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Rigouts L, Keysers J, Rabab R, Fissette K, van Deun A, de Jong BC. GeneXpert MTB/RIF Ultra performance to detect uncommon rpoB mutations in Mycobacterium tuberculosis. BMC Res Notes 2023; 16:146. [PMID: 37452349 PMCID: PMC10347863 DOI: 10.1186/s13104-023-06394-z] [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: 12/01/2022] [Accepted: 06/18/2023] [Indexed: 07/18/2023] Open
Abstract
OBJECTIVE To investigate the performance of GeneXpert MTB/RIF Ultra to accurately detect rifampicin resistance for less common rpoB mutations that potentially confer phenotypic resistance, we tested 28 such Mycobacterium tuberculosis cultures with Xpert Ultra. RESULTS They represented 22 different (combinations of) rpoB mutations. Of 28 isolates tested, one was reported by Xpert Ultra as "No rifampicin resistance detected", 8 yielded a "Rifampicin indeterminate" result, and 19 were identified as rifampicin resistant. Overall, our results corroborate previous observations on the "Indeterminate" results for mutations at codon 432, while we add Lys446Gln as additional "Indeterminate" result and Pro439Leu as a false rifampicin-susceptible result. Furthermore, we document other uncommon point mutations and indels across the rpoB gene that are mostly correctly identified as rifampicin resistant by Xpert ultra (V3). Taken together, "Indeterminate" results in Xpert Ultra may indicate underlying rpoB mutations within the rifampicin-resistance determining region and thus increase the post-test probability of rifampicin resistance, albeit to an unknown extent.
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Affiliation(s)
- Leen Rigouts
- Institute of Tropical Medicine, Mycobacteriology Unit, Nationalestraat 155, Antwerp, Belgium
| | - Jelle Keysers
- Institute of Tropical Medicine, Mycobacteriology Unit, Nationalestraat 155, Antwerp, Belgium
| | - Reenaers Rabab
- Institute of Tropical Medicine, Mycobacteriology Unit, Nationalestraat 155, Antwerp, Belgium
| | - Kristina Fissette
- Institute of Tropical Medicine, Mycobacteriology Unit, Nationalestraat 155, Antwerp, Belgium
| | | | - Bouke Catherine de Jong
- Institute of Tropical Medicine, Mycobacteriology Unit, Nationalestraat 155, Antwerp, Belgium
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Click ES, Kurbatova EV, Alexander H, Dalton TL, Chen MP, Posey JE, Ershova J, Cegielski JP. Isoniazid and Rifampin-Resistance Mutations Associated With Resistance to Second-Line Drugs and With Sputum Culture Conversion. J Infect Dis 2021; 221:2072-2082. [PMID: 32002554 DOI: 10.1093/infdis/jiaa042] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 01/28/2020] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Mutations in the genes inhA, katG, and rpoB confer resistance to anti-tuberculosis (TB) drugs isoniazid and rifampin. We questioned whether specific mutations in these genes were associated with different clinical and microbiological characteristics. METHODS In a multicountry prospective cohort study of multidrug-resistant TB, we identified inhA, katG, and rpoB mutations in sputum isolates using the Hain MTBDRplus line probe assay. For specific mutations, we performed bivariate analysis to determine relative risk of baseline or acquired resistance to other TB drugs. We compared time to sputum culture conversion (TSCC) using Kaplan-Meier curves and stratified Cox regression. RESULTS In total, 447 participants enrolled from January 2005 to December 2008 from 7 countries were included. Relative to rpoB S531L, isolates with rpoB D516V had less cross-resistance to rifabutin, increased baseline resistance to other drugs, and increased acquired fluoroquinolone resistance. Relative to mutation of katG only, mutation of inhA promoter and katG was associated with baseline extensively drug resistant (XDR) TB, increased acquired fluoroquinolone resistance, and slower TSCC (125.5 vs 89.0 days). CONCLUSIONS Specific mutations in inhA and katG are associated with differences in resistance to other drugs and TSCC. Molecular testing may make it possible to tailor treatment and assess additional drug resistance risk according to specific mutation profile.
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Affiliation(s)
- Eleanor S Click
- Division of Global HIV and TB, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Ekaterina V Kurbatova
- Division of Tuberculosis Elimination, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Heather Alexander
- Division of Global HIV and TB, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Tracy L Dalton
- Division of Tuberculosis Elimination, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Michael P Chen
- Division of Tuberculosis Elimination, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - James E Posey
- Division of Tuberculosis Elimination, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Julia Ershova
- Division of Global HIV and TB, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - J Peter Cegielski
- Division of Global HIV and TB, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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Gopie F, Commiesie E, Baldi S, Kamst M, Kaur D, de Lange W, Pinas P, Stijnberg D, Wongsokarijo M, Zijlmans C, de Zwaan R, van Soolingen D, Vreden S, de Vries G. Should treatment of low-level rifampicin mono-resistant tuberculosis be different? J Clin Tuberc Other Mycobact Dis 2021; 23:100222. [PMID: 33598570 PMCID: PMC7869001 DOI: 10.1016/j.jctube.2021.100222] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Background Rifampicin resistant tuberculosis (RR-TB) was frequently detected in Suriname after the introduction of Xpert MTB/RIF in 2012. Subsequent phenotypic drug-susceptibility testing (DST) was not conclusive at that moment, while RR-TB patients treated with first-line tuberculostatics had good treatment outcome. In our study, we analysed this interesting observation. Methods We collected demographic and clinical characteristics and treatment outcome of TB patients from May 2012-December 2018 and performed a univariate and multivariate analysis to assess possible associations with resistance to rifampicin. Secondly, we conducted whole genome sequencing on all available Mycobacterium tuberculosis isolates that had a rifampicin resistance in the Xpert MTB/RIF test and performed phenotypic DST on selected isolates. Findings RR-TB was detected in 59 (9.6%) patients confirmed by Xpert. These patients were treated with rifampicin-containing regimens in most (88%) of the cases. In all 32 samples examined, a D435Y mutation in the rpoB gene was identified; only one isolate revealed an additional isoniazid mutation. Phenotypic DST indicated low-level rifampicin resistance. In multivariate analysis, the Creole ethnicity was a factor associated with rifampicin resistance (aOR 3.5; 95%CI 1.9–6.4). The treatment success rate for patients with RR-TB (78.0%) was comparable to the treatment outcome in non-RR-TB patients 77.8%. Interpretation This study confirms a low-level rifampicin mono-resistance in TB patients of Suriname. These patients could benefit from a first-line regimen with high dose rifampicin (or rifabutin), rather than from the lengthy treatment regimens for rifampicin-resistant and multi-drug resistant TB, a concept of stratified medicine also advocated for the treatment of TB. Funding None.
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Affiliation(s)
- F.A. Gopie
- Academic Hospital Paramaribo, Paramaribo, Suriname
- Faculty of Medical Sciences, Anton de Kom University of Suriname, Paramaribo, Suriname
- Corresponding author at: Academic Hospital Paramaribo, Paramaribo, Suriname.
| | - E. Commiesie
- National Tuberculosis Program, Paramaribo, Suriname
| | - S. Baldi
- Central Laboratory, Paramaribo, Suriname
| | - M. Kamst
- National Tuberculosis Reference Laboratory, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - D. Kaur
- Massachusetts Supranational TB Reference Laboratory, University of Massachusetts Medical School, Jamaica Plane, MA, USA
| | - W.C.M. de Lange
- Department Pulmonary Diseases and Tuberculosis, University Medical Center Groningen, the Netherlands
| | - P.S. Pinas
- Central Laboratory, Paramaribo, Suriname
| | - D. Stijnberg
- National Tuberculosis Program, Paramaribo, Suriname
| | | | - C.W.R. Zijlmans
- Faculty of Medical Sciences, Anton de Kom University of Suriname, Paramaribo, Suriname
| | - R. de Zwaan
- National Tuberculosis Reference Laboratory, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - D. van Soolingen
- National Tuberculosis Reference Laboratory, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | | | - G. de Vries
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
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Miftahussurur M, Cruz M, Doohan D, Subsomwong P, Abreu JAJ, Hosking C, Waskito LA, Yamaoka Y. Five alternative Helicobacter pylori antibiotics to counter high levofloxacin and metronidazole resistance in the Dominican Republic. PLoS One 2019; 14:e0213868. [PMID: 30917150 PMCID: PMC6436749 DOI: 10.1371/journal.pone.0213868] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 03/01/2019] [Indexed: 12/19/2022] Open
Abstract
The prevalence of Helicobacter pylori resistance to levofloxacin and metronidazole was high in the Dominican Republic. We used two-fold agar dilution method to determine the minimum inhibitory concentration of five alternative antibiotics in 63 Dominican strains. We also assessed the genetic mutations associated with the antibiotic resistance using next-generation sequencing. We revealed that all 63 strains were sensitive towards sitafloxacin, furazolidone, and rifabutin. In contrast, the prevalence of rifaximin and garenoxacin resistance were high (82.5% and 34.9%, respectively). Patients more than or equal to 60 years old had the highest risk of double-antibiotic resistance (7/9, 77.8%, OR = 31.5, P = 0.009) and garenoxacin resistances (8/9, 88.9%, OR = 45.33, P = 0.002) with an increasing risk simultaneously by age (P = 0.004, r = 0.357). Almost all rifaximin resistant strains possessed multiple mutations with more than three mutations within rpoB including the most frequent novel mutations of S352L, I2726L, and V2465A. There was a significant association between vacA genotype and rifaximin resistance (P = 0.042). Among 23 levofloxacin-resistant strains, 82.6% (19/23, P <0.001) were also resistant to garenoxacin, and 39.1% (9/23) had a high minimal inhibitory concentration ≥8 μg/mL with positive trend correlation (P = <0.001, r = 0.84). Among 19 garenoxacin resistant strains, 16 (84.2%) contained mutations at D91 and N87 of gyrA. In conclusion, sitafloxacin, rifabutin, and furazolidone might be considered as alternative antibiotics to be included in H. pylori eradication regimen in regions with high prevalence of levofloxacin and metronidazole resistance, such as the Dominican Republic.
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Affiliation(s)
- Muhammad Miftahussurur
- Gastroentero-Hepatology Division, Department of Internal Medicine, Faculty of Medicine-Institute of Tropical Disease, Universitas Airlangga, Surabaya, Indonesia
- Institute of Tropical Disease, Universitas Airlangga, Surabaya, Indonesia
| | - Modesto Cruz
- Institute of Microbiology and Parasitology, Faculty of Science, Autonomous University of Santo Domingo, Santo Domingo, Dominican Republic
- Department of Biomedical Research, National Institute of Medicine and Diagnostic Imaging, Santo Domingo, Dominican Republic
| | - Dalla Doohan
- Institute of Tropical Disease, Universitas Airlangga, Surabaya, Indonesia
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Yufu, Japan
| | - Phawinee Subsomwong
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Yufu, Japan
| | - José A. Jiménez Abreu
- Dominican–Japanese Digestive Disease Center, Dr. Luis E. Aybar Health and Hygiene City, Santo Domingo, Dominican Republic
| | - Celso Hosking
- Department of Biomedical Research, National Institute of Medicine and Diagnostic Imaging, Santo Domingo, Dominican Republic
| | - Langgeng Agung Waskito
- Institute of Tropical Disease, Universitas Airlangga, Surabaya, Indonesia
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Yufu, Japan
| | - Yoshio Yamaoka
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Yufu, Japan
- Department of Medicine, Gastroenterology and Hepatology Section, Baylor College of Medicine, Houston, Texas, United States of America
- Faculty of Medicine, Universitas Airlangga, Surabaya, Indonesia
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5
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Su M, Satola SW, Read TD. Genome-Based Prediction of Bacterial Antibiotic Resistance. J Clin Microbiol 2019; 57:e01405-18. [PMID: 30381421 PMCID: PMC6425178 DOI: 10.1128/jcm.01405-18] [Citation(s) in RCA: 180] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 10/23/2018] [Indexed: 01/02/2023] Open
Abstract
Clinical microbiology has long relied on growing bacteria in culture to determine antimicrobial susceptibility profiles, but the use of whole-genome sequencing for antibiotic susceptibility testing (WGS-AST) is now a powerful alternative. This review discusses the technologies that made this possible and presents results from recent studies to predict resistance based on genome sequences. We examine differences between calling antibiotic resistance profiles by the simple presence or absence of previously known genes and single-nucleotide polymorphisms (SNPs) against approaches that deploy machine learning and statistical models. Often, the limitations to genome-based prediction arise from limitations of accuracy of culture-based AST in addition to an incomplete knowledge of the genetic basis of resistance. However, we need to maintain phenotypic testing even as genome-based prediction becomes more widespread to ensure that the results do not diverge over time. We argue that standardization of WGS-AST by challenge with consistently phenotyped strain sets of defined genetic diversity is necessary to compare the efficacy of methods of prediction of antibiotic resistance based on genome sequences.
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Affiliation(s)
- Michelle Su
- Department of Infectious Diseases, Emory University, Atlanta, Georgia, USA
- Antimicrobial Resistance and Therapeutic Discovery Training Program, Emory University, Atlanta, Georgia, USA
- Antibiotic Resistance Center, Emory University, Atlanta, Georgia, USA
| | - Sarah W Satola
- Department of Infectious Diseases, Emory University, Atlanta, Georgia, USA
- Antibiotic Resistance Center, Emory University, Atlanta, Georgia, USA
- Emory Investigational Clinical Microbiology Laboratory, Emory University, Atlanta, Georgia, USA
| | - Timothy D Read
- Department of Infectious Diseases, Emory University, Atlanta, Georgia, USA
- Antibiotic Resistance Center, Emory University, Atlanta, Georgia, USA
- Emory Investigational Clinical Microbiology Laboratory, Emory University, Atlanta, Georgia, USA
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Pyta K, Janas A, Szukowska M, Pecyna P, Jaworska M, Gajecka M, Bartl F, Przybylski P. Synthesis, docking and antibacterial studies of more potent amine and hydrazone rifamycin congeners than rifampicin. Eur J Med Chem 2019; 167:96-104. [PMID: 30769243 DOI: 10.1016/j.ejmech.2019.02.009] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2018] [Revised: 01/18/2019] [Accepted: 02/03/2019] [Indexed: 12/24/2022]
Abstract
New rifamycin congeners (1-33) with incorporated amine and hydrazone substituents leading to lipophilic and/or basic nature and altered rigidity of modified C(3) arm were synthesized and structurally characterized in detail. NMR spectroscopic studies at different temperatures indicate two types of structures of rifamycin congeners that are realized in solution: zwitterionic and non-ionic forms in dependence of the basicity of modified C(3) arm. The presence of rifamycin congeners in these two possible forms has a significant impact on the physico-chemical parameters such as lipophilicity (clogP) and water solubility and different binding mode of the C(3) arm of antibiotic at RNAP binding pocket (molecular target) leading to different antibacterial potency. The highest antibacterial potency against S. aureus (including MRSA and MLSB strains) and S. epidermidis strains, even higher than reference rifampicin (Rif) and rifaximin (Rifx) antibiotics, was found for rifamycin congeners bearing at the C(3) arm relatively rigid and basic substituents (bipiperidine and guanidine groups). These modifications provide favorable docking mode and excellent water solubility resulting in high potency (MICs 0.0078 μg/mL what gives ∼ 8.5 nM), irrespective whether rifamycin congener is a tertiary amine (15) or hydrazone (29). In turn, for a higher antibacterial potency of rifamycin congeners against E. faecalis strain (MICs 0.5 μg/mL that is 0.6 μM) as compared to Rif and Rifx, the most crucial factors are: bulkiness and the lipophilic character of the end of the C(3) rebuilt arm.
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Affiliation(s)
- Krystian Pyta
- Faculty of Chemistry, A. Mickiewicz University, Umultowska 89b, 61-614, Poznan, Poland
| | - Anna Janas
- Faculty of Chemistry, A. Mickiewicz University, Umultowska 89b, 61-614, Poznan, Poland
| | - Monika Szukowska
- Faculty of Chemistry, A. Mickiewicz University, Umultowska 89b, 61-614, Poznan, Poland
| | - Paulina Pecyna
- Department of Genetics and Pharmaceutical Microbiology, University of Medical Sciences, Swiecickiego 4, 60-781, Poznan, Poland
| | - Marcelina Jaworska
- Department of Genetics and Pharmaceutical Microbiology, University of Medical Sciences, Swiecickiego 4, 60-781, Poznan, Poland
| | - Marzena Gajecka
- Department of Genetics and Pharmaceutical Microbiology, University of Medical Sciences, Swiecickiego 4, 60-781, Poznan, Poland; Institute of Human Genetics, Polish Academy of Sciences, Strzeszynska 32, 60-479, Poznan, Poland
| | - Franz Bartl
- Humboldt-Universität zu Berlin, Lebenswissenschaftliche Fakultät, Institut für Biologie, Biophysikalische Chemie, Invalidenstr. 42, 10099, Berlin, Germany
| | - Piotr Przybylski
- Faculty of Chemistry, A. Mickiewicz University, Umultowska 89b, 61-614, Poznan, Poland.
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7
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Whitfield MG, Warren RM, Mathys V, Scott L, De Vos E, Stevens W, Streicher EM, Groenen G, Sirgel FA, Van Rie A. The potential use of rifabutin for treatment of patients diagnosed with rifampicin-resistant tuberculosis. J Antimicrob Chemother 2018; 73:2667-2674. [PMID: 29982641 PMCID: PMC6148329 DOI: 10.1093/jac/dky248] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 05/29/2018] [Accepted: 05/29/2018] [Indexed: 12/20/2022] Open
Abstract
Background Use of the Xpert MTB/RIF assay has increased the number of people diagnosed with rifampicin-resistant tuberculosis (RR-TB), especially in South Africa where Xpert is now the initial diagnostic for individuals with TB symptoms. We hypothesized that a proportion of RR-TB patients determined by Xpert can be treated with a rifabutin-containing regimen. Methods Rifabutin susceptibility by rpoB mutation was assessed in 349 individuals from South Africa and 172 from Belgium. rpoB polymorphisms were identified by Sanger sequencing. Rifampicin and rifabutin susceptibility was assessed phenotypically. A systematic review was performed to comprehensively collate information on rifabutin susceptibility by rpoB polymorphism. Rifabutin susceptibility was assigned to rpoB polymorphisms based on their positive likelihood ratios and ORs. Results One hundred and twelve rpoB polymorphisms (67.9% from literature) were identified from all 2045 RR-TB patients, of which 17 polymorphisms could be classified as susceptible/resistant to rifabutin. Eleven polymorphisms were associated with rifabutin susceptibility. The 516GTC mutation was the most common, representing 70% (South Africa) and 76% (Belgium) of all rifabutin-susceptible isolates. At a population level, the 11 polymorphisms associated with rifabutin susceptibility occurred in 33.2% and 16.6% of all South African and Belgian patients diagnosed with RR-TB, respectively. Conclusions Identification of the exact rpoB polymorphism leading to the diagnosis of RR-TB has the potential to allow inclusion of rifabutin in the treatment regimen of a substantial proportion of RR-TB patients. A randomized controlled trial evaluating the efficacy of a rifabutin-containing TB treatment regimen in these selected patients is needed to provide the evidence required for a change in policy.
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Affiliation(s)
- Michael G Whitfield
- South Africa Medical Research Council (SAMRC) Centre for Tuberculosis Research DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, Division of Molecular Biology and Human Genetics, Stellenbosch University, South Africa
| | - Robin M Warren
- South Africa Medical Research Council (SAMRC) Centre for Tuberculosis Research DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, Division of Molecular Biology and Human Genetics, Stellenbosch University, South Africa
| | - Vanessa Mathys
- Bacterial Diseases Service, Operational Direction Communicable and Infectious Diseases, Scientific Institute of Public Health (WIV-ISP), Brussels, Belgium
| | - Lesley Scott
- National Health Laboratory Services, South Africa
- Department of Molecular Medicine and Haematology, University of Witwatersrand, School of Pathology Faculty of Health Science, Johannesburg, South Africa
| | - Elise De Vos
- Global Health Institute, Epidemiology and Social Medicine Faculty of Medicine, University of Antwerp, Antwerp, Belgium
| | - Wendy Stevens
- National Health Laboratory Services, South Africa
- Department of Molecular Medicine and Haematology, University of Witwatersrand, School of Pathology Faculty of Health Science, Johannesburg, South Africa
| | - Elizabeth M Streicher
- South Africa Medical Research Council (SAMRC) Centre for Tuberculosis Research DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, Division of Molecular Biology and Human Genetics, Stellenbosch University, South Africa
| | - Guido Groenen
- Belgian Lung and Tuberculosis Association, Brussels, Belgium
| | - Frederick A Sirgel
- South Africa Medical Research Council (SAMRC) Centre for Tuberculosis Research DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, Division of Molecular Biology and Human Genetics, Stellenbosch University, South Africa
| | - Annelies Van Rie
- Global Health Institute, Epidemiology and Social Medicine Faculty of Medicine, University of Antwerp, Antwerp, Belgium
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Current Status of the Third-Line Helicobacter pylori Eradication. Gastroenterol Res Pract 2018; 2018:6523653. [PMID: 29853863 PMCID: PMC5954858 DOI: 10.1155/2018/6523653] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 04/08/2018] [Indexed: 02/08/2023] Open
Abstract
Antibiotic resistance is growing worldwide, and patients who have failed consecutive 1st- and 2nd-line H. pylori eradication regimens are increasing. Therefore, the role of the bacterial culture with antibiotic susceptibility testing and molecular susceptibility testing is important for avoiding the use of ineffective antibiotics. However, antibiotic susceptibility testing-guided treatment does not necessarily guarantee successful eradication, and there have been mixed results for the effectiveness of a 3rd-line rescue therapy. Therefore, providing patients with pretreatment medication instructions and education is important. It is also crucial to determine the reason of the eradication failure, including host-related factors (poor compliance to eradication regimen, smoking, and cytochrome P450 2C19 genetic polymorphism) or treatment-related factors (inadequate dosage or duration of therapy and gastric acidity), as such factors can be modified for a tailored therapy. Although the indications for H. pylori eradication have widened, patients at a high risk of gastric cancer can gain definitive benefits with a 3rd-line or even 4th-line therapy.
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Cabibbe AM, Sotgiu G, Izco S, Migliori GB. Genotypic and phenotypic M. tuberculosis resistance: guiding clinicians to prescribe the correct regimens. Eur Respir J 2017; 50:50/6/1702292. [DOI: 10.1183/13993003.02292-2017] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 12/11/2017] [Indexed: 11/05/2022]
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Jing W, Pang Y, Zong Z, Wang J, Guo R, Huo F, Jiang G, Ma Y, Huang H, Chu N. Rifabutin Resistance Associated with Double Mutations in rpoB Gene in Mycobacterium tuberculosis Isolates. Front Microbiol 2017; 8:1768. [PMID: 28959248 PMCID: PMC5603767 DOI: 10.3389/fmicb.2017.01768] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2017] [Accepted: 08/31/2017] [Indexed: 11/14/2022] Open
Abstract
The objective of this study was to investigate the cross-resistance between rifampin (RIF) and rifabutin (RFB) among clinical Mycobacterium tuberculosis (MTB) isolates, and the correlations between specific rpoB mutations and the minimum inhibitory concentrations (MICs) of RIF and RFB. A total of 256 RIF-resistant isolates were included from the National Tuberculosis Clinical Laboratory in China. The MICs of MTB isolates against RIF and RFB were determined by using a microplate alamarBlue assay. In addition, all the MTB isolates were sequenced for mutations in rpoB gene. 204 out of 256 isolates (79.7%) were resistant to RFB, whereas 52 (20.3%) were susceptible to RFB. RIF-resistant/INH-susceptible (RR) group had a significant lower proportion of RFB-resistance than MDR- (P = 0.04) and XDR-TB group (P < 0.01). DNA sequencing revealed that there were 218 isolates (85.2%) with a single mutation, 26 (10.1%) with double mutations, and 12 (4.7%) without mutation in rpoB gene. Notably, although the single substitution of Leu511Pro, Asp516Gly, and His526Asn did not result in RFB resistance, 77.8% (7/9) of the MTB isolates with these double mutations became resistant to RFB. Compared with RR group (38.9%, 7/18), MDR-TB (63.5%, 106/167) had significantly higher proportion of isolates with mutations in codon 531 of rpoB gene (P = 0.04). Our data demonstrate that various rpoB mutations are associated with differential resistance to RIF and RFB. A single specific mutation in codons 511, 516, 526, and 533 was linked to the susceptibility to RFB for MTB, while the strains with these double mutations irrelevantly conferring RFB resistance produced RFB-resistant phenotype.
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Affiliation(s)
- Wei Jing
- Department of Tuberculosis, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital Affiliated to Capital Medical UniversityBeijing, China
| | - Yu Pang
- National Clinical Laboratory on Tuberculosis, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital Affiliated to Capital Medical UniversityBeijing, China
| | - Zhaojing Zong
- National Clinical Laboratory on Tuberculosis, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital Affiliated to Capital Medical UniversityBeijing, China
| | - Jing Wang
- Department of Tuberculosis, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital Affiliated to Capital Medical UniversityBeijing, China
| | - Ru Guo
- Department of Tuberculosis, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital Affiliated to Capital Medical UniversityBeijing, China
| | - Fengmin Huo
- National Clinical Laboratory on Tuberculosis, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital Affiliated to Capital Medical UniversityBeijing, China
| | - Guanglu Jiang
- National Clinical Laboratory on Tuberculosis, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital Affiliated to Capital Medical UniversityBeijing, China
| | - Yifeng Ma
- National Clinical Laboratory on Tuberculosis, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital Affiliated to Capital Medical UniversityBeijing, China
| | - Hairong Huang
- National Clinical Laboratory on Tuberculosis, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital Affiliated to Capital Medical UniversityBeijing, China
| | - Naihui Chu
- Department of Tuberculosis, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital Affiliated to Capital Medical UniversityBeijing, China
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Zheng J, Chen L, Liu L, Li H, Liu B, Zheng D, Liu T, Dong J, Sun L, Zhu Y, Yang J, Zhang X, Jin Q. Proteogenomic Analysis and Discovery of Immune Antigens in Mycobacterium vaccae. Mol Cell Proteomics 2017; 16:1578-1590. [PMID: 28733429 DOI: 10.1074/mcp.m116.065813] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2016] [Revised: 07/05/2017] [Indexed: 11/06/2022] Open
Abstract
Tuberculosis (TB) is one of the leading causes of death worldwide, especially in developing countries. Neonatal BCG vaccination occurs in various regions, but the level of protection varies in different populations. Recently, Mycobacterium vaccae is found to be an immunomodulating therapeutic agent that could confer a significant level of protection against TB. It is the only vaccine in a phase III trial from WHO to assess its efficacy and safety in preventing TB disease in people with latent TB infection. However, the mechanism of immunotherapy of M. vaccae remains poorly understood. In this study, the full genome of M. vaccae was obtained by next-generation sequencing technology, and a proteogenomic approach was successfully applied to further perform genome annotation using high resolution and high accuracy MS data. A total of 3,387 proteins (22,508 unique peptides) were identified, and 581 proteins annotated as hypothetical proteins in the genome database were confirmed. Furthermore, 38 novel protein products not annotated at the genome level were detected and validated. Additionally, the translational start sites of 445 proteins were confirmed, and 98 proteins were validated through extension of their translational start sites based on N terminus-derived peptides. The physicochemical characteristics of the identified proteins were determined. Thirty-five immunogenic proteins of M. vaccae were identified by immunoproteomic analysis, and 20 of them were selected to be expressed and validated by Western blot for immunoreactivity to serum from patients infected with M. tuberculosis The results revealed that eight of them showed strong specific reactive signals on the immunoblots. Furthermore, cellular immune response was further examined and one protein displayed a higher cellular immune level in pulmonary TB patients. Twelve identified immunogenic proteins have orthologous in H37Rv and BCG. This is the first study to obtain the full genome and annotation of M. vaccae using a proteogenomic approach, and some immunogenic proteins that were validated by immunoproteomic analysis could contribute to the understanding of the mechanism of M. vaccae immunotherapy.
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Affiliation(s)
- Jianhua Zheng
- ‡From the MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Centre for Tuberculosis, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Lihong Chen
- ‡From the MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Centre for Tuberculosis, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Liguo Liu
- ‡From the MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Centre for Tuberculosis, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Haifeng Li
- ‡From the MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Centre for Tuberculosis, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Bo Liu
- ‡From the MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Centre for Tuberculosis, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Dandan Zheng
- ‡From the MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Centre for Tuberculosis, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Tao Liu
- ‡From the MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Centre for Tuberculosis, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jie Dong
- ‡From the MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Centre for Tuberculosis, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Lilian Sun
- ‡From the MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Centre for Tuberculosis, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yafang Zhu
- ‡From the MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Centre for Tuberculosis, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jian Yang
- ‡From the MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Centre for Tuberculosis, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xiaobing Zhang
- ‡From the MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Centre for Tuberculosis, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Qi Jin
- ‡From the MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Centre for Tuberculosis, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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12
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Classifying new anti-tuberculosis drugs: rationale and future perspectives. Int J Infect Dis 2017; 56:181-184. [DOI: 10.1016/j.ijid.2016.10.026] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Revised: 10/24/2016] [Accepted: 10/25/2016] [Indexed: 11/19/2022] Open
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13
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Rukasha I, Said HM, Omar SV, Koornhof H, Dreyer AW, Musekiwa A, Moultrie H, Hoosen AA, Kaplan G, Fallows D, Ismail N. Correlation of rpoB Mutations with Minimal Inhibitory Concentration of Rifampin and Rifabutin in Mycobacterium tuberculosis in an HIV/AIDS Endemic Setting, South Africa. Front Microbiol 2016; 7:1947. [PMID: 27994580 PMCID: PMC5136537 DOI: 10.3389/fmicb.2016.01947] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2016] [Accepted: 11/21/2016] [Indexed: 12/27/2022] Open
Abstract
Treatment of tuberculosis (TB) and HIV co-infections is often complicated by drug-to-drug interactions between anti-mycobacterial and anti-retroviral agents. Rifabutin (RFB) is an alternative to rifampin (RIF) for TB regimens and is recommended for HIV patients concurrently receiving protease inhibitors because of reduced induction of CYP3A4. This study sought to determine the proportion of RFB susceptible isolates among RIF-resistant strains in a high HIV prevalence setting in South Africa. In addition, the study explored the association between rpoB mutations and minimum inhibitory concentrations (MIC) of RIF and RFB. A total of 189 multidrug resistant (MDR) Mycobacterium tuberculosis isolates from the Centre for Tuberculosis repository were analyzed. The MICs were determined using a MYCOTB Sensititre plate method and the rpoB gene was sequenced. Of the 189 MDR isolates, 138 (73%) showed resistance to both RIF and RFB, while 51 (27%) isolates were resistant to RIF but retained susceptibility to RFB. The S531L was the most frequent rpoB point mutation in 105/189 (56%) isolates, followed by H526Y in 27/189 (14%) isolates. Resistance to both RIF and RFB was found predominantly in association with mutations S531L (91/105, 87%), H526Y (20/27, 74%), and H526D (15/19, 79%), while D516V (15/17, 88%), and L533P (3/4, 75%) were found in RIF-resistant, RFB-susceptible isolates. This study has shown that up to 27% of MDR-TB patients in South Africa may benefit from a treatment regimen that includes RFB.
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Affiliation(s)
- Ivy Rukasha
- Department of Medical Microbiology, Faculty of Health Sciences, University of the Free State Bloemfontein, South Africa
| | - Halima M Said
- Department of Medical Microbiology, Faculty of Health Sciences, University of the Free StateBloemfontein, South Africa; Centre for Tuberculosis, National Institute for Communicable DiseasesSandringham, South Africa
| | - Shaheed V Omar
- Centre for Tuberculosis, National Institute for Communicable Diseases Sandringham, South Africa
| | - Hendrik Koornhof
- Centre for Tuberculosis, National Institute for Communicable DiseasesSandringham, South Africa; Department of Medical Microbiology, Faculty of Health Sciences, University of the WitwatersrandJohannesburg, South Africa
| | - Andries W Dreyer
- Centre for Tuberculosis, National Institute for Communicable DiseasesSandringham, South Africa; Department of Medical Microbiology, Faculty of Health Sciences, University of the WitwatersrandJohannesburg, South Africa
| | - Alfred Musekiwa
- Centre for Evidence-based Health Care, Faculty of Medicine and Health Sciences, Stellenbosch University Cape Town, South Africa
| | - Harry Moultrie
- Medical Research Council, Respiratory and Meningeal Pathogens Research Unit, School of Pathology, University of the Witwatersrand Johannesburg, South Africa
| | - Anwar A Hoosen
- Department of Medical Microbiology, Faculty of Health Sciences, University of the Free State Bloemfontein, South Africa
| | - Gilla Kaplan
- The Bill and Melinda Gates Foundation, Seattle WA, USA
| | - Dorothy Fallows
- Public Health Research Institute, New Jersey Medical School, The State University of New Jersey, Rutgers University, Newark NJ, USA
| | - Nazir Ismail
- Centre for Tuberculosis, National Institute for Communicable DiseasesSandringham, South Africa; Department of Medical Microbiology, Faculty of Health Sciences, University of PretoriaPretoria, South Africa
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14
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Tuberculosis--advances in development of new drugs, treatment regimens, host-directed therapies, and biomarkers. THE LANCET. INFECTIOUS DISEASES 2016; 16:e34-46. [PMID: 27036358 DOI: 10.1016/s1473-3099(16)00070-0] [Citation(s) in RCA: 197] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Revised: 01/27/2016] [Accepted: 01/29/2016] [Indexed: 12/24/2022]
Abstract
Tuberculosis is the leading infectious cause of death worldwide, with 9·6 million cases and 1·5 million deaths reported in 2014. WHO estimates 480,000 cases of these were multidrug resistant (MDR). Less than half of patients who entered into treatment for MDR tuberculosis successfully completed that treatment, mainly due to high mortality and loss to follow-up. These in turn illustrate weaknesses in current treatment regimens and national tuberculosis programmes, coupled with operational treatment challenges. In this Review we provide an update on recent developments in the tuberculosis drug-development pipeline (including new and repurposed antimicrobials and host-directed drugs) as they are applied to new regimens to shorten and improve outcomes of tuberculosis treatment. Several new or repurposed antimicrobial drugs are in advanced trial stages for MDR tuberculosis, and two new antimicrobial drug candidates are in early-stage trials. Several trials to reduce the duration of therapy in MDR and drug-susceptible tuberculosis are ongoing. A wide range of candidate host-directed therapies are being developed to accelerate eradication of infection, prevent new drug resistance, and prevent permanent lung injury. As these drugs have been approved for other clinical indications, they are now ready for repurposing for tuberculosis in phase 2 clinical trials. We assess risks associated with evaluation of new treatment regimens, and highlight opportunities to advance tuberculosis research generally through regulatory innovation in MDR tuberculosis. Progress in tuberculosis-specific biomarkers (including culture conversion, PET and CT imaging, and gene expression profiles) can support this innovation. Several global initiatives now provide unique opportunities to tackle the tuberculosis epidemic through collaborative partnerships between high-income countries and middle-income and low-income countries for clinical trials training and research, allowing funders to coordinate several national and regional programmes for greatest overall effect.
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15
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Zuur MA, Bolhuis MS, Anthony R, den Hertog A, van der Laan T, Wilffert B, de Lange W, van Soolingen D, Alffenaar JWC. Current status and opportunities for therapeutic drug monitoring in the treatment of tuberculosis. Expert Opin Drug Metab Toxicol 2016; 12:509-21. [DOI: 10.1517/17425255.2016.1162785] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Marlanka A. Zuur
- Department of Clinical Pharmacy and Pharmacology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Mathieu S. Bolhuis
- Department of Clinical Pharmacy and Pharmacology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Richard Anthony
- Royal Tropical Institute (KIT), KIT Biomedical Research, Amsterdam, The Netherlands
| | - Alice den Hertog
- Royal Tropical Institute (KIT), KIT Biomedical Research, Amsterdam, The Netherlands
| | - Tridia van der Laan
- National Tuberculosis Reference Laboratory, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Bob Wilffert
- Department of Clinical Pharmacy and Pharmacology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- Department of Pharmacy, section Pharmacotherapy and Pharmaceutical Care, University of Groningen, Groningen, The Netherlands
| | - Wiel de Lange
- University of Groningen, University Medical Center Groningen, Tuberculosis Centre Beatrixoord, Haren, The Netherlands
- Department of Pulmonary Diseases and Tuberculosis, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Dick van Soolingen
- National Tuberculosis Reference Laboratory, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
- Departments of Pulmonary Diseases and Medical Microbiology, Radboud University Nijmegen Medical Center, Nijmegen, The Netherlands
| | - Jan-Willem C. Alffenaar
- Department of Clinical Pharmacy and Pharmacology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
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16
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Losurdo G, Iannone A, Giorgio F, Principi M, Di Leo A, Ierardi E. Rifabutin-based 10-day and 14-day triple therapy as a third-line and fourth-line regimen for Helicobacter pylori eradication: how should rifabutin be managed in rescue regimens? United European Gastroenterol J 2015; 4:474-5. [PMID: 27403315 DOI: 10.1177/2050640615623697] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 11/28/2015] [Indexed: 12/12/2022] Open
Affiliation(s)
- Giuseppe Losurdo
- Gastroenterology Section, Department of Emergency and Organ Transplantation, University of Bari, Italy
| | - Andrea Iannone
- Gastroenterology Section, Department of Emergency and Organ Transplantation, University of Bari, Italy
| | - Floriana Giorgio
- Gastroenterology Section, Department of Emergency and Organ Transplantation, University of Bari, Italy
| | - Mariabeatrice Principi
- Gastroenterology Section, Department of Emergency and Organ Transplantation, University of Bari, Italy
| | - Alfredo Di Leo
- Gastroenterology Section, Department of Emergency and Organ Transplantation, University of Bari, Italy
| | - Enzo Ierardi
- Gastroenterology Section, Department of Emergency and Organ Transplantation, University of Bari, Italy
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