Valeriu Crudu
@ifp.md
Microbiology
Phthisiopneumology Institute, Chisinau, Moldova
The main domains of my activities are scientific research in the field of tuberculosis control, microbiological diagnosis of infectious diseases, drug resistance.
During this period, I implemented over 40 international and local projects from the European Union research and development funding programme - FP7, H2020, NIH, CRDF Global, USAID, EDCTP. Authored or coauthored of more than 300 publications, scientific reports, trainings materials on national and international journals and forums and supervisor of junior researchers and doctoral students. Member of the European Society of Clinical Microbiology and Infectious Diseases, the UNION and the European Respiratory Society.
Number of citations: 4784, h-index: 27
EDUCATION
State Medical University, Chisinau, Moldova. Degree- MD; Medicine/Epidemiology (06/1980),
Academy of Sciences “I.Secenov”, Moscow, Russia. Degree – PhD, Medical Microbiology. (09/1991).
RESEARCH, TEACHING, or OTHER INTERESTS
Infectious Diseases, Microbiology, Epidemiology, Microbiology (medical)
Scopus Publications
Scopus Publications
Melanie H. Chitwood, Caroline Colijn, Chongguang Yang, Valeriu Crudu, Nelly Ciobanu, Alexandru Codreanu, Jaehee Kim, Isabel Rancu, Kyu Rhee, Ted Cohen,et al.
Springer Science and Business Media LLC
AbstractThe projected trajectory of multidrug resistant tuberculosis (MDR-TB) epidemics depends on the reproductive fitness of circulating strains of MDR M. tuberculosis (Mtb). Previous efforts to characterize the fitness of MDR Mtb have found that Mtb strains of the Beijing sublineage (Lineage 2.2.1) may be more prone to develop resistance and retain fitness in the presence of resistance-conferring mutations than other lineages. Using Mtb genome sequences from all culture-positive cases collected over two years in Moldova, we estimate the fitness of Ural (Lineage 4.2) and Beijing strains, the two lineages in which MDR is concentrated in the country. We estimate that the fitness of MDR Ural strains substantially exceeds that of other susceptible and MDR strains, and we identify several mutations specific to these MDR Ural strains. Our findings suggest that MDR Ural Mtb has been transmitting efficiently in Moldova and poses a substantial risk of spreading further in the region.
Sudhasini Panda, Jeffrey Morgan, Catherine Cheng, Mayuko Saito, Robert H. Gilman, Nelly Ciobanu, Valeriu Crudu, Donald G. Catanzaro, Antonino Catanzaro, Timothy Rodwell,et al.
Springer Science and Business Media LLC
AbstractThere is still incomplete knowledge of which Mycobacterium tuberculosis (Mtb) antigens can trigger distinct T cell responses at different stages of infection. Here, a proteome-wide screen of 20,610 Mtb-derived peptides in 21 patients mid-treatment for active tuberculosis (ATB) reveals IFNγ-specific T cell responses against 137 unique epitopes. Of these, 16% are recognized by two or more participants and predominantly derived from cell wall and cell processes antigens. There is differential recognition of antigens, including TB vaccine candidate antigens, between ATB participants and interferon-gamma release assay (IGRA + /−) individuals. We developed an ATB-specific peptide pool (ATB116) consisting of epitopes exclusively recognized by ATB participants. This pool can distinguish patients with pulmonary ATB from IGRA + /− individuals from various geographical locations, with a sensitivity of over 60% and a specificity exceeding 80%. This proteome-wide screen of T cell reactivity identified infection stage-specific epitopes and antigens for potential use in diagnostics and measuring Mtb-specific immune responses.
Victor Naestholt Dahl, Tetiana Butova, Alex Rosenthal, Alina Grinev, Andrei Gabrielian, Sergo Vashakidze, Natalia Shubladze, Bekzat Toxanbayeva, Lyailya Chingissova, Valeriu Crudu,et al.
Centers for Disease Control and Prevention (CDC)
In 2021, the World Health Organization recommended new extensively drug-resistant (XDR) and pre-XDR tuberculosis (TB) definitions. In a recent cohort of TB patients in Eastern Europe, we show that XDR TB as currently defined is associated with exceptionally poor treatment outcomes, considerably worse than for the former definition (31% vs. 54% treatment success).
Yu Lan, Valeriu Crudu, Nelly Ciobanu, Alexandru Codreanu, Melanie H. Chitwood, Benjamin Sobkowiak, Joshua L. Warren, and Ted Cohen
Elsevier BV
Elena Chesov, Dumitru Chesov, Maja Reimann, Viola Dreyer, Christian Utpatel, Matthias I. Gröschel, Nelly Ciobanu, Valeriu Crudu, Christoph Lange, Jan Heyckendorf,et al.
Elsevier BV
Sheng-Wei Pan, Donald G. Catanzaro, Marva Seifert, Rehan R. Syed, Naomi Hillery, Mei-Lin Ho, Valeriu Crudu, Elena Tudor, Nelly Ciobanu, Alexandru Codreanu,et al.
Elsevier BV
Ecaterina Noroc, Dumitru Chesov, Matthias Merker, Matthias I. Gröschel, Ivan Barilar, Viola Dreyer, Nelly Ciobanu, Maja Reimann, Valeriu Crudu, and Christoph Lange
Centers for Disease Control and Prevention (CDC)
Applying whole-genome-sequencing, we aimed to detect transmission events of multidrug-resistant/rifampin-resistant strains of Mycobacterium tuberculosis complex at a tuberculosis hospital in Chisinau, Moldova. We recorded ward, room, and bed information for each patient and monitored in-hospital transfers over 1 year. Detailed molecular and patient surveillance revealed only 2 nosocomial transmission events.
Rehan R. Syed, Donald G. Catanzaro, Rebecca E. Colman, Christopher G. Cooney, Yvonne Linger, Alexander V. Kukhtin, Rebecca C. Holmberg, Ryan Norville, Valeriu Crudu, Nelly Ciobanu,et al.
American Society for Microbiology
While the goal of universal drug susceptibility testing has been a key component of the WHO End TB Strategy, in practice, this remains inaccessible to many. Rapid molecular tests for tuberculosis (TB) and antituberculosis drug resistance could significantly improve access to testing.
Laura Rosu, Jason J Madan, Ewan M Tomeny, Malaisamy Muniyandi, Jasper Nidoi, Mamo Girma, Valentina Vilc, Priyanka Bindroo, Rajdeep Dhandhukiya, Adamu K Bayissa,et al.
Elsevier BV
Matthias Merker, Jean-Philippe Rasigade, Maxime Barbier, Helen Cox, Silke Feuerriegel, Thomas A. Kohl, Egor Shitikov, Kadri Klaos, Cyril Gaudin, Rudy Antoine,et al.
Springer Science and Business Media LLC
AbstractTransmission-driven multi-/extensively drug resistant (M/XDR) tuberculosis (TB) is the largest single contributor to human mortality due to antimicrobial resistance. A few major clades of the Mycobacterium tuberculosis complex belonging to lineage 2, responsible for high prevalence of MDR-TB in Eurasia, show outstanding transnational distributions. Here, we determined factors underlying the emergence and epidemic spread of the W148 clade by genome sequencing and Bayesian demogenetic analyses of 720 isolates from 23 countries. We dated a common ancestor around 1963 and identified two successive epidemic expansions in the late 1980s and late 1990s, coinciding with major socio-economic changes in the post-Soviet Era. These population expansions favored accumulation of resistance mutations to up to 11 anti-TB drugs, with MDR evolving toward additional resistances to fluoroquinolones and second-line injectable drugs within 20 years on average. Timescaled haplotypic density analysis revealed that widespread acquisition of compensatory mutations was associated with transmission success of XDR strains. Virtually all W148 strains harbored a hypervirulence-associated ppe38 gene locus, and incipient recurrent emergence of prpR mutation-mediated drug tolerance was detected. The outstanding genetic arsenal of this geographically widespread M/XDR strain clade represents a “perfect storm” that jeopardizes the successful introduction of new anti-M/XDR-TB antibiotic regimens.
L. Cates, A. Codreanu, N. Ciobanu, H. Fosburgh, C. J. Allender, H. Centner, D. M. Engelthaler, V. Crudu, T. Cohen, and N. A. Menzies
International Union Against Tuberculosis and Lung Disease
BACKGROUND Diagnosing drug resistance is critical for choosing effective TB treatment regimens. Next-generation sequencing (NGS) represents an alternative approach to conventional phenotypic drug susceptibility testing (pDST) for diagnosing TB drug resistance.METHODS We undertook a budget impact analysis estimating the costs of introduction and routine use of NGS in the Moldovan National TB Programme. We conducted an empirical costing study and collated price and operating characteristics for NGS platforms. We examined multiple NGS scenarios in comparison to the current approach (pDST) for pre-treatment drug resistance testing over 2021–2025.RESULTS Annual testing volume ranged from 912 to 1,926 patients. For the pDST scenario, we estimated total costs of US$362,000 (2021 USD) over the 5-year study period. Total costs for NGS scenarios ranged from US$475,000 to US$1,486,000. Lowest cost NGS options involved targeted sequencing as a replacement for pDST, and excluded individuals diagnosed as RIF-susceptible on Xpert® MTB/RIF. For all NGS scenarios, the majority (55–80%) of costs were devoted to reagent kits. Start-up costs of NGS were small relative to routine costs borne each year.CONCLUSION NGS adoption will require expanded resources compared to conventional pDST. Further work is required to better understand the feasibility of NGS in settings such as Moldova.
Iris Finci, Audrey Albertini, Matthias Merker, Sönke Andres, Nino Bablishvili, Ivan Barilar, Tatiana Cáceres, Valeriu Crudu, Eduardo Gotuzzo, Nchimunya Hapeela,et al.
Elsevier BV
Maryam Kheirandish, Donald Catanzaro, Valeriu Crudu, and Shengfan Zhang
Oxford University Press (OUP)
Abstract Objective This study aims to establish an informative dynamic prediction model of treatment outcomes using follow-up records of tuberculosis (TB) patients, which can timely detect cases when the current treatment plan may not be effective. Materials and Methods We used 122 267 follow-up records from 17 958 new cases of pulmonary TB in the Republic of Moldova. A dynamic prediction framework integrating landmark modeling and machine learning algorithms was designed to predict patient outcomes during the course of treatment. Sensitivity and positive predictive value (PPV) were calculated to evaluate performance of the model at critical time points. New measures were defined to determine when follow-up laboratory tests should be conducted to obtain most informative results. Results The random-forest algorithm performed better than support vector machine and penalized multinomial logistic regression models for predicting TB treatment outcomes. For all 3 outcome classes (ie, cured, not cured, and died after 24 months following treatment initiation), sensitivity and PPV of prediction models improved as more follow-up information was collected. Specifically, sensitivity and PPV increased from 0.55 to 0.84 and from 0.32 to 0.88, respectively, for the not cured class. Conclusion The dynamic prediction framework utilizes longitudinal laboratory test results to predict patient outcomes at various landmarks. Sputum culture and smear results are among the important variables for prediction; however, the most recent sputum result is not always the most informative one. This framework can potentially facilitate a more effective treatment monitoring program and provide insights for policymakers toward improved guidelines on follow-up tests.
Maximillian Marin, Roger Vargas, Michael Harris, Brendan Jeffrey, L Elaine Epperson, David Durbin, Michael Strong, Max Salfinger, Zamin Iqbal, Irada Akhundova,et al.
Oxford University Press (OUP)
Abstract Motivation Short-read whole-genome sequencing (WGS) is a vital tool for clinical applications and basic research. Genetic divergence from the reference genome, repetitive sequences and sequencing bias reduces the performance of variant calling using short-read alignment, but the loss in recall and specificity has not been adequately characterized. To benchmark short-read variant calling, we used 36 diverse clinical Mycobacterium tuberculosis (Mtb) isolates dually sequenced with Illumina short-reads and PacBio long-reads. We systematically studied the short-read variant calling accuracy and the influence of sequence uniqueness, reference bias and GC content. Results Reference-based Illumina variant calling demonstrated a maximum recall of 89.0% and minimum precision of 98.5% across parameters evaluated. The approach that maximized variant recall while still maintaining high precision (<99%) was tuning the mapping quality filtering threshold, i.e. confidence of the read mapping (recall = 85.8%, precision = 99.1%, MQ ≥ 40). Additional masking of repetitive sequence content is an alternative conservative approach to variant calling that increases precision at cost to recall (recall = 70.2%, precision = 99.6%, MQ ≥ 40). Of the genomic positions typically excluded for Mtb, 68% are accurately called using Illumina WGS including 52/168 PE/PPE genes (34.5%). From these results, we present a refined list of low confidence regions across the Mtb genome, which we found to frequently overlap with regions with structural variation, low sequence uniqueness and low sequencing coverage. Our benchmarking results have broad implications for the use of WGS in the study of Mtb biology, inference of transmission in public health surveillance systems and more generally for WGS applications in other organisms. Availability and implementation All relevant code is available at https://github.com/farhat-lab/mtb-illumina-wgs-evaluation. Supplementary information Supplementary data are available at Bioinformatics online.
Elena Chesov, Dumitru Chesov, Florian P. Maurer, Sönke Andres, Christian Utpatel, Ivan Barilar, Ana Donica, Maja Reimann, Stefan Niemann, Christoph Lange,et al.
European Respiratory Society (ERS)
RationaleBedaquiline has been classified as a group A drug for the treatment of multidrug-resistant tuberculosis (MDR-TB) by the World Health Organization; however, globally emerging resistance threatens the effectivity of novel MDR-TB treatment regimens.ObjectivesWe analysed pre-existing and emerging bedaquiline resistance in bedaquiline-based MDR-TB therapies, and risk factors associated with treatment failure and death.MethodsIn a cross-sectional cohort study, we employed patient data, whole-genome sequencing (WGS) and phenotyping of Mycobacterium tuberculosis complex (MTBC) isolates. We could retrieve baseline isolates from 30.5% (62 out of 203) of all MDR-TB patients who received bedaquiline between 2016 and 2018 in the Republic of Moldova. This includes 26 patients for whom we could also retrieve a follow-up isolate.Measurements and main resultsAt baseline, all MTBC isolates were susceptible to bedaquiline. Among 26 patients with available baseline and follow-up isolates, four (15.3%) patients harboured strains which acquired bedaquiline resistance under therapy, while one (3.8%) patient was re-infected with a second bedaquiline-resistant strain. Treatment failure and death were associated with cavitary disease (p=0.011), and any additional drug prescribed in the bedaquiline-containing regimen with WGS-predicted resistance at baseline (OR 1.92 per unit increase, 95% CI 1.15–3.21; p=0.012).ConclusionsMDR-TB treatments based on bedaquiline require a functional background regimen to achieve high cure rates and to prevent the evolution of bedaquiline resistance. Novel MDR-TB therapies with bedaquiline require timely and comprehensive drug resistance monitoring.
Chongguang Yang, Benjamin Sobkowiak, Vijay Naidu, Alexandru Codreanu, Nelly Ciobanu, Kenneth S. Gunasekera, Melanie H. Chitwood, Sofia Alexandru, Stela Bivol, Marcus Russi,et al.
Public Library of Science (PLoS)
Background The incidence of multidrug-resistant tuberculosis (MDR-TB) remains critically high in countries of the former Soviet Union, where >20% of new cases and >50% of previously treated cases have resistance to rifampin and isoniazid. Transmission of resistant strains, as opposed to resistance selected through inadequate treatment of drug-susceptible tuberculosis (TB), is the main driver of incident MDR-TB in these countries. Methods and findings We conducted a prospective, genomic analysis of all culture-positive TB cases diagnosed in 2018 and 2019 in the Republic of Moldova. We used phylogenetic methods to identify putative transmission clusters; spatial and demographic data were analyzed to further describe local transmission of Mycobacterium tuberculosis. Of 2,236 participants, 779 (36%) had MDR-TB, of whom 386 (50%) had never been treated previously for TB. Moreover, 92% of multidrug-resistant M. tuberculosis strains belonged to putative transmission clusters. Phylogenetic reconstruction identified 3 large clades that were comprised nearly uniformly of MDR-TB: 2 of these clades were of Beijing lineage, and 1 of Ural lineage, and each had additional distinct clade-specific second-line drug resistance mutations and geographic distributions. Spatial and temporal proximity between pairs of cases within a cluster was associated with greater genomic similarity. Our study lasted for only 2 years, a relatively short duration compared with the natural history of TB, and, thus, the ability to infer the full extent of transmission is limited. Conclusions The MDR-TB epidemic in Moldova is associated with the local transmission of multiple M. tuberculosis strains, including distinct clades of highly drug-resistant M. tuberculosis with varying geographic distributions and drug resistance profiles. This study demonstrates the role of comprehensive genomic surveillance for understanding the transmission of M. tuberculosis and highlights the urgency of interventions to interrupt transmission of highly drug-resistant M. tuberculosis.
Adam Penn-Nicholson, Sophia B Georghiou, Nelly Ciobanu, Mubin Kazi, Manpreet Bhalla, Anura David, Francesca Conradie, Morten Ruhwald, Valeriu Crudu, Camilla Rodrigues,et al.
Elsevier BV
Naomi Hillery, Marva Seifert, Donald G Catanzaro, Symone McKinnon, Rebecca E Colman, Peter G Chiles, Dumitru Chesov, Nelly Ciobanu, Christopher Hagan, Valeriu Crudu,et al.
JMIR Publications Inc.
Background The lack of accurate and efficient diagnostic devices for extensively drug-resistant tuberculosis (XDR-TB) makes it a severe threat to global public health. A prospective clinical study in an intended-use cohort was designed to evaluate the Akonni Biosystems XDR-TB TruArray and lateral flow cell (XDR-LFC) to address this gap in tuberculosis diagnostics. Objective This paper presents the protocol for a study that aims to document the conceptualization and design of this evaluation method for early dissemination while data collection and analysis are ongoing. Methods The clinical study was conducted in three phases. The first phase was to observe changes in bacterial load and culture positivity in patient sputa over time and better understand the diversity of prospective clinical samples. The second phase was to prospectively collect clinical samples for sensitivity and specificity testing of the Akonni Biosystems XDR-LFC device. Lastly, the third phase was to explore the anti-TB drug concentrations in serum throughout the drug-resistant tuberculosis treatment. Results The methodology described includes the study design, laboratory sample handling, data collection, and the protection elements of human subjects of this clinical study to evaluate a potential new XDR-TB diagnostic device. A total of 664 participants were enrolled across the three phases. The implemented complex systems facilitated a thorough clinical data collection for an objective evaluation of the device. The study is closed to recruitment. The follow-up data collection and analysis are in progress. Conclusions This paper outlined a prospective cohort study protocol to evaluate a rapid XDR-TB detection device, which may be informative for other researchers with similar goals. International Registered Report Identifier (IRRID) DERR1-10.2196/26748
Dumitru Chesov, Jan Heyckendorf, Sofia Alexandru, Ana Donica, Elena Chesov, Maja Reimann, Valeriu Crudu, Victor Botnaru, and Christoph Lange
European Respiratory Society (ERS)
BackgroundEvaluation of novel anti-tuberculosis (TB) drugs for the treatment of multidrug-resistant (MDR)-TB continues to be of high interest on the TB research agenda. We assessed treatment outcomes in patients with pulmonary MDR-TB who received bedaquiline-containing treatment regimens in the Republic of Moldova, a high-burden MDR-TB country.MethodWe systematically analysed the SIMETB national electronic TB database and performed a retrospective propensity score-matched comparison of treatment outcomes in a cohort of patients with MDR-TB who started treatment during 2016–2018 with a bedaquiline-containing regimen (bedaquiline cohort) and a cohort of patients treated without bedaquiline (non-bedaquiline cohort).ResultsFollowing propensity score matching, 114 patients were assigned to each cohort of MDR-TB patients. Patients in the bedaquiline cohort had a higher 6-month sputum culture conversion rate than those in the non-bedaquiline cohort (66.7% versus 40.3%; p<0.001). Patients under bedaquiline-containing regimens had a higher cure rate assessed by both World Health Organization (WHO) and TBnet definitions (55.3% versus 24.6%; p=0.001 and 43.5% versus 19.6%; p=0.004, respectively), as well as a lower mortality rate (8.8% versus 20.2%; p<0.001 and 10.9% versus 25.2%; p=0.01, respectively). In patients who previously failed on MDR-TB treatment, >40% of patients achieved a cure with a bedaquiline-containing regimen.ConclusionsBedaquiline-based MDR-TB treatment regimens result in better disease resolution when compared with bedaquiline-sparing MDR-TB treatment regimens under programmatic conditions in a country with a high burden of MDR-TB.
L. Cates, V. Crudu, A. Codreanu, N. Ciobanu, H. Fosburgh, T. Cohen, and N. A. Menzies
International Union Against Tuberculosis and Lung Disease
Dear Editor, Diagnosing drug resistance to TB requires substantial resources, yet there are few unit cost estimates for these services.1–3 We examined the laboratory costs of diagnosing TB and drug resistance in Moldova, where 29% of treatment-naı̈ve cases have multidrug-resistant TB (MDR-TB).4,5 This study was conducted at the Chiril Draganiuc Institute of Phthisiopneumology (IPP) in Chisinau, Moldova, where the National TB Reference Laboratory (NRL) is based. The NRL offers TB microscopy, culture testing and species identification, drug susceptibility testing (DST) and molecular diagnostics.6 This allowed cost estimation for a range of tests, including sputum smear microscopy (SSM), Löwenstein-Jenson (LJ) solid culture, BACTECe MGITe (BD, Franklin Lakes, NJ, USA), Xpertw MTB/RIF (Cepheid, Sunnyvale, CA, USA), phenotypic DST for firstand second-line drugs, and two Hain Lifescience (Nehren, Germany) line-probe assays (LPAs). We assessed costs from a provider perspective from January to December 2018. We included the direct costs of TB diagnostic and monitoring tests, plus laboratory-level overheads. Direct costs included staffing, laboratory equipment, reagents and consumables. Overheads included fuel, repairs and maintenance, office supplies, utilities, buildings, vehicles, recurrent and non-recurrent training courses, quality control, cleaning, management, and general-use laboratory items. We excluded institute-level overheads, research costs and nonlaboratory clinical costs, as well as transportation and time costs incurred by patients. For each cost category, we collected data on resource using established methods.7 For supplies and equipment, we extracted quantity and price data from accounting and inventory databases. Utilities, buildings, and maintenance costs were extracted from accounting records. Test quantities were extracted from the Moldova National Database for Notification and Follow-Up on Tuberculosis Cases (https://simetb.ifp. md/). Shared costs were directly allocated to different tests and laboratory activity categories, based on interviews with laboratory personnel. Useful life estimates were provided by laboratory personnel (non-recurrent training for 5 years, buildings for 20 years, vehicles for 10 years, laboratory equipment for 2–9 years depending on the item). Costs in Moldovan leu (MDL) were converted to United States dollars (USD) at MDL16.85251⁄4USD1.00 (as of 2 July 2018). We allocated all recurrent and capital costs across the different test types. Overheads were allocated across tests and activities proportional to personnel time spent on each test. The economic cost of capital items was calculated by annuitising the capital cost over the expected useful life, with a 3% discount rate. We analysed these data to describe the distribution of costs across budget categories and test types, the average per-test economic cost (unit cost) for each type of test, and the typical per-patient cost for diagnosis of TB and TB drug resistance. All results are reported in 2018 USD. The Table shows the distribution of costs across test types, with overhead costs either excluded or included. Based on these analyses, reagents and consumables represented almost half (46.5%) of the total laboratory costs in 2018. This was followed by staff salaries and benefits (19.0%); laboratory equipment (17.3%); buildings (10.3%); fuel, repairs and maintenance (2.5%); and utilities (2.0%). Training, vehicles, quality control and office supplies together accounted for 2.5% of total costs. We calculated unit costs by dividing total test costs, including overheads, by the total tests performed in 2018. These unit costs ranged from less than USD10 per test for LJ and SSM (USD7.59 and USD8.15, respectively) to USD44.78 and USD48.42 for LPA and second-line phenotypic DST panels, respectively. To contextualise our unit cost results, we compared these values to published estimates from a publicly available cost database.8 Based on these comparisons, our estimates were similar to published values for SSM, MGIT and Xpert. Our estimates were lower than the range of published values for LJ and first-line phenotypic DST, but higher for LPA. However, there were fewer published values for these tests.1,8 We found no published estimates for the unit cost of second-line phenotypic DST. The per-patient cost of TB diagnosis was calculated by estimating the number of each type of test that would be received by a typical patient (SSM x 1.94, LJ x 1.0, MGIT x 1.0, Xpert x 1.0), multiplied by the unit cost for each test, and summing across all tests. We estimated this cost to be USD73 per patient. Perpatient costs for firstand second-line DST were estimated using a similar approach. Diagnosis of first-
Tyler S. Brown, Vegard Eldholm, Ola Brynildsrud, Magnus Osnes, Natalie Levy, James Stimson, Caroline Colijn, Sofia Alexandru, Ecaterina Noroc, Nelly Ciobanu,et al.
Microbiology Society
The evolution and emergence of drug-resistant tuberculosis (TB) has been studied extensively in some contexts, but the ecological drivers of these two processes remain poorly understood. This study sought to describe the joint evolutionary and epidemiological histories of a novel multidrug-resistant Mycobacterium tuberculosis strain recently identified in the capital city of the Republic of Moldova (MDR Ural/4.2), where genomic surveillance of drug-resistant M. tuberculosis has been limited thus far. Using whole genome sequence data and Bayesian phylogenomic methods, we reconstruct the stepwise acquisition of drug resistance mutations in the MDR Ural/4.2 strain, estimate its historical bacterial population size over time, and infer the migration history of this strain between Eastern European countries. We infer that MDR Ural/4.2 likely evolved (via acquisition of rpoB S450L, which confers resistance to rifampin) in the early 1990s, during a period of social turmoil following Moldovan independence from the Soviet Union. This strain subsequently underwent substantial population size expansion in the early 2000s, at a time when national guidelines encouraged inpatient treatment of TB patients. We infer exportation of this strain and its isoniazid-resistant ancestral precursor from Moldova to neighbouring countries starting as early as 1985. Our findings suggest temporal and ecological associations between specific public health practices, including inpatient hospitalization of drug-resistant TB cases from the early 2000s until 2013, and the evolution of drug-resistant M. tuberculosis in Moldova. These findings underscore the need for regional coordination in TB control and expanded genomic surveillance efforts across Eastern Europe.
Barbara Molina-Moya, Nelly Ciobanu, Marta Hernandez, Cristina Prat-Aymerich, Valeriu Crudu, Emily R. Adams, Alexandru Codreanu, Derek J. Sloan, Luis E. Cuevas, and Jose Dominguez
MDPI AG
Tuberculosis (TB) diagnosis is increasingly based on the detection of Mycobacterium tuberculosis complex (MTBC) DNA in sputum using molecular diagnostic tests as the first test for diagnosis. However, sputum can be difficult to obtain in children, patients without productive cough, and the elderly and approaches testing non-sputum samples are needed. We evaluated whether TB can be detected from the oral mucosa of patients with TB. Adults with presumptive TB were examined using culture, Xpert MTB/RIF, smear microscopy and X-Rays. Oral mucosa swabs collected on PrimeStore-MTM, stored at room temperature if tested within 30 days or at −20 °C if examined at a later time. RT-PCR was performed to detect M. tuberculosis DNA. Eighty patients had bacteriologically-confirmed TB, 34 had bacteriologically-negative TB (negative tests but abnormal X-rays) and 152 were considered not to have TB (not TB). Oral swabs RT-PCR were positive in 29/80 (36.3%) bacteriologically-confirmed, 9/34 (26.5%) bacteriologically-negative and 29/152 (19.1%) not TB. The yield varied among samples stored for less and more than 30 days (p = 0.013) from 61% (11/18) and 29% (18/62) among bacteriologically confirmed, and 30.8% (4/13) and 23.8% (5/21) among bacteriologically-negative participants. Among not TB patients, the specificity was 80.9% (123/152), being 78.3% (18/23) among samples stored less than 30 days and 81.4% (105/129) among samples stored for more than 30 days (p = 0.46). The detection of M. tuberculosis in oral mucosa samples is feasible, but storage conditions may affect the yield.
D. Chesov, V. Lesanu, N. Ciobanu, A. Codreanu, V. Crudu, L. E. Cuevas, D. Kiss, N. Czoboly, and A. Somoskovi
International Union Against Tuberculosis and Lung Disease
Kurt Wollenberg, Michael Harris, Andrei Gabrielian, Nelly Ciobanu, Dumitru Chesov, Alyssa Long, Jessica Taaffe, Darrell Hurt, Alex Rosenthal, Michael Tartakovsky,et al.
Springer Science and Business Media LLC
Abstract Background Recurrence of drug-resistant tuberculosis (DR-TB) after treatment occurs through relapse of the initial infection or reinfection by a new drug-resistant strain. Outbreaks of DR-TB in high burden regions present unique challenges in determining recurrence status for effective disease management and treatment. In the Republic of Moldova the burden of DR-TB is exceptionally high, with many cases presenting as recurrent. Methods We performed a retrospective analysis of Mycobacterium tuberculosis from Moldova to better understand the genomic basis of drug resistance and its effect on the determination of recurrence status in a high DR-burden environment. To do this we analyzed genomes from 278 isolates collected from 189 patients, including 87 patients with longitudinal samples. These pathogen genomes were sequenced using Illumina technology, and SNP panels were generated for each sample for use in phylogenetic and network analysis. Discordance between genomic resistance profiles and clinical drug-resistance test results was examined in detail to assess the possibility of mixed infection. Results There were clusters of multiple patients with 10 or fewer differences among DR-TB samples, which is evidence of person-to-person transmission of DR-TB. Analysis of longitudinally collected isolates revealed that many infections exhibited little change over time, though 35 patients demonstrated reinfection by divergent (number of differences > 10) lineages. Additionally, several same-lineage sample pairs were found to be more divergent than expected for a relapsed infection. Network analysis of the H3/4.2.1 clade found very close relationships among 61 of these samples, making differentiation of reactivation and reinfection difficult. There was discordance between genomic profile and clinical drug sensitivity test results in twelve samples, and four of these had low level (but not statistically significant) variation at DR SNPs suggesting low-level mixed infections. Conclusions Whole-genome sequencing provided a detailed view of the genealogical structure of the DR-TB epidemic in Moldova, showing that reinfection may be more prevalent than currently recognized. We also found increased evidence of mixed infection, which could be more robustly characterized with deeper levels of genomic sequencing.
Juan F Vesga, Timothy B Hallett, Michael J A Reid, Kuldeep Singh Sachdeva, Raghuram Rao, Sunil Khaparde, Paresh Dave, Kiran Rade, Maureen Kamene, Eunice Omesa,et al.
Elsevier BV