss the most known factors as a vaccine candidate, including single (AhpC, BG, CagA, KatA, Fla, Hsp, HWC, Lpp, LPS, NAP, OMP, OMV, SOD, Tpx, Urease, VacA) and multi-component vaccines. Many promising results in the field of single and multivalent vaccine can be seen, but there is no satisfactory outcome and neither a prophylactic nor a therapeutic vaccine to treat or eradicate the infection in human has been acquired. Hence, selecting suitable antigen is an important factor as an appropriate adjuvant. Taken all together, the development of efficient anti-H. pylori vaccines relies on the fully understanding of the interactions between H. pylori and its host immune system. Therefore, more work should be done on epitope mapping, analysis of molecular structure, and determination of the antigen determinant region as well due to design a vaccine, preferably a multi-component vaccine to elicit specific CD4 T-cell responses that are required for H. pylori vaccine efficacy.

Helicobacter pylori isolated from Iranian drinking water: vacA, cagA, iceA, oipA and babA2 genotype status and antimicrobial resistance properties

Despite the clinical importance of Helicobacter pylori in human gastric disorders, its exact route of transmission is still uncertain. Based on the contentious hypothesis and findings of previous investigations, water may play an important role in the transmission of H. pylori to humans. This study was carried out to investigate the vacA, cagA, oipA, iceA and babA2 genotype status and antimicrobial resistance properties of H. pylori strains isolated from the drinking water samples of four major provinces in Iran. A total of 400 drinking water samples were cultured and tested. H. pylori-positive strains were analyzed for the presence of various genotypes and antimicrobial resistance. Twelve of 400 (3%) water samples were positive for H. pylori. Samples from Isfahan province had the highest, while those from Shiraz had the lowest prevalence of H. pylori. The seasonal distribution was also determined, with the highest prevalence of bacteria in the summer season (7.36%). H. pylori strains harbored the highest levels of resistance against ampicillin (100%), erythromycin (75%), clarithromycin (75%), and trimethoprim (58.3%). The most commonly detected genotypes were vacAs1a (83.3%), vacAm1a (66.6%), vacAs2 (50%) and cagA (50%). The presence of similar genotypes in the H. pylori strains of drinking water and those of human clinical samples suggest that contaminated water maybe the sources of bacteria. Spiramycin and furazolidone are suggested for the treatment of cases of H. pylori infection.