Whole Genome Sequencing Reveals Virulence Potentials of Helicobacter pylori Strain KE21 Isolated from a Kenyan Patient with Gastric Signet Ring Cell Carcinoma

Mwangi, Catherine; Njoroge, Stephen; Tshibangu‐Kabamba, Evariste; Moloo, Zahir; Rajula, Allan; Devani, Smita; Matsumoto, Takashi; Nyerere, Kimang'a; Kariuki, Samuel; Govind, Revathi; Yamaoka, Yoshio

doi:10.3390/toxins12090556

Cited by 13 publications

(16 citation statements)

References 93 publications

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“…In the study Mwangi et al, conducted in 2020, they stated that the H. pylori strain they isolated from a patient in Kenya was similar to Asian stains. Although the main virulence factors they detected were found in other African strains, it was reported that this strain was not similar to other African strains in terms of phylogeny (26). In our study, we found that our results were similar in terms of virulence factors, ORF and phylogenies, but that African strains we studied generally differed from European and Asian strains in terms of both virulence gene prevalence and phylogeny.…”

Section: In Silico Analysis Of H Pylori From Different Continentscontrasting

confidence: 58%

In silico Analysis of Virulence, Resistance Genes and Phylogeny of Helicobacter pylori Strains from Different Continents

Demırci¹,

Ünlü²,

Kocazeybek³

2021

experimed

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Objective: Helicobacter pylori (H. pylori) is a bacterium that infects the gastric mucosa of 50% of the world population. It is known that different regional treatment practices used against the infections of H. pylori affect both the expression of virulence and antimicrobial resistance genes, giving the bacteria geographic differentiation. The aim of this study was to perform in silico analysis of virulence, resistance genes and phylogeny of H. pylori strains obtained from people living in different continents.Material and Method: Complete gene sequences of 18 H. pylori strains from six continents were downloaded from the National Center for Biotechnology Information (NCBI) database. The phylogeny of the strains, resistance and virulence genes were analyzed by CSI phylogeny, CARD and VFanalyzer, respectively.Results: African strains were the most distant identity to European strains. A2147G single nucleotide polymorphism associated with clarithromycin resistance was detected in South American and Asian origin. It was determined that strains were differentiated by a total of 95 related virulence genes under eight headings. The cagA, cagE, cagL and vacA genes were found in all strains in Asia. Conclusion:In conclusion, our study demonstrated that H. pylori strains, whose data were collected in different continents, differ from each other in terms of similarities and there is a serious difference especially in terms of virulence genes.

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Section: In Silico Analysis Of H Pylori From Different Continentscontrasting

confidence: 58%

In silico Analysis of Virulence, Resistance Genes and Phylogeny of Helicobacter pylori Strains from Different Continents

Demırci¹,

Ünlü²,

Kocazeybek³

2021

experimed

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“…In Ethiopia, an East African country, reports on the diagnosis of HPI are largely based on serology and SAT [87,88,[107][108][109]. On the other hand, Kenya, a neighboring country, has reports on the use of SAT [89,90], endoscopy, RUT, histol-ogy, and culture [91,110]. Similarly, in Uganda, SAT [92], endoscopy, histology and RUT [93,94], serology and SAT [95] have been used in the diagnosis of HPI.…”

Section: Non-invasive Invasivementioning

confidence: 99%

Helicobacter pylori Infection in Africa: Update of the Current Situation and Challenges

Smith¹,

Ajayi²,

Jolaiya³

et al. 2021

Dig Dis

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Background: The burden of Helicobacter pylori infection (HPI) in Africa remains high with varying levels of prevalence among children and adults reported in different regions of the continent. Persistent and uneradicated HPI could result in gastric cancer, although less severe pathological outcomes have been reported among Africans – the so-called “African enigma.” Summary: Analysis of endoscopic findings of the upper gastrointestinal tract demonstrates similarities with that of patients from the West. Thus, it could be asserted that the true picture of HPI in Africa is yet to be unveiled due to several challenges including inadequate health-care system, lack of treatment guidelines and standardized protocol for diagnosis, and lack of data. This review explores the prevalence, diagnosis, treatment, and health-care system in Africa as it relates to HPI, thus providing an update and highlighting the need for an African HPI guideline. Key Messages: There is high prevalence of Helicobacter pylori infection (HPI) in Africa with an increasing burden of antibiotic resistance. Various methods including invasive and noninvasive methods are deployed in the diagnosis of HPI in Africa. There is a need for consensus on diagnosis and treatment of HPI in Africa.

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“…The final detection was performed with POD/TMB substrate (Nacalai Tesque, Inc., Japan). This ELISA system was optimized and calibrated using the training set of blood samples from Congolese patients whose H. pylori status was already established using culture, histology or rapid urease test applied as previously described (S2 Table) [31,33,34]. Polyclonal rabbit anti-Helicobacter pylori IgG (Dako, Danmark) with detection by 1:80,000 peroxidase-conjugated secondary anti-rabbit IgG antibodies (Jackson Immuno Research Laboratories, Inc; USA) was used as an internal positive control while water, PBS and carbonate buffer were set as negative controls during all reactions.…”

Section: Development Of the Hpafr-elisa And Laboratory Testingmentioning

confidence: 99%

Assessment of the diagnostic accuracy and relevance of a novel ELISA system developed for seroepidemiologic surveys of Helicobacter pylori infection in African settings

et al. 2021

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Beside diagnostic uncertainties due to the lack of a perfect gold standard test for Helicobacter pylori infection, the diagnosis and the prevalence estimation for this infection encounter particular challenges in Africa including limited diagnostic tools and specific genetic background. We developed and evaluated the accuracy of an enzyme-linked immunosorbent assay (ELISA) system tailored for H. pylori genetics in Africa (HpAfr-ELISA). Strains belonging to main genetic populations infecting Africans were exploited as sources for whole-cell antigens to establish in-house the ELISA system. A phase II unmatched case-control study explored the diagnostic accuracy of the HpAfr-ELISA using a training set of samples collected from dyspeptic patients from Kinshasa, the Democratic Republic of Congo (DRC) who had been tested with invasive standard tests (i.e., histology, culture, and rapid urease test) in 2017. Then the assay was cross-validated through a community-based survey assessing the prevalence of H. pylori and associated factors in 425 adults from Mbujimayi, DRC in 2018. Bayesian inferences were used to deal with statistical uncertainties of estimates (true prevalence, sensitivity, and specificity) in the study population. At its optimal cut-off-value 20.2 U/mL, the assay achieved an estimated sensitivity of 97.6% (95% credible interval [95%CrI]: 89.2; 99.9%) and specificity of 90.5% (95%CrI: 78.6; 98.5). Consistent outcomes obtained at repeated tests attested the robustness of the assay (negative and positive agreements always > 70%). The true prevalence of H. pylori was estimated 53.8% [95%CrI: 42.8; 62.7%]. Increasing age (adjusted odds ratio [aOR] = 1.0 [95% confidence interval (CI): 1.0; 1.1]; p<0.001), overcrowding households (aOR = 3.2 [95%CI: 2.0; 5.1]; p<0.001), and non-optimal hand hygiene (aOR = 4.5 [95%CI: 2.0; 11.4]; p = 0.001) were independently associated with the H. pylori-seropositivity. The novel ELISA system has demonstrated good diagnostic accuracy and potential usefulness for management and mitigation strategies for H. pylori infection in African settings.

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Whole Genome Sequencing Reveals Virulence Potentials of Helicobacter pylori Strain KE21 Isolated from a Kenyan Patient with Gastric Signet Ring Cell Carcinoma

Cited by 13 publications

References 93 publications

In silico Analysis of Virulence, Resistance Genes and Phylogeny of Helicobacter pylori Strains from Different Continents

In silico Analysis of Virulence, Resistance Genes and Phylogeny of Helicobacter pylori Strains from Different Continents

<b><i>Helicobacter pylori</i></b> Infection in Africa: Update of the Current Situation and Challenges

Assessment of the diagnostic accuracy and relevance of a novel ELISA system developed for seroepidemiologic surveys of Helicobacter pylori infection in African settings

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