Clustering of South African Helicobacter pylori isolates from peptic ulcer disease patients is demonstrated by repetitive extragenic palindromic-PCR fingerprinting

Effect of treatment failure on the CagA EPIYA motif in Helicobacter pylori strains from Colombian subjects

AIM

To evaluate effect of treatment failure on cagA and vacA genotypes in Helicobacter pylori (H. pylori) isolates from Colombia.

METHODS

One hundred and seventy-six participants infected with H. pylori from Colombia were treated during 14 d with the triple-standard therapy. Six weeks later, eradication was evaluated by ¹³C-Urea breath test. Patients with treatment failure were subjected to endoscopy control; biopsies obtained were used for histopathology and culture. DNA from H. pylori isolates was amplified using primers specific for cagA and vacA genes. The phylogenetic relationships among isolates obtained before and after treatment were established by conglomerate analysis based on random amplified polymorphic DNA (RAPD) fingerprinting.

RESULTS

Treatment effectiveness was at 74.6%. Of the participants with treatment failure, 25 accepted subjected to a second endoscopy. Prevalence of post-treatment infection was 64% (16/25) and 40% (10/25) by histology and culture, respectively. Upon comparing the cagA and vacA genotypes found before and after therapy, multiple cagA genotypes (cagA-positive and cagA-negative) were found before treatment; in contrast, cagA-negative genotypes decreased after treatment. vacA s1m1 genotype was highly prevalent in patients before and after therapy. The 3’cagA region was successfully amplified in 95.5% (21/22) of the isolates obtained before and in 81.8% (18/22) of the isolates obtained after treatment. In the isolates obtained from patients with treatment failure, it was found that 72.7% (16/22) presented alterations in the number of EPIYA motifs, compared to isolates found before treatment.

CONCLUSION

Unsuccessful treatment limits colonization by low-virulence strains resulting in partial and selective eradication in mixed infections, and acts on the cagA-positive strains inducing genetic rearrangements in cagA variable region that produces a loss or gain of EPIYA repetitions.

Clinical Application of the DiversiLab Microbial Typing System Using Repetitive Sequence-Based PCR for Characterization of Helicobacter pylori in Japan

We evaluated the DiversiLab (DL) system with universal primers, a semiautomated repetitive extragenic palindromic sequence-based polymerase chain reaction (PCR) (rep-PCR) system, for the characterization of Helicobacter pylori in Japan. All 135 isolates from Japanese patients with gastric cancer (GC, n = 55) or non-GC (n = 80) were used and subjected to the drug susceptibility examinations (amoxicillin, AMPC; metronidazole, MNZ; and clarithromycin, CAM) by E-test. There were 28 MNZ-resistant (20.7%), 35 CAM-resistant (25.9%), and 16 MNZ/CAM-resistant (11.9%) isolates. DL rep-PCR fingerprinting analysis at the level of 95% similarity revealed five major groups (A-E) and the other including 45 isolates. The occupation rates of GC-derived isolates in groups B (54.2%) and E (58.8%) were higher than in the other groups: A (26.7%), C (28.6%), D (30.0%), and the other (40.0%). Relative higher occupation rates of drug resistants, such as MNZ-, CAM- and double MNZ/CAM-resistant isolates, were observed in groups B (45.8%), C (42.6%), and D (40%). Five of eight GC-derived isolates with MNZ/CAM resistance were significantly assigned to group B (P = 0.0312, χ(2) -test). These results suggest that the isolates classified in group B have a potential to contribute to the development of severe gastric disorders. The DL system, rapid and high sensitive technology, would be widely available in clinical laboratory for pathological and epidemiological analyses even in H. pylori.

Molecular characterization and susceptibility testing of Helicobacter pylori strains isolated in western Argentina

OBJECTIVE

To characterize Helicobacter pylori isolates from western Argentina using virulence markers and antimicrobial susceptibility patterns in order to assess the association between virulent genotypes, antimicrobial resistance, and disease. DNA fingerprinting was also evaluated for the segregation of virulent or resistant strain clusters.

METHODS

Genotyping of 299 H. pylori isolates was performed by PCR using specific primers for the cagA, vacA and iceA genes. Random amplification of polymorphic DNA (RAPD)-PCR and rep-PCR genetic clustering were assessed using five random primers and BOXA1R and ERIC primers, respectively. Resistance to clarithromycin (Cla) and metronidazole (Mtz) was assessed by the agar dilution method.

RESULTS

It was observed that 40.8% of the genotypes were cagA-positive; 66.9% were vacA s1m1 genotype and the iceA1 allele was found in 40.8%. A significant correlation (p=0.0000) was observed between cagA positivity and vacA s1m1/iceA1 genotypes. Triple virulent genotypes were statistically associated with peptic ulcer (PU) (p=0.0001) and Cla resistance (p=0.0000). RAPD fingerprints obtained with AO2 primers identified clusters that were strongly associated with PU, virulence markers, and resistance to Cla and Mtz.

CONCLUSIONS

The H. pylori isolates that harbored two or three virulence markers were more resistant to Cla and Mtz. Combined analysis of virulent genotypes and resistance patterns may permit identification of high-risk patients to prevent PU later in life or to avoid antimicrobial treatment failure.

The association of vacA genotype and Helicobacter pylori-related disease in Latin American and African populations

In the populations of Western countries, particular genotypes of the vacuolating cytotoxin gene, vacA (vacA s, signal region variants; vacA m, middle region variants) of Helicobacter pylori are believed to be risk factors for the development of peptic ulcers and gastric cancer. However, it was unclear whether these vacA gene variants are associated with the development of gastrointestinal diseases in developing nations. The relationship between vacA genotypes and H. pylori-related disease development in Latin American and African populations was investigated using meta-analysis of 2612 patients from Latin America (2285 strains) and 520 patients from Africa (434 strains). The frequencies of vacA s and m genotypes differed between strains from Latin America (77.2% for s1 and 68.1% for m1) and Africa (83.9% for s1 and 56.7% for m1). Latin American strains with s1 and m1 genotypes increased the risk of gastric cancer (OR 4.17, 95% CI 2.49-6.98 for s1, and 3.59, 2.27-5.68 for m1) and peptic ulcers (e.g. 1.73, 1.37-2.20 for s1). African strains with the s1 or m1 genotypes also increased the risk of peptic ulcers (8.69, 1.16-64.75 for s1) and gastric cancer (10.18, 2.36-43.84 for m1). The cagA-positive genotype frequently coincided with s1 and m1 genotypes in both populations. Overall, the vacA s and m genotypes were related to gastric cancer and peptic ulcer development and might be useful markers of risk factors for gastrointestinal disease, especially in Latin America. Further studies will be required to evaluate the effects of vacA genotypes in African populations because of the small sample number currently available.

J. Análise das impressões digitais de DNA e de fatores de virulência de linhagens de Helicobacter pylori

RACIONAL: Helicobacter pylori é hoje aceito como o principal agente etiológico de gastrite em seres humanos e fator de risco para úlcera péptica e câncer gástrico. A evolução da infecção está relacionada a diversos fatores, inclusive bacterianos, como presença do gene cagA e o genótipo vacA s1m1, associados ao desenvolvimento de úlcera e adenocarcinoma gástrico. A técnica de RAPD ("random amplified polimorphic") tem sido amplamente utilizada para obtenção de impressões digitais de DNA para examinar a similaridade entre linhagens. OBJETIVOS: Avaliar a presença de cagA e alelos do vacA em amostras de H. pylori e associar os achados com a doença apresentada e também investigar possível clonicidade entre os fatores de virulência e as doenças com a impressão digital de DNA gerada pelo RAPD-PCR. MÉTODOS: Foram incluídas 112 amostras provenientes de pacientes com diferentes laudos endoscópicos: gastrite (n = 41), esofagite de refluxo (n = 14), úlcera gástrica (n = 19) e úlcera duodenal (n = 38). A análise dos fatores de virulência da bactéria foi feita por PCR e as impressões digitais de DNA foram estabelecidas pelo método de RAPD-PCR. RESULTADOS: Os resultados obtidos indicam que houve uma associação significativa entre úlcera duodenal e o mosaico vacA s1m1. Analisando-se os padrões de bandas geradas pelo RAPD-PCR, sete diferentes dendogramas foram construídos e não foi possível detectar associação significativa entre os agrupamentos, sugerindo que as amostras não possuem perfil clonal. CONCLUSÃO: Os resultados reforçam a importância do gene vacA como um marcador de virulência do H. pylori. O RAPD da impressão digital de DNA realizado foi incapaz de associar o padrão de bandas com as enfermidades e os genótipos de vacA e cagA.

Analysis of genetic variability, antimicrobial susceptibility and virulence markers in Helicobacter pylori identified in Central Italy

OBJECTIVE

To assess the relationship between the presence of mixed infection of Helicobacter pylori and both antimicrobial susceptibility and virulence markers.

MATERIAL AND METHODS

Thirty-six patients with H. pylori infection were included in the study. Three colonies were selected from each positive biopsy sample collected from each host for a total of 108 H. pylori strains. The genetic variability was evaluated through the amplified fragment length polymorphism (AFLP) analysis; the antibiotic susceptibility to amoxicillin, clarithromycin, moxifloxacin, rifabutin and tinidazole was determined using the minimum inhibitory concentrations (MICs) with the agar dilution method. Moreover, the vacA, cagA, iceA and babA2 statuse were detected by polymerase chain reaction (PCR).

RESULTS

There was a strong connection between mixed H. pylori infection and antimicrobial resistance. In particular, H. pylori strains with genetic variability, in the same host, expressed more resistance to clarithromycin, moxifloxacin and tinidazole than that expressed in strains with a unique genetic host pattern. VacA s1m1/s1m2 genotypes were found in 70% of strains isolated in mixed infection, whereas the same allelic combinations were found in 42% of strains, isolated in single infection. The cagA(+) status prevailed both in patients with mixed (97%) and in those with single infection (85%) without significant differences. The iceA1 status was more commonly found in patients with mixed infection, whereas the babA2 status was significantly prevalent in single H. pylori infection.

CONCLUSIONS

Mixed H. pylori infection harbouring in one patient is significantly related to strains that are more resistant to antibiotics and with a more virulent genotype (vacA s1m1/s1m2, cagA, iceA1) than strains responsible for single infection.

Microbial source tracking: state of the science

Although water quality of the Nation's lakes, rivers and streams has been monitored for many decades and especially since the passage of the Clean Water Act in 1972, many still do not meet the Act's goal of "fishable and swimmable". While waterways can be impaired in numerous ways, the protection from pathogenic microbe contamination is most important for waters used for human recreation, drinking water and aquaculture. Typically, monitoring methods used for detecting potential pathogenic microorganisms in environmental waters are based upon cultivation and enumeration of fecal indicator bacteria (i.e. fecal coliforms, E. coli, and fecal enterococci). Currently, there is increasing interest in the potential for molecular fingerprinting methods to be used not only for detection but also for identification of fecal contamination sources. Molecular methods have been applied to study the microbial ecology of environmental systems for years and are now being applied to help improve our waters by identifying problem sources and determining the effect of implemented remedial solutions. Management and remediation of water pollution would be more cost-effective if the correct sources could be identified. This review provides an outline of the main methods that either have been used or have been suggested for use in microbial source tracking and some of the limitations associated with those methods.

Phenotypic variation of Helicobacter pylori isolates from geographically distinct regions detected by lectin typing

A total of 309 Helicobacter pylori isolates from 18 different countries were analyzed with a previously developed lectin typing system. The system was developed by using a proteolytic pretreatment to enhance the carbohydrate fraction of the sample. Four lectins from Ulex europaeus, Lotus tetragonolobus, Erythrina cristigali, and Triticum vulgaris were used to type the strains. The lectins were chosen for their specificities for sugars commonly encountered in the lipopolysaccharide of H. pylori. The isolates were received from their parent institutions as pellets of biomass and were typed at one of three centers (in Ireland, Sweden, and Estonia). All 16 possible lectin reaction patterns were observed in the study, with the isolates with the predominant pattern exhibiting reactions with all the lectins in the panel. For European patients suffering from gastritis, an association was noted between lectin reaction pattern MH4 and atrophic chronic gastritis; isolates with lectin reaction pattern MH4 were isolated from patients with atrophic chronic gastritis, whereas isolates with this pattern were not isolated from patients with chronic gastritis (P = 0.0006). In addition, statistically significant relationships were noted between the lectin reaction pattern and the associated pathology of isolates from the Swedish population. Isolates with patterns MH13 and MH16, which had low lectin reactivities, correlated with nonulcer disease (P = 0.0025 and P = 0.0002, respectively), and all four isolates from adenocarcinoma patients were characterized as possessing reaction pattern MH16. In contrast, isolates with lectin reaction patterns MH1 and MH10, which had high lectin reactivities, were associated with ulcer disease (P = 0.046 and P = 0.0022, respectively).