Selective staining of gastric biopsies for H. pylori does not affect detection rates or turnaround time and improves cost compared to reflexive staining

Aims: Deep learning (DL), a sub-area of artificial intelligence, has demonstrated great promise at automating diagnostic tasks in pathology, yet its translation into clinical settings has been slow. Few studies have examined its impact on pathologist performance, when embedded into clinical workflows. The identification of H. pylori on H&E stain is a tedious, imprecise task which might benefit from DL assistance. Here, we developed a DL assistant for diagnosing H. pylori in gastric biopsies and tested its impact on pathologist diagnostic accuracy and turnaround time. Methods and results: H&E-stained whole-slide images (WSI) of 303 gastric biopsies with ground truth confirmation by immunohistochemistry formed the study dataset; 47 and 126 WSI were respectively used to train and optimize our DL assistant to detect H. pylori, and 130 were used in a clinical experiment in which 3 experienced GI pathologists reviewed the same test set with and without assistance. On the test set, the assistant achieved high performance, with a WSI-level area-under-the-receiver-operating-characteristic curve (AUROC) of 0.965 (95% CI 0.934-0.987). On H. pylori-positive cases, assisted diagnoses were faster (β, the fixed effect size for assistance= -0.557, p=0.003) and much more accurate (OR=13.37, p<0.001) than unassisted diagnoses. However, assistance increased diagnostic uncertainty on H. pylori-negative cases, resulting in an overall decrease in assisted accuracy (OR=0.435, p=0.016) and negligible impact on overall turnaround time (β for assistance=0.010, p=0.860). Conclusions: DL can assist pathologists with H. pylori diagnosis, but its integration into clinical workflows requires optimization to mitigate diagnostic uncertainty as a potential consequence of assistance.

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Analysis of babA, cagE and cagA Genes in Helicobacter pylori from Upper Gastric Patients in the North of Iran

Infectious Disorders - Drug Targets ◽

10.2174/1871526518666180515113218 ◽

2019 ◽

Vol 19 (3) ◽

pp. 274-278 ◽

Cited By ~ 1

Author(s):

Saba Fakhrieh Asl ◽

Mehrnaz Pourvahedi ◽

Ali Mojtahedi ◽

Mohammad Shenagari

Keyword(s):

Helicobacter Pylori ◽

Gastric Diseases ◽

Specific Primers ◽

The North ◽

Different Types ◽

North Of Iran ◽

Gastric Biopsies ◽

Pcr Method ◽

Non Ulcer Dyspepsia ◽

H Pylori

Objective:Helicobacter pylori is a Gram-negative bacterium which has a serious effect on up to half of the world’s population and has been related to different gastric diseases. The goal of this study was to assess the frequency of babA, cagE and cagA genotypes among H. pylori strains isolated from gastric biopsies of endoscopic patients in the north of Iran.Methods:The present study was performed on 90 strains of H. pylori isolated from patients with gastric diseases (Gastric ulcer (GU), Duodenal ulcer (DU), Gastritis (G), Non-ulcer dyspepsia (NUD) and Gastric adenocarcinoma (GC)). DNA was extracted from all isolated strains and PCR method was performed to detect the prevalence of babA2, cagE and cagA genes using specific primers.Results:Among 90 samples of H. pylori, babA2, cagE, and cagA genes were detected in 42.2%, 30% and 82.2% of strains respectively. The statistical analysis showed that the prevalence of cagA gene in GU, G, DU, and NUD was significantly higher than other genes. Moreover, cagA, and babA2 genes were significantly more prevalent in GC patients compared to cagE gene. Our isolates exhibited 8 distinct arrangements of virulence patterns. The occurrence of cagA (35.6%) was the most prevalent pattern followed by cagA/babA2 (20%) and cagA/babA2/cagE (14.4%).Conclusion:In summary, as first report from Guilan province in the north of Iran, we showed significant association between the presence of babA2, cagE, and cagA genes in different types of gastric disorders.

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Proteomics signature of autoimmune atrophic gastritis: towards a link with gastric cancer

Gastric Cancer ◽

10.1007/s10120-020-01148-3 ◽

2021 ◽

Author(s):

Ombretta Repetto ◽

Valli De Re ◽

Paolo Giuffrida ◽

Marco Vincenzo Lenti ◽

Raffaella Magris ◽

...

Keyword(s):

Gastric Cancer ◽

Atrophic Gastritis ◽

Tricarboxylic Acid Cycle ◽

Differential Abundance ◽

Expression Levels ◽

2D Dige ◽

Gastric Corpus ◽

Gastric Biopsies ◽

H Pylori ◽

Autoimmune Atrophic Gastritis

Abstract Background Autoimmune atrophic gastritis (AAG) is a chronic disease that can progress to gastric cancer (GC). To better understand AAG pathology, this proteomics study investigated gastric proteins whose expression levels are altered in this disease and also in GC. Methods Using two-dimensional difference gel electrophoresis (2D-DIGE), we compared protein maps of gastric corpus biopsies from AAG patients and controls. Differentially abundant spots (|fold change|≥ 1.5, P < 0.01) were selected and identified by LC–MS/MS. The spots were further assessed in gastric antrum biopsies from AAG patients (without and with Helicobacter pylori infection) and from GC patients and unaffected first-degree relatives of GC patients. Results 2D-DIGE identified 67 differentially abundant spots, with 28 more and 39 less abundant in AAG-corpus than controls. LC–MS/MS identified these as 53 distinct proteins. The most significant (adjusted P < 0.01) biological process associated with the less abundant proteins was “tricarboxylic acid cycle”. Of the 67 spots, 57 were similarly differentially abundant in AAG-antrum biopsies irrespective of H. pylori infection status. The differential abundance was also observed in GC biopsies for 14 of 28 more abundant and 35 of 39 less abundant spots, and in normal gastric biopsies of relatives of GC patients for 6 and 25 spots, respectively. Immunoblotting confirmed the different expression levels of two more abundant proteins (PDIA3, GSTP gene products) and four less abundant proteins (ATP5F1A, PGA3, SDHB, PGC). Conclusion This study identified a proteomics signature of AAG. Many differential proteins were shared by GC and may be involved in the progression of AAG to GC.

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Frequency of rdx A Deletion Mutation Conferring Metronidazole Resistance in Helicobacter pylori

10.51429/ejmm29308 ◽

2020 ◽

Vol 29 (3) ◽

pp. 59-64

Author(s):

Hanaa M. El Maghraby ◽

Samar Mohaseb

Keyword(s):

Helicobacter Pylori ◽

Epigastric Pain ◽

Deletion Mutation ◽

Rapid Urease Test ◽

Rrna Gene ◽

University Hospitals ◽

Metronidazole Resistance ◽

Urease Test ◽

Gastric Biopsies ◽

H Pylori

Background: Metronidazole is one of the antimicrobial drugs that can be used in combination with other drugs for eradication of Helicobacter pylori (H. pylori).Unfortunately, metronidazole resistance in H. plori is an increasing health problem which may be attributed to inactivation of many genes as rdx A gene. Objective: To determine the frequency of rdx A deletion mutation in H. pylori detected in infected patients attending at the Gastroenterology Unit, Zagazig University Hospitals. Methodology: Two gastric biopsies were taken from each enrolled patient by endoscopy. H.pylori detection was done by rapid urease test and polymerase chain reaction (PCR) amplification of 16S rRNA gene. Deletion mutation in rdx A gene was detected by conventional PCR. Results: Out of 134 doubled gastric biopsies obtained from 134 patients, 52.2% were positive for H. pylori. Epigastric pain, vomiting and gastritis were significantly associated with detection of H. pylori infection (p˂ 0.05). Deletion mutation of rdx A gene was detected in 28.6% of H. pylori positive specimens obtained from infected patients. Conclusion: Deletion mutation of rdx A gene is a frequent determinant of rdx A inactivation conferring metronidazole resistance among H. pylori.

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Evaluation of Better Staining Method among Hematoxylin and Eosin, Giemsa and Periodic Acid Schiff-Alcian Blue for the Detection of Helicobacter pylori in Gastric Biopsies

Malaysian Journal of Medical Sciences ◽

10.21315/mjms2020.27.5.6 ◽

2020 ◽

Vol 27 (5) ◽

pp. 53-61

Author(s):

Abdullah Saleh Alkhamiss

Keyword(s):

Helicobacter Pylori ◽

Alcian Blue ◽

National Guard ◽

Periodic Acid ◽

Giemsa Stain ◽

Periodic Acid Schiff ◽

Gastric Biopsies ◽

Hematoxylin And Eosin ◽

H Pylori ◽

Sensitivity Specificity

Background: This study was undertaken to evaluate the preferred method (Giemsa or periodic acid Schiff-Alcian blue [PAS-AB] stains) of detecting Helicobacter pylori (H. pylori) in gastric mucosal biopsies in terms of sensitivity, specificity and applicability. To the best of my knowledge, this is the first report comparing Giemsa and PAS-AB staining for the detection of H. pylori in such biopsies. Methods: The formalin-fixed paraffin-embedded blocks of 49 gastric biopsies from different patients were collected from the archive of anatomical pathology at King Abdulaziz Medical City, National Guard, Riyadh, Saudi Arabia. From each block, three slides were prepared and analysed using the hematoxylin and eosin (H&E), Giemsa and PAS-AB stains to detect the presence/absence of H. pylori, and the results were compared in terms of sensitivity, specificity and applicability. Results: The majority of the biopsies in this study showed antrum-type gastric mucosa. Only 15 biopsies showed active gastritis, whereas the rest showed chronic gastritis. Three biopsies showed intestinal metaplasia. All were detected by PAS-AB stain, but only two-thirds were detected by H&E stain. Fifteen gastric biopsies showed H. pylori infection in general and in 13 of them, active gastritis cases were discovered. Fourteen out of these 15 H. pylori infection cases were detected by Giemsa stain, whereas only 13 cases were detected by H&E stain. PAS-AB stain showed the worst results since it demonstrated only 40% sensitivity and 67.65% specificity in H. pylori detection. Conclusion: Giemsa stain has better sensitivity and specificity in gastric H. pylori infection detection than PAS-AB. Therefore, using PAS-AB stain to detect H. pylori infection is not recommended.

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Primary antibiotic resistance of Helicobacter pylori among a Chinese Tibetan population

Future Microbiology ◽

10.2217/fmb-2020-0206 ◽

2020 ◽

Vol 15 (14) ◽

pp. 1353-1361

Author(s):

Xiaoqiong Tang ◽

Xiaohong Chen ◽

Yalin Shen ◽

Tiankuo Yang ◽

Renwei Hu ◽

...

Keyword(s):

Helicobacter Pylori ◽

Antibiotic Resistance ◽

Primary Resistance ◽

Tibetan Population ◽

Disk Diffusion Assay ◽

Treatment Naïve ◽

Gastric Biopsies ◽

H Pylori ◽

Resistance Rates ◽

Diffusion Assay

Aim: To evaluate the primary antibiotic resistance in Helicobacter pylori strains isolated from a Chinese Tibetan population. Methods & materials: Gastric biopsies from 400 H. pylori treatment-naive Tibetan patients were collected for H. pylori isolation. Susceptibility to amoxicillin (AML)/clarithromycin (CLR)/levofloxacin (LEV)/metronidazole (MTZ)/tetracycline (TET)/rifampicin (RIF)/furazolidone (FZD) was determined by E-test or a disk diffusion assay. Results: Biopsies from 117 patients were H. pylori culture positive (29.3%). The primary resistance rates to MTZ, CLR, LEV, RIF, AML, TET and FZD were 90.6, 44.4, 28.2, 69.2, 7.7, 0.8 and 0.8%, respectively. Interestingly, 42.7% of the strains had simultaneous resistance to CLR and MTZ. Conclusion: Among Tibetan strains, primary resistance rates were high for CLR/MTZ/LEV, whereas primary resistance rates to AML/TET/FZD were low. The high resistance to RIF is a concerning finding.

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Antibiotic Resistance and Genotypes of Helicobacter pylori Strains in Patients with Gastroduodenal Disease in Southeast Poland

Journal of Clinical Medicine ◽

10.3390/jcm8071071 ◽

2019 ◽

Vol 8 (7) ◽

pp. 1071 ◽

Cited By ~ 3

Author(s):

Izabela Korona-Glowniak ◽

Halina Cichoz-Lach ◽

Radoslaw Siwiec ◽

Sylwia Andrzejczuk ◽

Andrzej Glowniak ◽

...

Keyword(s):

Genetic Diversity ◽

Helicobacter Pylori ◽

Test Method ◽

Rapid Urease Test ◽

Microbial Culture ◽

Virulence Markers ◽

Gastroduodenal Disease ◽

Urease Test ◽

Gastric Biopsies ◽

H Pylori

The aim of this study was to investigate genetic diversity of Helicobacter pylori virulence markers to predict clinical outcome as well as to determine an antibiotic susceptibility of H. pylori strains in Poland. Gastric biopsies from 132 patients with gastrointestinal disorders were tested for presence of H. pylori with the use of rapid urease test, microbial culture, and polymerase chain reaction (PCR) detection. The genetic diversity of 62 H. pylori positive samples was evaluated by detection of cagA and PCR-typing of vacA and iceA virulence-associated genes. Most common H. pylori genotypes were cagA(+)vacAs1m2 (27.4%) and cagA(−)vacAs2m2 (24.2%). In logistic regression analysis, we recognized the subsequent significant associations: gastritis with ureC, i.e., H. pylori infection (p = 0.006), BMI index (p = 0.032); and negatively with iceA1 (p = 0.049) and peptic ulcer with cagA (p = 0.018). Thirty-five H. pylori strains were cultured and tested by E-test method showing that 49% of strains were resistant to at least one of the tested antibiotics. This is the first study that reports the high incidence and diversity of allelic combination of virulence genes in gastroduodenitis patients in Poland. Genotyping of H. pylori strains confirmed the involvement of cagA gene and vacAs1m1 genotype in development and severity of gastric disorder.

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Deep learning for sensitive detection of Helicobacter Pylori in gastric biopsies

BMC Gastroenterology ◽

10.1186/s12876-020-01494-7 ◽

2020 ◽

Vol 20 (1) ◽

Author(s):

Sebastian Klein ◽

Jacob Gildenblat ◽

Michaele Angelika Ihle ◽

Sabine Merkelbach-Bruse ◽

Ka-Won Noh ◽

...

Keyword(s):

Helicobacter Pylori ◽

Deep Learning ◽

Decision Support ◽

Ground Truth ◽

Novel Technologies ◽

Therapeutic Decisions ◽

Gastric Biopsies ◽

H Pylori ◽

Microscopic Diagnosis ◽

Whole Slide Images

Abstract Background Helicobacter pylori, a 2 × 1 μm spiral-shaped bacterium, is the most common risk factor for gastric cancer worldwide. Clinically, patients presenting with symptoms of gastritis, routinely undergo gastric biopsies. The following histo-morphological evaluation dictates therapeutic decisions, where antibiotics are used for H. pylori eradication. There is a strong rational to accelerate the detection process of H. pylori on histological specimens, using novel technologies, such as deep learning. Methods We designed a deep-learning-based decision support algorithm that can be applied on regular whole slide images of gastric biopsies. In detail, we can detect H. pylori both on Giemsa- and regular H&E stained whole slide images. Results With the help of our decision support algorithm, we show an increased sensitivity in a subset of 87 cases that underwent additional PCR- and immunohistochemical testing to define a sensitive ground truth of HP presence. For Giemsa stained sections, the decision support algorithm achieved a sensitivity of 100% compared to 68.4% (microscopic diagnosis), with a tolerable specificity of 66.2% for the decision support algorithm compared to 92.6 (microscopic diagnosis). Conclusion Together, we provide the first evidence of a decision support algorithm proving as a sensitive screening option for H. pylori that can potentially aid pathologists to accurately diagnose H. pylori presence on gastric biopsies.

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Effects of different attractants and human scent on mesocarnivore detection at camera traps

Wildlife Research ◽

10.1071/wr19117 ◽

2020 ◽

Vol 47 (4) ◽

pp. 338

Author(s):

Bracy W. Heinlein ◽

Rachael E. Urbanek ◽

Colleen Olfenbuttel ◽

Casey G. Dukes

Keyword(s):

Fatty Acid ◽

Castor Oil ◽

Camera Trap ◽

Camera Traps ◽

Individual Species ◽

Detection Rates ◽

Capture Success ◽

Affect Detection ◽

Species Specific

Abstract ContextCamera traps paired with baits and scented lures can be used to monitor mesocarnivore populations, but not all attractants are equally effective. Several studies have investigated the efficacy of different attractants on the success of luring mesocarnivores to camera traps; fewer studies have examined the effect of human scent at camera traps. AimsWe sought to determine the effects of human scent, four attractants and the interaction between attractants and human scent in luring mesocarnivores to camera traps. Methods We compared the success of synthetic fermented egg (SFE), fatty acid scent (FAS) tablets, castor oil, and sardines against a control of no attractant in luring mesocarnivores to camera traps. We deployed each attractant and the control with either no regard to masking human scent or attempting to restrict human scent for a total of 10 treatments, and replicated treatments eight to nine times in two different phases. We investigated whether: (1) any attractants increased the probability of capturing a mesocarnivore at a camera trap; (2) not masking human scent affected the probability of capturing a mesocarnivore at a camera trap; and (3) any attractants increased the probability of repeat detections at a given camera trap. We also analysed the behaviour (i.e. speed and distance to attractant) of each mesocarnivore in relation to the attractants. Key resultsSardines improved capture success compared with the control treatments, whereas SFE, castor oil, and FAS tablets had no effect when all mesocarnivores were included in the analyses. Masking human scent did not affect detection rates in the multispecies analyses. Individually, the detection of some species depended on the interactions between masking (or not masking) human scent and some attractants. ConclusionsSardines were the most effective as a broad-based attractant for mesocarnivores. Mesocarnivores approached traps baited with sardines at slower rates, which allows for a higher success of capturing an image of the animal. ImplicationsHuman scent may not need to be masked when deploying camera traps for multispecies mesocarnivore studies, but researchers should be aware that individual species respond differently to attractants and may have higher capture success with species-specific attractants.

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A 14-Day Course of Triple Therapy is Superior to a 10-Day Course for the Eradication ofHelicobacter pylori: A Canadian Study Conducted in a ‘Real World’ Setting

Canadian Journal of Gastroenterology and Hepatology ◽

10.1155/2015/659390 ◽

2015 ◽

Vol 29 (8) ◽

pp. e7-e10 ◽

Cited By ~ 6

Author(s):

Yen-I Chen ◽

Carlo A Fallone

Keyword(s):

Triple Therapy ◽

Eradication Rate ◽

Day Treatment ◽

Office Visit ◽

First Line ◽

Intention To Treat ◽

Treatment Naïve ◽

Gastric Biopsies ◽

H Pylori ◽

Treat Analysis

BACKGROUND: SuccessfulHelicobacter pylorieradication with the traditional seven-day course of proton pump inhibitor (PPI) triple therapy is declining. Prolonging therapy to either 10 or 14 days is associated with better eradications rates.OBJECTIVE: To compare the effectiveness of 14-day course of triple therapy versus a 10-day course in the treatment ofH pyloriin Canada.METHODS: Consecutive treatment-naive patients with clinical indications forH pylorieradication underwent either a 10-day course or a 14-day course of traditional PPI triple therapy depending on the date of the office visit (an odd date received the 10-day course, whereas an even date received the 14-day treatment).H pylorieradication was ascertained via urea breath test or gastric biopsies performed ≥4 weeks after completion of therapy. Analyses were by both intention to treat and per-protocol.RESULTS: A total of 83 patients were included in the study (31 in the 10-day group and 52 in the 14-day group). In the intention-to-treat analysis, eradication rates were 82.7% (95% CI 70% to 92%) versus 45.2% (95% CI 27% to 64%), favouring the 14-day treatment (P<0.001). Similarly, in the per-protocol analysis, eradication rates were 91.5% (95% CI 80% to 98%) versus 63.6% (95% CI 41% to 83%), favouring the 14-day arm (P=0.01). Adverse events and compliance were not significantly different between the two groups.CONCLUSION: A 14-day course of standard PPI triple therapy was superior to a shorter-duration therapy and should be included as a first-line regimen forH pylorieradication in Canada. The 10-day course of treatment did not achieve an acceptable eradication rate and should no longer be used in this country.

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