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Buyuk F, Karakaya E, Akar M, Kayman T, Tarhane S, Ozcan HE, Celebi O, Saticioglu IB, Anuk T, Abay S, Otlu S, Aydin F. A comprehensive study of Helicobacter pylori infection: molecular analysis, antibacterial susceptibility, and histopathological examination. Antonie Van Leeuwenhoek 2023; 116:1261-1273. [PMID: 37603113 DOI: 10.1007/s10482-023-01868-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 08/07/2023] [Indexed: 08/22/2023]
Abstract
Helicobacter pylori is a pathogen associated with gastroduodenal diseases. This study aimed; (i) to investigate H. pylori presence by invasive tests in adult dyspeptic patients, (ii) to determine antibiotic susceptibility and genotypic characteristics of the H. pylori isolates, and (iii) to investigate the relationship between the H. pylori genotypes and the histopathological findings. In this cross-sectional study, gastric biopsy samples from 208 adult dyspeptic patients were used for culture, tissue Polymerase Chain Reaction (PCR), and histopathological analysis. Antibiotic susceptibility of the H. pylori isolates was analyzed by gradient method. Analysis of the virulence genes was performed by monoplex PCR. Genetic profiles (from A to H) were created based on the virulence genes presence. Enterobacterial Repetitive Intergenic Consensus-PCR (ERIC-PCR) was used for the genotyping of the H. pylori isolates. The mean age of the patients was 46 (± 15) years and 128 (61.5%) of them were female. H. pylori positivity was detected by culture, tissue PCR and histopathological examination in 59 (28.4%), 114 (54.8%) and 81 (38.9%) patients, respectively. The overall prevalence of H. pylori was found to be 63% (131/208). All H. pylori isolates were susceptible to tetracycline and amoxicillin. The resistance rates for metronidazole, clarithromycin, levofloxacin, and rifampicin were 67.2%, 27.9%, 34.4% and 13.11%, respectively. Multi drug resistance (MDR) was detected at the rate of 45.9% (28/61). While the most common virulence gene was cagA (93.44%), the least common was vacAm1 (23%). The predominant genetic profile was profile A (47.5%). ERIC-PCR results revealed a total of 26 different patterns. A high prevalence of H. pylori was detected in adult dyspeptic patients as in developing countries. It was observed significant genotypic heterogeneity and virulence gene diversity within the isolates. A considerable resistance rate detected against antibiotics such as clarithromycin, metronidazole, and levofloxacin, which are frequently used in the eradication of H. pylori, should be taken into consideration when creating regional empirical treatment regimens.
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Affiliation(s)
- Fatih Buyuk
- Department of Microbiology, Faculty of Veterinary Medicine, Kafkas University, Kars, Türkiye.
| | - Emre Karakaya
- Department of Microbiology, Faculty of Veterinary Medicine, Erciyes University, Kayseri, Türkiye
| | - Mustafa Akar
- Department of Gastroenterology, University of Health Sciences, Bursa Yüksek İhtisas Training and Research Hospital, Bursa, Türkiye
| | - Tuba Kayman
- Department of Medical Microbiology, Faculty of Medicine, Kırıkkale University, Kırıkkale, Türkiye
| | - Serdal Tarhane
- Veterinary Department, Eldivan Vocational School of Health Services, Çankırı Karatekin University, Çankırı, Türkiye
| | - Hacer Ece Ozcan
- Department of Medical Pathology, Mersin City Hospital, Mersin, Türkiye
| | - Ozgur Celebi
- Department of Microbiology, Faculty of Veterinary Medicine, Kafkas University, Kars, Türkiye
| | - Izzet Burcin Saticioglu
- Department of Aquatic Animal Diseases, Faculty of Veterinary Medicine, Uludağ University, Bursa, Türkiye
| | - Turgut Anuk
- Department of General Surgery, Erzurum Faculty of Medicine, University of Health Sciences, Erzurum, Türkiye
| | - Secil Abay
- Department of Microbiology, Faculty of Veterinary Medicine, Erciyes University, Kayseri, Türkiye
| | - Salih Otlu
- Department of Microbiology, Faculty of Veterinary Medicine, Kafkas University, Kars, Türkiye
| | - Fuat Aydin
- Department of Microbiology, Faculty of Veterinary Medicine, Erciyes University, Kayseri, Türkiye
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Milani M, Moaddab Y, Sharifi Y. One piece biopsy for both rapid urease test and cultivation of Helicobacter pylori. J Microbiol Methods 2019; 164:105674. [PMID: 31348953 DOI: 10.1016/j.mimet.2019.105674] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2019] [Revised: 07/22/2019] [Accepted: 07/22/2019] [Indexed: 01/03/2023]
Abstract
BACKGROUND & AIMS Increasing antibiotic resistance among Helicobacter pylori isolates and the unsuccessful attempts at eradication can impose many costs to both healthcare systems and patients. The present study intended to find a way from which H. pylori could be isolated from biopsies with less invasive procedures undertaken on infected patients. METHODS A biopsy specimen from each patient with gastric disorders was put into urea-containing agar. After two hours, the specimens were removed from agar and placed into tubes containing 1 ml 20% glucose solution. Then, the specimens were inoculated onto the Columbia agar and incubated under microaerophilic conditions. The grown colonies were identified as H.pylori based on the microbiology tests and PCR. RESULTS Overall, 449 biopsy specimens were collected from the patients. Of all biopsies, 219 (48.8%) revealed positive results in the rapid urease test. Using the aforementioned method, 158 (35.2%) culture positive biopsy specimens were obtained. CONCLUSION The researchers attempted to use one biopsy specimen for both rapid urease and culture tests. This method causes fewer injuries of gastric tissue and allows antimicrobial susceptibility testing and characterization in detail of the isolated organism.
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Affiliation(s)
- Morteza Milani
- Infectious and Tropical Diseases Research Center, Tabriz University of Medical Science, Tabriz, Iran; Department of Medical Nanotechnology, Faculty of Advanced Medical Science, Medical University of Tabriz, Tabriz, Iran
| | - Yaghuob Moaddab
- Liver and Gastrointestinal disease research center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Yaeghob Sharifi
- Department of Microbiology, Faculty of Medicine, Urmia University of Medical Sciences, Urmia, Iran; Cellular and molecular research center, Faculty of Medicine, Urmia University of Medical Sciences, Urmia, Iran.
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González-Vázquez R, Herrera-González S, Cordova-Espinoza MG, Zúñiga G, Giono-Cerezo S, Hernández-Hernández JM, León-Ávila G. Helicobacter pylori: detection of iceA1 and iceA2 genes in the same strain in Mexican isolates. Arch Med Res 2012; 43:339-46. [PMID: 22884501 DOI: 10.1016/j.arcmed.2012.07.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2011] [Accepted: 07/04/2012] [Indexed: 12/11/2022]
Abstract
BACKGROUND AND AIMS Helicobacter pylori iceA1 and iceA2 gene amplification is usually performed to identify mixed populations as both genes are apparently reportedly exclusive. However, some strains isolated from Mexico show both iceA genes. The aim of this study was to establish the frequency of these genes in Mexican isolates and genomic diversity of the H. pylori strains. METHODS One hundred thirty six biopsies were obtained from 68 patients (39 children and 29 adults). The presence of H. pylori was confirmed in 3/18 children and 6/19 adults by culture. There were 93 clinical strains isolated from nine patients. Additionally, we studied 37 strains from a strain collection isolated from 10 patients. The strains were genotyped and dual iceA genes were identified by polymerase chain reaction (PCR) and amplicons were sequenced. In addition, an enterobacterial repetitive intergenic consensus PCR (ERIC-PCR) assay was performed as fingerprinting method. RESULTS The genotypification of the H. pylori isolates indicated that all strains were vacA+; 86% babA2+, 86% cagA+, 82% vacA s1m1+, 19% iceA1+, 9% iceA2+, and 72% of them carried both iceA1 and iceA2 genes. The ERIC-PCR profiling revealed that the strains clustered in eight genetic groups depending on the presence of iceA1, iceA2 or both. A basic local multiple alignment analysis of the nucleotide sequences revealed that the iceA1 and iceA2 genes exhibited no relevant similarity. CONCLUSION The results here showed the presence of triple-positive strains (babA, cagA, vacA) of H. pylori and strains carrying simultaneously both iceA1 and iceA2 genes.
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Affiliation(s)
- Rosa González-Vázquez
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, México, DF, Mexico
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Impact of transgenic Bt-cotton on the diversity of pink-pigmented facultative methylotrophs. World J Microbiol Biotechnol 2008. [DOI: 10.1007/s11274-008-9713-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Hussain MA, Naveed SA, Sechi LA, Ranjan S, Alvi A, Ahmed I, Ranjan A, Mukhopadhyay S, Ahmed N. Isocitrate dehydrogenase of Helicobacter pylori potentially induces humoral immune response in subjects with peptic ulcer disease and gastritis. PLoS One 2008; 3:e1481. [PMID: 18213389 PMCID: PMC2195454 DOI: 10.1371/journal.pone.0001481] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2007] [Accepted: 12/24/2007] [Indexed: 01/11/2023] Open
Abstract
Background H. pylori causes gastritis and peptic ulcers and is a risk factor for the development of gastric carcinoma. Many of the proteins such as urease, porins, flagellins and toxins such as lipo-polysaccharides have been identified as potential virulence factors which induce proinflammatory reaction. We report immunogenic potentials of isocitrate dehydrogenase (ICD), an important house keeping protein of H. pylori. Methodology/Principal Findings Amino acid sequences of H. pylori ICD were subjected to in silico analysis for regions with predictably high antigenic indexes. Also, computational modelling of the H. pylori ICD as juxtaposed to the E. coli ICD was carried out to determine levels of structure similarity and the availability of surface exposed motifs, if any. The icd gene was cloned, expressed and purified to a very high homogeneity. Humoral response directed against H. pylori ICD was detected through an enzyme linked immunosorbent assay (ELISA) in 82 human subjects comprising of 58 patients with H. pylori associated gastritis or ulcer disease and 24 asymptomatic healthy controls. The H. pylori ICD elicited potentially high humoral immune response and revealed high antibody titers in sera corresponding to endoscopically-confirmed gastritis and ulcer disease subjects. However, urea-breath-test negative healthy control samples and asymptomatic control samples did not reveal any detectable immune responses. The ELISA for proinflammatory cytokine IL-8 did not exhibit any significant proinflammatory activity of ICD. Conclusions/Significance ICD of H. pylori is an immunogen which interacts with the host immune system subsequent to a possible autolytic-release and thereby significantly elicits humoral responses in individuals with invasive H. pylori infection. However, ICD could not significantly stimulate IL8 induction in a cultured macrophage cell line (THP1) and therefore, may not be a notable proinflammatory agent.
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Affiliation(s)
- M. Abid Hussain
- Pathogen Evolution Laboratory, Centre for DNA Fingerprinting and Diagnostics (CDFD), Hyderabad, India
| | - Shaik A. Naveed
- Centre for Liver Research and Diagnostics, Deccan College of Medical Sciences and Allied Hospitals, Hyderabad, India
| | - Leonardo A. Sechi
- Dipartimento di Scienze Biomediche, Sezione Microbiologia sperimentale e clinica, Facoltà di Medicina, Universiti degli studi de Sassari, Sassari, Italy
| | - Sarita Ranjan
- Computational and Functional Genomics Group, Centre for DNA Fingerprinting and Diagnostics (CDFD), Hyderabad, India
| | - Ayesha Alvi
- Pathogen Evolution Laboratory, Centre for DNA Fingerprinting and Diagnostics (CDFD), Hyderabad, India
| | - Irshad Ahmed
- Centre for Liver Research and Diagnostics, Deccan College of Medical Sciences and Allied Hospitals, Hyderabad, India
| | - Akash Ranjan
- Computational and Functional Genomics Group, Centre for DNA Fingerprinting and Diagnostics (CDFD), Hyderabad, India
| | - Sangita Mukhopadhyay
- Laboratory of Molecular and Cellular Biology, Centre for DNA Fingerprinting and Diagnostics (CDFD), Hyderabad, India
| | - Niyaz Ahmed
- Pathogen Evolution Laboratory, Centre for DNA Fingerprinting and Diagnostics (CDFD), Hyderabad, India
- * To whom correspondence should be addressed. E-mail:
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Ahmed N, Majeed AA, Ahmed I, Hussain MA, Alvi A, Devi SM, Rizwan M, Ranjan A, Sechi LA, Mégraud F. genoBASE pylori: A genotype search tool and database of the human gastric pathogen Helicobacter pylori. INFECTION GENETICS AND EVOLUTION 2007; 7:463-8. [PMID: 17320487 DOI: 10.1016/j.meegid.2007.01.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2006] [Revised: 01/10/2007] [Accepted: 01/19/2007] [Indexed: 01/24/2023]
Abstract
Helicobacter pylori is the pathogenic bacterium linked to gastric and duodenal ulcers and gastric carcinoma. Genomic diversity of the organism has enabled new insights into its population biology through comparative genomics. genoBASE pylori is an online databank of several virulence-linked and phylogenetic markers of H. pylori strains obtained from different human populations. This knowledgebase is built upon a relational database management system which is connected to visualize the presence of known, pathogenicity markers such as the co-ordinates within the cag pathogenicity island (cagPAI), the cagA gene and motifs surrounding it, the vacA allotypes and the oipA gene frame status, together with genotypic details in the form of DNA profiling traces and candidate gene sequences for individual strains. This flexible search tool allows inter-laboratory comparison of DNA fingerprinting data in the form of fluorescent amplified fragment length polymorphism (FAFLP), enterobacterial repetitive intergenic consensus (ERIC) and repetitive extragenic palindromic (REP) signature profiles. Besides this, the database also displays diversity of strains based on nucleotide sequences of several house keeping genes and two membrane proteins. Being the first of its kind, genoBASE pylori is expected to be a helpful online tool in strengthening the concept of 'geographic genomics' and will be useful to molecular epidemiologists, clinical laboratory scientists and those interested in diagnostic development for H. pylori. The database can be accessed through its website (http://www.cdfd.org.in/amplibase/HP).
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Affiliation(s)
- Niyaz Ahmed
- Pathogen Evolution Group, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India.
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Tsesmeli NE, Kotsaftis PS, Savopoulos CG, Hatzitolios AI, Kaiafa GD, Kounanis AD, Karamitsos DT. Incidence and etiology of acute non-malignant upper gastrointestinal bleeding in northern Greece. J Gastroenterol Hepatol 2007; 22:1009-13. [PMID: 17608846 DOI: 10.1111/j.1440-1746.2006.04775.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
AIM To evaluate the incidence and etiology of acute non-malignant upper gastrointestinal bleeding (ANMUGIB) in northern Greece due to increased use of non-steroidal anti-inflammatory drugs (NSAIDs), including low-dose aspirin (L-A), exposure and geographical variability of Helicobacter pylori (Hp) seroprevalence. METHODS A retrospective study of 110 patients admitted for hematemesis or melena during a 6-month period. All patients had undergone a gastrointestinal (GI) endoscopy during hospitalization. The presence of Hp was identified by biopsies and a (13)C-urea breath test in the case of Hp(-) biopsy bleeding peptic ulcer (BPU). The activity of ANMUGIB was assessed according to Forrest's classification. Statistical analysis was made by the chi(2)-test and Yates' correction. RESULTS Most patients were in the two medium age groups with no significant difference between them (P < 0.001). NSAID or L-A (100 mg/day) use was reported in 42.73% of patients in a ratio 1:1 (P > 0.1) and Hp infection was found in 29.09% of patients. BPU, with approximately two-thirds in the bulb, erosions and varices were the most frequent sources. Hp infection was found in 60.65% of BPU, 65.57% were related to NSAIDs or L-A and 8.19% were non-Hp non-NSAID/L-A BPU. Flat spots were most commonly found with a significant difference (P < 0.001) to other stigmata of recent bleeding, except for clean base. CONCLUSIONS In northern Greece, persons aged over 40 years are prone to ANMUGIB with a non-significant relationship to males. Hp infection and medication use, such as NSAIDS and L-A, are deeply involved in its etiology. Non-Hp non-NSAID/L-A BPU are a small proportion. ANMUGIB seems to have a generally good prognosis.
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Affiliation(s)
- Niki E Tsesmeli
- First Medical Propedeutic Department, AHEPA Hospital, Aristotle University of Thessaloniki, Thessaloniki, Greece
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Chong PP, Abdul Hadi SR, Lee YL, Phan CL, Tan BC, Ng KP, Seow HF. Genotyping and drug resistance profile of Candida spp. in recurrent and one-off vaginitis, and high association of non-albicans species with non-pregnant status. INFECTION GENETICS AND EVOLUTION 2007; 7:449-56. [PMID: 17324639 DOI: 10.1016/j.meegid.2007.01.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2006] [Accepted: 01/12/2007] [Indexed: 11/27/2022]
Abstract
Recurrent vulvovaginal candidiasis affects women worldwide and the resistance to azole drugs may be an important factor. The extent of strain-to-strain variation within a species and its relationship to the ability of the organism to colonize the vulvovaginal mucosa is not well established. The aims of this study were to compare: (i) the genotypes of Candida strains in sequential infections in patients with recurrent vaginitis, (ii) the genotypes of strains in patients with only one episode of infection in a period of 1 year and (iii) determine the in vitro antifungal susceptibilities of strains that cause recurrent vaginitis. Fifty-one cultured specimens from six distinct Candida species were genotyped via random amplified polymorphic DNA-polymerase chain reaction (RAPD-PCR) method using the ERIC1 and ERIC2 primers (ERIC, enterobacterial repetitive intergenic consensus). Statistical analyses allowed three different scenarios to be discerned for recurrent cases: (i) strain maintenance without genetic variation, (ii) strain maintenance with minor genetic variation and (iii) outright strain replacement. The genetic relatedness between strains from patients with recurrent vaginitis and patients with single episode of vaginitis were demonstrated by the dendogramme and the mean pairwise similarity coefficient S(AB) for the intergroup comparison was 0.223. However, intragroup genetic relatedness was slightly higher than intergroup comparison, with mean S(AB) of 0.261 and 0.331 for Groups I and II, respectively. A high proportion of Group I isolates (87.5%) causing recurrent infections were resistant to ketoconazole, whereas 41.7% of these isolates were cross-resistant to both clotrimazole and ketoconazole as shown by the in vitro antifungal susceptibility test, especially for C. glabrata isolates. Pregnancy status of patients displayed a highly significant association with C. albicans species whereas non-albicans species had a markedly higher prevalence in non-pregnant patients (p<0.001). These results may have a profound impact on the management of vaginal candidiasis, especially in recurrent cases.
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Affiliation(s)
- Pei Pei Chong
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, University Putra Malaysia, 43400 Serdang, Selangor, Malaysia.
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Finger SA, Velapatiño B, Kosek M, Santivañez L, Dailidiene D, Quino W, Balqui J, Herrera P, Berg DE, Gilman RH. Effectiveness of enterobacterial repetitive intergenic consensus PCR and random amplified polymorphic DNA fingerprinting for Helicobacter pylori strain differentiation. Appl Environ Microbiol 2006; 72:4713-6. [PMID: 16820463 PMCID: PMC1489368 DOI: 10.1128/aem.00894-06] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
We compared the robustness and discriminatory power of the enterobacterial repetitive intergenic consensus (ERIC) and random amplified polymorphic DNA (RAPD) fingerprinting methods for detecting cases of mixed Helicobacter pylori infection in Peruvian shantytown residents. H. pylori isolates from 63 participants were cultured, and five single colonies and a pool of additional colonies from each participant were analyzed by ERIC-PCR and by RAPD tests with four 10-nucleotide primers (one primer per reaction). There was 94% agreement between the ERIC and RAPD profiles in classifying sets of isolates as uniform versus closely related but not identical versus probably unrelated, indicating a high kappa statistic of 0.8942. Subtle differences in related ERIC or RAPD patterns likely reflect gene transfer between strains, recombination, and/or mutation, whereas markedly different patterns reflect infection by unrelated strains. At least half of infected shantytown residents seemed to carry more than one H. pylori strain, although in 19 of 31 persons, the strains were closely related. Three RAPD tests, each with a different primer, were needed to achieve the sensitivity of one ERIC test. ERIC-PCR constitutes a resource- and time-efficient method for H. pylori strain differentiation.
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Affiliation(s)
- S Alison Finger
- Departamento de Microbiología, Universidad Peruana Cayetano Heredia, Lima, Peru
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Singh A, Goering RV, Simjee S, Foley SL, Zervos MJ. Application of molecular techniques to the study of hospital infection. Clin Microbiol Rev 2006; 19:512-30. [PMID: 16847083 PMCID: PMC1539107 DOI: 10.1128/cmr.00025-05] [Citation(s) in RCA: 176] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Nosocomial infections are an important source of morbidity and mortality in hospital settings, afflicting an estimated 2 million patients in United States each year. This number represents up to 5% of hospitalized patients and results in an estimated 88,000 deaths and 4.5 billion dollars in excess health care costs. Increasingly, hospital-acquired infections with multidrug-resistant pathogens represent a major problem in patients. Understanding pathogen relatedness is essential for determining the epidemiology of nosocomial infections and aiding in the design of rational pathogen control methods. The role of pathogen typing is to determine whether epidemiologically related isolates are also genetically related. To determine molecular relatedness of isolates for epidemiologic investigation, new technologies based on DNA, or molecular analysis, are methods of choice. These DNA-based molecular methodologies include pulsed-field gel electrophoresis (PFGE), PCR-based typing methods, and multilocus sequence analysis. Establishing clonality of pathogens can aid in the identification of the source (environmental or personnel) of organisms, distinguish infectious from noninfectious strains, and distinguish relapse from reinfection. The integration of molecular typing with conventional hospital epidemiologic surveillance has been proven to be cost-effective due to the associated reduction in the number of nosocomial infections. Cost-effectiveness is maximized through the collaboration of the laboratory, through epidemiologic typing, and the infection control department during epidemiologic investigations.
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Affiliation(s)
- Aparajita Singh
- Department of Medicine, Section of Infectious Diseases, Henry Ford Hospital, Wayne State University School of Medicine, Detroit, MI 48202, USA
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Prouzet-Mauléon V, Hussain MA, Lamouliatte H, Kauser F, Mégraud F, Ahmed N. Pathogen evolution in vivo: genome dynamics of two isolates obtained 9 years apart from a duodenal ulcer patient infected with a single Helicobacter pylori strain. J Clin Microbiol 2005; 43:4237-41. [PMID: 16081988 PMCID: PMC1233956 DOI: 10.1128/jcm.43.8.4237-4241.2005] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
The survival and microevolution of Helicobacter pylori strains in the niches of the stomach after eradication therapy have largely been unexplored. We analyzed genomic signatures for two successive isolates obtained 9 years apart from a duodenal ulcer patient who underwent eradication therapy for H. pylori. These isolates were genotyped based on 50 different parameters involving three different fingerprinting approaches and several evolutionarily significant and virulence-associated landmarks in the genome, including nine informative gene loci, the cag pathogenicity island and its right junction, members of the plasticity region cluster, and vacA and iceA alleles. Our observations reveal that the two isolates were derived from the same strain that colonized the patient for almost a decade and were almost identical. Microevolution, however, was observed in the cagA gene and its right junction, the vacA m1 allele, and a member of the plasticity region cluster (JHP926). These results suggest that H. pylori has a great ability to survive and reemerge as a microevolved strain posteradication, thereby hinting at the requirement for follow-up of patients after therapy.
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Affiliation(s)
- Valérie Prouzet-Mauléon
- Pathogen Evolution Group, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India, INSERM ERI 10 and Centre National de Référence des Campylobacters et Hélicobacters, Laboratoire de Bactériologie, Université Victor Segalen Bordeaux 2, France, Service Hépato-Gastroentérologie, Hôpital Saint André, Bordeaux, France
| | - M. Abid Hussain
- Pathogen Evolution Group, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India, INSERM ERI 10 and Centre National de Référence des Campylobacters et Hélicobacters, Laboratoire de Bactériologie, Université Victor Segalen Bordeaux 2, France, Service Hépato-Gastroentérologie, Hôpital Saint André, Bordeaux, France
| | - Hervé Lamouliatte
- Pathogen Evolution Group, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India, INSERM ERI 10 and Centre National de Référence des Campylobacters et Hélicobacters, Laboratoire de Bactériologie, Université Victor Segalen Bordeaux 2, France, Service Hépato-Gastroentérologie, Hôpital Saint André, Bordeaux, France
| | - Farhana Kauser
- Pathogen Evolution Group, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India, INSERM ERI 10 and Centre National de Référence des Campylobacters et Hélicobacters, Laboratoire de Bactériologie, Université Victor Segalen Bordeaux 2, France, Service Hépato-Gastroentérologie, Hôpital Saint André, Bordeaux, France
| | - Francis Mégraud
- Pathogen Evolution Group, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India, INSERM ERI 10 and Centre National de Référence des Campylobacters et Hélicobacters, Laboratoire de Bactériologie, Université Victor Segalen Bordeaux 2, France, Service Hépato-Gastroentérologie, Hôpital Saint André, Bordeaux, France
| | - Niyaz Ahmed
- Pathogen Evolution Group, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India, INSERM ERI 10 and Centre National de Référence des Campylobacters et Hélicobacters, Laboratoire de Bactériologie, Université Victor Segalen Bordeaux 2, France, Service Hépato-Gastroentérologie, Hôpital Saint André, Bordeaux, France
- Corresponding author. Mailing address: Pathogen Evolution Group, CDFD, ECIL Rd., Nacharam, Hyderabad 500 076, India. Phone: 91 40 27150008. Fax: 91 40 27155610. E-mail:
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Kauser F, Hussain MA, Ahmed I, Ahmad N, Habeeb A, Khan AA, Ahmed N. Comparing genomes of Helicobacter pylori strains from the high-altitude desert of Ladakh, India. J Clin Microbiol 2005; 43:1538-45. [PMID: 15814963 PMCID: PMC1081395 DOI: 10.1128/jcm.43.4.1538-1545.2005] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
The genomic diversity of Helicobacter pylori from the vast Indian subcontinent is largely unknown. We compared the genomes of 10 H. pylori strains from Ladakh, North India. Molecular analysis was carried out to identify rearrangements within and outside the cag pathogenicity island (cag PAI) and DNA sequence divergence in candidate genes. Analyses of virulence genes (such as the cag PAI as a whole, cagA, vacA, iceA, oipA, babB, and the plasticity cluster) revealed that H. pylori strains from Ladakh are genetically distinct and possibly less virulent than the isolates from East Asian countries, such as China and Japan. Phylogenetic analyses based on the cagA-glr motifs, enterobacterial repetitive intergenic consensus patterns, repetitive extragenic palindromic signatures, the glmM gene mutations, and several genomic markers representing fluorescent amplified fragment length polymorphisms revealed that Ladakhi strains share features of the Indo-European, as well as the East Asian, gene pools. However, the contribution of genetic features from the Indo-European gene pool was more prominent.
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Affiliation(s)
- Farhana Kauser
- Pathogen Evolution Group, Centre for DNA Fingerprinting and Diagnostics, Nacharam, Hyderabad 500 076, India
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Kauser F, Hussain MA, Ahmed I, Srinivas S, Devi SM, Majeed AA, Rao KR, Khan AA, Sechi LA, Ahmed N. Comparative genomics of Helicobacter pylori isolates recovered from ulcer disease patients in England. BMC Microbiol 2005; 5:32. [PMID: 15916705 PMCID: PMC1180443 DOI: 10.1186/1471-2180-5-32] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2005] [Accepted: 05/25/2005] [Indexed: 12/16/2022] Open
Abstract
Background Genomic diversity of H. pylori from many different human populations is largely unknown. We compared genomes of 65 H. pylori strains from Nottingham, England. Molecular analysis was carried out to identify rearrangements within and outside the cag-pathogenicity-island (cag PAI) and DNA sequence divergence in candidate genes. Phylogenetic analysis was carried out based on various high-resolution genotyping techniques. Results Analyses of virulence genes (cagT, cagE, cagA, vacA, iceA, oipA and babB) revealed that H. pylori strains from England are genetically distinct from strains obtained from other countries. The toxigenic vacA s1m1 genotype was found to be less common and the plasticity region cluster was found to be disrupted in all the isolates. English isolates showed a predominance of iceA1 alleles and a functional proinflammatory oipA gene. The English H. pylori gene pool revealed several Asian/oriental features. This included the predominance of cagA – glr (cagA right junction) motif types III and II (up to 42%), presence of vacA m1c alleles and phylogenetic affinity towards East Asian / Amerindian gene pools based on fluorescent amplified fragment length polymorphism (FAFLP) analysis and glmM sequence analysis. Conclusion Overall, our results demonstrated genetic affinities of H. pylori in England with both European and the Asian gene pools and some distinctive genetic features of virulence genes that may have evolved in this important European population.
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Affiliation(s)
- Farhana Kauser
- Pathogen Evolution Group, Laboratory of Molecular and Cell Biology, Centre for DNA Fingerprinting and Diagnostics (CDFD), Hyderabad, India
| | - M Abid Hussain
- Pathogen Evolution Group, Laboratory of Molecular and Cell Biology, Centre for DNA Fingerprinting and Diagnostics (CDFD), Hyderabad, India
| | - Irshad Ahmed
- Deccan Medical College and Allied Hospitals, Hyderabad, India
| | - Sriramula Srinivas
- Pathogen Evolution Group, Laboratory of Molecular and Cell Biology, Centre for DNA Fingerprinting and Diagnostics (CDFD), Hyderabad, India
| | - S Manjulata Devi
- Pathogen Evolution Group, Laboratory of Molecular and Cell Biology, Centre for DNA Fingerprinting and Diagnostics (CDFD), Hyderabad, India
| | - Ahmed A Majeed
- Pathogen Evolution Group, Laboratory of Molecular and Cell Biology, Centre for DNA Fingerprinting and Diagnostics (CDFD), Hyderabad, India
| | - K Rajender Rao
- Pathogen Evolution Group, Laboratory of Molecular and Cell Biology, Centre for DNA Fingerprinting and Diagnostics (CDFD), Hyderabad, India
| | - Aleem A Khan
- ISOGEM Working Group on Genetics of Helicobacters [International Society for Genomic and Evolutionary Microbiology (ISOGEM)], Hyderabad, India
- Deccan Medical College and Allied Hospitals, Hyderabad, India
| | - Leonardo A Sechi
- ISOGEM Working Group on Genetics of Helicobacters [International Society for Genomic and Evolutionary Microbiology (ISOGEM)], Hyderabad, India
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Niyaz Ahmed
- Pathogen Evolution Group, Laboratory of Molecular and Cell Biology, Centre for DNA Fingerprinting and Diagnostics (CDFD), Hyderabad, India
- ISOGEM Working Group on Genetics of Helicobacters [International Society for Genomic and Evolutionary Microbiology (ISOGEM)], Hyderabad, India
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Kauser F, Khan AA, Hussain MA, Carroll IM, Ahmad N, Tiwari S, Shouche Y, Das B, Alam M, Ali SM, Habibullah CM, Sierra R, Megraud F, Sechi LA, Ahmed N. The cag pathogenicity island of Helicobacter pylori is disrupted in the majority of patient isolates from different human populations. J Clin Microbiol 2005; 42:5302-8. [PMID: 15528729 PMCID: PMC525253 DOI: 10.1128/jcm.42.11.5302-5308.2004] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The cag pathogenicity island (cag-PAI) is one of the major virulence determinants of Helicobacter pylori. The chromosomal integrity of this island or the lack thereof is speculated to play an important role in the progress of the gastroduodenal pathology caused by H. pylori. We determined the integrity of the cag-PAI by using specific flanking and internally anchored PCR primers to know the biogeographical distribution of strains carrying fully integral cag-PAI with proinflammatory behavior in vivo. Genotypes based on eight selected loci were studied in 335 isolates obtained from eight different geographic regions. The cag-PAI appeared to be disrupted in the majority of patient isolates throughout the world. Conservation of cag-PAI was highest in Japanese isolates (57.1%). However, only 18.6% of the Peruvian and 12% of the Indian isolates carried an intact cag-PAI. The integrity of cag-PAI in European and African strains was minimal. All 10 strains from Costa Rica had rearrangements. Overall, a majority of the strains of East Asian ancestry were found to have intact cag-PAI compared to strains of other descent. We also found that the cagE and cagT genes were less often rearranged (18%) than the cagA gene (27%). We attempted to relate cag-PAI rearrangement patterns to disease outcome. Deletion frequencies of cagA, cagE, and cagT genes were higher in benign cases than in isolates from severe ulcers and gastric cancer. Conversely, the cagA promoter and the left end of the cag-PAI were frequently rearranged or deleted in isolates linked to severe pathology. Analysis of the cag-PAI genotypes with a different biogeoclimatic history will contribute to our understanding of the pathogen-host interaction in health and disease.
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Affiliation(s)
- Farhana Kauser
- Pathogen Evolution Group, Center for DNA Fingerprinting and Diagnostics, Hyderabad 500 076, India
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