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Burger Z, Aung HT, Seifert M, Mar TT, Harris V, Colman RE, Rodwell TC, Aung ST. Contributions of GeneXpert ® to TB diagnosis in Myanmar. Int J Tuberc Lung Dis 2022; 26:875-879. [PMID: 35996278 PMCID: PMC9423018 DOI: 10.5588/ijtld.22.0009] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND: Xpert® MTB/RIF, a rapid, molecular TB diagnostic assay, can detect Mycobacterium tuberculosis and rifampin resistance directly from clinical sputum samples in <2 h with high sensitivity and specificity. The added diagnostic value of Xpert over smear microscopy at a national level in Myanmar has not been previously reported.METHODS: We evaluated 339,358 Xpert and demographic records captured from January 2015 to December 2018 as part of the Myanmar National TB Program Data Utilization and Connectivity Project to examine the additional diagnostic yield of Xpert relative to smear for the detection of M. tuberculosis for TB diagnosis in Myanmar, with a focus on people living with HIV (PLHIV) and sample type.RESULTS: Use of Xpert increased TB case detection by 40% compared to smear microscopy results. Among PLHIV, use of Xpert increased TB case detection by almost 100% compared to smear microscopy results.CONCLUSION: Xpert testing identified more patients with TB than smear microscopy alone, particularly in cohorts with significant proportions of PLHIV. The use of Xpert as a screening tool in countries with a high burden of TB could lead to significantly increased diagnosis of TB at a regional and national level.
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Affiliation(s)
- Z Burger
- University of California San Diego, La Jolla, CA, USA
| | - H T Aung
- Clinton Health Access Initiative, Yangon, Myanmar
| | - M Seifert
- University of California San Diego, La Jolla, CA, USA
| | - T T Mar
- Ministry of Health and Sports, Naypyitaw, Myanmar
| | - V Harris
- Foundation for Innovative New Diagnostics, Geneva, Switzerland
| | - R E Colman
- University of California San Diego, La Jolla, CA, USA
| | - T C Rodwell
- University of California San Diego, La Jolla, CA, USA
| | - S T Aung
- Ministry of Health and Sports, Naypyitaw, Myanmar
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2
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Ramirez-Busby SM, Rodwell TC, Fink L, Catanzaro D, Jackson RL, Pettigrove M, Catanzaro A, Valafar F. A Multinational Analysis of Mutations and Heterogeneity in PZase, RpsA, and PanD Associated with Pyrazinamide Resistance in M/XDR Mycobacterium tuberculosis. Sci Rep 2017; 7:3790. [PMID: 28630430 PMCID: PMC5476565 DOI: 10.1038/s41598-017-03452-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 04/28/2017] [Indexed: 11/28/2022] Open
Abstract
Pyrazinamide (PZA) is an important first-line drug in all existing and new tuberculosis (TB) treatment regimens. PZA-resistance in M. tuberculosis is increasing, especially among M/XDR cases. Noted issues with PZA Drug Susceptibility Testing (DST) have driven the search for alternative tests. This study provides a comprehensive assessment of PZA molecular diagnostics in M/XDR TB cases. A set of 296, mostly XDR, clinical M. tuberculosis isolates from four countries were subjected to DST for eight drugs, confirmatory Wayne's assay, and whole-genome sequencing. Three genes implicated in PZA resistance, pncA, rpsA, and panD were investigated. Assuming all non-synonymous mutations cause resistance, we report 90% sensitivity and 65% specificity for a pncA-based molecular test. The addition of rpsA and panD potentially provides 2% increase in sensitivity. Molecular heterogeneity in pncA was associated with resistance and should be evaluated as a diagnostic tool. Mutations near the N-terminus and C-terminus of PZase were associated with East-Asian and Euro-American lineages, respectively. Finally, Euro-American isolates are most likely to have a wild-type PZase and escape molecular detection. Overall, the 8-10% resistance without markers may point to alternative mechanisms of resistance. Confirmatory mutagenesis may improve the disconcertingly low specificity but reduce sensitivity since not all mutations may cause resistance.
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Affiliation(s)
- S M Ramirez-Busby
- Biological and Medical Informatics Research Center, San Diego State University, San Diego, California, USA
| | - T C Rodwell
- Department of Medicine, University of California, San Diego, California, USA
| | - L Fink
- Biological and Medical Informatics Research Center, San Diego State University, San Diego, California, USA
| | - D Catanzaro
- Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas, USA
| | - R L Jackson
- Department of Medicine, University of California, San Diego, California, USA
| | - M Pettigrove
- Department of Medicine, University of California, San Diego, California, USA
| | - A Catanzaro
- Department of Medicine, University of California, San Diego, California, USA
| | - F Valafar
- Biological and Medical Informatics Research Center, San Diego State University, San Diego, California, USA.
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Seifert M, Ajbani K, Georghiou SB, Catanzaro D, Rodrigues C, Crudu V, Victor TC, Garfein RS, Catanzaro A, Rodwell TC. A performance evaluation of MTBDRplus version 2 for the diagnosis of multidrug-resistant tuberculosis. Int J Tuberc Lung Dis 2017; 20:631-7. [PMID: 27084817 DOI: 10.5588/ijtld.15.0788] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
OBJECTIVE To evaluate the performance of a recently updated rapid molecular diagnostic test, GenoType® MTBDRplus version 2, designed to detect drug resistance in both acid-fast bacilli (AFB) smear-negative and -positive specimens. DESIGN Sputum samples from 1128 patients at risk for multidrug-resistant tuberculosis (MDR-TB) were tested using MTBDRplus v2 and compared with reference standard MGIT™ 960™ drug susceptibility testing. The relationship of participant human immunodeficiency virus (HIV) status, diabetic status, previous treatment, and smear gradation to the likelihood of obtaining an interpretable result was assessed using logistic regression. RESULTS The sensitivity and specificity of MTBDRplus v2 for detecting MDR-TB, when compared to a reference standard, were respectively 96.0% (95%CI 93.5-97.6) and 99.2% (95%CI 97.0-99.9) in AFB smear-positive specimens and 82.8% (95%CI 63.5-93.5) and 98.3% (95%CI 89.9-99.9) in AFB smear-negative specimens. A dose-response relationship was observed between the proportion of interpretable test results and AFB smear bacterial load after adjusting for age, sex, body mass index, HIV status, previous treatment and diabetic status. CONCLUSION While MTBDRplus v2 performs well among both AFB smear-positive and -negative specimens, smear gradation appears to influence both the probability of obtaining an interpretable result and test sensitivity, indicating a significant association between bacillary load and test performance.
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Affiliation(s)
- M Seifert
- University of California, San Diego, California, USA
| | - K Ajbani
- Hinduja National Hospital, Mumbai, India
| | - S B Georghiou
- University of California, San Diego, California, USA
| | - D Catanzaro
- University of Arkansas, Fayetteville, Arkansas, USA
| | | | - V Crudu
- Institute of Phthisiopneumology, Chisinau, Moldova
| | - T C Victor
- Stellenbosch University, Cape Town, South Africa
| | - R S Garfein
- University of California, San Diego, California, USA
| | - A Catanzaro
- University of California, San Diego, California, USA
| | - T C Rodwell
- University of California, San Diego, California, USA
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4
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Nikam C, Patel R, Sadani M, Ajbani K, Kazi M, Soman R, Shetty A, Georghiou SB, Rodwell TC, Catanzaro A, Rodrigues C. Redefining MTBDRplus test results: what do indeterminate results actually mean? Int J Tuberc Lung Dis 2017; 20:154-9. [PMID: 26792465 DOI: 10.5588/ijtld.15.0319] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Although line-probe assays (LPAs) are promising, little research has been conducted to elucidate the true nature of indeterminate LPA results or assess the ability of these assays to perform on a wide range of clinical samples. OBJECTIVE To evaluate the performance of the commercially available GenoType(®) MTBDRplus LPA against conventional BACTEC™ MGIT™ 960 culture and drug susceptibility testing (DST) among 308 pulmonary tuberculosis (PTB) and 32 extra-pulmonary TB samples. RESULTS Invalid LPA results (defined as those with a missing Mycobacterium tuberculosis identification band) were obtained for 18 PTB samples, which were excluded from further analysis. The sensitivity and specificity of the MTBDRplus assay for multidrug-resistant TB, based upon the results obtained for the remaining 322 samples, was respectively 95.2% and 95.1%. Of 290 PTB samples, 40 (13.7%) were indeterminate on LPA (defined as the absence of both wild-type and corresponding mutation bands) for isoniazid (INH) and/or rifampicin (RMP), and were further evaluated by pyrosequencing (PSQ). Contrary to standard LPA interpretation, INH and RMP susceptibility were confirmed by both DST and PSQ in respectively 7.5% (3/40) and 27.5% (11/40) of indeterminate samples. CONCLUSION PSQ was found to be a valuable and rapid technique to resolve discrepancies in LPA test results that were not interpretable.
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Affiliation(s)
- C Nikam
- Department of Microbiology, P D Hinduja Hospital and Medical Research Centre, Mumbai, India
| | - R Patel
- Department of Microbiology, P D Hinduja Hospital and Medical Research Centre, Mumbai, India
| | - M Sadani
- Department of Microbiology, P D Hinduja Hospital and Medical Research Centre, Mumbai, India
| | - K Ajbani
- Department of Microbiology, P D Hinduja Hospital and Medical Research Centre, Mumbai, India
| | - M Kazi
- Department of Microbiology, P D Hinduja Hospital and Medical Research Centre, Mumbai, India
| | - R Soman
- Department of Microbiology, P D Hinduja Hospital and Medical Research Centre, Mumbai, India
| | - A Shetty
- Department of Microbiology, P D Hinduja Hospital and Medical Research Centre, Mumbai, India
| | - S B Georghiou
- Department of Medicine, University of California San Diego, La Jolla, California, USA
| | - T C Rodwell
- Department of Medicine, University of California San Diego, La Jolla, California, USA
| | - A Catanzaro
- Department of Medicine, University of California San Diego, La Jolla, California, USA
| | - C Rodrigues
- Department of Microbiology, P D Hinduja Hospital and Medical Research Centre, Mumbai, India
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Conners E, Garfein RS, Rodwell TC, Udwadia ZF, Catanzaro DG. Mobility patterns of persons at risk for drug-resistant tuberculosis in Mumbai, India. Int J Tuberc Lung Dis 2016; 20:1633-1638. [PMID: 27931339 PMCID: PMC10424886 DOI: 10.5588/ijtld.16.0187] [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] [Indexed: 11/10/2022] Open
Abstract
SETTING Tuberculosis (TB) hospital in Mumbai, India. OBJECTIVE To describe the mobility patterns of persons with suspected drug-resistant tuberculosis (DR-TB) and to assess whether there were significant differences in demographic or risk characteristics based on mobility. DESIGN Observational cohort study of TB clinic patients at risk for DR-TB. RESULTS Among 602 participants, 37% had ever moved from their place of birth; 14% were local movers (within state), and 23% were distant movers, between states or countries. Univariate multinomial logistic regression models showed that distant movers were more likely than non-movers to have lower income, less education, a greater number of previous TB episodes, and to have ever smoked. Compared to non-movers, local movers were more likely to have lower income and were more likely to have seen a doctor in the past 2 years. Clinical outcomes, including DR-TB, diabetes, and human immunodeficiency virus (HIV), did not differ between the three mobility groups. CONCLUSION Mobility was common among patients at risk for DR-TB in Mumbai. TB programs should consider the implications of mobility on the protracted treatment for DR-TB in India.
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Affiliation(s)
- E Conners
- Department of Medicine, University of California, San Diego, San Diego State University, San Diego, California, USA
| | - R S Garfein
- Department of Medicine, University of California, San Diego
| | - T C Rodwell
- Department of Medicine, University of California, San Diego
| | | | - D G Catanzaro
- University of Arkansas, Department of Biological Sciences, Fayetteville, Arkansas, USA
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ElMaraachli W, Slater M, Berrada ZL, Lin SYG, Catanzaro A, Desmond E, Rodrigues C, Victor TC, Crudu V, Gler MT, Rodwell TC. Predicting differential rifamycin resistance in clinical Mycobacterium tuberculosis isolates by specific rpoB mutations. Int J Tuberc Lung Dis 2016; 19:1222-6. [PMID: 26459537 DOI: 10.5588/ijtld.14.0936] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
SETTING Rifampin (RMP) resistant Mycobacterium tuberculosis is usually assumed to be resistant to all rifamycins. Increasing evidence indicates, however, that some rpoB mutations, detectable by rapid molecular diagnostics, confer resistance to RMP but not to rifabutin (RBT), suggesting that RBT may be effective for the treatment of M. tuberculosis with these mutations. OBJECTIVE To determine if specific rpoB mutations reliably predict differential phenotypic resistance to RMP and RBT. DESIGN We selected 60 clinical M. tuberculosis isolates from a repository of multinational multidrug-resistant tuberculosis isolates and stratified them into two groups: 1) those with rpoB mutations suspected to confer differential resistance to RMP and RBT, and 2) those expected to be cross-resistant to RMP and RBT. These assumptions were tested by comparing the phenotypic susceptibilities of RMP/RBT with those predicted by mutations in the rpoB gene. RESULTS Of 20 suspected RMP-resistant/RBT-susceptible isolates, 15 were RMP-resistant but RBT-susceptible, 3 were RMP- and RBT-susceptible, and 2 were cross-resistant to both RMP and RBT. In comparison, 40 of 40 suspected cross-resistant isolates were both RMP- and RBT-resistant. CONCLUSION Our data support the association between specific rpoB mutations and differential resistance of M. tuberculosis to RMP and RBT. Clinical studies are required to investigate the efficacy of RBT in the treatment of M. tuberculosis harboring these mutations.
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Affiliation(s)
- W ElMaraachli
- Department of Medicine, University of California San Diego, San Diego, USA
| | - M Slater
- Department of Medicine, Stanford University School of Medicine, Stanford, USA
| | - Z L Berrada
- California Department of Public Health, Richmond, California, USA
| | - S-Y G Lin
- California Department of Public Health, Richmond, California, USA
| | - A Catanzaro
- Department of Medicine, University of California San Diego, San Diego, USA
| | - E Desmond
- California Department of Public Health, Richmond, California, USA
| | - C Rodrigues
- Department of Microbiology, P D Hinduja Hospital Medical Research Centre, Veer Sarvarkar Marg, Mumbai, India
| | - T C Victor
- Department of Biomedical Sciences, Stellenbosch University, Cape Town, South Africa
| | - V Crudu
- Microbiology and Morphology Laboratory, Institute of Phthisiopneumology, Chisinau, Moldova
| | - M T Gler
- Tropical Disease Foundation/Makati Medical Center, Makati City, The Philippines
| | - T C Rodwell
- Department of Medicine, University of California San Diego, San Diego, USA
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Garfein RS, Collins K, Muñoz F, Moser K, Cerecer-Callu P, Raab F, Rios P, Flick A, Zúñiga ML, Cuevas-Mota J, Liang K, Rangel G, Burgos JL, Rodwell TC, Patrick K. Feasibility of tuberculosis treatment monitoring by video directly observed therapy: a binational pilot study. Int J Tuberc Lung Dis 2016; 19:1057-64. [PMID: 26260824 DOI: 10.5588/ijtld.14.0923] [Citation(s) in RCA: 86] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Although directly observed therapy (DOT) is recommended worldwide for monitoring anti-tuberculosis treatment, transportation and personnel requirements limit its use. OBJECTIVE To evaluate the feasibility and acceptability of 'video DOT' (VDOT), which allows patients to record and transmit medication ingestion via videos watched remotely by health care providers to document adherence. METHODS We conducted a single-arm trial among tuberculosis (TB) patients in San Diego, California, USA, (n = 43) and Tijuana, Mexico (n = 9) to represent high- and low-resource settings. Pre-/post-treatment interviews assessed participant characteristics and experiences. Adherence was defined as the proportion of observed doses to expected doses. RESULTS The mean age was 37 years (range 18-86), 50% were male, and 88% were non-Caucasian. The mean duration of VDOT use was 5.5 months (range 1-11). Adherence was similar in San Diego (93%) and Tijuana (96%). Compared to time on in-person DOT, 92% preferred VDOT, 81% thought VDOT was more confidential, 89% never/rarely had problems recording videos, and 100% would recommend VDOT to others. Seven (13%) participants were returned to in-person DOT and six (12%) additional participants had their phones lost, broken or stolen. CONCLUSIONS VDOT was feasible and acceptable, with high adherence in both high- and low-resource settings. Efficacy and cost-effectiveness studies are needed.
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Affiliation(s)
- R S Garfein
- Division of Global Public Health, Department of Medicine, University of California, San Diego, La Jolla, USA
| | - K Collins
- Division of Global Public Health, Department of Medicine, University of California, San Diego, La Jolla, USA
| | - F Muñoz
- Division of Global Public Health, Department of Medicine, University of California, San Diego, La Jolla, USA
| | - K Moser
- San Diego County Health and Human Services Agency, San Diego, California, USA
| | - P Cerecer-Callu
- Instituto de Servicios de Salud, Tijuana, Baja California, México
| | - F Raab
- Department of Preventive Medicine and Public Health, University of California, San Diego, La Jolla, USA
| | - P Rios
- Qualcomm Institute, University of California, San Diego, La Jolla, USA
| | - A Flick
- Qualcomm Institute, University of California, San Diego, La Jolla, USA
| | - M L Zúñiga
- School of Social Work, San Diego State University, San Diego, California, USA
| | - J Cuevas-Mota
- Division of Global Public Health, Department of Medicine, University of California, San Diego, La Jolla, USA
| | - K Liang
- San Diego County Health and Human Services Agency, San Diego, California, USA
| | - G Rangel
- Comision de Salud Fronteriza, Sección México-Secretaria de Salud, Tijuana, Baja California, México
| | - J L Burgos
- Division of Global Public Health, Department of Medicine, University of California, San Diego, La Jolla, USA
| | - T C Rodwell
- Division of Global Public Health, Department of Medicine, University of California, San Diego, La Jolla, USA
| | - K Patrick
- Department of Preventive Medicine and Public Health, University of California, San Diego, La Jolla, USA; Qualcomm Institute, University of California, San Diego, La Jolla, USA
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Georghiou SB, Ajbani K, Rodrigues C, Rodwell TC. Performance of a pyrosequencing platform in diagnosing drug-resistant extra-pulmonary tuberculosis in India. Int J Tuberc Lung Dis 2016; 20:160-5. [PMID: 26792466 DOI: 10.5588/ijtld.15.0459] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
SETTING Pyrosequencing diagnostic assays have shown great utility in identifying and characterizing pulmonary drug-resistant tuberculosis (TB) infections. However, the method has yet to be evaluated for the diagnosis of drug-resistant extra-pulmonary TB (EPTB). OBJECTIVE To evaluate the performance of a pyrosequencing platform in establishing molecular drug resistance profiles for 79 clinical EPTB specimens at a referral center for drug-resistant TB in India. DESIGN Genotypic drug resistance profiles were established for all 79 non-pulmonary, culture-positive TB clinical specimens. Acid-fast bacilli smear microscopy, MGIT™ 960™ culture and drug susceptibility testing were performed on all specimens for reference. RESULTS In comparison to MGIT 960, the sensitivity and specificity of pyrosequencing in detecting drug resistance among specimens was found to be respectively 100% and 100%, 67% and 98%, and 100% and 100% for isoniazid, rifampicin, and the fluoroquinolones. No EPTB specimens were phenotypically resistant to any of the injectables, but the specificity of the assay was determined to be 100%, 98%, and 98% for amikacin, kanamycin, and capreomycin. CONCLUSIONS Pyrosequencing is a rapid, appropriate technology for the diagnosis of isoniazid-, fluoroquinolone-, and potentially injectable drug-resistant EPTB clinical specimens, and should be considered as an alternative to conventional growth-based diagnostic methods for EPTB when resistance to these drugs is suspected.
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Affiliation(s)
- S B Georghiou
- Division of Global Public Health, School of Medicine, University of California San Diego, La Jolla, California, USA
| | - K Ajbani
- Section Microbiology, Department of Laboratory Medicine, P D Hinduja National Hospital and Medical Research Centre, Mumbai, India
| | - C Rodrigues
- Section Microbiology, Department of Laboratory Medicine, P D Hinduja National Hospital and Medical Research Centre, Mumbai, India
| | - T C Rodwell
- Division of Global Public Health, School of Medicine, University of California San Diego, La Jolla, California, USA
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Garfein RS, Catanzaro DG, Rodwell TC, Avalos E, Jackson RL, Kaping J, Evasco H, Rodrigues C, Crudu V, Lin SYG, Groessl E, Groessel E, Hillery N, Trollip A, Ganiats T, Victor TC, Eisenach K, Valafar F, Channick J, Qian L, Catanzaro A. Phenotypic and genotypic diversity in a multinational sample of drug-resistant Mycobacterium tuberculosis isolates. Int J Tuberc Lung Dis 2016; 19:420-7. [PMID: 25859997 DOI: 10.5588/ijtld.14.0488] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
OBJECTIVE To develop and evaluate rapid, molecular-based drug susceptibility testing (DST) for extensively drug-resistant tuberculosis (XDR-TB), we assembled a phenotypically and genotypically diverse collection of Mycobacterium tuberculosis isolates from patients evaluated for drug resistance in four high-burden countries. METHODS M. tuberculosis isolates from India (n = 111), Moldova (n = 90), the Philippines (n = 96), and South Africa (n = 103) were selected from existing regional and national repositories to maximize phenotypic diversity for resistance to isoniazid, rifampin (RMP), moxifloxacin, ofloxacin, amikacin, kanamycin, and capreomycin. MGIT™ 960 was performed on viable isolates in one laboratory using standardized procedures and drug concentrations. Genetic diversity within drug resistance phenotypes was assessed. RESULTS Nineteen distinct phenotypes were observed among 400 isolates with complete DST results. Diversity was greatest in the Philippines (14 phenotypes), and least in South Africa (9 phenotypes). Nearly all phenotypes included multiple genotypes. All sites provided isolates resistant to injectables but susceptible to fluoroquinolones. Many patients were taking drugs to which their disease was resistant. DISCUSSION Diverse phenotypes for XDR-TB-defining drugs, including resistance to fluoroquinolones and/or injectable drugs in RMP-susceptible isolates, indicate that RMP susceptibility does not ensure effectiveness of a standard four-drug regimen. Rapid, low-cost DST assays for first- and second-line drugs are thus needed.
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Affiliation(s)
- R S Garfein
- Department of Medicine, University of California, San Diego, California, USA
| | - D G Catanzaro
- University of Arkansas, Department of Biological Sciences, Fayetteville, Arkansas, USA
| | - T C Rodwell
- Department of Medicine, University of California, San Diego, California, USA
| | - E Avalos
- Department of Family Medicine and Public Health, University of California, San Diego, California, USA
| | - R L Jackson
- Department of Medicine, University of California, San Diego, California, USA
| | - J Kaping
- Department of Medicine, University of California, San Diego, California, USA
| | - H Evasco
- Tropical Disease Foundation, Inc, Philippine Institute of Tuberculosis Building, Makati City, Philippines
| | | | - V Crudu
- Microbiology and Morphology Laboratory, Institute of Phthisiopneumology, Chisinau, Moldova
| | - S-Y G Lin
- California Department of Public Health, Richmond, California, USA
| | | | - E Groessel
- Department of Family Medicine and Public Health, University of California, San Diego, California, USA
| | - N Hillery
- Department of Family Medicine and Public Health, University of California, San Diego, California, USA
| | - A Trollip
- Department of Biomedical Sciences, Stellenbosch University, Cape Town, South Africa
| | - T Ganiats
- Department of Family Medicine and Public Health, University of California, San Diego, California, USA
| | - T C Victor
- Department of Biomedical Sciences, Stellenbosch University, Cape Town, South Africa
| | - K Eisenach
- Department of Pathology, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - F Valafar
- University of Arkansas, Department of Biological Sciences, Fayetteville, Arkansas, USA
| | - J Channick
- Department of Medicine, University of California, San Diego, California, USA
| | - L Qian
- Department of Microbiology, University of Hawaii, Honolulu, Hawaii, USA
| | - A Catanzaro
- Department of Medicine, University of California, San Diego, California, USA
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10
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Valafar F, Ramirez-Busby SM, Torres J, Paul LV, Rodwell TC, Victor TC, Rodrigues C, Gler MT, Crudu V, Catanzaro T. Prognostic significance of novel katG mutations in Mycobacterium tuberculosis. Int J Mycobacteriol 2015; 4:51-52. [PMID: 27695670 DOI: 10.1016/j.ijmyco.2014.11.043] [Citation(s) in RCA: 3] [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: 11/17/2022] Open
Abstract
BACKGROUND By using whole genome sequencing (WGS), researchers are beginning to understand the genetic diversity of Mycobacterium tuberculosis (MTB) and its consequences for the diagnosis of multidrug-resistant tuberculosis (MDR-TB) on a genomic scale. The Global Consortium for Drug-resistant TB Diagnostics (GCDD) conducted a genome scale variant analyses of 366 clinical MTB genomes (mostly MDR/XDR [extensively drug resistant]) from four countries in order to inform the development of rapid molecular diagnostics. This project has been extended by performing an evolutionary analysis of isoniazid (INH)-resistant isolates for prognostic purposes. METHODS 151 (130 INHR, 21 INHS) clinical MTB isolates from India (19: 17 INHR, 2 INHS), Moldova (48: 42 INHR, 6 INHS), the Philippines (26: 20 INHR, 6 INHS), and South Africa (58: 51 INHR, 7 INHS) were included in this study. INH drug susceptibility was determined by using MGIT 960 and WHO (World Health Organization)-recommended critical concentration of 0.1 mg/L. Isolates were sequenced using PacBio RS WGS platform. A genome-wide variant analysis was conducted using a proprietary pipeline (PacDAP) developed at San Diego State University. To infer the amino acid changes in katG that confer resistance, PAML was utilized to detect sites in silico that are under positive selection. The dN/dS method was used in combination with Bayes empirical Bayes to determine sites under positive selection and Chi-Squared analysis to determine the significance of the selected sites. RESULTS PacDAP variant analysis revealed 22 novel catalase-peroxidase (katG product) mutations. Of these, 14 were single nucleotide polymorphisms, while 8 novel mutations appeared in combination with katG S315T and/or with inhA promoter C-15T. These SNPs have not been previously reported. Additionally, 11 previously observed, but uncommon, katG mutations were also observed in these clinical isolates. These results suggest that 17 amino acids in the enzyme are under positive selective pressure; most significantly in South Africa and the Philippines. No selective pressure on codons other than 315 was observed in isolates from Moldova. Due to the low number of isolates from India, the significance of the sites under positive selection was low and no prediction for India could be made based on this study. CONCLUSIONS Eleven of the 14 SNPs are resistance conferring, and it is believed that the remaining 8 combinatorial mutations are either compensatory in nature or, in combination with known SNPs, could increase resistance levels. Positive selection results indicate a diversifying evolutionary path to resistance more in line with long tail statistics and therefore indicate a departure from the traditional point mutation (or "hotspot") model that current molecular diagnostics are based on. Positive selection pressures indicate a future with elevated diagnostic and prognostic significance of the "long tail" (i.e., alternative mechanisms of resistance) and potentially diminishing significance of the canonical mutations (especially in South Africa and the Philippines), which could have significant future implications on narrowly targeting molecular diagnostics.
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Affiliation(s)
- F Valafar
- Bioinformatics & Medical Informatics Research Center, San Diego State University, San Diego, USA
| | - S M Ramirez-Busby
- Bioinformatics & Medical Informatics Research Center, San Diego State University, San Diego, USA
| | - J Torres
- Bioinformatics & Medical Informatics Research Center, San Diego State University, San Diego, USA
| | - Lynthia V Paul
- Department of Biomedical Sciences, Stellenbosch University, Tygerberg, South Africa
| | - T C Rodwell
- Department of Medicine, University of California, San Diego, CA, USA
| | - T C Victor
- Department of Biomedical Sciences, Stellenbosch University, Tygerberg, South Africa
| | | | - M T Gler
- Tropical Disease Foundation, Makati City, Philippines
| | - V Crudu
- Microbiology and Morphology Laboratory, Institute of Phthisiopneumology, Chisinau, Republic of Moldova
| | - T Catanzaro
- Department of Medicine, University of California, San Diego, CA, USA
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11
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Trollip AP, Moore D, Coronel J, Caviedes L, Klages S, Victor T, Romancenco E, Crudu V, Ajbani K, Vineet VP, Rodrigues C, Jackson RL, Eisenach K, Garfein RS, Rodwell TC, Desmond E, Groessl EJ, Ganiats TG, Catanzaro A. Second-line drug susceptibility breakpoints for Mycobacterium tuberculosis using the MODS assay. Int J Tuberc Lung Dis 2014; 18:227-32. [PMID: 24429318 DOI: 10.5588/ijtld.13.0229] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
OBJECTIVE To establish breakpoint concentrations for the fluoroquinolones (moxifloxacin [MFX] and ofloxacin [OFX]) and injectable second-line drugs (amikacin [AMK], kanamycin [KM] and capreomycin [CPM]) using the microscopic observation drug susceptibility (MODS) assay. SETTING A multinational study conducted between February 2011 and August 2012 in Peru, India, Moldova and South Africa. DESIGN In the first phase, breakpoints for the fluoroquinolones and injectable second-line drugs (n = 58) were determined. In the second phase, MODS second-line drug susceptibility testing (DST) as an indirect test was compared to MGIT™ DST (n = 89). In the third (n = 30) and fourth (n = 156) phases, we determined the reproducibility and concordance of MODS second-line DST directly from sputum. RESULTS Breakpoints for MFX (0.5 μg/ml), OFX (1 μg/ml), AMK (2 μg/ml), KM (5 μg/ml) and CPM (2.5 μg/ml) were determined. In all phases, MODS results were highly concordant with MGIT DST. The few discrepancies suggest that the MODS breakpoint concentrations for some drugs may be too low. CONCLUSION MODS second-line DST yielded comparable results to MGIT second-line DST, and is thus a promising alternative. Further studies are needed to confirm the accuracy of the drug breakpoints and the reliability of MODS second-line DST as a direct test.
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Affiliation(s)
- A P Trollip
- Biomedical Sciences, Department of Science and Technology/National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research, Medical Research Council Centre for Molecular and Cellular Biology, Stellenbosch University, Cape Town, South Africa
| | - D Moore
- TB Centre and Department of Clinical Research, London School of Hygiene & Tropical Medicine, London, UK; Laboratorio de Investigación de Enfermedades Infecciosas, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - J Coronel
- Laboratorio de Investigación de Enfermedades Infecciosas, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - L Caviedes
- Laboratorio de Investigación de Enfermedades Infecciosas, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - S Klages
- Biomedical Sciences, Department of Science and Technology/National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research, Medical Research Council Centre for Molecular and Cellular Biology, Stellenbosch University, Cape Town, South Africa
| | - T Victor
- Biomedical Sciences, Department of Science and Technology/National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research, Medical Research Council Centre for Molecular and Cellular Biology, Stellenbosch University, Cape Town, South Africa
| | - E Romancenco
- Microbiology and Morphology Laboratory, Phthisiopneumology Institute, Chisinau, Moldova
| | - V Crudu
- Microbiology and Morphology Laboratory, Phthisiopneumology Institute, Chisinau, Moldova
| | - K Ajbani
- Department of Microbiology, Parmanand Deepchand Hinduja National Hospital and Medical Research Centre Tertiary Care Hospital, Mumbai, India
| | - V P Vineet
- Department of Microbiology, Parmanand Deepchand Hinduja National Hospital and Medical Research Centre Tertiary Care Hospital, Mumbai, India
| | - C Rodrigues
- Department of Microbiology, Parmanand Deepchand Hinduja National Hospital and Medical Research Centre Tertiary Care Hospital, Mumbai, India
| | - R L Jackson
- University of California San Diego School of Medicine, La Jolla, California, USA
| | - K Eisenach
- Department of Pathology, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - R S Garfein
- University of California San Diego School of Medicine, La Jolla, California, USA
| | - T C Rodwell
- Division of Global Public Health, University of California San Diego School of Medicine, La Jolla, California, USA
| | - E Desmond
- Mycobacteriology and Mycology Section, Microbial Diseases Laboratory, California Department of Public Health, Richmond, California, USA
| | - E J Groessl
- University of California San Diego, Veterans' Affairs San Diego Healthcare System, La Jolla, California, USA
| | - T G Ganiats
- University of California San Diego Health Services Research Center, UCSD, La Jolla, California, USA
| | - A Catanzaro
- University of California San Diego School of Medicine, La Jolla, California, USA
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12
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Yen YF, Rodwell TC, Yen MY, Shih HC, Hu BS, Li LH, Shie YH, Chuang P, Garfein RS. DOT associated with reduced all-cause mortality among tuberculosis patients in Taipei, Taiwan, 2006-2008. Int J Tuberc Lung Dis 2012; 16:178-84. [PMID: 22236917 PMCID: PMC3289585 DOI: 10.5588/ijtld.11.0034] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [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: 11/10/2022] Open
Abstract
OBJECTIVE To determine whether patients receiving directly observed treatment (DOT) had lower all-cause mortality than those treated with self-administered treatment (SAT) and to identify factors associated with mortality among tuberculosis (TB) patients. DESIGN All TB patients in Taipei, Taiwan, diagnosed between 2006 and 2008 were included in a retrospective cohort study. RESULTS Among 3624 TB patients, 45.5% received DOT, which was disproportionately offered to older patients and those with more underlying illness and severe TB disease. After controlling for patients' sociodemographic factors, clinical findings and underlying comorbidities, the odds of death were 40% lower (aOR 0.60, 95%CI 0.5-0.8) among patients treated with DOT than those on SAT. After adjusting for DOT, independent predictors of death included non-Taiwan birth, increasing age, male, unemployment, end-stage renal disease requiring dialysis, malignancy, acid-fast bacilli smear positivity and pleural effusion. CONCLUSION DOT was associated with lower all-cause mortality after controlling for confounding factors. DOT should be expanded in Taiwan to improve critical treatment outcomes among TB patients.
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Affiliation(s)
- Y-F Yen
- Section of Infectious Diseases, Taipei City Hospital, Taipei City Government, Taipei, Taiwan
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13
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Garfein RS, Lozada R, Liu L, Laniado-Laborin R, Rodwell TC, Deiss R, Alvelais J, Catanzaro A, Chiles PG, Strathdee SA. High prevalence of latent tuberculosis infection among injection drug users in Tijuana, Mexico. Int J Tuberc Lung Dis 2009; 13:626-632. [PMID: 19383197 PMCID: PMC2744313] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023] Open
Abstract
BACKGROUND We studied prevalence and correlates of latent tuberculosis infection (LTBI) among injection drug users (IDUs) in Tijuana, Mexico, where tuberculosis (TB) is endemic. METHODS IDUs aged > or =18 years were recruited via respondent-driven sampling (RDS) and underwent standardized interviews, human immunodeficiency virus (HIV) antibody testing and LTBI screening using Quanti-FERON((R))-TB Gold In-Tube, a whole-blood interferon-gamma release assay (IGRA). LTBI prevalence was estimated and correlates were identified using RDS-weighted logistic regression. RESULTS Of 1020 IDUs, 681 (67%) tested IGRA-positive and 44 (4%) tested HIV-positive. Mean age was 37 years, 88% were male and 98% were Mexican-born. IGRA positivity was associated with recruitment nearest the US border (aOR 1.64, 95%CI 1.09-2.48), increasing years of injection (aOR 1.20/5 years, 95%CI 1.07-1.34), and years lived in Tijuana (aOR 1.10/5 years, 95%CI 1.03-1.18). Speaking some English (aOR 0.38, 95%CI 0.25-0.57) and injecting most often at home in the past 6 months (aOR 0.68, 95%CI 0.45-0.99) were inversely associated with IGRA positivity. DISCUSSION Increased LTBI prevalence among IDUs in Tijuana appears to be associated with greater drug involvement. Given the high risk for HIV infection among Tijuana's IDUs, interventions are urgently needed to prevent HIV infection and treat LTBI among IDUs before these epidemics collide.
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Affiliation(s)
- R S Garfein
- University of California San Diego, School of Medicine, San Diego, California, USA
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14
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O’Connell-Rodwell CE, Wood JD, Rodwell TC, Puria S, Partan SR, Keefe R, Shriver D, Arnason BT, Hart LA. Wild elephant (Loxodonta africana) breeding herds respond to artificially transmitted seismic stimuli. Behav Ecol Sociobiol 2006. [DOI: 10.1007/s00265-005-0136-2] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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15
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Rodwell TC, Kriek NP, Bengis RG, Whyte IJ, Viljoen PC, de Vos V, Boyce WM. Prevalence of bovine tuberculosis in African buffalo at Kruger National Park. J Wildl Dis 2001; 37:258-64. [PMID: 11310876 DOI: 10.7589/0090-3558-37.2.258] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Bovine tuberculosis (BTB) was first detected in Kruger National Park (KNP) in a single African buffalo (Syncerus caffer) in 1990. In 1991/1992, 2,071 African buffalo were examined for BTB as part of a culling program that removed animals from all known herds in KNP. The prevalence of BTB in 1991/1992 was estimated to be 0%, 4.4% (+/-0.6%), and 27.1% (+/-1.4%), in the north, central, and south zones of KNP, respectively. In 1998, a stratified, two-stage cluster sampling method was used to estimate that the prevalence of BTB was 1.5% (+/-2.5%), 16% (+/-5.3%), and 38.2% (+/-6.3%), in the north, central, and south zones, respectively. This represented a significant increase in prevalence (P < or = 0.05) in the south and central zones, but not in the north zone. Continued monitoring of BTB in KNP is important for understanding disease transmission risks, potential population effects, and the efficacy of disease management strategies. The methodology and sample sizes used in 1998 are appropriate for future BTB monitoring in KNP.
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Affiliation(s)
- T C Rodwell
- Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California, Davis 95616, USA
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16
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Boyce WM, Ramey RR, Rodwell TC, Rubin ES, Singer RS. Population subdivision among desert bighorn sheep (Ovis canadensis) ewes revealed by mitochondrial DNA analysis. Mol Ecol 1999; 8:99-106. [PMID: 9919700 DOI: 10.1046/j.1365-294x.1999.00536.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We used behavioural observations and mitochondrial DNA (mtDNA) sequence analysis to examine demographic and genetic structure within and among home-range groups of desert bighorn sheep (Ovis canadensis) ewes in the Peninsular Ranges of southern California, USA. We identified substantial genetic variation in the first 515 bp of the mtDNA control region and determined that seven haplotypes were distributed in a nonrandom fashion among these ewe subpopulations. Although a significant (P < 0.01) amount of mtDNA variation (33%) was partitioned among home-range groups, we did not find strong evidence for matrilineal substructuring within these groups. Based on analyses of molecular variance, and comparisons of behavioural associations and distances between centres of activity, we concluded that within a given home-range group, bighorn sheep ewes generally associate with other ewes based on their availability rather than their matrilineal relationships. Our results also supported the conclusion that multiple ewe subpopulations exist within the Peninsular Ranges, and that these subpopulations are the most basic demographic and genetic units.
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Affiliation(s)
- W M Boyce
- Department of Pathology, Microbiology and Immunology, University of California, Davis 95616, USA.
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17
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Crosbie PR, Boyce WM, Rodwell TC. DNA sequence variation in Dermacentor hunteri and estimated phylogenies of Dermacentor spp. (Acari: Ixodidae) in the New World. J Med Entomol 1998; 35:277-288. [PMID: 9615547 DOI: 10.1093/jmedent/35.3.277] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
The genus Dermacentor is represented by 12 species in the New World. We sequenced a 300-bp portion of the mitochondrial 16S ribosomal DNA gene for 28 individual ticks representing 9 of these species and analyzed their phylogenetic relationships. Maximum parsimony, distance (neighbor-joining), and maximum likelihood were all used to resolve tree topologies. Eleven specimens of Dermacentor hunteri Bishopp representing populations across the tick's entire geographic range showed negligible genetic variation, with only single base-pair differences between each of 5 haplotypes. We found high degrees of bootstrap support (66-86%) for monophyly of the genus, but variable support for monophyly of species within the genus. D. hunteri, D. occidentalis Marx, and D. variabilis (Say) each resolved as a monophyletic taxon (79-99% support). D. andersoni Stiles and D. parumapertus Neumann formed a paraphyletic clade (99% support). D. albipictus Packard showed substantial intraspecific variation and warrants further investigation. D. imitans Warburton was distinct from all other Dermacentor spp. on all trees.
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Affiliation(s)
- P R Crosbie
- Department of Veterinary Pathology, Microbiology and Immunology, University of California, Davis 95616-8739, USA
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