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Nandwani S, Singhal S, Gothi D, Singhal R, Perween N, Gupta K, Bir R, Gunasekaran J, Soni A, Chaudhary U. Evaluation of Diagnostic Performance of Line Probe Assay on Smear-Negative Samples of Pulmonary Tuberculosis. Cureus 2024; 16:e58298. [PMID: 38752058 PMCID: PMC11094765 DOI: 10.7759/cureus.58298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/15/2024] [Indexed: 05/18/2024] Open
Abstract
BACKGROUND This study aims to compare the performance of line probe assay (LPA) on smear-negative samples with that of smear-positive samples for diagnosing pulmonary tuberculosis (PTB) and first-line drug sensitivity testing (FL DST). METHODS A total of 196 sputum samples including both smear-positive (112) and negative (84) samples of patients suspected of PTB were subjected to LPA for TB detection and FL DST. TB culture followed by MPT 64 Ag was done and conventional FL DST was performed on all culture-positive isolates. Results of LPA on smear-negative were compared with smear-positive samples. RESULTS The LPA confirmed the diagnosis of PTB in 104/112 smear-positive cases but in only 36/84 smear-negative cases. The assay had 47.36%, 72.72%, and 88.88% sensitivity and 86.96%, 95.23%, and 95.65% specificity in smear-negative cases compared to 89.09%, 95.83%, and 98.07% sensitivity and 100%, 98.36%, and 98.24% specificity in smear-positive cases for detecting Mycobacterium tuberculosis (MTB), rifampicin (RMP) resistance, and isoniazid (INH) resistance, respectively. CONCLUSION LPA performance was better on smear-positive than smear-negative sputum samples. Further larger studies are needed to justify the use of LPA on smear-negative pulmonary samples for diagnosis.
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Affiliation(s)
- Sumi Nandwani
- Microbiology, Post Graduate Institute of Child Health, Noida, IND
| | - Sanjay Singhal
- Microbiology, Employee's State Insurance Corporation (ESIC) Hospital, Postgraduate Institute of Medical Sciences and Research (PGIMSR), New Delhi, IND
| | - Dipti Gothi
- Pulmonary and Critical Care Medicine, Employee's State Insurance Corporation (ESIC) Hospital, Postgraduate Institute of Medical Sciences and Research (PGIMSR), New Delhi, IND
| | - Ritu Singhal
- Microbiology, WHO National Reference Laboratory and Center of Excellence (TB) and National Institute of Tuberculosis and Respiratory Diseases, New Delhi, IND
| | - Naz Perween
- Microbiology, Post Graduate Institute of Child Health, Noida, IND
| | - Kavita Gupta
- Microbiology, Post Graduate Institute of Child Health, Noida, IND
| | - Raunak Bir
- Microbiology, Post Graduate Institute of Child Health, Noida, IND
| | | | - Anushka Soni
- Microbiology, Post Graduate Institute of Child Health, Noida, IND
| | - Urmila Chaudhary
- Microbiology, Post Graduate Institute of Child Health, Noida, IND
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Scott LE, Shapiro AN, Da Silva MP, Tsoka J, Jacobson KR, Emch M, Moultrie H, Jenkins HE, Moore D, Van Rie A, Stevens WS. Integrating Molecular Diagnostics and GIS Mapping: A Multidisciplinary Approach to Understanding Tuberculosis Disease Dynamics in South Africa Using Xpert MTB/RIF. Diagnostics (Basel) 2023; 13:3163. [PMID: 37891984 PMCID: PMC10606157 DOI: 10.3390/diagnostics13203163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 08/30/2023] [Accepted: 09/14/2023] [Indexed: 10/29/2023] Open
Abstract
An investigation was carried out to examine the use of national Xpert MTB/RIF data (2013-2017) and GIS technology for MTB/RIF surveillance in South Africa. The aim was to exhibit the potential of using molecular diagnostics for TB surveillance across the country. The variables analysed include Mycobacterium tuberculosis (Mtb) positivity, the mycobacterial proportion of rifampicin-resistant Mtb (RIF), and probe frequency. The summary statistics of these variables were generated and aggregated at the facility and municipal level. The spatial distribution patterns of the indicators across municipalities were determined using the Moran's I and Getis Ord (Gi) statistics. A case-control study was conducted to investigate factors associated with a high mycobacterial load. Logistic regression was used to analyse this study's results. There was striking spatial heterogeneity in the distribution of Mtb and RIF across South Africa. The median patient age, urban setting classification, and number of health care workers were found to be associated with the mycobacterial load. This study illustrates the potential of using data generated from molecular diagnostics in combination with GIS technology for Mtb surveillance in South Africa. Spatially targeted interventions can be implemented in areas where high-burden Mtb persists.
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Affiliation(s)
- Lesley Erica Scott
- Wits Diagnostic Innovation Hub, Faculty of Health Science, University of the Witwatersrand, Johannesburg 2093, South Africa; (M.P.D.S.); (J.T.); (W.S.S.)
| | - Anne Nicole Shapiro
- Department of Biostatistics, Boston University School of Public Health, Boston, MA 02118, USA; (A.N.S.); (H.E.J.)
| | - Manuel Pedro Da Silva
- Wits Diagnostic Innovation Hub, Faculty of Health Science, University of the Witwatersrand, Johannesburg 2093, South Africa; (M.P.D.S.); (J.T.); (W.S.S.)
- National Priority Program of the National Health Laboratory Services (NHLS), Johannesburg 2131, South Africa
| | - Jonathan Tsoka
- Wits Diagnostic Innovation Hub, Faculty of Health Science, University of the Witwatersrand, Johannesburg 2093, South Africa; (M.P.D.S.); (J.T.); (W.S.S.)
| | - Karen Rita Jacobson
- Division of Infectious Diseases, Boston Medical Center, Boston, MA 02118, USA;
| | - Michael Emch
- Department of Epidemiology, University of North Carolina School, Chapel Hill, NC 27127, USA;
- Department of Geography and Environment, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Harry Moultrie
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg 2192, South Africa;
| | - Helen Elizabeth Jenkins
- Department of Biostatistics, Boston University School of Public Health, Boston, MA 02118, USA; (A.N.S.); (H.E.J.)
| | - David Moore
- Department of Clinical Research, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK;
| | - Annelies Van Rie
- Faculty of Medicine and Health Sciences, University of Antwerp, 2000 Antwerpen, Belgium;
| | - Wendy Susan Stevens
- Wits Diagnostic Innovation Hub, Faculty of Health Science, University of the Witwatersrand, Johannesburg 2093, South Africa; (M.P.D.S.); (J.T.); (W.S.S.)
- National Priority Program of the National Health Laboratory Services (NHLS), Johannesburg 2131, South Africa
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Cutugno L, O'Byrne C, Pané‐Farré J, Boyd A. Rifampicin-resistant RpoB S522L Vibrio vulnificus exhibits disturbed stress response and hypervirulence traits. Microbiologyopen 2023; 12:e1379. [PMID: 37877661 PMCID: PMC10493491 DOI: 10.1002/mbo3.1379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 08/15/2023] [Accepted: 08/31/2023] [Indexed: 10/26/2023] Open
Abstract
Rifampicin resistance, which is genetically linked to mutations in the RNA polymerase β-subunit gene rpoB, has a global impact on bacterial transcription and cell physiology. Previously, we identified a substitution of serine 522 in RpoB (i.e., RpoBS522L ) conferring rifampicin resistance to Vibrio vulnificus, a human food-borne and wound-infecting pathogen associated with a high mortality rate. Transcriptional and physiological analysis of V. vulnificus expressing RpoBS522L showed increased basal transcription of stress-related genes and global virulence regulators. Phenotypically these transcriptional changes manifest as disturbed osmo-stress responses and toxin-associated hypervirulence as shown by reduced hypoosmotic-stress resistance and enhanced cytotoxicity of the RpoBS522L strain. These results suggest that RpoB-linked rifampicin resistance has a significant impact on V. vulnificus survival in the environment and during infection.
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Affiliation(s)
- Laura Cutugno
- School of Natural SciencesUniversity of GalwayGalwayIreland
| | - Conor O'Byrne
- School of Biological and Chemical SciencesUniversity of GalwayGalwayIreland
| | - Jan Pané‐Farré
- Centre for Synthetic Microbiology (SYNMIKRO) & Department of ChemistryPhilipps‐University MarburgMarburgGermany
| | - Aoife Boyd
- School of Natural SciencesUniversity of GalwayGalwayIreland
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Mishra D, Singh A, Yadav RK, Verma M. Diagnostic Utility of Cartridge-Based Nucleic Acid Amplification Test (CBNAAT) on Induced Sputum Versus Gastric Aspirate Samples for the Diagnosis of Paediatric Pulmonary Tuberculosis. Cureus 2023; 15:e47246. [PMID: 38022348 PMCID: PMC10654686 DOI: 10.7759/cureus.47246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/18/2023] [Indexed: 12/01/2023] Open
Abstract
BACKGROUND Tuberculosis (TB) in children is neglected, mainly due to a lack of sensitive diagnostic tools. Paediatric TB is now a global priority. More paediatric TB cases are being recorded as a result of the introduction of Xpert® Mycobacterium tuberculosis (MTB)/rifampicin (RIF) (Cepheid Inc., Sunnyvale, USA). This study was undertaken to evaluate the performance of Xpert MTB/RIF in the diagnosis of pulmonary TB in children. METHODS We recruited 70 paediatric patients with probable pulmonary TB and their gastric aspirate (GA), and induced sputum (IS) samples were collected between January 2021 and June 2022 in Saifai, Etawah, Uttar Pradesh, at the Microbiology Department of the Uttar Pradesh University of Medical Sciences (U.P.U.M.S.). All samples were subjected to smear examination, Bacterial Activation of Continuous Temperature and Environmental Control - Mycobacterial Growth Indicator Tube (BACTEC-MGIT) culture, and Xpert MTB/RIF. RESULTS The specimens included 70 GAs and 70 IS samples. The total number of specimens were 140 and we collected GA as well as IS from each of the patient enrolled in the study. When compared to microscopy, GeneXpert provides a quicker and earlier detection of paediatric TB. The sensitivity of the cartridge-based nucleic acid amplification test (CBNAAT) against mycobacterial growth indicator tube (MGIT) was 75.0% for GA samples and 63.64% for IS samples. CONCLUSION Paediatric TB, owing to its paucibacillary nature and difficulty in the collection of samples, makes the diagnosis difficult by conventional methods. Our study shows that smear and culture yield in GA samples are superior to those of IS samples and the sensitivity of Xpert MTB/RIF assay is also significantly different in GA and IS samples, but a combination of GA and IS yielded the best results.
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Affiliation(s)
- Dipti Mishra
- Microbiology, Uttar Pradesh University of Medical Sciences, Etawah, IND
| | - Amit Singh
- Microbiology, Uttar Pradesh University of Medical Sciences, Etawah, IND
| | - Rajesh K Yadav
- Pediatrics, Uttar Pradesh University of Medical Sciences, Etawah, IND
| | - Mudit Verma
- Community Medicine, Uttar Pradesh University of Medical Sciences, Etawah, IND
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Lazarinis S, Hailer NP, Järhult JD, Brüggemann A. Incidence of Rifampicin Resistance in Periprosthetic Joint Infection: A Single-Centre Cohort Study on 238 Patients. Antibiotics (Basel) 2023; 12:1499. [PMID: 37887200 PMCID: PMC10603907 DOI: 10.3390/antibiotics12101499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Revised: 09/18/2023] [Accepted: 09/27/2023] [Indexed: 10/28/2023] Open
Abstract
BACKGROUND Rifampicin is a pillar in the treatment of periprosthetic joint infection (PJI). However, rifampicin resistance is an increasing threat to PJI treatment. This study explores the incidence of rifampicin-resistant bacteria over time in a Swedish tertiary referral centre and the association of rifampicin resistance with infection-free survival after PJI. METHODS The study included 238 staphylococcal PJIs treated between 2001 and 2020 for which susceptibility data for rifampicin were available. Data on causative bacteria, rifampicin resistance, treatment, and outcome were obtained. Kaplan-Meier survival analysis and Cox regression modelling estimated the infection-free cumulative survival and adjusted hazard ratios (HRs) for the risk of treatment failure. RESULTS Rifampicin-resistant causative bacteria were identified in 40 cases (17%). The proportion of rifampicin-resistant agents decreased from 24% in 2010-2015 to 12% in 2016-2020. The 2-year infection-free survival rates were 78.6% (95% CI, 66.4-93.1%) for the rifampicin-resistant group and 90.0% (95% CI, 85.8-94.4%) for the rifampicin-sensitive group. Patients with PJI caused by rifampicin-resistant bacteria had an increased risk of treatment failure (adjusted HR, 4.2; 95% CI, 1.7-10.3). CONCLUSIONS The incidence of PJI caused by rifampicin-resistant bacteria did not increase over the past 20 years. The risk of treatment failure in PJI caused by rifampicin-resistant bacteria is more than four times that caused by rifampicin-sensitive bacteria, highlighting the importance of limiting the development of rifampicin resistance.
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Affiliation(s)
- Stergios Lazarinis
- Department of Surgical Sciences, Orthopaedics, Uppsala University, SE-751 85 Uppsala, Sweden; (N.P.H.); (A.B.)
| | - Nils P. Hailer
- Department of Surgical Sciences, Orthopaedics, Uppsala University, SE-751 85 Uppsala, Sweden; (N.P.H.); (A.B.)
| | - Josef D. Järhult
- Department of Medical Sciences, Zoonosis Science Center, Uppsala University, SE-751 85 Uppsala, Sweden;
| | - Anders Brüggemann
- Department of Surgical Sciences, Orthopaedics, Uppsala University, SE-751 85 Uppsala, Sweden; (N.P.H.); (A.B.)
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Hang NTL, Hijikata M, Maeda S, Thuong PH, Huan HV, Hoang NP, Tam DB, Anh PT, Huyen NT, Cuong VC, Kobayashi N, Wakabayashi K, Miyabayashi A, Seto S, Keicho N. Host-pathogen relationship in retreated tuberculosis with major rifampicin resistance-conferring mutations. Front Microbiol 2023; 14:1187390. [PMID: 37469437 PMCID: PMC10352910 DOI: 10.3389/fmicb.2023.1187390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 06/09/2023] [Indexed: 07/21/2023] Open
Abstract
Introduction It is assumed that host defense systems eliminating the pathogen and regulating tissue damage make a strong impact on the outcome of tuberculosis (TB) disease and that these processes are affected by rifampicin (RIF) resistance-conferring mutations of Mycobacterium tuberculosis (Mtb). However, the host responses to the pathogen harboring different mutations have not been studied comprehensively in clinical settings. We analyzed clinico-epidemiological factors and blood transcriptomic signatures associated with major rpoB mutations conferring RIF resistance in a cohort study. Methods Demographic data were collected from 295 active pulmonary TB patients with treatment history in Hanoi, Vietnam. When recruited, drug resistance-conferring mutations and lineage-specific variations were identified using whole-genome sequencing of clinical Mtb isolates. Before starting retreatment, total RNA was extracted from the whole blood of HIV-negative patients infected with Mtb that carried either the rpoB H445Y or rpoB S450L mutation, and the total RNA was subjected to RNA sequencing after age-gender matching. The individual RNA expression levels in the blood sample set were also measured using real-time RT-PCR. Logistic and linear regression models were used to assess possible associations. Results In our cohort, rpoB S450L and rpoB H445Y were major RIF resistance-conferring mutations [32/87 (36.8%) and 15/87 (17.2%), respectively]. H445Y was enriched in the ancient Beijing genotype and was associated with nonsynonymous mutations of Rv1830 that has been reported to regulate antibiotic resilience. H445Y was also more frequently observed in genetically clustered strains and in samples from patients who had received more than one TB treatment episode. According to the RNA sequencing, gene sets involved in the interferon-γ and-α pathways were downregulated in H445Y compared with S450L. The qRT-PCR analysis also confirmed the low expression levels of interferon-inducible genes, including BATF2 and SERPING1, in the H445Y group, particularly in patients with extensive lesions on chest X-ray. Discussion Our study results showed that rpoB mutations as well as Mtb sublineage with additional genetic variants may have significant effects on host response. These findings strengthen the rationale for investigation of host-pathogen interactions to develop countermeasures against epidemics of drug-resistant TB.
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Affiliation(s)
| | - Minako Hijikata
- Department of Pathophysiology and Host Defense, The Research Institute of Tuberculosis, JATA, Tokyo, Japan
| | - Shinji Maeda
- Faculty of Pharmaceutical Sciences, Hokkaido University of Science, Sapporo, Hokkaido, Japan
| | | | | | | | - Do Bang Tam
- Department of Biochemistry, Hematology and Blood Transfusion, Hanoi Lung Hospital, Hanoi, Vietnam
| | - Pham Thu Anh
- Tuberculosis Network Management Office, Hanoi Lung Hospital, Hanoi, Vietnam
| | - Nguyen Thu Huyen
- NCGM-BMH Medical Collaboration Center, Hanoi, Vietnam
- Department of Health Policy and Economics, Hanoi University of Public Health, Hanoi, Vietnam
| | | | | | - Keiko Wakabayashi
- Department of Pathophysiology and Host Defense, The Research Institute of Tuberculosis, JATA, Tokyo, Japan
| | - Akiko Miyabayashi
- Department of Pathophysiology and Host Defense, The Research Institute of Tuberculosis, JATA, Tokyo, Japan
| | - Shintaro Seto
- Department of Pathophysiology and Host Defense, The Research Institute of Tuberculosis, JATA, Tokyo, Japan
| | - Naoto Keicho
- The Research Institute of Tuberculosis, JATA, Tokyo, Japan
- National Center for Global Health and Medicine, Tokyo, Japan
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Rich ML, Khan U, Zeng C, LaHood A, Franke MF, Atwood S, Bastard M, Burhan E, Danielyan N, Dzhazibekova PM, Gadissa D, Ghafoor A, Hewison C, Islam MS, Kazmi E, Khan PY, Lecca L, Maama LB, Melikyan N, Naing YY, Philippe K, Saki NA, Seung KJ, Skrahina A, Tefera GB, Varaine F, Vilbrun SC, Võ L, Mitnick CD, Huerga H. Outcomes of WHO-conforming, longer, all-oral multidrug-resistant TB regimens and analysis implications. Int J Tuberc Lung Dis 2023; 27:451-457. [PMID: 37231598 PMCID: PMC10237267 DOI: 10.5588/ijtld.22.0613] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 02/02/2023] [Indexed: 05/27/2023] Open
Abstract
BACKGROUND: Evidence of the effectiveness of the WHO-recommended design of longer individualized regimens for multidrug- or rifampicin-resistant TB (MDR/RR-TB) is limited.OBJECTIVES: To report end-of-treatment outcomes for MDR/RR-TB patients from a 2015-2018 multi-country cohort that received a regimen consistent with current 2022 WHO updated recommendations and describe the complexities of comparing regimens.METHODS: We analyzed a subset of participants from the endTB Observational Study who initiated a longer MDR/RR-TB regimen that was consistent with subsequent 2022 WHO guidance on regimen design for longer treatments. We excluded individuals who received an injectable agent or who received fewer than four likely effective drugs.RESULTS: Of the 759 participants analyzed, 607 (80.0%, 95% CI 77.0-82.7) experienced successful end-of-treatment outcomes. The frequency of success was high across groups, whether stratified on number of Group A drugs or fluoroquinolone resistance, and ranged from 72.1% to 90.0%. Regimens were highly variable regarding composition and the duration of individual drugs.CONCLUSIONS: Longer, all-oral, individualized regimens that were consistent with 2022 WHO guidance on regimen design had high frequencies of treatment success. Heterogeneous regimen compositions and drug durations precluded meaningful comparisons. Future research should examine which combinations of drugs maximize safety/tolerability and effectiveness.
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Affiliation(s)
- M L Rich
- Division of Global Health Equity, Brigham and Women´s Hospital, Boston, MA, Partners In Health, Boston, MA, USA
| | - U Khan
- Interactive Research & Development Global, Singapore, Singapore
| | - C Zeng
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, MA, USA
| | - A LaHood
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, MA, USA
| | - M F Franke
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, MA, USA
| | - S Atwood
- Division of Global Health Equity, Brigham and Women´s Hospital, Boston, MA
| | | | - E Burhan
- Persahabatan General Hospital, Jakarta, Indonesia
| | - N Danielyan
- Médecins Sans Frontières (MSF), Tbilisi, Georgia
| | | | - D Gadissa
- Partners In Health (PIH), Addis Ababa, Ethiopia
| | - A Ghafoor
- National Tuberculosis Programme (NTP), Ministry of National Health, Islamabad, Pakistan
| | | | - M S Islam
- Interactive Research & Development, Dhaka, Bangladesh
| | - E Kazmi
- Directorate General Health Services, Centers for Disease Control and Prevention, Sindh, Pakistan
| | - P Y Khan
- Partners In Health, Boston, MA, USA, Department of Clinical Research, London School of Hygiene & Tropical Medicine, London, UK
| | - L Lecca
- Socios En Salud Sucursal, Lima, Peru
| | - L B Maama
- PIH, Maseru, Lesotho, NTP, Maseru, Lesotho
| | - N Melikyan
- Epicentre, Paris, France, MSF, Yerevan, Armenia
| | | | | | - N A Saki
- World Health Organization, Country Office, Dhaka, Bangladesh
| | - K J Seung
- Division of Global Health Equity, Brigham and Women´s Hospital, Boston, MA, Partners In Health, Boston, MA, USA
| | | | - G B Tefera
- Partners In Health (PIH), Addis Ababa, Ethiopia
| | | | - S C Vilbrun
- GHESKIO Institute of Infectious Diseases and Reproductive Health, NTP, Port-au-Prince, Haiti
| | - L Võ
- Friends for International TB Relief, Ho Chi Minh City, Vietnam
| | - C D Mitnick
- Division of Global Health Equity, Brigham and Women´s Hospital, Boston, MA, Partners In Health, Boston, MA, USA, Department of Global Health and Social Medicine, Harvard Medical School, Boston, MA, USA
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Niem JM, Billones-Baaijens R, Stodart BJ, Reveglia P, Savocchia S. Biocontrol Potential of an Endophytic Pseudomonas poae Strain against the Grapevine Trunk Disease Pathogen Neofusicoccum luteum and Its Mechanism of Action. Plants (Basel) 2023; 12:plants12112132. [PMID: 37299111 DOI: 10.3390/plants12112132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 05/11/2023] [Accepted: 05/21/2023] [Indexed: 06/12/2023]
Abstract
Grapevine trunk diseases (GTDs) impact the sustainability of vineyards worldwide and management options are currently limited. Biological control agents (BCAs) may offer a viable alternative for disease control. With an aim to develop an effective biocontrol strategy against the GTD pathogen Neofusicoccum luteum, this study investigated the following: (1) the efficacy of the strains in suppressing the BD pathogen N. luteum in detached canes and potted vines; (2) the ability of a strain of Pseudomonas poae (BCA17) to colonize and persist within grapevine tissues; and (3) the mode of action of BCA17 to antagonize N. luteum. Co-inoculations of the antagonistic bacterial strains with N. luteum revealed that one strain of P. poae (BCA17) suppressed infection by 100% and 80% in detached canes and potted vines, respectively. Stem inoculations of a laboratory-generated rifampicin-resistant strain of BCA17 in potted vines (cv. Shiraz) indicated the bacterial strain could colonize and persist in the grapevine tissues, potentially providing some protection against GTDs for up to 6 months. The bioactive diffusible compounds secreted by BCA17 significantly reduced the spore germination and fungal biomass of N. luteum and the other representative GTD pathogens. Complementary analysis via MALDI-TOF revealed the presence of an unknown cyclic lipopeptide in the bioactive diffusible compounds, which was absent in a non-antagonistic strain of P. poae (JMN13), suggesting this novel lipopeptide may be responsible for the biocontrol activity of the BCA17. Our study provided evidence that P. poae BCA17 is a potential BCA to combat N. luteum, with a potential novel mode of action.
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Affiliation(s)
- Jennifer Millera Niem
- Gulbali Institute, Charles Sturt University, Locked Bag 588, Wagga Wagga, NSW 2678, Australia
- Faculty of Science and Health, School of Agricultural, Environmental and Veterinary Sciences, Charles Sturt University, Locked Bag 588, Wagga Wagga, NSW 2678, Australia
- UPLB Museum of Natural History, University of the Philippines Los Baños, College, Los Baños 4031, Laguna, Philippines
- Institute of Weed Science, Entomology, and Plant Pathology, College of Agriculture and Food Science, University of the Philippines Los Baños, College, Los Baños 4031, Laguna, Philippines
| | | | - Benjamin J Stodart
- Gulbali Institute, Charles Sturt University, Locked Bag 588, Wagga Wagga, NSW 2678, Australia
- Faculty of Science and Health, School of Agricultural, Environmental and Veterinary Sciences, Charles Sturt University, Locked Bag 588, Wagga Wagga, NSW 2678, Australia
| | - Pierluigi Reveglia
- Gulbali Institute, Charles Sturt University, Locked Bag 588, Wagga Wagga, NSW 2678, Australia
- Faculty of Science and Health, School of Agricultural, Environmental and Veterinary Sciences, Charles Sturt University, Locked Bag 588, Wagga Wagga, NSW 2678, Australia
- Institute for Sustainable Agriculture, CSIC, 14004 Córdoba, Spain
| | - Sandra Savocchia
- Gulbali Institute, Charles Sturt University, Locked Bag 588, Wagga Wagga, NSW 2678, Australia
- Faculty of Science and Health, School of Agricultural, Environmental and Veterinary Sciences, Charles Sturt University, Locked Bag 588, Wagga Wagga, NSW 2678, Australia
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9
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Cattaneo P, Mulongo CM, Morino G, De Vita MV, Paone G, Scarlata S, Kinyita S, Odhiambo H, Mazzi C, Gobbi F, Buonfrate D. Burden of Pulmonary Rifampicin-Resistant Tuberculosis in Kajiado, Kenya: An Observational Study. Microorganisms 2023; 11:1280. [PMID: 37317254 DOI: 10.3390/microorganisms11051280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Revised: 05/08/2023] [Accepted: 05/10/2023] [Indexed: 06/16/2023] Open
Abstract
BACKGROUND Rifampicin resistance (RR) is a major challenge in the clinical management of tuberculosis (TB), but data on its prevalence are still sparse in many countries. Our study aimed at estimating the prevalence of RR-TB in Kajiado County, Kenya. Secondary objectives were to estimate the incidence of pulmonary TB in adults and the rate of HIV-TB coinfection. METHODS We conducted an observational study in the context of the ATI-TB Project, carried out in Kajiado. The project was based on an active-case-finding campaign implemented with the aid of village chiefs, traditional healers and community health volunteers. Diagnosis relied on Xpert MTB/RIF, including a mobile machine that could be used to cover areas where testing would otherwise be difficult. RESULTS In sum, 3840 adults were screened for active TB during the campaign. RR cases among all TB diagnoses were 4.6%. The annual incidence of pulmonary TB among adults was 521 cases per 100,000 population. The rate of HIV coinfection was 22.2% among pulmonary TB diagnoses. CONCLUSION The prevalence of RR-TB was four times that what could be inferred from official notifications in Kajiado, and higher than overall prevalence in Kenya. In addition, our estimate of incidence of pulmonary TB in adults in Kajiado significantly differed from cases notified in the same area. In contrast, the rate of HIV coinfection was in line with national and regional data. TB diagnostic capability must be strengthened in Kajiado to improve patients' management and public health interventions.
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Affiliation(s)
- Paolo Cattaneo
- Department of Infectious, Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Negrar di Valpolicella, 37024 Verona, Italy
| | | | - Gianfranco Morino
- World Friends Amici del Mondo Onlus, Ruaraka Uhai Neema Hospital, off Thika Highway, Nairobi P.O. Box 39433-00623, Kenya
| | - Maria Vittoria De Vita
- World Friends Amici del Mondo Onlus, Ruaraka Uhai Neema Hospital, off Thika Highway, Nairobi P.O. Box 39433-00623, Kenya
| | - Gabriele Paone
- World Friends Amici del Mondo Onlus, Ruaraka Uhai Neema Hospital, off Thika Highway, Nairobi P.O. Box 39433-00623, Kenya
| | - Simone Scarlata
- Unit of Internal Medicine, Respiratory Pathophysiology and Thoracic Endoscopy, Fondazione Policlinico Universitario Campus Bio Medico, 00128 Rome, Italy
| | | | | | - Cristina Mazzi
- Department of Infectious, Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Negrar di Valpolicella, 37024 Verona, Italy
| | - Federico Gobbi
- Department of Infectious, Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Negrar di Valpolicella, 37024 Verona, Italy
| | - Dora Buonfrate
- Department of Infectious, Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Negrar di Valpolicella, 37024 Verona, Italy
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10
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Huang W, Lee MKT, Sin ATK, Nazari RS, Chua SY, Sng LH. Evaluation of Xpert MTB/RIF ultra assay for detection of Mycobacterium tuberculosis and rifampicin resistance. Pathology 2023:S0031-3025(23)00116-2. [PMID: 37268484 DOI: 10.1016/j.pathol.2023.03.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 01/05/2023] [Accepted: 03/14/2023] [Indexed: 06/04/2023]
Abstract
Tuberculosis (TB) is a public health challenge globally, and molecular testing is recommended to expedite diagnosis. Concerns that Xpert MTB/RIF assay (Xpert) may be less sensitive when testing paucibacillary samples led to the development of the Xpert MTB/RIF Ultra assay (Ultra). We evaluated the performance of Ultra against Xpert on clinical samples sent to the national reference laboratory in Singapore. In total, 149 samples collected between January 2019 and November 2020 were analysed. Mycobacterium tuberculosis complex (MTBC) was isolated from 55 cultures. Using culture as the reference standard, Ultra demonstrated higher sensitivity (96.4% vs 85.5%) and marginally lower specificity (88.3% vs 89.4%) compared to Xpert in the full cohort. When considering only paucibacillary specimens such as extrapulmonary and smear-negative samples, similar results were obtained. Reclassifying Ultra trace results (low levels of MTB are detected but no rifampicin resistant result is detected) as negative in the full cohort led to a decrease in sensitivity by 10.9% and a marginal increase in specificity by 1.1%. In instances of low bacillary load, Ultra also identified rifampicin resistance more accurately than Xpert, when corroborated against other methods such as broth microdilution, line probe assay and whole genome sequencing (WGS). One isolate tested rifampicin-resistant using Xpert and Ultra, but was phenotypically susceptible and WGS demonstrated the presence of the silent mutation Thr444Thr. Ultra is more sensitive than Xpert in the detection of MTBC and rifampicin resistance in our local setting. Nevertheless, the results of molecular testing should still be correlated with phenotypic studies.
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Affiliation(s)
- Wenjie Huang
- Central Tuberculosis Laboratory, Department of Microbiology, Singapore General Hospital, Singapore.
| | - Melody Kee Tai Lee
- Central Tuberculosis Laboratory, Department of Microbiology, Singapore General Hospital, Singapore
| | - Amanda Teo Kai Sin
- Central Tuberculosis Laboratory, Department of Microbiology, Singapore General Hospital, Singapore
| | | | - Syn Yu Chua
- Central Tuberculosis Laboratory, Department of Microbiology, Singapore General Hospital, Singapore
| | - Li-Hwei Sng
- Central Tuberculosis Laboratory, Department of Microbiology, Singapore General Hospital, Singapore
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11
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Dolya B, Hryhorieva O, Sorochynska K, Lopatniuk M, Ostash I, Tseduliak VM, Sterndorff EB, Jørgensen TS, Gren T, Dacyuk Y, Weber T, Luzhetskyy A, Fedorenko V, Ostash B. Properties of Multidrug-Resistant Mutants Derived from Heterologous Expression Chassis Strain Streptomyces albidoflavus J1074. Microorganisms 2023; 11:1176. [PMID: 37317150 DOI: 10.3390/microorganisms11051176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Revised: 03/30/2023] [Accepted: 04/28/2023] [Indexed: 06/16/2023] Open
Abstract
Streptomyces albidoflavus J1074 is a popular platform to discover novel natural products via the expression of heterologous biosynthetic gene clusters (BGCs). There is keen interest in improving the ability of this platform to overexpress BGCs and, consequently, enable the purification of specialized metabolites. Mutations within gene rpoB for the β-subunit of RNA polymerase are known to increase rifampicin resistance and augment the metabolic capabilities of streptomycetes. Yet, the effects of rpoB mutations on J1074 remained unstudied, and we decided to address this issue. A target collection of strains that we studied carried spontaneous rpoB mutations introduced in the background of the other drug resistance mutations. The antibiotic resistance spectra, growth, and specialized metabolism of the resulting mutants were interrogated using a set of microbiological and analytical approaches. We isolated 14 different rpoB mutants showing various degrees of rifampicin resistance; one of them (S433W) was isolated for the first time in actinomycetes. The rpoB mutations had a major effect on antibiotic production by J1074, as evident from bioassays and LC-MS data. Our data support the idea that rpoB mutations are useful tools to enhance the ability of J1074 to produce specialized metabolites.
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Affiliation(s)
- Borys Dolya
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, 79005 Lviv, Ukraine
| | - Olena Hryhorieva
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, 79005 Lviv, Ukraine
| | - Khrystyna Sorochynska
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, 79005 Lviv, Ukraine
| | - Maria Lopatniuk
- Department of Pharmacy, Saarland University, 66123 Saarbrucken, Germany
| | - Iryna Ostash
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, 79005 Lviv, Ukraine
| | - Vasylyna-Marta Tseduliak
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, 79005 Lviv, Ukraine
| | - Eva Baggesgaard Sterndorff
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, 2800 Kongens Lyngby, Denmark
| | - Tue Sparholt Jørgensen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, 2800 Kongens Lyngby, Denmark
| | - Tetiana Gren
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, 2800 Kongens Lyngby, Denmark
| | - Yuriy Dacyuk
- Department of Mineral Geology and Geophysics, Ivan Franko National University of Lviv, 79005 Lviv, Ukraine
| | - Tilmann Weber
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, 2800 Kongens Lyngby, Denmark
| | - Andriy Luzhetskyy
- Department of Pharmacy, Saarland University, 66123 Saarbrucken, Germany
| | - Victor Fedorenko
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, 79005 Lviv, Ukraine
| | - Bohdan Ostash
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, 79005 Lviv, Ukraine
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12
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Devrari JC, Chauhan M. Study the prevalence of rifampicin resistance among pulmonary tuberculosis patients by genexpert assay from a tertiary care hospital of North India. Int J Mycobacteriol 2023; 12:175-178. [PMID: 37338480 DOI: 10.4103/ijmy.ijmy_219_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2023] Open
Abstract
Background Rifampicin (RIF) resistance (RR) tuberculosis (TB) has posed a great challenge to TB control programs globally. Evidence of RIF-RR can help as a surrogate marker to find out multidrug-resistance cases. The study aimed to determine the prevalence of RIF-RR in pulmonary TB (PTB) patients over the 4 years at Dr. RPGMC, Tanda, from the year 2018 to 2021. Methods This was a retrospective study conducted at Dr. RPGMC, Tanda at Kangra, where we checked (from January 2018 to December 2021) clinically suspected PTB patients, whose samples were sent to the laboratory for GeneXpert assay to identify Mycobacterium TB/RIF (MTB/RIF) testing. Results Of the total 11,774 clinically suspected PTB specimens were collected, and identified by GeneXpert MTB/RIF assay, in which 2358 samples were MTB positive and 9416 were MTB negative. Among 2358 MTB-positive samples, 2240 (95%) samples were RIF sensitive, in which 1553 (65.9%) were males and 687 (29.1%) were females, 76 (3.2%) samples were RIF-RR, in which 51 (2.2%) were males and 25 (1%) were females, and 42 (1.8%) samples were RIF indeterminate, in which 25 (1%) were males and 17 (0.8%) were females. Conclusion The rate of RIF-RR was found 3.2% of total samples which was more in males. The overall positivity rate was 20%, and the rate of positivity decreased from 32% to 14% over the 4 years in sputum samples. Hence, the GeneXpert assay was found to be very important tool to detect RIF-RR among suspected PTB patients.
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Affiliation(s)
- Jitendra Chandra Devrari
- Department of Microbiology, Dr. Rajendra Prasad Government Medical College, Kangra, Himachal Pradesh, India
| | - Madhu Chauhan
- Department of Microbiology, Dr. Rajendra Prasad Government Medical College, Kangra, Himachal Pradesh, India
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13
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Beyene N, Sitotaw AL, Telila EG, Gebre HA, Alemu NB, Burny R, Cox C, Soka J, Tegegn B, Wassie L, Bobosha K, Agizew T. The use of rats to detect drug-resistant TB. Public Health Action 2023; 13:1-3. [PMID: 37152211 PMCID: PMC10162364 DOI: 10.5588/pha.22.0059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 12/18/2022] [Indexed: 05/09/2023] Open
Abstract
Although detection of drug-susceptible TB by Anti-Persoonsmijnen Ontmijnende Product Ontwikkeling-trained African giant pouched rats has been known for more than a decade, the detection of drug-resistant TB (DR-TB) using rats has never been explored before. We present what we believe to be the first report on rifampicin-resistant TB (RR-TB) detected using Xpert® MTB/RIF Ultra, comparably identified by rats sniffing sputum samples from presumptive TB patients: 88% of RR-TB detected using Ultra were identified by the rats. Further evaluation of the usefulness of rats for large-scale DR-TB contact triage testing is needed, especially in low- and middle-income countries, where resources are limited.
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Affiliation(s)
- N. Beyene
- Anti-Persoonsmijnen Ontmijnende Product Ontwikkeling (APOPO) TB Research Project, Armauer Hansen Research Institute (AHRI), Addis Ababa, Ethiopia
- APOPO, Tuberculosis Department, Sokoine University of Agriculture, Morogoro, Tanzania
- Department of Biology, University of Antwerp, Belgium
| | - A. L. Sitotaw
- Anti-Persoonsmijnen Ontmijnende Product Ontwikkeling (APOPO) TB Research Project, Armauer Hansen Research Institute (AHRI), Addis Ababa, Ethiopia
| | - E. G. Telila
- Anti-Persoonsmijnen Ontmijnende Product Ontwikkeling (APOPO) TB Research Project, Armauer Hansen Research Institute (AHRI), Addis Ababa, Ethiopia
| | - H. A. Gebre
- Anti-Persoonsmijnen Ontmijnende Product Ontwikkeling (APOPO) TB Research Project, Armauer Hansen Research Institute (AHRI), Addis Ababa, Ethiopia
| | - N. B. Alemu
- Anti-Persoonsmijnen Ontmijnende Product Ontwikkeling (APOPO) TB Research Project, Armauer Hansen Research Institute (AHRI), Addis Ababa, Ethiopia
| | - R. Burny
- APOPO, Tuberculosis Department, Sokoine University of Agriculture, Morogoro, Tanzania
- APOPO, Research Project, Eduardo Mondlane University, Maputo, Mozambique
| | - C. Cox
- APOPO, Tuberculosis Department, Sokoine University of Agriculture, Morogoro, Tanzania
- Department of Biology, University of Antwerp, Belgium
| | - J. Soka
- APOPO, Tuberculosis Department, Sokoine University of Agriculture, Morogoro, Tanzania
- APOPO, Research Project, Tanzanian Veterinary Research Institute, Dar es Salaam, Tanzania
| | - B. Tegegn
- Addis Ababa City Administration Health Bureau, Tuberculosis/HIV, Addis Ababa, Ethiopia
| | - L. Wassie
- AHRI, Mycobacterium, Diseases Research Directorate, Addis Ababa, Ethiopia
| | - K. Bobosha
- AHRI, Mycobacterium, Diseases Research Directorate, Addis Ababa, Ethiopia
| | - T. Agizew
- Anti-Persoonsmijnen Ontmijnende Product Ontwikkeling (APOPO) TB Research Project, Armauer Hansen Research Institute (AHRI), Addis Ababa, Ethiopia
- APOPO, Tuberculosis Department, Sokoine University of Agriculture, Morogoro, Tanzania
- Department of Biology, University of Antwerp, Belgium
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14
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Wang S, Hao J, Yang J, Zhang Q, Li A. The Attenuation Mechanism and Live Vaccine Potential of a Low-Virulence Edwardsiella ictaluri Strain Obtained by Rifampicin Passaging Culture. J Microbiol Biotechnol 2023; 33:167-179. [PMID: 36734130 PMCID: PMC9998210 DOI: 10.4014/jmb.2210.10013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 11/23/2022] [Accepted: 12/02/2022] [Indexed: 02/04/2023]
Abstract
The rifampicin-resistant strain E9-302 of Edwardsiella ictaluri strain 669 (WT) was generated by continuous passage on BHI agar plates containing increasing concentrations of rifampicin. E9-302 was attenuated significantly by 119 times to zebrafish Danio rerio compared to WT in terms of the 50% lethal dose (LD50). Zebrafish vaccinated with E9-302 via intraperitoneal (IP) injection at a dose of 1 × 103 CFU/fish had relative percentage survival (RPS) rates of 85.7% when challenged with wild-type E. ictaluri via IP 14 days post-vaccination (dpv). After 14 days of primary vaccination with E9-302 via immersion (IM) at a dose of 4 × 107 CFU/ml, a booster IM vaccination with E9-302 at a dose of 2 × 107 CFU/ml exhibited 65.2% RPS against challenge with wild-type E. ictaluri via IP 7 days later. These results indicated that the rifampicin-resistant attenuated strain E9-302 had potential as a live vaccine against E. ictaluri infection. A previously unreported amino acid site change at position 142 of the RNA polymerase (RNAP) β subunit encoded by the gene rpoB associated with rifampicin resistance was identified. Analysis of the whole-genome sequencing results revealed multiple missense mutations in the virulence-related genes esrB and sspH2 in E9-302 compared with WT, and a 189 bp mismatch in one gene, whose coding product was highly homologous to glycosyltransferase family 39 protein. This study preliminarily explored the molecular mechanism underlying the virulence attenuation of rifampicin-resistant strain E9-302 and provided a new target for the subsequent study of the pathogenic mechanism of E. ictaluri.
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Affiliation(s)
- Shuyi Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, P.R. China.,University of Chinese Academy of Sciences, Beijing 100049, P.R. China
| | - Jingwen Hao
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, P.R. China.,University of Chinese Academy of Sciences, Beijing 100049, P.R. China
| | - Jicheng Yang
- Dalian Ocean University, Dalian 116023, P.R. China
| | - Qianqian Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, P.R. China
| | - Aihua Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, P.R. China.,University of Chinese Academy of Sciences, Beijing 100049, P.R. China
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15
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Alao MA, Ogunbosi BO, Ibrahim OR. Trends in Rifampicin Resistance Among Children With Presumptive TB in the Pre-COVID and COVID-Era. Glob Pediatr Health 2023; 10:2333794X231156048. [PMID: 36814532 PMCID: PMC9939620 DOI: 10.1177/2333794x231156048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Accepted: 01/20/2023] [Indexed: 02/19/2023] Open
Abstract
Publications on COVID-19's impact on the global tuberculosis burden are from adult cohorts, pediatric data are lacking for inform decision. We compared the TB trends in southern Nigerian children in the pre-COVID-19 and COVID-19 era. This was a retrospective, cross-sectional study of early morning sputum/gastric washing or stool samples from children with presumptive TB evaluated using GeneXpert in a tertiary hospital from January 2016 to May 2022. Of the 20 589 persons screened for presumed TB in the pre-COVID-19 and the COVID-19 era, only 1104 (88.7%) of 1245 children had complete data for analysis. In the COVID era, a significantly higher number of children were presumed to have TB 755 (68.4%), P < .001. The overall incidence of MTB detected by Xpert MTB/RIF during the study period was 6.4% (71/1104). The incidence of MTB in the pre-COVID-19 era was 24/349 (6.9%), which was slightly higher than the COVID-19 era (47/755; 6.2%), P > .05). The annual trends of MTB detected peaked in 2019 [18/115; 15.7%] in the pre-COVID-19 era, then plummeted to 12/228 (5.3%) in 2020 in the COVID-19 era, and reached its all-time low of 6/160 (3.8%) in the first half of 2022, (P < .001). The overall incidence of Rifampicin-resistant TB (RR-TB) was 2.8% among the MTB detected cases and all occurred in the COVID-19 era. This study found a significant decline in MTB diagnosis and in the emergence of RR-TB in the COVID-19 era. This necessitates re-prioritizing worldwide efforts to manage childhood tuberculosis, including increased testing, if the aim of eliminating tuberculosis by 2035 is to be met.
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Affiliation(s)
- Michael Abel Alao
- Bowen University Teaching Hospital, Oyo State, Nigeria
- College of Medicine University of Ibadan & University College Hospital, Ibadan, Oyo State, Nigeria
- Michael Abel Alao, Department of Pediatrics, University College Hospital, PMB 5116, Ibadan, Oyo State 200212, Nigeria and the Department of Pediatrics, Bowen University Teaching Hospital, Box 15, Ogbomoso, Oyo State, Nigeria. Emails: ;
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16
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Mvelase NR, Cele LP, Singh R, Naidoo Y, Giandhari J, Wilkinson E, de Oliveira T, Swe-Han KS, Mlisana KP. Consequences of rpoB mutations missed by the GenoType MTBDR plus assay in a programmatic setting in South Africa. Afr J Lab Med 2023; 12:1975. [PMID: 36873290 PMCID: PMC9982466 DOI: 10.4102/ajlm.v12i1.1975] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 10/24/2022] [Indexed: 02/05/2023] Open
Abstract
Background Rifampicin resistance missed by commercial rapid molecular assays but detected by phenotypic assays may lead to discordant susceptibility results and affect patient management. Objective This study was conducted to evaluate the causes of rifampicin resistance missed by the GenoType MTBDRplus and its impact on the programmatic management of tuberculosis in KwaZulu-Natal, South Africa. Methods We analysed routine tuberculosis programme data from January 2014 to December 2014 on isolates showing rifampicin susceptibility on the GenoType MTBDRplus assay but resistance on the phenotypic agar proportion method. Whole-genome sequencing was performed on a subset of these isolates. Results Out of 505 patients with isoniazid mono-resistant tuberculosis on the MTBDRplus, 145 (28.7%) isolates showed both isoniazid and rifampicin resistance on the phenotypic assay. The mean time from MTBDRplus results to initiation of drug-resistant tuberculosis therapy was 93.7 days. 65.7% of the patients had received previous tuberculosis treatment. The most common mutations detected in the 36 sequenced isolates were I491F (16; 44.4%) and L452P (12; 33.3%). Among the 36 isolates, resistance to other anti-tuberculosis drugs was 69.4% for pyrazinamide, 83.3% for ethambutol, 69.4% for streptomycin, and 50% for ethionamide. Conclusion Missed rifampicin resistance was mostly due to the I491F mutation located outside the MTBDRplus detection area and the L452P mutation, which was not included in the initial version 2 of the MTBDRplus. This led to substantial delays in the initiation of appropriate therapy. The previous tuberculosis treatment history and the high level of resistance to other anti-tuberculosis drugs suggest an accumulation of resistance.
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Affiliation(s)
- Nomonde R Mvelase
- Department of Medical Microbiology, KwaZulu-Natal Academic Complex, National Health Laboratory Service, Durban, South Africa.,School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Lindiwe P Cele
- Department of Public Health, Epidemiology and Biostatistics Unit, Sefako Makgatho Health Sciences University, Pretoria, South Africa
| | - Ravesh Singh
- Department of Medical Microbiology, KwaZulu-Natal Academic Complex, National Health Laboratory Service, Durban, South Africa.,School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Yeshnee Naidoo
- KwaZulu-Natal Research Innovation and Sequencing Platform, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa.,Centre for Epidemic Response and Innovation, School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
| | - Jennifer Giandhari
- KwaZulu-Natal Research Innovation and Sequencing Platform, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Eduan Wilkinson
- KwaZulu-Natal Research Innovation and Sequencing Platform, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa.,Centre for Epidemic Response and Innovation, School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
| | - Tulio de Oliveira
- KwaZulu-Natal Research Innovation and Sequencing Platform, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa.,Centre for Epidemic Response and Innovation, School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa.,Centre for the AIDS Programme of Research in South Africa, University of KwaZulu-Natal, Durban, South Africa
| | - Khine Swe Swe-Han
- Department of Medical Microbiology, KwaZulu-Natal Academic Complex, National Health Laboratory Service, Durban, South Africa.,School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Koleka P Mlisana
- Department of Medical Microbiology, KwaZulu-Natal Academic Complex, National Health Laboratory Service, Durban, South Africa.,School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa.,Centre for the AIDS Programme of Research in South Africa, University of KwaZulu-Natal, Durban, South Africa
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17
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Saikaew S, Thongprachum A, Pongsararuk R, Thanraka A, Kunyanone N, Chaiyasirinroje B, Luangsook P, Butr-Indr B, Phunpae P, Wattananandkul U. Genotypic Distribution and the Epidemiology of Multidrug Resistant Tuberculosis in Upper Northern Thailand. Antibiotics (Basel) 2022; 11:antibiotics11121733. [PMID: 36551389 PMCID: PMC9774302 DOI: 10.3390/antibiotics11121733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 11/26/2022] [Accepted: 11/28/2022] [Indexed: 12/03/2022] Open
Abstract
The epidemiology and genotypes of multidrug-resistant tuberculosis (MDR-TB), a global public health threat, remain limited. The genotypic distribution and factors associated with MDR-TB in upper northern Thailand between 2015 and 2019 were investigated. The DNA sequencing of rpoB, katG, and inhA promoter of 51 multidrug-resistant Mycobacterium tuberculosis isolates revealed nine patterns of the rpoB gene mutation distributed in seven provinces. The S531L mutation was the most common mutation in all provinces. The rpoB mutation in Chiang Rai, Chiang Mai, and Lampang was highly diverse compared to other areas. Here, the mutation profiles that have yet to be reported in northern Thailand (H526P, Q513P, and H526C) were detected in Chiang Rai province. The S315T katG mutation was the most common genotype associated with INH resistance, especially in Chiang Mai and Lampang. Further analysis of data from 110 TB patients (42 MDR-TB and 68 drug-susceptible TB) revealed that <60 years of age was a significant factor associated with MDR-TB (OR = 0.316, 95% CI 0.128−0.784, p = 0.011) and ≥60 years of age was a significant factor associated with the S315T katG-mutation (OR = 8.867, 95% CI 0.981−80.177, p = 0.047). This study highlighted the necessity for continuous surveillance and risk factor monitoring for effective control of MDR-TB.
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Affiliation(s)
- Sukanya Saikaew
- Faculty of Public Health, Chiang Mai University, Muang District, Chiang Mai 50200, Thailand
- Division of Clinical Microbiology, Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Aksara Thongprachum
- Faculty of Public Health, Chiang Mai University, Muang District, Chiang Mai 50200, Thailand
| | - Rodjana Pongsararuk
- Office of Disease Prevention and Control, 1 (ODPC 1) Chiang Mai, Department of Disease Control, Ministry of Public Health Thailand, Chiang Mai 50000, Thailand
| | - Aungkana Thanraka
- Department of Medical Technology, Chiangrai Prachanukroh Hospital, Chiang Rai 57000, Thailand
| | - Naowarat Kunyanone
- Department of Medical Technology, Chiangrai Prachanukroh Hospital, Chiang Rai 57000, Thailand
| | | | - Praphan Luangsook
- Division of Clinical Microbiology, Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand
- Infectious Diseases Research Unit (IDRU), Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Bordin Butr-Indr
- Division of Clinical Microbiology, Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand
- Infectious Diseases Research Unit (IDRU), Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Ponrut Phunpae
- Division of Clinical Microbiology, Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand
- Infectious Diseases Research Unit (IDRU), Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Usanee Wattananandkul
- Division of Clinical Microbiology, Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand
- Infectious Diseases Research Unit (IDRU), Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand
- Epidemiology Research Group of Infectious Disease (ERGID), Chiang Mai University, Chiang Mai 50200, Thailand
- Correspondence: ; Tel.: +66-53-93-5068 (ext. 15)
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18
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Diriba G, Alemu A, Tola HH, Eshetu K, Yenew B, Amare M, Dagne B, Mollalign H, Sinshaw W, Abebaw Y, Seid G, Tadesse M, Zerihun B, Getu M, Moga S, Meaza A, Gamtesa DF, Tefera Z, Wondimu A, Hailu M, Buta B, Getahun M, Kebede A. Detection of Mycobacterium tuberculosis and rifampicin resistance by Xpert® MTB/RIF assay among presumptive tuberculosis patients in Addis Ababa, Ethiopia from 2014 to 2021. IJID Reg 2022; 5:97-103. [PMID: 36247095 PMCID: PMC9556786 DOI: 10.1016/j.ijregi.2022.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 08/31/2022] [Accepted: 09/01/2022] [Indexed: 12/02/2022]
Abstract
Objective This study aimed to determine the frequencies and trends of Mycobacterium tuberculosis and rifampicin resistance among presumptive tuberculosis patients in Ethiopia, who were tested using the Xpert MTB/RIF assay between 2014 and 2021. Methods Data were collected retrospectively from patient registries. Laboratory-based data were extracted from the national tuberculosis (TB) referral laboratory database. All patients referred to the National Tuberculosis Reference Laboratory (NTRL) for TB diagnosis from all over the country between March 1, 2014 and September 30, 2021, and tested using the Xpert MTB/RIF assay, were included. The extracted data were entered into a Microsoft Excel sheet and analyzed by Statistical Package for Social Sciences (SPSS) version 23. Results Among a total of 13 772 individuals tested using the Xpert MTB/RIF assay, the majority (8223; 59.7%) were males, and 48.5% (6678) of the individuals were aged between 15 and 39 years. Mycobacterium tuberculosis (MTB) was detected in 17.0% (2347) of the examined individuals. Of the detected MTB cases, nearly 9.9% (233) were rifampicin resistant (RR-TB), while 24 (1.0%) were RR-intermediate. Among all RR-TB cases, more than half (125; 53.6%) were detected in males, and 105 were new TB cases. Extrapulmonary (EPTB) patients had a greater rate of rifampicin resistance (11.0%) than pulmonary (PTB) patients (9.6%). Conclusion The frequency of TB and RR-TB remains high in the study setting. RR-TB was found to have a statistically significant association with previous anti-TB medication treatment. As a result, improving treatment adherence in recognized instances could assist in preventing MTB and RR-TB cases.
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Key Words
- EPHI, Ethiopian Public Health Institute
- EPTB, extrapulmonary tuberculosis
- MDR, multidrug resistance
- MTB, Mycobacterium tuberculosis
- MTBC, Mycobacterium tuberculosis complex
- Mycobacterium tuberculosis
- NTRL, National Tuberculosis Reference Laboratory
- PTB, pulmonary tuberculosis
- RIF, rifampicin
- RR-TB, rifampicin-resistant tuberculosis
- SPSS, Statistical Package for Social Sciences
- TB, tuberculosis
- WHO, World Health Organization
- Xpert MTB/RIF
- frequency
- rifampicin resistance
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Affiliation(s)
- Getu Diriba
- National Tuberculosis Reference Laboratory, Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Ayinalem Alemu
- National Tuberculosis Reference Laboratory, Ethiopian Public Health Institute, Addis Ababa, Ethiopia
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Habteyes Hailu Tola
- Department of Public Health, College of Health Sciences, Selale University, Fiche, Ethiopia
| | - Kirubel Eshetu
- USAID Eliminate TB Project, Management Sciences for Health, Addis Ababa, Ethiopia
| | - Bazezew Yenew
- National Tuberculosis Reference Laboratory, Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Misikir Amare
- National Tuberculosis Reference Laboratory, Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Biniyam Dagne
- National Tuberculosis Reference Laboratory, Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Hilina Mollalign
- National Tuberculosis Reference Laboratory, Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Waganeh Sinshaw
- National Tuberculosis Reference Laboratory, Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Yeshiwork Abebaw
- National Tuberculosis Reference Laboratory, Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Getachew Seid
- National Tuberculosis Reference Laboratory, Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Mengistu Tadesse
- National Tuberculosis Reference Laboratory, Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Betselot Zerihun
- National Tuberculosis Reference Laboratory, Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Melak Getu
- National Tuberculosis Reference Laboratory, Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Shewki Moga
- National Tuberculosis Reference Laboratory, Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Abyot Meaza
- National Tuberculosis Reference Laboratory, Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Dinka Fekadu Gamtesa
- National Tuberculosis Reference Laboratory, Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Zigba Tefera
- National Tuberculosis Reference Laboratory, Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Amanuel Wondimu
- National Tuberculosis Reference Laboratory, Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Michael Hailu
- National Tuberculosis Reference Laboratory, Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Bedo Buta
- National Tuberculosis Reference Laboratory, Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Muluwork Getahun
- National Tuberculosis Reference Laboratory, Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Abebaw Kebede
- Department of Microbial, Cellular and Molecular Biology, College of Natural and Computational Sciences, Addis Ababa University, Addis Ababa, Ethiopia
- Africa Centers for Disease Control and Prevention, Addis Ababa, Ethiopia
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Bae S, Kim ES, Kim HS, Yang E, Chung H, Lee YW, Jung J, Kim MJ, Chong YP, Kim SH, Choi SH, Lee SO, Kim YS. Risk Factors of Recurrent Infection in Patients with Staphylococcus aureus Bacteremia: a Competing Risk Analysis. Antimicrob Agents Chemother 2022; 66:e0012622. [PMID: 35762799 DOI: 10.1128/aac.00126-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Although several clinical variables have been reported as risk factors for recurrence of Staphylococcus aureus infection, most studies have not considered competing risk events that may overestimate the risk. In this study, we performed competing risk analysis to identify risk factors related to 90-day recurrence in patients with S. aureus bacteremia (SAB) using a large cohort data from a single tertiary hospital in South Korea. All adults who experienced SAB during admission were prospectively enrolled from August 2008 to December 2019. After the day of the first positive blood culture, recurrence and all-cause mortality were assessed for 90 days. Recurrence was defined as a development of symptoms or signs of infection with or without repeated bacteremia after >7 days of negative blood culture and clinically apparent improvement. Subdistribution hazard ratios (sHR) for recurrence and all-cause mortality were estimated using Fine and Gray models. Of 1,725 SAB patients, including 885 cases (51.3%) of methicillin-resistant S. aureus (MRSA) bacteremia, 85 (5.0%) experienced recurrence during the study period. In a multivariate Fine and Gray regression model, the presence of a vascular graft (subdistribution HR [sHR], 3.48; 95% confidence interval [CI], 1.90-6.40), nasal MRSA carriage (sHR, 2.10; 95% CI, 1.28-3.44), methicillin resistance (sHR, 1.69; 95% CI, 1.00-2.84), and rifampicin resistance (sHR, 2.20; 95% CI, 1.12-4.33) were significantly associated with 90-day recurrence. In a large cohort of SAB patients with a high prevalence of MRSA, indwelling vascular graft, nasal MRSA carriage, methicillin resistance, and rifampicin resistance were potential risk factors for recurrence of S. aureus infection.
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Sereda Y, Korotych O, Klimuk D, Zhurkin D, Solodovnikova V, Grzemska M, Grankov V, Hurevich H, Yedilbayev A, Skrahina A. Tuberculosis Co-Infection Is Common in Patients Requiring Hospitalization for COVID-19 in Belarus: Mixed-Methods Study. Int J Environ Res Public Health 2022; 19. [PMID: 35410048 DOI: 10.3390/ijerph19074370] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 03/22/2022] [Accepted: 03/30/2022] [Indexed: 12/24/2022]
Abstract
A significant drop in tuberculosis (TB) case-finding has been widely reported during the period of the COVID-19 pandemic. To address a decrease in TB notification, Belarus introduced laboratory TB testing in patients with the laboratory-confirmed coronavirus disease 2019 (COVID-19). We conducted a secondary analysis of health records among 844 patients with laboratory-confirmed COVID-19 diagnosis who were admitted to repurposed departments at TB hospitals and who were tested by Xpert MTB/RIF (Cepheid Inc., Sunnyvale, CA, USA) in five Belarus regions between April and October 2021. Quantitative analysis followed by 13 individual interviews with health managers, physicians, and nurses participating in the intervention. Most patients were male (64%) and mean age was 43.5 ± 16 years. One in twenty (n = 47, 5.6%) patients were co-infected with active pulmonary TB, and over one-third of them (n = 18) had rifampicin resistance. In-hospital mortality was comparable in patients with and without TB co-infection (2.1% and 2.3% respectively, p > 0.99). Laboratory TB testing among patients with COVID-19 at repurposed departments of TB hospitals is feasible in Belarus and may improve TB case-finding.
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He W, Tan Y, Liu C, Wang Y, He P, Song Z, Liu D, Zheng H, Ma A, Zhao B, Ou X, Xia H, Wang S, Zhao Y. Drug-Resistant Characteristics, Genetic Diversity, and Transmission Dynamics of Rifampicin-Resistant Mycobacterium tuberculosis in Hunan, China, Revealed by Whole-Genome Sequencing. Microbiol Spectr 2022;:e0154321. [PMID: 35171016 DOI: 10.1128/spectrum.01543-21] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
To gain a deep insight into the additional drug-resistant profiles, genetic diversity, and transmission dynamics of rifampicin-resistant tuberculosis (RR-TB) circulating in Hunan province, drug susceptibility testing and whole-genome-sequencing were performed among RR-TB strains collected from Jan. 2013 to Jun. 2018 in Hunan province. A total of 124 RR-TB strains were recovered successfully and included into the final analysis. Lineage 2.2.1 was the dominant sublineage, accounting for 72.6% (90/124), followed by lineage 4.5 (11.3%, 14/124), lineage 4.4 (8.1%, 10/124), lineage 4.2 (6.5%, 8/124) and lineage 2.2.2 (1.6%, 2/124). Overall, 83.1% (103/124) and 3.2% (4/124) of RR-TB were MDR-TB and XDR-TB, respectively. Nearly 30% of RR-TB isolates were resistant to fluoroquinolones, and 26.6% (33/124) were pre-XDR-TB. Moreover, 30.6% (38/124) of RR-TB strains were identified as phenotypically resistance to pyrazinamide. Totally, 17 clusters containing 48 (38.7%, 48/124) RR-TB strains were identified, ranging in size from 2 to 10 isolates. No significant difference was detected in clustering rate between lineage 2 and lineage 4 (χ2 = 0.027, P = 0.870). Our study revealed the complexity of RR-TB strains circulating in Hunan province with complex additional drug-resistant profile and relatively higher clustering rates. Comprehensive information based on WGS should be used to guide the design of treatment regimens and tailor public interventions. IMPORTANCE Comprehensive information such as genetic background and drug-resistant profile of MTB strains could help to tailor public interventions. However, these data are limited in Hunan province, one of the provinces with high-TB burden in China. So, this study aimed to provide us with deep insight into the molecular epidemiology of RR-TB isolates circulating in Hunan province by combining phenotypic drug susceptibility testing and whole-genome sequencing. To our knowledge, this is the first study to use whole-genome sequencing data of RR-TB strains spanning more than 5 years for molecular epidemiology analysis in Hunan province, which allows us to identify genetic background information and clustered strains more accurately. Our study revealed the complexity of RR-TB strains circulating in Hunan province with complex additional drug-resistant profile and relatively higher clustering rates. Comprehensive information based on WGS should be used to guide the design of treatment regimens and tailor public interventions.
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Huang J, Zhang F, Zhang J, Dai J, Rong D, Zhao M, Wang J, Ding Y, Chen M, Xue L, Gu Q, Wu S, Wu Q. Molecular Characterization of Rifampicin-Resistant Staphylococcus aureus Isolates from Retail Foods in China. Antibiotics (Basel) 2021; 10:1487. [PMID: 34943699 DOI: 10.3390/antibiotics10121487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 11/24/2021] [Accepted: 11/26/2021] [Indexed: 11/17/2022] Open
Abstract
This study investigated the molecular characteristics of rifampin-resistant (RIF-R) Staphylococcus aureus isolates recovered from 4300 retail food samples covering most provincial capitals in China, from 2011 to 2016. Of the 1463 S. aureus enrolled, 149 isolates (142 MSSA and 7 MRSA) were identified as rifampicin-resistant, including 20 high-level (MICs ≥ 8 μg/mL) and 129 low-level (MICs between 2 and 4 μg/mL) rifampicin-resistant strains. Most of the RIF-R S. aureus isolates were resistant to more than three antibiotics. The mutations in the rifampicin resistance-determining region of the rpoB gene were studied in all RIF-R strains. All of the strains presented the mutational change 481 His/Asn and five isolates presented an additional mutation, including 477 Asp/Tyr, 527 Ile/Met, and 466 Leu/Ser, respectively. Thirteen STs and twenty-one spa types were represented, in which five MRSA showed non-type SCCmec and the remaining MRSA belonged to SCCmec type IV-where, ST1-t127 was the predominant type from all of the isolates, while ST398-t034 was the predominant type for the MRSA isolates. In this study, we found that the food-related RIF-R S. aureus may have a unique genetic background selection. However, the scenario regarding the presence of RIF-R S. aureus, especially MRSA, in retail food in China is not favorable and warrants public attention.
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23
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Das A, Gupta V, Anupurba S. Rifampicin-Resistant Disseminated Tuberculosis in an Immunocompetent Adolescent Male Presenting with Retropharyngeal Abscess and Spinal Involvement. J Lab Physicians 2021; 13:277-279. [PMID: 34602794 PMCID: PMC8478508 DOI: 10.1055/s-0041-1730754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Abstract
Retropharyngeal abscess is a rare manifestation in spinal tuberculosis. Early clinical diagnosis followed by microbiological confirmation and effective treatment is crucial to avoid irreversible damage to the spine. Here, we report a case of disseminated tuberculosis in an immunocompetent adolescent male who presented with retropharyngeal abscess, multifocal involvement of the spine, and skin tuberculids. Xpert MTB/RIF assay in this patient facilitated early lifesaving treatment by detecting rifampicin-resistant Mycobacterium tuberculosis (MTB) in the clinical specimen.
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Affiliation(s)
- Arghya Das
- Department of Microbiology, Institute of Medical Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Vineeta Gupta
- Department of Pediatrics, Institute of Medical Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Shampa Anupurba
- Department of Microbiology, Institute of Medical Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, India
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24
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Kabała M, Gofron Z, Aptekorz M, Sacha K, Harmanus C, Kuijper E, Martirosian G. Clostridioides difficile Ribotype 027 (RT027) Outbreak Investigation Due to the Emergence of Rifampicin Resistance Using Multilocus Variable-Number Tandem Repeat Analysis (MLVA). Infect Drug Resist 2021; 14:3247-3254. [PMID: 34429622 PMCID: PMC8380304 DOI: 10.2147/idr.s324745] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 07/24/2021] [Indexed: 12/29/2022] Open
Abstract
Objective The aim of this study was Clostridioides difficile outbreak investigation due to the emergence of rifampicin resistant ribotype 027 (RT 027) fecal isolates from patients of Polish tertiary care hospital between X. 2017 and II. 2018 using multilocus variable tandem repeat analysis (MLVA). Materials and Methods Twenty-nine C. difficile fecal isolates from patients of tertiary care hospital in Southern Poland were ribotyped and analyzed by MLVA. Multiplex PCR (mPCR) for genes encoding GDH (gluD), toxins A (tcdA)/ B (tcdB), 16S rDNA and binary toxin genes (ctdA and ctdB) was performed. The antibiotic susceptibility profile was determined by E-test. Results The A, B and binary toxins encoding genes were detected in all 29 C. difficile strains which were sensitive to metronidazole, vancomycin and were resistant to erythromycin, clindamycin, and moxifloxacin; resistance to imipenem demonstrated 97%, to rifampicin – 45% isolates. C. difficile strains could be grouped by MLVA into 5 distinct clusters, and the largest cluster II contains 16 strains. The comparison of rifampicin GM MIC of cluster II (n=16 strains) with all others (n=13) showed that strains from clusters I, III, IV and V possessed significantly (p <0.005) higher GM MIC and were more resistant to rifampicin. Conclusion MLVA analysis proved transmission and recognized outbreak due to multidrug-resistant RT 027 C. difficile among patients of tertiary care hospital in Southern Poland. The reason for this is probably the widespread occurrence of spores in the hospital environment, which includes, among others, neglect of hygienic procedures and epidemic supervision. High resistance to imipenem (97%) and to rifampicin (45%) among C. difficile RT 027 Silesian isolates is threatening and requires further studies to elucidate this phenomenon.
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Affiliation(s)
- Monika Kabała
- Department of Medical Microbiology Medical University of Silesia in Katowice, Katowice, Poland
| | - Zygmunt Gofron
- Department of Medical Microbiology Medical University of Silesia in Katowice, Katowice, Poland
| | - Małgorzata Aptekorz
- Department of Medical Microbiology Medical University of Silesia in Katowice, Katowice, Poland
| | - Krzysztof Sacha
- Department of Medical Microbiology Medical University of Silesia in Katowice, Katowice, Poland
| | - Celine Harmanus
- Department of Medical Microbiology Leiden University Medical Center, Leiden, the Netherlands
| | - Ed Kuijper
- Department of Medical Microbiology Leiden University Medical Center, Leiden, the Netherlands
| | - Gayane Martirosian
- Department of Medical Microbiology Medical University of Silesia in Katowice, Katowice, Poland
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Ma P, Luo T, Ge L, Chen Z, Wang X, Zhao R, Liao W, Bao L. Compensatory effects of M. tuberculosis rpoB mutations outside the rifampicin resistance-determining region. Emerg Microbes Infect 2021; 10:743-752. [PMID: 33775224 PMCID: PMC8057087 DOI: 10.1080/22221751.2021.1908096] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Mycobacterium tuberculosis has been observed to develop resistance to the frontline anti-tuberculosis drug rifampicin, primarily through mutations in the rifampicin resistance-determining region (RRDR) of rpoB. While these mutations have been determined to confer a fitness cost, compensatory mutations in rpoA and rpoC that may enhance the fitness of resistant strains have been demonstrated. Recent genomic studies identified several rpoB non-RRDR mutations that co-occurred with RRDR mutations in clinical isolates without rpoA/rpoC mutations and may confer fitness compensation. In this study, we identified 33 evolutionarily convergent rpoB non-RRDR mutations through phylogenomic analysis of public genomic data for clinical M. tuberculosis isolates. We found that none of these mutations, except V170F and I491F, can cause rifampin resistance in Mycolicibacterium smegmatis. The compensatory effects of five representative mutations across rpoB were evaluated by an in vitro competition assay, through which we observed that each of these mutations can significantly improve the relative fitness of the initial S450L mutant (0.97–1.08 vs 0.87). Furthermore, we observed that the decreased RNAP transcription efficiency introduced by S450L was significantly alleviated by each of the five mutations. Structural analysis indicated that the fitness compensation observed for the non-RRDR mutations might be achieved by modification of the RpoB active centre or by changes in interactions between RNAP subunits. Our results provide experimental evidence supporting that compensatory effects are exerted by several rpoB non-RRDR mutations, which could be utilized as additional molecular markers for predicting the fitness of clinical rifampin-resistant M. tuberculosis strains.
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Affiliation(s)
- Pengjiao Ma
- Laboratory of Infection and Immunity, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, People's Republic of China
| | - Tao Luo
- Laboratory of Infection and Immunity, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, People's Republic of China
| | - Liang Ge
- Laboratory of Infection and Immunity, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, People's Republic of China
| | - Zonghai Chen
- Laboratory of Infection and Immunity, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, People's Republic of China
| | - Xinyan Wang
- Laboratory of Infection and Immunity, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, People's Republic of China
| | - Rongchuan Zhao
- Laboratory of Infection and Immunity, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, People's Republic of China
| | - Wei Liao
- Laboratory of Infection and Immunity, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, People's Republic of China
| | - Lang Bao
- Laboratory of Infection and Immunity, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, People's Republic of China
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Liu X, Zu X, Wang Z, Zhao P, Gao L, Zhao Z, Xue Y. [Development of molecular markers of Mycobacterium tuberculosis rifampicin resistance gene rpoB by PARMS technology]. Sheng Wu Gong Cheng Xue Bao 2021; 37:2503-2512. [PMID: 34327915 DOI: 10.13345/j.cjb.200487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The purpose of this study is to provide a simple and reliable genetic typing approach for molecular drug susceptibility test of Mycobacterium tuberculosis, through the developing of fluorescence molecular marker of rifampicin resistance gene rpoB. Eleven fluorescent molecular markers of the rpoB gene were established by using the sequence difference between the amino acid positions 531, 526, 516, 511 and 513 of rpoB gene of rifampicin-resistant strains and the alleles of rifampicin-sensitive strains, combined with the PARMS technique (Penta-primer amplification refractory mutation system). We used 104 clinical isolates of Mycobacterium tuberculosis to validate this marker and it was verified by sequencing as 100% correct. These samples were also tested with proportional drug sensitivity test. The coincidence rate was 94.23%. The molecular markers had high reliability for genotyping of rpoB gene. It can also detect low-concentration drug-resistant samples (511/533 unit point mutations) whose phenotypic susceptibility cannot be detected. The eleven sets of fluorescent molecular markers could cover 92%-96% of rpoB gene mutation types of rifampicin-resistant strains, and provide new idea for rapid detection of rifampin-resistant Mycobacterium tuberculosis.
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Affiliation(s)
- Xiaohui Liu
- College of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang 471023, Henan, China
| | - Xiangyang Zu
- College of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang 471023, Henan, China
| | - Zhenzhen Wang
- Department of Laboratory Medicine, the First Affiliated Hospital of Henan University of Science and Technology, Luoyang 471023, Henan, China
| | - Pengchao Zhao
- College of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang 471023, Henan, China
| | - Lei Gao
- College of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang 471023, Henan, China
| | - Zhanqin Zhao
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471023, Henan, China
| | - Yun Xue
- College of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang 471023, Henan, China
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Aljanazreh B, Alzatari K, Tamimi A, Alsaafeen MH, Hassouneh W, Ashhab Y. Brucellosis re-emergence after a decade of quiescence in Palestine, 2015-2017: A seroprevalence and molecular characterization study. Transbound Emerg Dis 2021; 69:e130-e140. [PMID: 34331742 DOI: 10.1111/tbed.14270] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 03/09/2021] [Accepted: 07/29/2021] [Indexed: 01/23/2023]
Abstract
Brucellosis is an endemic disease in many developing countries and ranked by the World Health Organization among the top seven "neglected zoonoses". Although a Palestinian brucellosis control program was launched in 1998, the disease re-emerged after 2012. Interestingly, a similar re-emerging pattern was reported in the neighbouring Israeli regions. The aim of this work was to characterize the re-emerging strains and delineate their genetic relatedness. During 2015-2017, blood samples from 1324 suspected human cases were analyzed using two serological tests. Seropositive samples were cultured, and their DNAs were analyzed by different genetic markers to determine the involved Brucella species and rule out any possible involvement of the Rev.1 vaccine strain. The rpoB gene was sequenced from nine isolates to screen for rifampicin resistance mutations. Multi locus VNTR analysis (MLVA-16) was used for genotyping the isolates. The molecular analysis showed that all isolates were Brucella melitensis strains unrelated to the Rev.1 vaccine. The rpoB gene sequences showed four single nucleotide variations (SNVs) not associated with rifampicin resistance. MLVA-16 analysis clustered the isolates into 22 unique genotypes that belonged to the East Mediterranean lineage. Altogether, our findings show that the re-emergence of brucellosis was due to B. melitensis strains of local origin, the Palestinian and Israeli control programs' weaknesses could be a major factor behind the re-emergence of the disease. However, other socioeconomic and environmental factors must be investigated. Moreover, strengthening brucellosis control programs and enhancing cooperation between all stakeholders is essential to ensure long-term program outcomes to fight brucellosis.
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Affiliation(s)
- Bessan Aljanazreh
- Palestine Korea Biotechnology Center, Palestine Polytechnic University, Hebron, Palestine
| | - Khaled Alzatari
- Palestine Korea Biotechnology Center, Palestine Polytechnic University, Hebron, Palestine.,Palestine Red Crescent Specialized Hospital, Hebron, Palestine
| | - Asmaa Tamimi
- Palestine Korea Biotechnology Center, Palestine Polytechnic University, Hebron, Palestine
| | - Mohammad H Alsaafeen
- Department of Preventive Medicine, Hebron Health Directorate, Palestinian Ministry of Health, Hebron, Palestine
| | | | - Yaqoub Ashhab
- Palestine Korea Biotechnology Center, Palestine Polytechnic University, Hebron, Palestine
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Zheng X, Fang R, Wang C, Tian X, Lin J, Zeng W, Zhou T, Xu C. Resistance Profiles and Biological Characteristics of Rifampicin-Resistant Staphylococcus aureus Small-Colony Variants. Infect Drug Resist 2021; 14:1527-1536. [PMID: 33911880 PMCID: PMC8071703 DOI: 10.2147/idr.s301863] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 03/12/2021] [Indexed: 01/01/2023] Open
Abstract
Background Staphylococcus aureus (S. aureus) is a major contributor to nosocomial and community-acquired infections. S. aureus small colony variants (SCVs) which changed in relevant phenotype have made more limited and difficult for therapeutic options against S. aureus infections increasingly. Rifampicin is considered as the "last-resort" antibiotic against S. aureus. Our study investigated resistance profiles and biological characteristics of rifampicin-resistant S. aureus SCVs. Methods We collected S. aureus SCVs that were selected from 41 rifampicin-resistant clinical isolates. Then, biological characteristics, resistance spectrum, and rifampicin resistance mechanisms of tested S. aureus SCVs and corresponding parental strains were investigated by classic microbiological methods, agar dilution method, polymerase chain reaction (PCR). Moreover, the fitness cost of S. aureus SCVs, including growth, biofilm formation ability, and virulence profile, was also determined by bacterial growth curve assay, biofilm formation assay, and Galleria mellonella infection model. Results There were three S. aureus SCVs (JP310 SCVs, JP1450 SCVs, JP1486 SCVs) that were selected from 41 rifampicin-resistant S. aureus. S. aureus SCVs colonies were tiny, with decreased pigmentation, and the hemolysis circle was not obvious compared with corresponding parental strains. And SCVs could not be restored to normal-colony phenotype after hemin, menaquinone, or thymidine supplementation. Different rpoB mutations occurred in JP1486 SCVs. Antimicrobial susceptibility testing revealed MICs of SCVs were higher than corresponding parental strains. Besides, the growth ability and virulence of SCVs were lower, and biofilm formation ability of which increased compared with parental strains. Conclusion S. aureus SCVs share the rifampicin resistance mechanisms with parental strains, although there were some differences in the position of rpoB mutations. Moreover, we found that the biological characteristics of SCVs were significantly different from corresponding parental strains. In contrast, decreased susceptibility to other antibiotics of SCVs was observed during phenotype switch. Furthermore, SCVs incur the fitness cost.
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Affiliation(s)
- Xiangkuo Zheng
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325035, People's Republic of China
| | - Renchi Fang
- Department of Laboratory Medicine, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, 310003, People's Republic of China
| | - Chong Wang
- Department of Laboratory Medicine, Qingdao Municipal Hospital, Qingdao, 266000, People's Republic of China
| | - Xuebin Tian
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, 325035, People's Republic of China
| | - Jie Lin
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325035, People's Republic of China
| | - Weiliang Zeng
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, 325035, People's Republic of China
| | - Tieli Zhou
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325035, People's Republic of China
| | - Chunquan Xu
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325035, People's Republic of China
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Faulkner V, Cox AA, Goh S, van Bohemen A, Gibson AJ, Liebster O, Wren BW, Willcocks S, Kendall SL. Re-sensitization of Mycobacterium smegmatis to Rifampicin Using CRISPR Interference Demonstrates Its Utility for the Study of Non-essential Drug Resistance Traits. Front Microbiol 2021; 11:619427. [PMID: 33597931 PMCID: PMC7882622 DOI: 10.3389/fmicb.2020.619427] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 12/21/2020] [Indexed: 12/24/2022] Open
Abstract
A greater understanding of the genes involved in antibiotic resistance in Mycobacterium tuberculosis (Mtb) is necessary for the design of improved therapies. Clustered regularly interspaced short palindromic repeat interference (CRISPRi) has been previously utilized in mycobacteria to identify novel drug targets by the demonstration of gene essentiality. The work presented here shows that it can also be usefully applied to the study of non-essential genes involved in antibiotic resistance. The expression of an ADP-ribosyltransferase (Arr) involved in rifampicin resistance in Mycobacterium smegmatis was silenced using CRISPRi and the impact on rifampicin susceptibility was measured. Gene silencing resulted in a decrease in the minimum inhibitory concentration (MIC) similar to that previously reported in an arr deletion mutant. There is contradictory evidence for the toxicity of Streptococcus pyogenes dCas9 (dCas9Spy) in the literature. In this study the expression of dCas9Spy in M. smegmatis showed no impact on viability. Silencing was achieved with concentrations of the aTc inducer lower than previously described and with shorter induction times. Finally, designing small guide RNAs (sgRNAs) that target transcription initiation, or the early stages of elongation had the most impact on rifampicin susceptibility. This study demonstrates that CRISPRi based gene silencing can be as impactful as gene deletion for the study of non-essential genes and further contributes to the knowledge on the design and induction of sgRNAs for CRISPRi. This approach can be applied to other non-essential antimicrobial resistance genes such as drug efflux pumps.
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Affiliation(s)
- Valwynne Faulkner
- Pathobiology and Population Sciences, The Royal Veterinary College, Hatfield, United Kingdom
| | - Adrienne Adele Cox
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Shan Goh
- Department of Clinical, Pharmaceutical & Biological Science, School of Life & Medical Sciences, University of Hertfordshire, Hatfield, United Kingdom
| | - Annelies van Bohemen
- Pathobiology and Population Sciences, The Royal Veterinary College, Hatfield, United Kingdom
| | - Amanda J Gibson
- Pathobiology and Population Sciences, The Royal Veterinary College, Hatfield, United Kingdom.,Centre of Excellence for Bovine TB, Aberystwyth University, Aberystwyth, United Kingdom
| | - Oliver Liebster
- Pathobiology and Population Sciences, The Royal Veterinary College, Hatfield, United Kingdom
| | - Brendan W Wren
- Department of Infection Biology, The London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Sam Willcocks
- Department of Infection Biology, The London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Sharon L Kendall
- Pathobiology and Population Sciences, The Royal Veterinary College, Hatfield, United Kingdom
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30
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Ngabonziza JCS, Decroo T, Maniliho R, Habimana YM, Van Deun A, de Jong BC. Low Cycle Threshold Value in Xpert MTB/RIF Assay May Herald False Detection of Tuberculosis and Rifampicin Resistance: A Study of Two Cases. Open Forum Infect Dis 2021; 8:ofab034. [PMID: 33614819 PMCID: PMC7885858 DOI: 10.1093/ofid/ofab034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Accepted: 01/19/2021] [Indexed: 11/15/2022] Open
Abstract
We report 2 cases for whom Xpert MTB/RIF falsely signaled rifampicin-resistant tuberculosis, based on unusually low cycle threshold and 3 of 5 probes missing. Other mycobacterial tests were negative. Further optimization of the Xpert MTB/RIF algorithm is warranted.
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Affiliation(s)
- Jean Claude S Ngabonziza
- National Reference Laboratory Division, Department of Biomedical Services, Rwanda Biomedical Centre, Kigali, Rwanda
- Mycobacteriology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Tom Decroo
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
- Research Foundation Flanders, Brussels, Belgium
| | | | - Yves M Habimana
- Tuberculosis and Other Respiratory Diseases Division, Institute of HIV/AIDS Disease Prevention and Control, Rwanda Biomedical Center, Kigali, Rwanda
| | | | - Bouke C de Jong
- Mycobacteriology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
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31
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Srinivasan V, Ha VTN, Vinh DN, Thai PVK, Ha DTM, Lan NH, Hai HT, Walker TM, Thu DDA, Dunstan SJ, Thwaites GE, Ashton PM, Caws M, Thuong NTT. Sources of Multidrug Resistance in Patients With Previous Isoniazid-Resistant Tuberculosis Identified Using Whole Genome Sequencing: A Longitudinal Cohort Study. Clin Infect Dis 2020; 71:e532-e539. [PMID: 32166306 PMCID: PMC7744982 DOI: 10.1093/cid/ciaa254] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 03/10/2020] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND Meta-analysis of patients with isoniazid-resistant tuberculosis (TB) given standard first-line anti-TB treatment indicated an increased risk of multidrug-resistant TB (MDR-TB) emerging (8%), compared to drug-sensitive TB (0.3%). Here we use whole genome sequencing (WGS) to investigate whether treatment of patients with preexisting isoniazid-resistant disease with first-line anti-TB therapy risks selecting for rifampicin resistance, and hence MDR-TB. METHODS Patients with isoniazid-resistant pulmonary TB were recruited and followed up for 24 months. Drug susceptibility testing was performed by microscopic observation drug susceptibility assay, mycobacterial growth indicator tube, and by WGS on isolates at first presentation and in the case of re-presentation. Where MDR-TB was diagnosed, WGS was used to determine the genomic relatedness between initial and subsequent isolates. De novo emergence of MDR-TB was assumed where the genomic distance was 5 or fewer single-nucleotide polymorphisms (SNPs), whereas reinfection with a different MDR-TB strain was assumed where the distance was 10 or more SNPs. RESULTS Two hundred thirty-nine patients with isoniazid-resistant pulmonary TB were recruited. Fourteen (14/239 [5.9%]) patients were diagnosed with a second episode of TB that was multidrug resistant. Six (6/239 [2.5%]) were identified as having evolved MDR-TB de novo and 6 as having been reinfected with a different strain. In 2 cases, the genomic distance was between 5 and 10 SNPs and therefore indeterminate. CONCLUSIONS In isoniazid-resistant TB, de novo emergence and reinfection of MDR-TB strains equally contributed to MDR development. Early diagnosis and optimal treatment of isoniazid-resistant TB are urgently needed to avert the de novo emergence of MDR-TB during treatment.
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Affiliation(s)
- Vijay Srinivasan
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Vu T N Ha
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Dao N Vinh
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Phan V K Thai
- Pham Ngoc Thach Hospital for Tuberculosis and Lung Disease, Ho Chi Minh City, Vietnam
| | - Dang T M Ha
- Pham Ngoc Thach Hospital for Tuberculosis and Lung Disease, Ho Chi Minh City, Vietnam
| | - Nguyen H Lan
- Pham Ngoc Thach Hospital for Tuberculosis and Lung Disease, Ho Chi Minh City, Vietnam
| | - Hoang T Hai
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Timothy M Walker
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Do D A Thu
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Sarah J Dunstan
- Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, Australia
| | - Guy E Thwaites
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Philip M Ashton
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Maxine Caws
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
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Cutugno L, Mc Cafferty J, Pané-Farré J, O’Byrne C, Boyd A. rpoB mutations conferring rifampicin-resistance affect growth, stress response and motility in Vibrio vulnificus. Microbiology (Reading) 2020; 166:1160-1170. [PMID: 33186092 PMCID: PMC7819355 DOI: 10.1099/mic.0.000991] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 10/29/2020] [Indexed: 12/16/2022]
Abstract
Rifampicin is a broad-spectrum antibiotic that binds to the bacterial RNA polymerase (RNAP), compromising DNA transcription. Rifampicin resistance is common in several microorganisms and it is typically caused by point mutations in the gene encoding the β subunit of RNA polymerase, rpoB. Different rpoB mutations are responsible for various levels of rifampicin resistance and for a range of secondary effects. rpoB mutations conferring rifampicin resistance have been shown to be responsible for severe effects on transcription, cell fitness, bacterial stress response and virulence. Such effects have never been investigated in the marine pathogen Vibrio vulnificus, even though rifampicin-resistant strains of V. vulnificus have been isolated previously. Moreover, spontaneous rifampicin-resistant strains of V. vulnificus have an important role in conjugation and mutagenesis protocols, with poor consideration of the effects of rpoB mutations. In this work, effects on growth, stress response and virulence of V. vulnificus were investigated using a set of nine spontaneous rifampicin-resistant derivatives of V. vulnificus CMCP6. Three different mutations (Q513K, S522L and H526Y) were identified with varying incidence rates. These three mutant types each showed high resistance to rifampicin [minimal inhibitory concentration (MIC) >800 µg ml-1], but different secondary effects. The strains carrying the mutation H526Y had a growth advantage in rich medium but had severely reduced salt stress tolerance in the presence of high NaCl concentrations as well as a significant reduction in ethanol stress resistance. Strains possessing the S522L mutation had reduced growth rate and overall biomass accumulation in rich medium. Furthermore, investigation of virulence characteristics demonstrated that all the rifampicin-resistant strains showed compromised motility when compared with the wild-type, but no major effects on exoenzyme production were observed. These findings reveal a wide range of secondary effects of rpoB mutations and indicate that rifampicin resistance is not an appropriate selectable marker for studies that aim to investigate phenotypic behaviour in this organism.
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Affiliation(s)
- Laura Cutugno
- Discipline of Microbiology, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
| | - Jennifer Mc Cafferty
- Discipline of Microbiology, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
| | - Jan Pané-Farré
- Institute of Microbiology, University of Greifswald, D-17489 Greifswald, Germany
- Center for Synthetic Microbiology (SYNMIKRO) & Department of Chemistry, Philipps-University Marburg, Hans-Meerwein-Strasse, C07, 35043 Marburg, Germany
| | - Conor O’Byrne
- Discipline of Microbiology, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
| | - Aoife Boyd
- Discipline of Microbiology, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
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Araya S, Negesso AE, Tamir Z. Rifampicin-Resistant Mycobacterium tuberculosis Among Patients with Presumptive Tuberculosis in Addis Ababa, Ethiopia. Infect Drug Resist 2020; 13:3451-3459. [PMID: 33116664 PMCID: PMC7547769 DOI: 10.2147/idr.s263023] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 08/25/2020] [Indexed: 01/16/2023] Open
Abstract
Background Drug-resistant tuberculosis remains a major public health threat complicating tuberculosis control programs globally. Data on rifampicin resistance (RR), which is a surrogate marker for multidrug resistance, are limited among Ethiopian tuberculosis patients. This study aimed to determine the magnitude of rifampicin-resistant Mycobacterium tuberculosis (RR-MTB) among presumptive tuberculosis patients attending St. Peter Tuberculosis Specialized Hospital, Addis Ababa, Ethiopia. Patients and Methods A retrospective cross-sectional study was conducted at St. Peter Tuberculosis Specialized Hospital from January 2016 to December 2018. After checking completeness of the necessary information, data of tuberculosis-presumptive cases who underwent Gene Xpert® testing were collected from medical records using a data-extraction format prepared for this study purpose. Data were double entered and analyzed using SPSS version 20 statistical software. Results A total of 12,685 presumptive tuberculosis patients were included; of whom 54.5% were males and the mean age of the study participants was 40.3±18.7 years. Mycobacterium tuberculosis (MTB) was detected in 1714 participants (13.5%). Of these MTB cases, 169 cases (9.8%) were confirmed to have RR-MTB. Prevalence of MTB was relatively higher among males (15.1%, P=0.78); whereas RR-MTB was higher among females (10.3%, P=0.81). The incidence of MTB and RR-MTB was significantly associated with treatment history (P=0.042 and P=0.025), respectively. HIV infection has significantly associated with incidence of RR-MTB (P=0.032), but not with MTB (P˃0.05). Prevalence of MTB and RR-MTB had a declining trend through time, being 16.7% and 12.9%, 12.8% and 9.1%, and 12.2% and 7.9% in 2016, 2017 and 2018, respectively. Conclusion This study showed a decreasing trend of both MTB and RR-MTB from 2016 to 2018 in an MTB, MDR-MTB, and TB/HIV co-infection high-burden setting, Addis Ababa, Ethiopia. Occurrence of MTB and RR-MTB was associated with treatment history. Therefore, improvement in treatment adherence of identified cases would be helpful to prevent emergence or re-emergence of MTB and RR-MTB cases.
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Affiliation(s)
- Shambel Araya
- Department of Medical Laboratory Sciences, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Abebe Edao Negesso
- Department of Medical Laboratory Sciences, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Zemenu Tamir
- Department of Medical Laboratory Sciences, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
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34
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Kouemo Motse FD, Nsagha DS, Teyim PM, Adiogo D, Kojom Foko LP, Kedy Koum DC, Ngaba GP, Assob Nguedia JC. Rifampicin resistance among Mycobacterium tuberculosis-infected individuals using GeneXpert MTB/RIF ultra: a hospital-based study. Trop Med Int Health 2020; 26:159-165. [PMID: 32946180 DOI: 10.1111/tmi.13489] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
OBJECTIVES To determine the prevalence and risk factors associated with rifampicin (RIF)-resistant tuberculosis using GeneXpert technology. METHODS A cross-sectional study was conducted from April 2018 to November 2019 among tuberculosis (TB)-infected Cameroonian patients in the Littoral Region using records from patients presenting with clinically suspected or documented TB. The patients were screened for TB using GeneXpert MDR/RIF ultra. Data were documented with an ad hoc survey form and analysed with SPSS version 22. RESULTS 153 patients were included in the study. 64.1% were males; mean age was 37.9 ± 14.7 years and median age 37 years (range: 2-82). Most patients were new cases (76.4%). Relapses accounted for 8.5% and recurrences for 2.6%. Pulmonary TB was diagnosed among 98.7% patients using mostly sputum samples (85%). The prevalence of RIF resistance was 6.7% (95% CI: 3.4%-12.7%). This prevalence was significantly higher in samples of mucus and mucopurulent aspect (P-value = 0.04). RIF-resistant M. tuberculosis strains were significantly more frequent among relapses than new cases (23.1% vs. 2.3% P-value < 0.0001). A statistically significant association was found between GeneXpert-based quantification results and type and aspect of samples. CONCLUSION This study confirms the circulation of RIF-resistant M. tuberculosis strains in the Littoral region. There is a need for extensive studies in other parts of the country.
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Affiliation(s)
- Francine D Kouemo Motse
- Department of Medical Laboratory Sciences, Faculty of Health Sciences, University of Buea, Buea, SW Region, Cameroon
| | - Dickson Shey Nsagha
- Department of Public Health and Hygiene, Faculty of Health Sciences, University of Buea, Buea, SW Region, Cameroon
| | - Pride M Teyim
- Tuberculosis Reference Laboratory, Littoral Regional Delegation of Public Health, Douala, Littoral Region, Cameroon
| | - Dieudonné Adiogo
- Department of Biological Sciences, Faculty of Medicine and Pharmaceutical Sciences, The University of Douala, Douala, Littoral Region, Cameroon
| | - Loick P Kojom Foko
- Department of Animal Organisms, The University of Douala, Douala, Cameroon
| | - Danielle C Kedy Koum
- Department of Biological Sciences, Faculty of Medicine and Pharmaceutical Sciences, The University of Douala, Douala, Littoral Region, Cameroon
| | - Guy P Ngaba
- Department of Biological Sciences, Faculty of Medicine and Pharmaceutical Sciences, The University of Douala, Douala, Littoral Region, Cameroon
| | - Jules C Assob Nguedia
- Department of Medical Laboratory Sciences, Faculty of Health Sciences, University of Buea, Buea, SW Region, Cameroon
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Pokam BDT, Yeboah-Manu D, Lawson L, Guemdjom PW, Okonu R, Madukaji L, Yhiler NY, Asuquo AE. Molecular Analysis of Mycobacterium tuberculosis Isolated in the North Central Zone of Nigeria. J Epidemiol Glob Health 2020; 9:259-265. [PMID: 31854167 PMCID: PMC7310797 DOI: 10.2991/jegh.k.191015.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Accepted: 10/05/2019] [Indexed: 11/10/2022] Open
Abstract
Tuberculosis (TB) incidence in Nigeria is high, with a significant burden of TB/Human Immunodeficiency Virus (HIV). Genotyping and drug susceptibility of Mycobacterium tuberculosis Complex (MTBC) are important in order to improve the control of the disease. This study sought to determine drug susceptibility and genetic diversity of MTBC in the country. The sputum samples of 202 patients [133 (65.8%) males/69 (34.2%) females] were collected in the North Central zone of Nigeria and cultured using Lowenstein–Jensen medium. Immunochromatography for the primary identification and Drug Susceptibility Testing (DST) by proportion method, as well as IS6110 typing, regions of difference 1, 4, 9, 12, 702, and 711, and spoligotyping were carried out on the isolates. Following the DST on 202 isolates, 51 (25.2%) showed resistance to at least one drug. Multidrug resistance was observed in 29/202 (14.4%) cases. HIV positivity [37/202 (18.3%) patients] was associated with rifampicin 9/37 (24.3%) resistance (p = 0.012) as well as gender (p = 0.009). Of the 202 isolates, 150 (74.3%) were identified as the Cameroon sublineage, followed by the UgandaI, Haarlem, and West Africa 1 with 18 (8.9%), 10 (5%), and 6 (3%), respectively. The LAM10_CAM was the most prevalent genetic family [128/202 (63.4%)], with the shared international type 61 [111 (55%) isolates] the largest cluster. Gender (p = 0.038) and age (p = 0.015) had significant associations with the LAM10_CAM family but neither with HIV (p = 0.479) nor drug resistance. Rifampicin resistance in TB/HIV coinfected patient is a major concern in the study area. The Mycobacterium africanum lineage showed a marked decrease, and the need to educate females most at risk of TB/HIV coinfection is advocated.
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Affiliation(s)
- Benjamin David Thumamo Pokam
- Department of Medical Laboratory Science, Faculty of Health Sciences, University of Buea, Buea, Cameroon.,Bacteriology Department, Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Accra, Ghana
| | - Dorothy Yeboah-Manu
- Bacteriology Department, Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Accra, Ghana
| | | | - Prisca Wabo Guemdjom
- Department of Public Health, Faculty of Health Sciences, University of Buea, Buea, Cameroon
| | - Ruth Okonu
- Bacteriology Department, Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Accra, Ghana
| | | | - Nchawa Yangkam Yhiler
- Department of Medical Laboratory Science, Faculty of Health Sciences, University of Buea, Buea, Cameroon.,Department of Allied Health, Biaka University Institute, Buea, Cameroon
| | - Anne Ebri Asuquo
- Department of Medical Laboratory Science, Faculty of Allied Medical Sciences, College of Medicine, University of Calabar, Calabar, Nigeria
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36
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Arefzadeh S, Azimi T, Nasiri M, Nikpor Z, Dabiri H, Doustdar F, Goudarzi H, Allahyartorkaman M. High-resolution melt curve analysis for rapid detection of rifampicin resistance in Mycobacterium tuberculosis: a single-centre study in Iran. New Microbes New Infect 2020; 35:100665. [PMID: 32257224 PMCID: PMC7125345 DOI: 10.1016/j.nmni.2020.100665] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 03/05/2020] [Indexed: 11/29/2022] Open
Abstract
This study aimed to compare the diagnostic accuracy of high-resolution melting (HRM) analysis in comparison with Xpert MTB/RIF as well as conventional drug susceptibility testing (DST) for the detection of rifampicin (RIF) resistance in Mycobacterium tuberculosis in Iran. A comparative cross-sectional study was carried out from April 2017 to September 2018. A total of 80 culture-positive clinical samples selected during the study period were analysed for detection of RIF-resistant TB by conventional DST, Xpert MTB/RIF, and sequencing. Sensitivity and specificity of the HRM calculated according to DST was our reference standard test in this study. The overall sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) of HRM assay were found to be 100%, 89.33%, 38.46%, and 100% respectively. The analysis demonstrated that the diagnostic accuracy of HRM tests is insufficient to replace Xpert MTB/RIF and conventional DST. HRM tests have the advantage of time to result and may be used in combination with culture. Further work to improve molecular tests would benefit from standardized reference standards and the methodology.
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Affiliation(s)
- S. Arefzadeh
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - T. Azimi
- Department of Pathobiology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - M.J. Nasiri
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Z. Nikpor
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - H. Dabiri
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - F. Doustdar
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - H. Goudarzi
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - M. Allahyartorkaman
- Regional Tuberculosis Reference laboratory, Tehran University of Medical Sciences, Tehran, Iran
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Vargas AP, Rios AA, Grandjean L, Kirwan DE, Gilman RH, Sheen P, Zimic MJ. Determination of potentially novel compensatory mutations in rpoc associated with rifampin resistance and rpob mutations in Mycobacterium tuberculosis Clinical isolates from peru. Int J Mycobacteriol 2020; 9:121-137. [PMID: 32474533 PMCID: PMC10022416 DOI: 10.4103/ijmy.ijmy_27_20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
Background Rifampicin (RIF) resistance in Mycobacterium tuberculosis is frequently caused by mutations in the rpoB gene. These mutations are associated with a fitness cost, which can be overcome by compensatory mutations in other genes, among which rpoC may be the most important. We analyzed 469 Peruvian M. tuberculosis clinical isolates to identify compensatory mutations in rpoC/rpoA associated with RIF resistance. Methods The M. tuberculosis isolates were collected and tested for RIF susceptibility and spoligotyping. Samples were sequenced and aligned to the reference genome to identify mutations. By analyzing the sequences and the metadata, we identified a list of rpoC mutations exclusively associated with RIF resistance and mutations in rpoB. We then evaluated the distribution of these mutations along the protein sequence and tridimensional structure. Results One hundred and twenty-five strains were RIF susceptible and 346 were resistant. We identified 35 potential new compensatory mutations, some of which were distributed on the interface surface between rpoB and rpoC, arising in clusters and suggesting the presence of hotspots for compensatory mutations. Conclusion This study identifies 35 putative novel compensatory mutations in the β' subunit of M. tuberculosis RNApol. Six of these (S428T, L507V, A734V, I997V, and V1252LM) are considered most likely to have a compensatory role, as they fall in the interaction zone of the two subunits and the mutation did not lead to any change in the protein's physical-chemical properties.
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Affiliation(s)
- Ana Paula Vargas
- Department of Cellular and Molecular Sciences, Laboratory of Bioinformatics and Molecular Biology, Faculty of Science and Philosophy, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Angela A. Rios
- Department of Cellular and Molecular Sciences, Laboratory of Bioinformatics and Molecular Biology, Faculty of Science and Philosophy, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Louis Grandjean
- Department of Paediatric Infectious Diseases, Imperial College, University of London, London, England
| | - Daniela E. Kirwan
- Infection and Immunity Research Institute, St. George’s, University of London, London, England
| | - Robert H. Gilman
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Patricia Sheen
- Department of Cellular and Molecular Sciences, Laboratory of Bioinformatics and Molecular Biology, Faculty of Science and Philosophy, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Mirko J. Zimic
- Department of Cellular and Molecular Sciences, Laboratory of Bioinformatics and Molecular Biology, Faculty of Science and Philosophy, Universidad Peruana Cayetano Heredia, Lima, Peru
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Loss G, Simões PM, Valour F, Cortês MF, Gonzaga L, Bergot M, Trouillet-Assant S, Josse J, Diot A, Ricci E, Vasconcelos AT, Laurent F. Staphylococcus aureus Small Colony Variants (SCVs): News From a Chronic Prosthetic Joint Infection. Front Cell Infect Microbiol 2019; 9:363. [PMID: 31696062 PMCID: PMC6817495 DOI: 10.3389/fcimb.2019.00363] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 10/07/2019] [Indexed: 12/21/2022] Open
Abstract
Small colony variants (SCV) of Staphylococcus aureus have been reported as implicated in chronic infections. Here, we investigated the genomic and transcriptomic changes involved in the evolution from a wild-type to a SCV from in a patient with prosthetic joint infection relapse. The SCV presented a stable phenotype with no classical auxotrophy and the emergence of rifampicin resistance. Whole Genome Sequencing (WGS) analysis showed only the loss of a 42.5 kb phage and 3 deletions, among which one targeting the rpoB gene, known to be the target of rifampicin and to be associated to SCV formation in the context of a constitutively active stringent response. Transcriptomic analysis highlighted a specific signature in the SCV strain including a complex, multi-level strategy of survival and adaptation to chronicity within the host including a protection from the inflammatory response, an evasion of the immune response, a constitutively activated stringent response and a scavenging of iron sources.
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Affiliation(s)
- Guilherme Loss
- Laboratório Nacional de Computação Científica, Rio de Janeiro, Brazil
| | - Patricia Martins Simões
- National Reference Center for Staphylococci - Hospices Civils de Lyon, IAI-Department of Clinical Microbiology, Northern Hospital Group, Lyon, France.,Centre International de Recherche en Infectiologie (CIRI), Lyon, France
| | - Florent Valour
- Centre International de Recherche en Infectiologie (CIRI), Lyon, France.,Hospices Civils de Lyon, Infectious Diseases Department, Northern Hospital Group, Lyon, France
| | - Marina Farrel Cortês
- Institute of Microbiology Professor Paulo de Góes, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Luiz Gonzaga
- Laboratório Nacional de Computação Científica, Rio de Janeiro, Brazil
| | - Marine Bergot
- Centre International de Recherche en Infectiologie (CIRI), Lyon, France
| | - Sophie Trouillet-Assant
- Hospices Civils de Lyon, Joint Research Unit HCL-BioMerieux, Centre Hospitalier Lyon Sud, Pierre-Benite, France
| | - Jêrome Josse
- Centre International de Recherche en Infectiologie (CIRI), Lyon, France
| | - Alan Diot
- Centre International de Recherche en Infectiologie (CIRI), Lyon, France
| | - Emiliano Ricci
- Centre International de Recherche en Infectiologie (CIRI), Lyon, France
| | | | - Frédéric Laurent
- National Reference Center for Staphylococci - Hospices Civils de Lyon, IAI-Department of Clinical Microbiology, Northern Hospital Group, Lyon, France.,Centre International de Recherche en Infectiologie (CIRI), Lyon, France
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Saranathan R, Padmapriyadarsini C, Sivaramakrishnan GN, Perumal BK, Kannayan S, Joseph B, Gopalan N, Hanna LE. Pulmonary Mycobacterium kyorinense disease: A case report and review of literature. Indian J Med Microbiol 2019; 37:127-131. [PMID: 31424025 DOI: 10.4103/ijmm.ijmm_19_94] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
We report here the first case of pulmonary infection due to Mycobacterium kyorinense in a 55-year-old hypertensive woman treated for pulmonary tuberculosis earlier on two occasions. She presented with productive cough, intermittent episode of left-sided chest pain, loss of appetite, low-grade fever, and breathlessness. Sputum cultures revealed non-tuberculous mycobacteria (NTM). She remained persistently symptomatic with sputum cultures positive for acid-fast bacilli even after 6 months of treatment. Hence, a 16SrRNA gene amplification and sequencing were done that revealed M. kyorinense. Based on the guidelines of the American Thoracic Society, she was started on weight-based dosing of clarithromycin, levofloxacin, ethambutol, isoniazid and injection amikacin daily. The patient improved symptomatically and became culture-negative after 3 months of therapy with the above regimen and continued to be culture negative for 12 months of treatment. She continues to remain symptom-free without evidence of any clinical or bacteriological relapse.
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Affiliation(s)
- Rajagopalan Saranathan
- Department of HIV, ICMR-National Institute for Research in Tuberculosis, Chennai, Tamil Nadu, India
| | | | | | - Bhavani K Perumal
- Department of Clinical Research, ICMR-National Institute for Research in Tuberculosis, Chennai, Tamil Nadu, India
| | - Silambuchelvi Kannayan
- Department of Bacteriology, ICMR-National Institute for Research in Tuberculosis, Chennai, Tamil Nadu, India
| | - Bency Joseph
- Department of Clinical Research, ICMR-National Institute for Research in Tuberculosis, Chennai, Tamil Nadu, India
| | - Narendran Gopalan
- Department of Clinical Research, ICMR-National Institute for Research in Tuberculosis, Chennai, Tamil Nadu, India
| | - Luke Elizabeth Hanna
- Department of HIV, ICMR-National Institute for Research in Tuberculosis, Chennai, Tamil Nadu, India
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Abstract
Introduction The WHO endorsed Xpert Mycobacterium tuberculosis/rifampicin (MTB/RIF) assay, has been evaluated for pulmonary TB in a number of studies but very few have investigated it for extrapulmonary specimens. The present study evaluates the performance of Xpert MTB/RIF assay in the diagnosis of extrapulmonary TB (EPTB). Aim and Objectives The aim of the study is to determine sensitivity and specificity of Xpert MTB/RIF assay for diagnosis of EPTB and RIF resistance in comparison to culture on Lowenstein-Jensen (LJ) medium and proportion method (PM), respectively. Materials and Methods A total of 738 specimens from clinically suspected cases of EPTB were subjected to Ziehl-Neelsen staining, Xpert MTB/RIF assay and culture on LJ medium. PM was done on MTB isolates. Results The sensitivity, specificity of Xpert MTB/RIF assay for diagnosis of EPTB were 84.91% (95% confidence interval [CI] 72.41%-93.25%) and 86.72% (95% CI 83.94%-89.17%) and for RIF resistance detection were 60.00% (95% CI 32.29%-83.66%) and 94.74% (95% CI 73.97%-99.87%), respectively. Among culture-positive cases, the sensitivity of Xpert MTB/RIF assay was 94.12% in smear positive and 80.56% in smear-negative cases. Xpert MTB/RIF showed maximum sensitivity of MTB detection from lymph node specimens (100% [95% CI 54.07%-100.00%]) and other body fluids (100% [95% CI 15.81%-100.00%]). Conclusion The present study establishes Xpert MTB/RIF assay as a promising tool in the rapid diagnosis of EPTB and detection of RIF resistance.
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Affiliation(s)
- Sheetal Bankar
- Department of Microbiology, T.N. Medical College and B Y L Nair Ch. Hospital, Mumbai, Maharashtra, India
| | - Reena Set
- Department of Microbiology, T.N. Medical College and B Y L Nair Ch. Hospital, Mumbai, Maharashtra, India
| | - Disha Sharma
- Department of Microbiology, T.N. Medical College and B Y L Nair Ch. Hospital, Mumbai, Maharashtra, India
| | - Daksha Shah
- City TB Officer, Mumbai District Tuberculosis Control Society, Mumbai, Maharashtra, India
| | - Jayanthi Shastri
- Department of Microbiology, T.N. Medical College and B Y L Nair Ch. Hospital, Mumbai, Maharashtra, India
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Diandé S, Badoum G, Combary A, Zombra I, Saouadogo T, Sawadogo LT, Nébié B, Gnanou S, Zigani A, Ouédraogo SM, Diallo A, Kaboré S, Sangaré L. Multidrug-Resistant Tuberculosis in Burkina Faso from 2006 to 2017: Results of National Surveys. Eur J Microbiol Immunol (Bp) 2019; 9:23-28. [PMID: 30967972 PMCID: PMC6444799 DOI: 10.1556/1886.2018.00029] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Accepted: 01/07/2019] [Indexed: 11/19/2022] Open
Abstract
Setting A survey of the prevalence of drug-resistant tuberculosis (DR-TB) in new and previously treated patients (PTPs) was performed in Burkina Faso from 2016 to 2017. Design In this cross-sectional survey, a structured questionnaire was administered to eligible smear-positive patients in all 86 diagnostic and treatment centers of the country to collect their socio-demographic characteristics and medical histories. Their sputa were tested using the Mycobacterium tuberculosis/rifampicin (MTB/RIF) Xpert assay. Those which were found to be positive for TB and rifampicin-resistant were also tested with GenoType MTBDRplus2.0 and MTBDRsl2.0. Univariate and multivariate logistic regressions were performed to determine risk factors associated with rifampicin resistance. Results Of the 1140 smear-positive patients enrolled, 995 new and 145 PTPs were positive for MTB complex by Xpert. Of these, 2.0% (20/995, 95% confidence interval (CI): 1.1–2.9) of the new cases and 14.5% (95% CI: 14.2–20.2) of the PTPs were resistant to rifampicin; 83% of them has multidrug-resistant tuberculosis (MDR-TB). None were pre-extensively drug-resistant TB (pre-XDR-TB) or XDR-TB. Only the previous treatment was significantly associated with rifampicin resistance, p < 0.0001. Conclusion Similar to global trends, rifampicin resistance was significantly higher in patients with prior TB treatment (14.5%) than in naïve patients (2.0%). These percentages are slightly below the global averages, but nonetheless suggest the need for continued vigilance. Extending the use of Xpert testing should strengthen the surveillance of DR-TB in Burkina Faso.
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Affiliation(s)
- Souba Diandé
- Programme National de Lutte contre la Tuberculose, Ministère de la Santé, Ouagadougou, Burkina Faso
| | - Gisèle Badoum
- Université Ouaga-I Pr Joseph Ki-Zerbo, Unité de Formation en Sciences de la Santé, Ouagadougou, Burkina Faso.,CHU Yalgado Ouédraogo, Département de Médecine, Services de Pneumologie, Ouagadougou, Burkina Faso
| | - Adjima Combary
- Programme National de Lutte contre la Tuberculose, Ministère de la Santé, Ouagadougou, Burkina Faso
| | - Issaka Zombra
- Programme National de Lutte contre la Tuberculose, Ministère de la Santé, Ouagadougou, Burkina Faso
| | - Tandaogo Saouadogo
- Programme National de Lutte contre la Tuberculose, Ministère de la Santé, Ouagadougou, Burkina Faso
| | - Léon T Sawadogo
- Programme National de Lutte contre la Tuberculose, Ministère de la Santé, Ouagadougou, Burkina Faso
| | - Bayéma Nébié
- Programme National de Lutte contre la Tuberculose, Ministère de la Santé, Ouagadougou, Burkina Faso
| | - Saïdou Gnanou
- Programme National de Lutte contre la Tuberculose, Ministère de la Santé, Ouagadougou, Burkina Faso
| | - Adama Zigani
- Centre National de Lutte Antituberculeuse, Ministère de la Santé, Ouagadougou, Burkina Faso
| | - Seydou Mohamed Ouédraogo
- Direction de la Protection de la Santé et de la Population, Ministère de la Santé, Ouagadougou, Burkina Faso
| | - Adama Diallo
- Programme National de Lutte contre la Tuberculose, Ministère de la Santé, Ouagadougou, Burkina Faso
| | - Seydou Kaboré
- Programme National de Lutte contre la Tuberculose, Ministère de la Santé, Ouagadougou, Burkina Faso
| | - Lassana Sangaré
- Université Ouaga-I Pr Joseph Ki-Zerbo, Unité de Formation en Sciences de la Santé, Ouagadougou, Burkina Faso.,CHU Yalgado Ouédraogo, Département des laboratoires, Service de Bactériologie-Virologie Ouagadougou, Burkina Faso
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42
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Boyle KK, Kuo FC, Horcajada JP, Hughes H, Cavagnaro L, Marculescu C, McLaren A, Nodzo SR, Riccio G, Sendi P, Silibovsky R, Stammers J, Tan TL, Wimmer M. General Assembly, Treatment, Antimicrobials: Proceedings of International Consensus on Orthopedic Infections. J Arthroplasty 2019; 34:S225-S237. [PMID: 30360976 DOI: 10.1016/j.arth.2018.09.074] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
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43
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Xu Z, Zhou A, Wu J, Zhou A, Li J, Zhang S, Wu W, Karakousis PC, Yao YF. Transcriptional Approach for Decoding the Mechanism of rpoC Compensatory Mutations for the Fitness Cost in Rifampicin-Resistant Mycobacterium tuberculosis. Front Microbiol 2018; 9:2895. [PMID: 30555440 PMCID: PMC6283890 DOI: 10.3389/fmicb.2018.02895] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2018] [Accepted: 11/12/2018] [Indexed: 12/31/2022] Open
Abstract
Multidrug-resistant tuberculosis (TB), defined as TB resistant to the two first-line drugs, isoniazid and rifampin, is a serious challenge to global TB eradication efforts. Although mutations in rpoA or rpoC have been proposed to compensate for this fitness cost due to rpoB mutation in rifampicin-resistant Mycobacterium tuberculosis mutants, whether the compensatory effect exists and the underlying mechanisms of compensation remain unclear. Here, we used RNA sequencing to investigate the global transcriptional profiles of 6 rifampin-resistant clinical isolates with either single mutation in rpoB or dual mutations in rpoB/rpoC, as well as 3 rifampin-susceptible clinical isolates, trying to prove the potential compensatory effect of rpoC by transcriptomic alteration. In rifampin-free conditions, rpoC mutation was associated with M. tuberculosis upregulation of ribosomal protein-coding genes, dysregulation of growth-related essential genes and balancing the expression of arginine and glutamate synthesis-associated genes. Upon rifampin exposure of M. tuberculosis isolates, rpoC mutations were associated with the upregulation of the oxidative phosphorylation machinery, which was inhibited in the rpoB single mutants, as well as stabilization of the expression of rifampin-regulated essential genes and balancing the expression of genes involved in metabolism of sulfur-containing amino acids. Taken together, our data suggest that rpoC mutation may compensate for the fitness defect of rifampicin-resistant M. tuberculosis by altering gene expression in response to rifampin exposure.
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Affiliation(s)
- Zhihong Xu
- Laboratory of Bacterial Pathogenesis, Department of Microbiology and Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Aiping Zhou
- Department of Laboratory Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Jiawei Wu
- Faculty of Basic Medicine, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Aiwu Zhou
- Faculty of Basic Medicine, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jun Li
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Shulin Zhang
- Laboratory of Bacterial Pathogenesis, Department of Microbiology and Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wenjuan Wu
- Department of Laboratory Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Petros C Karakousis
- Department of Medicine, Center for Tuberculosis Research, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Yu-Feng Yao
- Laboratory of Bacterial Pathogenesis, Department of Microbiology and Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Department of Laboratory Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
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44
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Ikuabe PO, Ebuenyi ID. Prevalence of rifampicin resistance by automated Genexpert rifampicin assay in patients with pulmonary tuberculosis in Yenagoa, Nigeria. Pan Afr Med J 2018; 29:204. [PMID: 30100958 PMCID: PMC6080957 DOI: 10.11604/pamj.2018.29.204.14579] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2017] [Accepted: 03/14/2018] [Indexed: 11/21/2022] Open
Abstract
Introduction The diagnosis of tuberculosis and its treatment is challenging in resource – limited settings. The growth and speed of multi drug – resistant tuberculosis (MDR-TB) in high burden countries like Nigeria is a growing concern. This study is aimed at determining the prevalence of rifampicin resistance in sputum specimens of patients with pulmonary tuberculosis in Yenagoa, Nigeria. Methods A descriptive survey of all consecutive sputum specimens of adults greater than 15 years of age that presented to the Tuberculosis Referral Hospital Laboratory were subjected to the automated Genexpert test between January and December 2016. Results All 446 specimens were tested using the Genexpert automated system. 102 (22.9%) of the sputum specimens were positive for Mycobacterium tuberculosis, with 15 (14.7%) showing rifampicin resistance. Conclusion There was significantly high prevalence of MDR-TB much higher than the World Health Organisation (WHO) prediction of 3.2 -5.4% for Nigeria. Pan African Medical Journal – ISSN: 1937- 8688 (www.panafrican-med-journal.com) Published in partnership with the African Field Epidemiology Network (AFENET). (www.afenet.net) Pan African Medical Journal – ISSN: 1937- 8688 (www.panafrican-med-journal.com) Published in partnership with the African Field Epidemiology Network (AFENET). (www.afenet.net)
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Affiliation(s)
- Peter Ogie Ikuabe
- Department of Internal Medicine Niger Delta University Teaching Hospital Okolobiri, Bayelsa State, Nigeria
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Lavania M, Singh I, Turankar RP, Gupta AK, Ahuja M, Pathak V, Sengupta U. Enriched whole genome sequencing identified compensatory mutations in the RNA polymerase gene of rifampicin-resistant Mycobacterium leprae strains. Infect Drug Resist 2018; 11:169-175. [PMID: 29416362 PMCID: PMC5790067 DOI: 10.2147/idr.s152082] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Despite more than three decades of multidrug therapy (MDT), leprosy remains a major public health issue in several endemic countries, including India. The emergence of drug resistance in Mycobacterium leprae (M. leprae) is a cause of concern and poses a threat to the leprosy-control program, which might ultimately dampen the achievement of the elimination program of the country. Rifampicin resistance in clinical strains of M. leprae are supposed to arise from harboring bacterial strains with mutations in the 81-bp rifampicin resistance determining region (RRDR) of the rpoB gene. However, complete dynamics of rifampicin resistance are not explained only by this mutation in leprosy strains. To understand the role of other compensatory mutations and transmission dynamics of drug-resistant leprosy, a genome-wide sequencing of 11 M. leprae strains - comprising five rifampicin-resistant strains, five sensitive strains, and one reference strain - was done in this study. We observed the presence of compensatory mutations in two rifampicin-resistant strains in rpoC and mmpL7 genes, along with rpoB, that may additionally be responsible for conferring resistance in those strains. Our findings support the role for compensatory mutation(s) in RNA polymerase gene(s), resulting in rifampicin resistance in relapsed leprosy patients.
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Affiliation(s)
- Mallika Lavania
- Stanley Browne Laboratory, The Leprosy Mission Trust India, TLM Community Hospital Nand Nagari
| | - Itu Singh
- Stanley Browne Laboratory, The Leprosy Mission Trust India, TLM Community Hospital Nand Nagari
| | - Ravindra P Turankar
- Stanley Browne Laboratory, The Leprosy Mission Trust India, TLM Community Hospital Nand Nagari
| | - Anuj Kumar Gupta
- Agilent Technologies India Pvt Ltd, Jasola District Centre, New Delhi, India
| | - Madhvi Ahuja
- Stanley Browne Laboratory, The Leprosy Mission Trust India, TLM Community Hospital Nand Nagari
| | - Vinay Pathak
- Stanley Browne Laboratory, The Leprosy Mission Trust India, TLM Community Hospital Nand Nagari
| | - Utpal Sengupta
- Stanley Browne Laboratory, The Leprosy Mission Trust India, TLM Community Hospital Nand Nagari
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Abstract
Rifampicin is one of the major drugs used on its own and also in combination to treat numerous infections sustained by methicillin-resistant Staphylococcus aureus (MRSA). In Italy, rifampicin resistance (RIF-R) is increasing in multidrug-resistant-MRSA isolates (16.4%), with respect to Europe (5.7%). In our study, the relationship between clones, rpoB mutations, and susceptibility profiles in 50 RIF-R MRSA isolated from hospitalized patients was evaluated. Antimicrobial susceptibility testing was performed by the broth microdilution method. Isolates were typed by MLST/SCCmec/spa-typing. The rpoB gene was analyzed by PCR and sequence analysis. RIF-R isolates were 60% heterogeneous vancomycin-intermediate S. aureus (hVISA) and 22% daptomycin nonsusceptible and belonged to the major MRSA clones: ST228-SCCmec I (44%), ST8-SCCmec IV (18%), ST239-SCCmec III (16%), ST5-SCCmec II (14%), and ST22-SCCmec IVh (4%). Thirteen diverse RpoB amino acid substitutions were identified. Half of the strains harbored the H481N substitution, conferring low-level resistance. Different single mutations at the equivalent locus (H481D; H481Y) or in other loci, and multiple mutations conferred high-level resistance. In conclusion, this study investigated the nature of RIF-R in Italy among RIF-R-MRSA strains, finding a prevalence of ST228, strongly associated with reduced susceptibility to glycopeptides (hVISA). The spread of RIF-R strains in clinical settings represents a serious threat, due to their complex resistance nature even to new anti-Gram-positive drugs, making these infections particularly difficult to treat.
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Affiliation(s)
- Dafne Bongiorno
- Medical Molecular Microbiology and Antibiotic Resistance Laboratory (MMAR Lab), Department of Biomedical and Biotechnological Sciences (BIOMETEC), University of Catania , Catania, Italy
| | - Gino Mongelli
- Medical Molecular Microbiology and Antibiotic Resistance Laboratory (MMAR Lab), Department of Biomedical and Biotechnological Sciences (BIOMETEC), University of Catania , Catania, Italy
| | - Stefania Stefani
- Medical Molecular Microbiology and Antibiotic Resistance Laboratory (MMAR Lab), Department of Biomedical and Biotechnological Sciences (BIOMETEC), University of Catania , Catania, Italy
| | - Floriana Campanile
- Medical Molecular Microbiology and Antibiotic Resistance Laboratory (MMAR Lab), Department of Biomedical and Biotechnological Sciences (BIOMETEC), University of Catania , Catania, Italy
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Liu J, Zhao Z, Deng Y, Shi Y, Liu Y, Wu C, Luo P, Hu C. Complete Genome Sequence of Vibrio campbellii LMB 29 Isolated from Red Drum with Four Native Megaplasmids. Front Microbiol 2017; 8:2035. [PMID: 29109705 PMCID: PMC5660062 DOI: 10.3389/fmicb.2017.02035] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 10/05/2017] [Indexed: 01/22/2023] Open
Abstract
Vibrio spp. are the most common pathogens for animals reared in aquaculture. Vibrio campbellii, which is often involved in shrimp, fish and mollusks diseases, is widely distributed in the marine environment worldwide, but our knowledge about its pathogenesis and antimicrobial resistance is very limited. The existence of this knowledge gap is at least partially because that V. campbellii was originally classified as Vibrio harveyi, and the detailed information of its comparative genome analysis to other Vibrio spp. is currently lacking. In this study, the complete genome of a V. campbellii predominant strain, LMB29, was determined by MiSeq in conjunction with PacBio SMRT sequencing. This genome consists of two circular DNA chromosomes and four megaplasmids. Comparative genome analysis indicates that LMB29 shares a 96.66% similarity (average nucleotide identity) with the V. campbellii ATCC strain BAA-1116 based on a 75% AF (average fraction) calculations, and its functional profile is very similar to V. campbellii E1 and V. campbellii CAIM115. Both type III secretion system (T3SS) and type VI secretion system (T6SS), along with the tlh gene which encodes a thermolabile hemolysin, are present in LMB29 which may contribute to the bacterial pathogenesis. The virulence of this strain was experimental confirmed by performing a LDH assay on a fish cell infection model, and cell death was observed as early as within 3 h post infection. Thirty-seven antimicrobial resistance genes (>45% identity) were predicted in LMB29 which includes a novel rifampicin ADP ribosyltransferase, arr-9, in plasmid pLMB157. The gene arr-9 was predicted on a genomic island with horizontal transferable potentials which may facilitate the rifampicin resistance dissemination. Future researches are needed to explore the pathogenesis of V. campbellii LMB29, but the availability of this genome sequence will certainly aid as a basis for further analysis.
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Affiliation(s)
- Jinxin Liu
- Institute of Marine Biology, College of Oceanography, Hohai University, Nanjing, China.,Department of Food Science and Technology, University of California, Davis, Davis, CA, United States
| | - Zhe Zhao
- Institute of Marine Biology, College of Oceanography, Hohai University, Nanjing, China.,Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Yiqing Deng
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Yan Shi
- Institute of Marine Biology, College of Oceanography, Hohai University, Nanjing, China
| | - Yupeng Liu
- Institute of Marine Biology, College of Oceanography, Hohai University, Nanjing, China
| | - Chao Wu
- Institute of Marine Biology, College of Oceanography, Hohai University, Nanjing, China
| | - Peng Luo
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Chaoqun Hu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
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48
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Abstract
OBJECTIVES Xpert MTB/RIF assay, a rapid and automated real-time nucleic acid amplification test, has been reported for the diagnosis of musculoskeletal tuberculosis (TB) in current years. This meta-analysis aims to determine the diagnostic accuracy of Xpert for the detection of musculoskeletal TB and rifampicin (RIF) resistance. METHODS We searched PubMed, Embase, China National Knowledge Infrastructure, and Wanfang for original articles published up to 1st June 2017 to identify studies in which the Xpert assay was applied to diagnose musculoskeletal TB. Pooled estimates were calculated using a random-effects model or a fixed-effects model according to heterogeneity. Summary receiver operating characteristic curves and the area under the curve (AUC) were used to summarize overall diagnostic performance. Deeks' test was performed to evaluate potential publication bias. RESULTS Twelve studies were identified with a pooled sensitivity and specificity of respectively 0.81 (95% confidence interval [CI] 0.78-0.83) and 0.83 (95% CI 0.80-0.86) of Xpert for the diagnosis of musculoskeletal TB. Xpert was highly sensitive (0.89, 95% CI 0.79-0.95) and highly specific (0.96, 95% CI 0.92-0.98) in detecting RIF resistance. AUC (over 0.9) suggested a relatively high level of overall diagnostic accuracy of Xpert for detecting musculoskeletal TB and RIF resistance. Prevalence and reference standard were indicated to be sources of heterogeneity between studies. No publication bias was found. CONCLUSION This study provides available evidence of the rapid and effective role of Xpert in diagnosing musculoskeletal TB and detecting RIF resistance.
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Affiliation(s)
- Hai Wen
- Department of Spine Surgery, The Second Xiangya Hospital of Central South University, Changsha, People’s Republic of China
| | - Pengzhi Li
- Department of Spine Surgery, The Second Xiangya Hospital of Central South University, Changsha, People’s Republic of China
| | - Hong Ma
- Department of Spine Surgery, The Second Xiangya Hospital of Central South University, Changsha, People’s Republic of China
| | - Guohua Lv
- Department of Spine Surgery, The Second Xiangya Hospital of Central South University, Changsha, People’s Republic of China
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Tóth Á, Berta B, Tirczka T, Jekkel C, Ábrahám A, Prohászka Z, Bognár Z, Erdősi T. First description of a rifampicin-resistant Neisseria meningitidis serogroup Y strain causing recurrent invasive meningococcal disease in Hungary. Acta Microbiol Immunol Hung 2017; 64:1-7. [PMID: 28220707 DOI: 10.1556/030.64.2017.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
A Hungarian soldier previously immunized against Neisseria meningitidis by quadrivalent polysaccharide vaccine was twice infected with meningococci within six weeks. The patient was treated with ceftriaxone during both episodes and he successfully recovered. His close contacts received rifampicin prophylaxis. An investigation was performed to characterize the genetic background of the pathogens to ascertain if the recurrent invasive meningococcal disease was caused by the same strain and to find out the reason for reinfection. Both meningococci belonged to the fine type Y:P1.5-2,10-1:F4-1:ST-23. This is the first description of the Europe-wide prevalent N. meningitidis serogroup Y in Hungary. In the first episode, we found wild-type rpoB allele in the non-culturable sample implying the susceptibility to rifampicin. The culturable isolate from the second episode proved resistant to rifampicin and had a point mutation in the rpoB gene. The rifampicin resistance might have evolved during the prophylactic treatment of contacts. Previous immunization of the patient with polysaccharide vaccine was ineffective due to his immunodeficiency, thus immunization with conjugate vaccine was proposed. We have proposed the implementation of centralized rifampicin susceptibility testing of N. meningitidis strains within a defined time frame to intervene and administer appropriate prophylaxis to close contacts.
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Affiliation(s)
- Ákos Tóth
- 1 National Center for Epidemiology, Budapest, Hungary
- 2 European Program for Public Health Microbiology Training (EUPHEM), European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden
| | | | - Tamás Tirczka
- 1 National Center for Epidemiology, Budapest, Hungary
| | | | | | | | - Zsófia Bognár
- 1 National Center for Epidemiology, Budapest, Hungary
| | - Tímea Erdősi
- 1 National Center for Epidemiology, Budapest, Hungary
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50
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Cai XC, Xi H, Liang L, Liu JD, Liu CH, Xue YR, Yu XY. Rifampicin-Resistance Mutations in the rpoB Gene in Bacillus velezensis CC09 have Pleiotropic Effects. Front Microbiol 2017; 8:178. [PMID: 28243227 PMCID: PMC5303731 DOI: 10.3389/fmicb.2017.00178] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2016] [Accepted: 01/24/2017] [Indexed: 12/31/2022] Open
Abstract
Rifampicin resistance (Rifr) mutations in the RNA polymerase β subunit (rpoB) gene exhibit pleiotropic phenotypes as a result of their effects on the transcription machinery in prokaryotes. However, the differences in the effects of the mutations on the physiology and metabolism of the bacteria remain unknown. In this study, we isolated seven Rifr mutations in rpoB, including six single point mutations (H485Y, H485C, H485D, H485R, Q472R, and S490L) and one double point mutation (S490L/S617F) from vegetative cells of an endophytic strain, Bacillus velezensis CC09. Compared to the wild-type (WT) strain (CC09), the H485R and H485D mutants exhibited a higher degree of inhibition of Aspergillus niger spore germination, while the H485Y, S490L, Q472R, and S490L/S617F mutants exhibited a lower degree of inhibition due to their lower production of the antibiotic iturin A. These mutants all exhibited defective phenotypes in terms of pellicle formation, sporulation, and swarming motility. A hierarchical clustering analysis of the observed phenotypes indicated that the four mutations involving amino acid substitutions at H485 in RpoB belonged to the same cluster. In contrast, the S490L and Q472R mutations, as well as the WT strain, were in another cluster, indicating a functional connection between the mutations in B. velezensis and phenotypic changes. Our data suggest that Rifr mutations cannot only be used to study transcriptional regulation mechanisms, but can also serve as a tool to increase the production of bioactive metabolites in B. velezensis.
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Affiliation(s)
- Xun-Chao Cai
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University Nanjing, China
| | - Huan Xi
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University Nanjing, China
| | - Li Liang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University Nanjing, China
| | - Jia-Dong Liu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University Nanjing, China
| | - Chang-Hong Liu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University Nanjing, China
| | - Ya-Rong Xue
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University Nanjing, China
| | - Xiang-Yang Yu
- Institute of Food Safety and Inspection - Jiangsu Academy of Agricultural Sciences Nanjing, China
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