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Clinical and Microbiological Characteristics of Mycobacterium kansasii Pulmonary Infections in China. Microbiol Spectr 2022; 10:e0147521. [PMID: 35019778 PMCID: PMC8754148 DOI: 10.1128/spectrum.01475-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Mycobacterium kansasii, an important opportunistic pathogen of humans, causes serious pulmonary disease. Sixty M. kansasii isolates were collected for investigating the clinical characteristics of patients with M. kansasii infections as well as drug susceptibility and genotypes of M. kansasii. More than 90% of the patients infected with M. kansasii were from eastern China. According to the internal transcribed spacers (ITS), rpoB, hsp65, and tuf, all M. kansasii isolates were classified as molecular type I, irrespective of the disease manifestation. Sixty M. kansasii isolates from China were diverse and separated into four branches. Pairwise average nucleotide identity (ANI) values for M. kansasii isolates affiliated with different genotypes were more than 85%. The earliest isolate was isolated from Jiangsu in 1983. Of the isolates, 78.3% (47/60) were isolated since 1999. All isolates were sensitive to rifabutin. All but one isolate was sensitive to clarithromycin. Sensitivity rates to rifampin, amikacin, moxifloxacin, and linezolid were 80.0%, 90.0%, 88.3%, and 91.7%, respectively. A high rate of resistance was noted for ciprofloxacin (44 isolates, 73.3%) and ethambutol (46 isolates, 76.7%). Compared with M. tuberculosis H37Rv, 12 mutations of embCA were observed in all M. kansasii isolates. All these 60 M. kansasii isolates shared identical sequences of rpoB, inhA, katG, rrl, rrs, rpsL, gyrA, and gyrB. In conclusion, M. kansasii isolates are exhibiting greater genetic diversity globally. The resistance mechanism of M. kansasii is not necessarily related to gene mutation. IMPORTANCEM. kansasii type I is the main genotype spreading worldwide. The molecular history of the global spread of type I isolates remains largely unclear. We conducted a detailed analysis of genomic evolution of global M. kansasii isolates. Our results suggest that M. kansasii isolates exhibit greater genetic diversity globally.
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Kim YG, Lee HY, Kwak N, Park JH, Kim TS, Kim MJ, Lee JS, Park SS, Yim JJ, Seong MW. Determination of Clinical Characteristics of Mycobacterium kansasii-Derived Species by Reanalysis of Isolates Formerly Reported as M. kansasii. Ann Lab Med 2021; 41:463-468. [PMID: 33824234 PMCID: PMC8041593 DOI: 10.3343/alm.2021.41.5.463] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 11/01/2020] [Accepted: 03/20/2021] [Indexed: 11/19/2022] Open
Abstract
Background Seven genotypic subtypes of Mycobacterium kansasii were recently demonstrated to represent distinct species based on phylogenomic analysis. Mycobacterium kansasii sensu stricto (formerly known as subtype 1) is most frequently associated with human diseases; only a few studies have compared the diverse clinical characteristics of M. kansasii subtypes, including their drug susceptibilities. We determined the actual incidence of infections caused by each subtype of M. kansasii and identified their clinical characteristics. Methods We subtyped isolates identified as M. kansasii over the last 10 years at a tertiary care hospital. Percent identity score of stored sequencing data was calculated using curated reference sequences of all M. kansasii subtypes. Clinical characteristics were compared between those classified as subtype 1 and other subtypes. Student's t-test, Wilcoxon rank-sum test, and Fisher's exact test were used for comparisons. Results Overall, 21.7% of the isolates were identified as species distinct from M. kansasii. The proportion of patients with subtype 1 M. kansasii infection who received treatment was significantly higher than that of patients with other subtype infections (55.3% vs. 7.7%, P=0.003). Only patients with subtype 1 infection received surgical treatment. Non-subtype 1 M. kansasii isolates showed a higher frequency of resistance to ciprofloxacin and trimethoprim/sulfamethoxazole. Conclusions Non-subtype 1 M. kansasii isolates should be separately identified in routine clinical laboratory tests for appropriate treatment selection.
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Affiliation(s)
- Young-Gon Kim
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul, Korea
| | - Hong Yeul Lee
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Seoul National University Hospital, Seoul, Korea
| | - Nakwon Kwak
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Seoul National University Hospital, Seoul, Korea
| | - Jae Hyeon Park
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul, Korea
| | - Taek Soo Kim
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul, Korea
| | - Man Jin Kim
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul, Korea
| | - Jee-Soo Lee
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul, Korea
| | - Sung-Sup Park
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul, Korea
| | - Jae-Joon Yim
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Seoul National University Hospital, Seoul, Korea.,Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Moon-Woo Seong
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul, Korea
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Pathogenic Determinants of the Mycobacterium kansasii Complex: An Unsuspected Role for Distributive Conjugal Transfer. Microorganisms 2021; 9:microorganisms9020348. [PMID: 33578772 PMCID: PMC7916490 DOI: 10.3390/microorganisms9020348] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 02/02/2021] [Accepted: 02/05/2021] [Indexed: 01/15/2023] Open
Abstract
The Mycobacterium kansasii species comprises six subtypes that were recently classified into six closely related species; Mycobacterium kansasii (formerly M. kansasii subtype 1), Mycobacterium persicum (subtype 2), Mycobacterium pseudokansasii (subtype 3), Mycobacterium ostraviense (subtype 4), Mycobacterium innocens (subtype 5) and Mycobacterium attenuatum (subtype 6). Together with Mycobacterium gastri, they form the M. kansasii complex. M. kansasii is the most frequent and most pathogenic species of the complex. M. persicum is classically associated with diseases in immunosuppressed patients, and the other species are mostly colonizers, and are only very rarely reported in ill patients. Comparative genomics was used to assess the genetic determinants leading to the pathogenicity of members of the M. kansasii complex. The genomes of 51 isolates collected from patients with and without disease were sequenced and compared with 24 publicly available genomes. The pathogenicity of each isolate was determined based on the clinical records or public metadata. A comparative genomic analysis showed that all M. persicum, M. ostraviense, M innocens and M. gastri isolates lacked the ESX-1-associated EspACD locus that is thought to play a crucial role in the pathogenicity of M. tuberculosis and other non-tuberculous mycobacteria. Furthermore, M. kansasii was the only species exhibiting a 25-Kb-large genomic island encoding for 17 type-VII secretion system-associated proteins. Finally, a genome-wide association analysis revealed that two consecutive genes encoding a hemerythrin-like protein and a nitroreductase-like protein were significantly associated with pathogenicity. These two genes may be involved in the resistance to reactive oxygen and nitrogen species, a required mechanism for the intracellular survival of bacteria. Three non-pathogenic M. kansasii lacked these genes likely due to two distinct distributive conjugal transfers (DCTs) between M. attenuatum and M. kansasii, and one DCT between M. persicum and M. kansasii. To our knowledge, this is the first study linking DCT to reduced pathogenicity.
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Khosravi AD, Asban B, Hashemzadeh M, Nashibi R. Molecular Identification, and Characterization of Mycobacterium kansasii Strains Isolated from Four Tuberculosis Regional Reference Laboratories in Iran During 2016-2018. Infect Drug Resist 2020; 13:2171-2180. [PMID: 32753913 PMCID: PMC7354002 DOI: 10.2147/idr.s245295] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 06/04/2020] [Indexed: 12/31/2022] Open
Abstract
Background Non-tuberculous mycobacterial (NTM) infections are growing concern in many countries around the globe including Iran. Among them, Mycobacterium kansasii (M. kansasii) causes both pulmonary and extra-pulmonary infections. Despite the high prevalence of M. kansasii isolates in Iran, unfortunately little is known about the epidemiological aspects of M. kansasii infection. Hence, the aim of the present study was to investigate the molecular identification, determination of subtypes variation and geographic distribution of clinical isolates of M. kansasii isolates. Methods In the present study, 108 clinical pulmonary isolates suspected to NTM were collected from four Tuberculosis Regional Reference Laboratories in Iran during 2016–2018. The isolates were confirmed as NTM using conventional and molecular methods. Among them, M. kansasii isolates were subjected to rpoB gene sequencing. For determination of subtyping of M. kansasii isolates, polymerase chain reaction-restriction enzyme analysis (PCR-REA) based on the hsp65 gene was performed. Results Based on the rpoB gene sequence analysis, 33 (30.5%) isolates were identified as M. kansasii species, compared to 31 (28.7%) isolates using phenotypic methods. The subtype I was the most frequent subtype (n=24; 72.7%), followed by subtype II (n=8; 24.2%). Conclusion We indicated that the rate of M. kansasii isolation with clinical significance appears to be increasing in Iran, especially in highly industrialized cities. The high rate of M. kansasii subtype I may suggest that this genotype has a particular potency for colonization, and a higher epidemiological potential for causing infection in humans. More studies are needed to provide a better understanding of the biology and pathogenicity of M. kansasii subtype I.
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Affiliation(s)
- Azar Dokht Khosravi
- Department of Microbiology, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.,Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Bahareh Asban
- Department of Microbiology, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Mohammad Hashemzadeh
- Department of Microbiology, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.,Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Roohangiz Nashibi
- Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.,Infectious Diseases & Tropical Medicine Ward, Razi Teaching Hospital, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
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Jagielski T, Borówka P, Bakuła Z, Lach J, Marciniak B, Brzostek A, Dziadek J, Dziurzyński M, Pennings L, van Ingen J, Žolnir-Dovč M, Strapagiel D. Genomic Insights Into the Mycobacterium kansasii Complex: An Update. Front Microbiol 2020; 10:2918. [PMID: 32010067 PMCID: PMC6974680 DOI: 10.3389/fmicb.2019.02918] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2019] [Accepted: 12/04/2019] [Indexed: 12/31/2022] Open
Abstract
Only very recently, has it been proposed that the hitherto existing Mycobacterium kansasii subtypes (I-VI) should be elevated, each, to a species rank. Consequently, the former M. kansasii subtypes have been denominated as Mycobacterium kansasii (former type I), Mycobacterium persicum (II), Mycobacterium pseudokansasii (III), Mycobacterium innocens (V), and Mycobacterium attenuatum (VI). The present work extends the recently published findings by using a three-pronged computational strategy, based on the alignment fraction-average nucleotide identity, genome-to-genome distance, and core-genome phylogeny, yet essentially independent and much larger sample, and thus delivers a more refined and complete picture of the M. kansasii complex. Furthermore, five canonical taxonomic markers were used, i.e., 16S rRNA, hsp65, rpoB, and tuf genes, as well as the 16S-23S rRNA intergenic spacer region (ITS). The three major methods produced highly concordant results, corroborating the view that each M. kansasii subtype does represent a distinct species. This work not only consolidates the position of five of the currently erected species, but also provides a description of the sixth one, i.e., Mycobacterium ostraviense sp. nov. to replace the former subtype IV. By showing a close genetic relatedness, a monophyletic origin, and overlapping phenotypes, our findings support the recognition of the M. kansasii complex (MKC), accommodating all M. kansasii-derived species and Mycobacterium gastri. None of the most commonly used taxonomic markers was shown to accurately distinguish all the MKC species. Likewise, no species-specific phenotypic characteristics were found allowing for species differentiation within the complex, except the non-photochromogenicity of M. gastri. To distinguish, most reliably, between the MKC species, and between M. kansasii and M. persicum in particular, whole-genome-based approaches should be applied. In the absence of clear differences in the distribution of the virulence-associated region of difference 1 genes among the M. kansasii-derived species, the pathogenic potential of each of these species can only be speculatively assessed based on their prevalence among the clinically relevant population. Large-scale molecular epidemiological studies are needed to provide a better understanding of the clinical significance and pathobiology of the MKC species. The results of the in vitro drug susceptibility profiling emphasize the priority of rifampicin administration in the treatment of MKC-induced infections, while undermining the use of ethambutol, due to a high resistance to this drug.
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Affiliation(s)
- Tomasz Jagielski
- Department of Applied Microbiology, Faculty of Biology, Institute of Microbiology, University of Warsaw, Warsaw, Poland
| | - Paulina Borówka
- Biobank Lab, Department of Molecular Biophysics, Faculty of Biology and Environmental Protection, University of Łódź, Łódź, Poland
- Department of Anthropology, Faculty of Biology and Environmental Protection, University of Łódź, Łódź, Poland
| | - Zofia Bakuła
- Department of Applied Microbiology, Faculty of Biology, Institute of Microbiology, University of Warsaw, Warsaw, Poland
| | - Jakub Lach
- Biobank Lab, Department of Molecular Biophysics, Faculty of Biology and Environmental Protection, University of Łódź, Łódź, Poland
- BBMRI.pl Consortium, Wroclaw, Poland
| | - Błażej Marciniak
- Biobank Lab, Department of Molecular Biophysics, Faculty of Biology and Environmental Protection, University of Łódź, Łódź, Poland
- BBMRI.pl Consortium, Wroclaw, Poland
| | - Anna Brzostek
- Institute of Medical Biology, Polish Academy of Sciences, Łódź, Poland
| | - Jarosław Dziadek
- Institute of Medical Biology, Polish Academy of Sciences, Łódź, Poland
| | - Mikołaj Dziurzyński
- Department of Bacterial Genetics, Faculty of Biology, Institute of Microbiology, University of Warsaw, Warsaw, Poland
| | - Lian Pennings
- Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, Netherlands
| | - Jakko van Ingen
- Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, Netherlands
| | - Manca Žolnir-Dovč
- Laboratory for Mycobacteria, University Clinic of Respiratory and Allergic Diseases, Golnik, Slovenia
| | - Dominik Strapagiel
- Biobank Lab, Department of Molecular Biophysics, Faculty of Biology and Environmental Protection, University of Łódź, Łódź, Poland
- BBMRI.pl Consortium, Wroclaw, Poland
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da Silva WMV, Duarte MH, de Carvalho LD, de Souza Caldas PC, Campos CED, Redner P, Ramos JP. Discovery of a novel Mycobacterium asiaticum PRA-hsp65 pattern. INFECTION GENETICS AND EVOLUTION 2019; 76:104040. [PMID: 31533063 DOI: 10.1016/j.meegid.2019.104040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 09/07/2019] [Accepted: 09/12/2019] [Indexed: 11/16/2022]
Abstract
Twenty-one pulmonary sputum samples from nine Brazilian patients were analyzed by the PRA-hsp65 method for identification of Mycobacterium species and the results were compared by sequencing. We reported a mutation at the position 381, that generates a suppression cutting site in the BstEII enzyme, thus leading to a new PRA-hsp65 pattern for M. asiaticum identification.
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Affiliation(s)
- William Marco Vicente da Silva
- National Reference Laboratory for Tuberculosis, Centro de Referência Professor Hélio Fraga, Escola Nacional de Saúde Pública, Fiocruz, RJ, Brazil.
| | - Mayara Henrique Duarte
- National Reference Laboratory for Tuberculosis, Centro de Referência Professor Hélio Fraga, Escola Nacional de Saúde Pública, Fiocruz, RJ, Brazil
| | - Luciana Distásio de Carvalho
- National Reference Laboratory for Tuberculosis, Centro de Referência Professor Hélio Fraga, Escola Nacional de Saúde Pública, Fiocruz, RJ, Brazil
| | - Paulo Cesar de Souza Caldas
- National Reference Laboratory for Tuberculosis, Centro de Referência Professor Hélio Fraga, Escola Nacional de Saúde Pública, Fiocruz, RJ, Brazil
| | - Carlos Eduardo Dias Campos
- National Reference Laboratory for Tuberculosis, Centro de Referência Professor Hélio Fraga, Escola Nacional de Saúde Pública, Fiocruz, RJ, Brazil
| | - Paulo Redner
- National Reference Laboratory for Tuberculosis, Centro de Referência Professor Hélio Fraga, Escola Nacional de Saúde Pública, Fiocruz, RJ, Brazil
| | - Jesus Pais Ramos
- National Reference Laboratory for Tuberculosis, Centro de Referência Professor Hélio Fraga, Escola Nacional de Saúde Pública, Fiocruz, RJ, Brazil
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Tagini F, Aeby S, Bertelli C, Droz S, Casanova C, Prod'hom G, Jaton K, Greub G. Phylogenomics reveal that Mycobacterium kansasii subtypes are species-level lineages. Description of Mycobacterium pseudokansasii sp. nov., Mycobacterium innocens sp. nov. and Mycobacterium attenuatum sp. nov. Int J Syst Evol Microbiol 2019; 69:1696-1704. [PMID: 30950782 DOI: 10.1099/ijsem.0.003378] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Among the species Mycobacterium kansasii, seven subtypes have been previously reported based on the PCR and the restriction fragment length polymorphism of the gene hsp65. Here, we used whole-genome sequencing to refine M. kansasii taxonomy and correct multiple inconsistencies. Average nucleotide identity (ANI) values between M. kansasii subtypes ranged from 88.4 to 94.2 %, lower than the accepted 95-96 % cut-off for species delineation. In addition, Mycobacterium gastri was closer to the M. kansasii subtypes 1, 2, 3, 4 and 5 than M. kansasii subtype 6. The recently described species Mycobacterium persicum shared 99.77 % ANI with M. kansasii subtype 2. Consistent with the ANI results, the digital DNA-DNA hybridization value was below the 70 % threshold for species delineation between subtypes and above it within subtypes as well as between subtype 2 and M. persicum. Furthermore, core-genome phylogeny confirmed the current M. kansasii species to be polyphyletic. Hence, we propose (i) Mycobacterium pseudokansasii sp. nov., replacing subtype 3, with the type strain MK142T(=CCUG 72128T=DSM 107152T), (ii) Mycobacterium innocens sp. nov., replacing subtype 5, with the type strain MK13T (=CCUG 72126T=DSM 107161T), and (iii) Mycobacterium attenuatum sp. nov., replacing subtype 6, with the type strain MK41T(=CCUG 72127T=DSM 107153T). Subtype 4 represents a new species-level lineage based on the genomic data but no strain was available. No genome sequence or strain was available for subtype 7. The proposed nomenclature will facilitate the identification of the most pathogenic subtype 1 as M. kansasii by clinicians while the new species names suggest the attenuated pathogenicity of the other subtypes.
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Affiliation(s)
- Florian Tagini
- 1Institute of Microbiology, Department of Laboratory Medicine, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Sébastien Aeby
- 1Institute of Microbiology, Department of Laboratory Medicine, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Claire Bertelli
- 1Institute of Microbiology, Department of Laboratory Medicine, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Sara Droz
- 2Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Carlo Casanova
- 2Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Guy Prod'hom
- 1Institute of Microbiology, Department of Laboratory Medicine, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Katia Jaton
- 1Institute of Microbiology, Department of Laboratory Medicine, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Gilbert Greub
- 1Institute of Microbiology, Department of Laboratory Medicine, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland.,3Division of Infectious Diseases, Department of Medicine, Lausanne University Hospital, Lausanne, Switzerland
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Bakuła Z, Kościuch J, Safianowska A, Proboszcz M, Bielecki J, van Ingen J, Krenke R, Jagielski T. Clinical, radiological and molecular features of Mycobacterium kansasii pulmonary disease. Respir Med 2018; 139:91-100. [PMID: 29858008 DOI: 10.1016/j.rmed.2018.05.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 04/26/2018] [Accepted: 05/08/2018] [Indexed: 12/21/2022]
Abstract
BACKGROUND Studies concerning sociodemographic, clinical, and laboratory features of Mycobacterium kansasii pulmonary disease are few and based on small patient cohorts. The objective of the study was to evaluate characteristics of patients from whom M. kansasii respiratory isolates were recovered and to provide a detailed description of M. kansasii disease. BASIC PROCEDURES Retrospective review of electronic medical records of all patients for whom at least one positive M. kansasii culture was obtained at the Department of Internal Medicine, Pulmonology and Allergology of the Warsaw Medical University between the year 2000 and 2015. Patients were categorized as having mycobacterial disease or as isolation cases based on the American Thoracic Society and Infectious Diseases Society of America (ATS/IDSA) diagnostic criteria. MAIN FINDINGS The study comprised of 105 patients (63 females, 42 males, mean age 64.6 ± 17.8 years). Of these, 86 (81.9%) were diagnosed as having M. kansasii disease. The proportion of positive smear microscopy was significantly higher in patients with M. kansasii disease compared to M. kansasii isolation (P < 0.001). There were no statistically significant differences between M. kansasii disease and isolation cases in terms of clinical symptoms or comorbidities. Patients with M. kansasii disease presented most commonly (43/86, 50%) fibro-cavitary disease upon radiology. Lesion distribution usually showed bilateral upper lobe involvement. Among the 191 isolates genotyped, all were identified as M. kansasii type I. PRINCIPAL CONCLUSIONS The findings from this study support the relaxation of the diagnostic criteria for the definition of M. kansasii disease, set forth by ATS/IDSA. Molecular typing did not differentiate isolates from patients with true disease from those with isolation only; the role of bacterial virulence factors thus remains elusive.
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Affiliation(s)
- Zofia Bakuła
- Department of Applied Microbiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland.
| | - Justyna Kościuch
- Department of Internal Medicine, Pulmonary Diseases & Allergy, Medical University of Warsaw, Warsaw, Poland.
| | - Aleksandra Safianowska
- Department of Internal Medicine, Pulmonary Diseases & Allergy, Medical University of Warsaw, Warsaw, Poland.
| | - Małgorzata Proboszcz
- Department of Internal Medicine, Pulmonary Diseases & Allergy, Medical University of Warsaw, Warsaw, Poland.
| | - Jacek Bielecki
- Department of Applied Microbiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland.
| | - Jakko van Ingen
- Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, The Netherlands.
| | - Rafał Krenke
- Department of Internal Medicine, Pulmonary Diseases & Allergy, Medical University of Warsaw, Warsaw, Poland.
| | - Tomasz Jagielski
- Department of Applied Microbiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland.
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9
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Murugaiyan J, Lewin A, Kamal E, Bakuła Z, van Ingen J, Ulmann V, Unzaga Barañano MJ, Humięcka J, Safianowska A, Roesler UH, Jagielski T. MALDI Spectra Database for Rapid Discrimination and Subtyping of Mycobacterium kansasii. Front Microbiol 2018; 9:587. [PMID: 29670585 PMCID: PMC5893902 DOI: 10.3389/fmicb.2018.00587] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 03/14/2018] [Indexed: 11/13/2022] Open
Abstract
Mycobacterium kansasii is an emerging non-tuberculous mycobacterial (NTM) pathogen capable of causing severe lung disease. Of the seven currently recognized M. kansasii genotypes (I-VII), genotypes I and II are most prevalent and have been associated with human disease, whereas the other five (III-VII) genotypes are predominantly of environmental origin and are believed to be non-pathogenic. Subtyping of M. kansasii serves as a valuable tool to guide clinicians in pursuing diagnosis and to initiate the proper timely treatment. Most of the previous rapid diagnostic tests for mycobacteria employing the matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) technology focused on species-level identification. The purpose of this study was to establish MALDI-TOF MS reference spectra database for discrimination of M. kansasii at the genotype level. A panel of 32 strains, representatives of M. kansasii genotypes I-VI were selected, whole cell proteins extracted and measured with MALDI-TOF MS. A unique main spectra (MSP) library was created using MALDI Biotyper Compass Explorer software. The spectra reproducibility was assessed by computing composite correlation index and MSPs cross-matching. One hundred clinical M. kansasii isolates used for testing of the database resulted in 90% identification at genus-level, 7% identification at species-level and 2% identification was below the threshold of log score value 1.7, of which all were correct at genotype level. One strain could not be identified. On the other hand, 37% of strains were identified at species level, 40% at genus level and 23% was not identified with the manufacturer's database. The MALDI-TOF MS was proven a rapid and robust tool to detect and differentiate between M. kansasii genotypes. It is concluded that MALDI-TOF MS has a potential to be incorporated into the routine diagnostic workflow of M. kansasii and possibly other NTM species.
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Affiliation(s)
- Jayaseelan Murugaiyan
- Centre for Infectious Medicine, Institute of Animal Hygiene and Environmental Health, Freie Universität Berlin, Berlin, Germany
| | - Astrid Lewin
- Division 16, Mycotic and Parasitic Agents and Mycobacteria, Robert Koch Institute, Berlin, Germany
| | - Elisabeth Kamal
- Division 16, Mycotic and Parasitic Agents and Mycobacteria, Robert Koch Institute, Berlin, Germany
| | - Zofia Bakuła
- Department of Applied Microbiology, Faculty of Biology, Institute of Microbiology, University of Warsaw, Warsaw, Poland
| | - Jakko van Ingen
- Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, Netherlands
| | - Vit Ulmann
- Institute of Public Health, Ostrava, Czechia
| | | | - Joanna Humięcka
- Hospital for Infectious Diseases in Warsaw, Medical University of Warsaw, Warsaw, Poland
| | - Aleksandra Safianowska
- Department of Internal Medicine, Pulmonology, and Allergology, Medical University of Warsaw, Warsaw, Poland
| | - Uwe H Roesler
- Centre for Infectious Medicine, Institute of Animal Hygiene and Environmental Health, Freie Universität Berlin, Berlin, Germany
| | - Tomasz Jagielski
- Department of Applied Microbiology, Faculty of Biology, Institute of Microbiology, University of Warsaw, Warsaw, Poland
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10
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Drug Susceptibility Profiling and Genetic Determinants of Drug Resistance in Mycobacterium kansasii. Antimicrob Agents Chemother 2018; 62:AAC.01788-17. [PMID: 29437627 DOI: 10.1128/aac.01788-17] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Accepted: 01/20/2018] [Indexed: 11/20/2022] Open
Abstract
Very few studies have examined drug susceptibility of Mycobacterium kansasii, and they involve a limited number of strains. The purpose of this study was to determine drug susceptibility profiles of M. kansasii isolates representing a spectrum of species genotypes (subtypes) with two different methodologies, i.e., broth microdilution and Etest assays. To confirm drug resistance, drug target genes were sequenced. A collection of 85 M. kansasii isolates, including representatives of eight different subtypes (I to VI, I/II, and IIB) from eight countries, was used. Drug susceptibility against 13 and 8 antimycobacterial agents was tested by using broth microdilution and Etest, respectively. For drug-resistant or high-MIC isolates, eight structural genes (rrl, katG, inhA, embB, rrs, rpsL, gyrA, and gyrB) and one regulatory region (embCA) were PCR amplified and sequenced in the search for resistance-associated mutations. All isolates tested were susceptible to rifampin (RIF), amikacin (AMK), co-trimoxazole (SXT), rifabutin (RFB), moxifloxacin (MXF), and linezolid (LZD) according to the microdilution method. Resistance to ethambutol (EMB), ciprofloxacin (CIP), and clarithromycin (CLR) was found in 83 (97.7%), 17 (20%), and 1 (1.2%) isolate, respectively. The calculated concordance between the Etest and dilution method was 22.6% for AMK, 4.8% for streptomycin (STR), 3.2% for CLR, and 1.6% for RIF. For EMB, INH, and SXT, not even a single MIC value determined by one method equaled that by the second method. The only mutations disclosed were A2266C transversion at the rrl gene (CLR-resistant strain) and A128G transition at the rpsL gene (strain with STR MIC of >64 mg/liter). In conclusion, eight drugs, including RIF, CLR, AMK, SXT, RFB, MXF, LZD, and ethionamide (ETO), showed high in vitro activity against M. kansasii isolates. Discrepancies of the results between the reference microdilution method and Etest preclude the use of the latter for drug susceptibility determination in M. kansasii Drug resistance in M. kansasii may have different genetic determinants than resistance to the same drugs in M. tuberculosis.
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Bakuła Z, Brzostek A, Borówka P, Żaczek A, Szulc-Kiełbik I, Podpora A, Parniewski P, Strapagiel D, Dziadek J, Proboszcz M, Bielecki J, van Ingen J, Jagielski T. Molecular typing of Mycobacterium kansasii using pulsed-field gel electrophoresis and a newly designed variable-number tandem repeat analysis. Sci Rep 2018; 8:4462. [PMID: 29535391 PMCID: PMC5849605 DOI: 10.1038/s41598-018-21562-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 02/06/2018] [Indexed: 11/09/2022] Open
Abstract
Molecular epidemiological studies of Mycobacterium kansasii are hampered by the lack of highly-discriminatory genotyping modalities. The purpose of this study was to design a new, high-resolution fingerprinting method for M. kansasii. Complete genome sequence of the M. kansasii ATCC 12478 reference strain was searched for satellite-like repetitive DNA elements comprising tandem repeats. A total of 24 variable-number tandem repeat (VNTR) loci were identified with potential discriminatory capacity. Of these, 17 were used to study polymorphism among 67 M. kansasii strains representing six subtypes (I-VI). The results of VNTR typing were compared with those of pulsed-field gel electrophoresis (PFGE) with AsnI digestion. Six VNTRs i.e. (VNTR 1, 2, 8, 14, 20 and 23) allow to differentiate analyzed strains with the same discriminatory capacities as use of a 17-loci panel. VNTR typing and PFGE in conjunction revealed 45 distinct patterns, including 11 clusters with 33 isolates and 34 unique patterns. The Hunter-Gaston's discriminatory index was 0.95 and 0.66 for PFGE and VNTR typing respectively, and 0.97 for the two methods combined. In conclusion, this study delivers a new typing scheme, based on VNTR polymorphism, and recommends it as a first-line test prior to PFGE analysis in a two-step typing strategy for M. kansasii.
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Affiliation(s)
- Zofia Bakuła
- Department of Applied Microbiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Anna Brzostek
- Institute of Medical Biology, Polish Academy of Sciences, Łódź, Poland
| | - Paulina Borówka
- Department of Anthropology, University of Łódź, Łódź, Poland
| | - Anna Żaczek
- Department of Biochemistry and Cell Biology, University of Rzeszów, Rzeszów, Poland
| | | | - Agata Podpora
- Department of Applied Microbiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Paweł Parniewski
- Institute of Medical Biology, Polish Academy of Sciences, Łódź, Poland
| | - Dominik Strapagiel
- Biobank Lab, Department of Molecular Biophysics, Faculty of Biology and Environmental Protection, University of Łódź, Łódź, Poland
| | - Jarosław Dziadek
- Institute of Medical Biology, Polish Academy of Sciences, Łódź, Poland
| | - Małgorzata Proboszcz
- Department of Internal Medicine, Pulmonary Diseases and Allergy, Medical University of Warsaw, Warsaw, Poland
| | - Jacek Bielecki
- Department of Applied Microbiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Jakko van Ingen
- Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Tomasz Jagielski
- Department of Applied Microbiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland.
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Draft Genome Sequences of Mycobacterium kansasii Clinical Strains. GENOME ANNOUNCEMENTS 2017; 5:5/22/e00406-17. [PMID: 28572311 PMCID: PMC5454194 DOI: 10.1128/genomea.00406-17] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Mycobacterium kansasii is a nontuberculous mycobacterial (NTM) pathogen, frequently isolated from clinical samples and responsible for a large part of NTM infections in the human population. Here, we report the draft genome sequences of 12 M. kansasii strains isolated from clinical and host-associated sources from the Netherlands, Germany, and Poland.
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Draft Genome Sequences of Mycobacterium kansasii Strains 1010001454, 1010001458, 1010001468, 1010001493, 1010001495, and 1010001469, Isolated from Environmental Sources. GENOME ANNOUNCEMENTS 2016; 4:4/3/e00456-16. [PMID: 27257194 PMCID: PMC4891640 DOI: 10.1128/genomea.00456-16] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Mycobacterium kansasii belongs to the nontuberculous mycobacteria (NTM) and causes opportunistic infections with both pulmonary and extrapulmonary manifestations. Here, we report the draft genome sequences of six environmental M. kansasii strains, designated 1010001495 (type I), 1010001469 (type II), 1010001468 (type III), 1010001458 (type IV), 1010001454 (type V), and 1010001493 (type V), originally isolated in five different European countries.
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