Heterogeneity and clonality among isolates of Mycobacterium kansasii: implications for epidemiological and pathogenicity studies

Drug susceptibility profiling of pulmonary Mycobacterium kansasii and its correlation with treatment outcome

OBJECTIVES:

With the introduction of newer molecular diagnostic tools to identify Mycobacterium tuberculosis, an increasing number of nontuberculous mycobacterium (NTM) is being identified. However, the drug resistance pattern of the NTM species identified is less explored. The objective of this study is to study the drug resistance patterns of Mycobacterium kansasii species isolated in a tuberculosis-endemic setting at South India.

METHODS:

A wide profile of NTM species were reported earlier from a prospective cohort of adults during 2017–2020. Out of this profile, a total of 22 M. kansasii species were subjected to drug susceptibility testing by two different methods: proportion sensitivity testing method and Sensititre testing method.

RESULTS:

Out of the 18 strains of M. kansasii subjected to Sensititre method of testing, the resistance pattern was demonstrated to be high for doxycycline (13) followed by rifampicin and trimethoprim/sulfamethoxazole (7). Out of the 22 strains subjected to proportion sensitivity testing method, 20 and 10 were resistant to isoniazid and ethambutol, respectively.

CONCLUSION:

There was a poor correlation between the treatment outcome and the resistance pattern of the antibiotics tested. With increasing numbers of NTM being reported, early and correct identification of NTM species is essential for the prompt initiation of appropriate treatment to achieve better outcome.

A Murine Model of Mycobacterium kansasii Infection Reproducing Necrotic Lung Pathology Reveals Considerable Heterogeneity in Virulence of Clinical Isolates

Among non-tuberculous mycobacteria, Mycobacterium kansasii is one of the most pathogenic, able to cause pulmonary disease indistinguishable from tuberculosis in immunocompetent susceptible adults. The lack of animal models that reproduce human-like lung disease, associated with the necrotic lung pathology, impairs studies of M. kansasii virulence and pathogenicity. In this study, we examined the ability of the C57BL/6 mice, intratracheally infected with highly virulent M. kansasii strains, to produce a chronic infection and necrotic lung pathology. As a first approach, we evaluated ten M. kansasii strains isolated from Brazilian patients with pulmonary disease and the reference strain M. kansasii ATCC 12478 for virulence-associated features in macrophages infected in vitro; five of these strains differing in virulence were selected for in vivo analysis. Highly virulent isolates induced progressive lung disease in mice, forming large encapsulated caseous granulomas in later stages (120–150 days post-infection), while the low-virulent strain was cleared from the lungs by day 40. Two strains demonstrated increased virulence, causing premature death in the infected animals. These data demonstrate that C57BL/6 mice are an excellent candidate to investigate the virulence of M. kansasii isolates. We observed considerable heterogeneity in the virulence profile of these strains, in which the presence of highly virulent strains allowed us to establish a clinically relevant animal model. Comparing public genomic data between Brazilian isolates and isolates from other geographic regions worldwide demonstrated that at least some of the highly pathogenic strains isolated in Brazil display remarkable genomic similarities with the ATCC strain 12478 isolated in the United States 70 years ago (less than 100 SNPs of difference), as well as with some recent European clinical isolates. These data suggest that few pathogenic clones have been widely spread within M. kansasii population around the world.

Determination of Clinical Characteristics of Mycobacterium kansasii-Derived Species by Reanalysis of Isolates Formerly Reported as M. kansasii

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.

A Small Protein but with Diverse Roles: A Review of EsxA in Mycobacterium-Host Interaction

As a major effector of the ESX-1 secretion system, EsxA is essential for the virulence of pathogenic mycobacteria, such as Mycobacterium tuberculosis (Mtb) and Mycobacterium marinum (Mm). EsxA possesses an acidic pH-dependent membrane permeabilizing activity and plays an essential role by mediating mycobacterial escape from the phagosome and translocation to the cytosol for intracellular replication. Moreover, EsxA regulates host immune responses as a potent T-cell antigen and a strong immunoregulator. EsxA interacts with multiple cellular proteins and stimulates several signal pathways, such as necrosis, apoptosis, autophagy, and antigen presentation. Interestingly, there is a co-dependency in the expression and secretion of EsxA and other mycobacterial factors, which greatly increases the complexity of dissecting the precise roles of EsxA and other factors in mycobacterium-host interaction. In this review, we summarize the current understandings of the roles and functions of EsxA in mycobacterial infection and discuss the challenges and future directions.

Population genomics provides insights into the evolution and adaptation to humans of the waterborne pathogen Mycobacterium kansasii

Mycobacterium kansasii can cause serious pulmonary disease. It belongs to a group of closely-related species of non-tuberculous mycobacteria known as the M. kansasii complex (MKC). Here, we report a population genomics analysis of 358 MKC isolates from worldwide water and clinical sources. We find that recombination, likely mediated by distributive conjugative transfer, has contributed to speciation and on-going diversification of the MKC. Our analyses support municipal water as a main source of MKC infections. Furthermore, nearly 80% of the MKC infections are due to closely-related M. kansasii strains, forming a main cluster that apparently originated in the 1900s and subsequently expanded globally. Bioinformatic analyses indicate that several genes involved in metabolism (e.g., maintenance of the methylcitrate cycle), ESX-I secretion, metal ion homeostasis and cell surface remodelling may have contributed to M. kansasii's success and its ongoing adaptation to the human host.

Pathogenic Determinants of the Mycobacterium kansasii Complex: An Unsuspected Role for Distributive Conjugal Transfer

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.

Genomic Insights Into the Mycobacterium kansasii Complex: An Update

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.

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

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 MK142^T(=CCUG 72128^T=DSM 107152^T), (ii) Mycobacterium innocens sp. nov., replacing subtype 5, with the type strain MK13^T (=CCUG 72126^T=DSM 107161^T), and (iii) Mycobacterium attenuatum sp. nov., replacing subtype 6, with the type strain MK41^T(=CCUG 72127^T=DSM 107153^T). 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.

Nontuberculous mycobacteria: Insights on taxonomy and evolution

Seventy years have passed since Ernest H. Runyon presented a phenotypic classification approach for nontuberculous mycobacteria (NTM), primarily as a starting point in trying to understand their clinical relevance. From numerical taxonomy (biochemical testing) to 16S rRNA gene sequencing to whole genome sequencing (WGS), our understanding of NTM has also evolved. Novel species are described at a rapid pace, while taxonomical relationships are re-defined in large part due to the accessibility of WGS. The evolutionary course of clonal complexes within species is better known for some NTM and less for others. In contrast with M. tuberculosis, much is left to learn about NTM as a whole.

NK Cell-Derived IFN-γ Protects against Nontuberculous Mycobacterial Lung Infection

In developed countries, pulmonary nontuberculous mycobacteria (NTM) infections are more prevalent than Mycobacterium tuberculosis infections. Given the differences in the pathogenesis of NTM and M. tuberculosis infections, separate studies are needed to investigate the pathological effects of NTM pathogens. Our previous study showed that anti-IFN-γ autoantibodies are detected in NTM-infected patients. However, the role of NK cells and especially NK cell-derived IFN-γ in this context has not been studied in detail. In the current study, we show that NK1.1 cell depletion increases bacterial load and mortality in a mouse model of pulmonary NTM infection. NK1.1 cell depletion exacerbates NTM-induced pathogenesis by reducing macrophage phagocytosis, dendritic cell development, cytokine production, and lung granuloma formation. Similar pathological phenomena are observed in IFN-γ-deficient (IFN-γ^-/-) mice following NTM infection, and adoptive transfer of wild-type NK cells into IFN-γ^-/- mice considerably reduces NTM pathogenesis. Injection of rIFN-γ also prevents NTM-induced pathogenesis in IFN-γ^-/- mice. We observed that NK cells represent the main producers of IFN-γ in the lungs and production starts as soon as 1 d postinfection. Accordingly, injection of rIFN-γ into IFN-γ^-/- mice 1 d (but not 2 wk) postinfection significantly improves immunity against NTM infection. NK cells also stimulate mycobacterial killing and IL-12 production by macrophages. Our results therefore indicate that IFN-γ production by NK cells plays an important role in activating and enhancing innate and adaptive immune responses at early stages of pulmonary NTM infection.

Whole genome sequence of Mycobacterium kansasii isolates of the genotype 1 from Brazilian patients with pulmonary disease demonstrates considerable heterogeneity

Mycobacterium kansasii is an opportunistic pathogen and one of the most commonly encountered species in individuals with lung disease. We here report the complete genome sequence of 12 clinical isolates of M. kansasii from patients with pulmonary disease in Brazil.

Clinical, radiological and molecular features of Mycobacterium kansasii pulmonary disease

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.

MALDI Spectra Database for Rapid Discrimination and Subtyping of Mycobacterium kansasii

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.

Molecular typing of Mycobacterium kansasii using pulsed-field gel electrophoresis and a newly designed variable-number tandem repeat analysis

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.

Mycobacterium kansasii Subtype I Is Associated With Clarithromycin Resistance in China

Mycobacterium kansasii is the second most common cause of slowly growing non-tuberculous mycobacteria diseases in China. The aim of the present study was to analyze M. kansasii subtypes isolated from patients in China, and to explore the antimicrobial susceptibility of the differentiation among these diverse subtypes. A total of 78 M. kansasii strains from 16 provinces of China were enrolled in this study. Amikacin (AMK) was the most highly active against M. kansasii strains, and only 4 isolates (5.1%) exhibited in vitro resistance to AMK. The percentage of levofloxacin (LFX) resistant strains among the 78 M. kansasii isolates was 39.7% (31/78), which was significantly higher than that of moxifloxacin (16.7%, P = 0.001) and gatifloxacin (19.2%, P = 0.005). By using PCR-restriction fragment analysis of the hsp65 gene (PRA), all the isolates were classified as four different subtypes. Of these four subtypes, M. kansasii subtype I was the most frequent genotype in China, accounting for 71.8% (56/78) of M. kansasii isolates. Resistance to clarithromycin (CLA) was noted in 26.8% (15/56) of subtype I isolates, which was significant higher than that of other subtypes (4.5%, P = 0.031). DNA sequencing revealed that the presence of mutations in 23S rRNA was associated with 56.2% (9/16) of CLA-resistant M. kansasii isolates. In conclusion, our data demonstrate that AMK is the most active agent against M. kansasii in vitro, while the high proportion of CLA resistance is noted in M. kansasii isolates. In addition, the predominant subtype I is associated with CLA resistance in China.

Molecular characterisation of clinical and environmental isolates of Mycobacterium kansasii isolates from South African gold mines

Mycobacterium kansasii (M. kansasii) is a major cause of non-tuberculous mycobacterial pulmonary disease in the South African gold-mining workforce, but the source of infection and molecular epidemiology are unknown. This study investigated the presence of M. kansasii in gold and coal mine and associated hostel water supplies and compared the genetic diversity of clinical and environmental isolates of M. kansasii. Five M. kansasii and ten other potentially pathogenic mycobacteria were cultured mainly from showerhead biofilms. Polymerase chain reaction-restriction analysis of the hsp65 gene on 196 clinical and environmental M. kansasii isolates revealed 160 subtype I, eight subtype II and six subtype IV strains. Twenty-two isolates did not show the typical M. kansasii restriction patterns, suggesting that these isolates may represent new subtypes of M. kansasii. In contrast to the clonal population structure found amongst the subtype I isolates from studies in other countries, DNA fingerprinting of 114 clinical and three environmental subtype I isolates demonstrated genetic diversity amongst the isolates. This study demonstrated that showerheads are possible sources of M. kansasii and other pathogenic non-tuberculous mycobacterial infection in a gold-mining region, that subtype I is the major clinical isolate of M. kansasii strain and that this subtype exhibits genetic diversity.

Insights on the emergence of Mycobacterium tuberculosis from the analysis of Mycobacterium kansasii

By phylogenetic analysis, Mycobacterium kansasii is closely related to Mycobacterium tuberculosis. Yet, although both organisms cause pulmonary disease, M. tuberculosis is a global health menace, whereas M. kansasii is an opportunistic pathogen. To illuminate the differences between these organisms, we have sequenced the genome of M. kansasii ATCC 12478 and its plasmid (pMK12478) and conducted side-by-side in vitro and in vivo investigations of these two organisms. The M. kansasii genome is 6,432,277 bp, more than 2 Mb longer than that of M. tuberculosis H37Rv, and the plasmid contains 144,951 bp. Pairwise comparisons reveal conserved and discordant genes and genomic regions. A notable example of genomic conservation is the virulence locus ESX-1, which is intact and functional in the low-virulence M. kansasii, potentially mediating phagosomal disruption. Differences between these organisms include a decreased predicted metabolic capacity, an increased proportion of toxin–antitoxin genes, and the acquisition of M. tuberculosis-specific genes in the pathogen since their common ancestor. Consistent with their distinct epidemiologic profiles, following infection of C57BL/6 mice, M. kansasii counts increased by less than 10-fold over 6 weeks, whereas M. tuberculosis counts increased by over 10,000-fold in just 3 weeks. Together, these data suggest that M. kansasii can serve as an image of the environmental ancestor of M. tuberculosis before its emergence as a professional pathogen, and can be used as a model organism to study the switch from an environmental opportunistic pathogen to a professional host-restricted pathogen.

Strain variation amongst clinical and potable water isolates of M. kansasii using automated repetitive unit PCR

Mycobacterium kansasii is a pulmonary pathogen that has been grown readily from municipal water, but rarely isolated from natural waters. A definitive link between water exposure and disease has not been demonstrated and the environmental niche for this organism is poorly understood. Strain typing of clinical isolates has revealed seven subtypes with Type 1 being highly clonal and responsible for most infections worldwide. The prevalence of other subtypes varies geographically. In this study 49 water isolates are compared with 72 patient isolates from the same geographical area (Brisbane, Australia), using automated repetitive unit PCR (Diversilab) and ITS_RFLP. The clonality of the dominant clinical strain type is again demonstrated but with rep-PCR, strain variation within this group is evident comparable with other reported methods. There is significant heterogeneity of water isolates and very few are similar or related to the clinical isolates. This suggests that if water or aerosol transmission is the mode of infection, then point source contamination likely occurs from an alternative environmental source.

Short communication: subtyping of Mycobacterium kansasii by PCR-restriction enzyme analysis of the hsp65 gene

Mycobacterium kansasii is one of the most common causes of pulmonary disease resulting from nontuberculous mycobacteria (NTM). It is also the most frequently isolated NTM species from clinical specimens in Poland. The aim of this study was to investigate the distribution of M. kansasii subtypes among patients suspected of having pulmonary NTM disease. Fifty clinical isolates of M. kansasii recovered from as many patients with suspected mycobacterial lung disease between 2000 and 2010 in Poland were genotyped by PCR-restriction enzyme analysis (PCR-REA) of partial hsp65 gene. Mycobacterium kansasii subtype I was the only genotype to be identified among the isolates, both disease-associated and non-disease-associated. Isolation of M. kansasii subtype I from clinical specimens may be indicative of infection but may also merely represent colonization.

hsp65 PCR-restriction analysis (PRA) with capillary electrophoresis for species identification and differentiation of Mycobacterium kansasii and Mycobacterium chelonae-Mycobacterium abscessus group

OBJECTIVES

The aim of the present study was to identify and differentiate Mycobacterium kansasii and Mycobacterium chelonae-Mycobacterium abscessus group strains isolated from clinical and environmental sources in different countries.

METHODS

PCR-restriction analysis of the hsp65 gene (PRA) with automated capillary electrophoresis was applied to the isolates previously identified by conventional biochemical testing and the molecular INNO-LiPA MYCOBACTERIA assay.

RESULTS

PRA performed very well in comparison with the two other methods (96.4% concordance). Among 27 M. kansasii isolates, this method detected five genetic types, of which type 1 represented the most common clinical isolate, as it is worldwide. PRA differentiated 29 M. chelonae-M. abscessus group isolates into Mycobacterium immunogenum type 2 (n=13), M. chelonae (n=12), and M. abscessus types 1 (n=1) and 2 (n=1). M. immunogenum was the most frequent (69%) isolate from humans, but only one of 11 cases was clinically significant. M. chelonae was the most commonly (83%) recovered from water. PRA also identified two isolates with hsp65 alleles representing previously unreported patterns.

CONCLUSIONS

PRA based on automated capillary electrophoresis is a rapid, simple, and reliable method for the identification and differentiation of both clinically relevant and environmental isolates of M. kansasii and M. chelonae-M. abscessus group.

Comprehensive multicenter evaluation of a new line probe assay kit for identification of Mycobacterium species and detection of drug-resistant Mycobacterium tuberculosis

We evaluated a new line probe assay (LiPA) kit to identify Mycobacterium species and to detect mutations related to drug resistance in Mycobacterium tuberculosis. A total of 554 clinical isolates of Mycobacterium tuberculosis (n = 316), Mycobacterium avium (n = 71), Mycobacterium intracellulare (n = 51), Mycobacterium kansasii (n = 54), and other Mycobacterium species (n = 62) were tested with the LiPA kit in six hospitals. The LiPA kit was also used to directly test 163 sputum specimens. The results of LiPA identification of Mycobacterium species in clinical isolates were almost identical to those of conventional methods. Compared with standard drug susceptibility testing results for the clinical isolates, LiPA showed a sensitivity and specificity of 98.9% and 97.3%, respectively, for detecting rifampin (RIF)-resistant clinical isolates; 90.6% and 100%, respectively, for isoniazid (INH) resistance; 89.7% and 96.0%, respectively, for pyrazinamide (PZA) resistance; and 93.0% and 100%, respectively, for levofloxacin (LVX) resistance. The LiPA kit could detect target species directly in sputum specimens, with a sensitivity of 85.6%. Its sensitivity and specificity for detecting RIF-, PZA-, and LVX-resistant isolates in the sputum specimens were both 100%, and those for detecting INH-resistant isolates were 75.0% and 92.9%, respectively. The kit was able to identify mycobacterial bacilli at the species level, as well as drug-resistant phenotypes, with a high sensitivity and specificity.

The rise and fall of the Mycobacterium tuberculosis genome

When studied from the perspective of non-tuberculous mycobacteria (NTM) it is apparent that Mycobacterium tuberculosis has undergone a biphasic evolutionary process involving genome expansion (gene acquisition and duplication) and reductive evolution (deletions). This scheme can instruct descriptive and experimental studies that determine the importance of ancestral events (including horizontal gene transfer) in shaping the present-day pathogen. For example, heterologous complementation in an NTM can test the functional importance of M. tuberculosis-specific genetic insertions. An appreciation of both phases of M. tuberculosis evolution is expected to improve our fundamental understanding of its pathogenicity and facilitate the evaluation of novel diagnostics and vaccines.

Isolation of novel mycobacteria contaminating an aquarium fish tank in a Japanese university hospital

AIMS

To better understand nontuberculous mycobacteria (NTM) contamination in a hospital setting, six freshwater fish gut homogenates and water in an aquarium fish tank placed on the reception counter of a nursing station were cultured for mycobacteria.

METHODS AND RESULTS

By direct sequencing of 16s rRNA, rpoB and hsp65, scotochromogenic and nonchromogenic Mycobacterium szulgai isolates containing hsp65 type II (GenBank accession nos. FJ384762 and FJ384764, respectively), Mycobacterium gordonae isolates containing rpoB clusters B and E (GenBank accession no. FJ384766), and Mycobacterium kansasii isolates containing hsp65 type VI were collected from the gut homogenates and water from the fish tank. However, no isolates were obtained from the tap water used to refill the fish tank. A randomly amplified polymorphic DNA (RAPD) analysis using a 10-mer primer (5'-TGGTCGCGGC) showed that some NTM from the fish tank water were identical to those obtained from the gut homogenates.

CONCLUSIONS

Fish and water in the tank were contaminated by the novel NTM.

SIGNIFICANCE AND IMPACT OF THE STUDY

These findings could help to elucidate infection routes and contamination sources of novel NTM from water sources.

Molecular epidemiology of nontuberculous mycobacteria

The emergence of nontuberculous mycobacteria (NTM) as important environmental pathogens has stimulated the search for molecular markers to identify NTM sources, determine virulence mechanisms and describe their population structure. The availability of genome sequence data for a number of NTM isolates has permitted a more definitive approach to classification of these organisms based on sequence analysis of polymorphic targets, such as 16S rRNA, hsp65 and the internal transcribed spacer. An alternative approach, based on assessment of conserved inserted and deleted elements, also permits robust branding of clinical and laboratory isolates. Complementary to 'top-down' approaches that classify organisms at the species, subspecies and strain level, 'bottom-up' methods to determine the genetic similarity of pairs or groups of isolates have also been developed and used. Analysis of large restriction fragments by pulsed-field gel electrophoresis, restriction fragment length polymorphisms of insertion sequences, repetitive genetic elements, arbitrary primed PCR fragments and multilocus sequencing have largely supplanted phenotypic methods for strain comparison, such as serotyping, biotyping and multilocus enzyme electrophoresis. Together, these two sets of tools can provide an enhanced portrait of the NTM and be useful in epidemiologic investigations of the geographic and ecologic provenance of NTM infections. With further study, it is anticipated that the application of these genetic tools to well-defined collections of organisms will not only lead to an improved understanding of the source of NTM infection, but also help identify clinically relevant bacterial subtypes and eventually uncover genetic markers of bacterial virulence.

Immune responses in cattle inoculated with Mycobacterium bovis, Mycobacterium tuberculosis, or Mycobacterium kansasii

Cattle were inoculated with Mycobacterium bovis, Mycobacterium tuberculosis, or Mycobacterium kansasii to compare the antigen-specific immune responses to various patterns of mycobacterial disease. Disease expression ranged from colonization with associated pathology (M. bovis infection) and colonization without pathology (M. tuberculosis infection) to no colonization or pathology (M. kansasii infection). Delayed-type hypersensitivity and gamma interferon responses were elicited by each mycobacterial inoculation; however, the responses by the M. bovis- and M. tuberculosis-inoculated animals exceeded those of the M. kansasii-inoculated animals. Specific antibody responses were detected in all M. tuberculosis- and M. bovis-inoculated cattle 3 weeks after inoculation. From 6 to 16 weeks after M. tuberculosis inoculation, the antibody responses waned, whereas the responses persisted with M. bovis infection. With M. kansasii inoculation, initial early antibody responses waned by 10 weeks after inoculation and then increased 2 weeks after the injection of purified protein derivative for the skin test at 18 weeks after challenge. These findings indicate that antibody responses are associated with the antigen burden rather than the pathology, cellular immune responses to tuberculin correlate with infection but not necessarily with the pathology or bacterial burden, and exposure to mycobacterial antigens may elicit an antibody response in a presensitized animal.

The biology of environmental mycobacteria

Although the environmental mycobacteria are slow growing relative to other microorganisms in water and soil which would suggest that they are poor competitors, compensating factors permit survival, growth and persistence in natural and human-engineered environments. Factors such as the hydrophobic, lipid-rich impermeable envelope, biofilm formation, acid resistance, anaerobic survival and metabolism of recalcitrant carbon compounds permit survival and growth of the environmental mycobacteria in a wide range of natural and human-engineered habitats. High numbers of environmental mycobacteria are found in coastal swamps and estuaries and boreal, peat-rich forest soils and waters. The hydrophobic surface results in concentration of the environmental mycobacteria at interfaces (air-water and surface-water) and in aerosolized droplets ejected from water. The survival and growth in protozoa and amoebae permit environmental mycobacteria to persist in habitats subject to predation and likely led to survival and growth in phagocytic cells of animals. Finally, slow growth allows time for mycobacterial cells to adapt to changing conditions before loss of viability.

Surrounded by mycobacteria: nontuberculous mycobacteria in the human environment

A majority of the Mycobacterium species, called the nontuberculous mycobacteria (NTM), are natural inhabitants of natural waters, engineered water systems, and soils. As a consequence of their ubiquitous distribution, humans are surrounded by these opportunistic pathogens. A cardinal feature of mycobacterial cells is the presence of a hydrophobic, lipid-rich outer membrane. The hydrophobicity of NTM is a major determinant of aerosolization, surface adherence, biofilm-formation, and disinfectant- and antibiotic resistance. The NTM are oligotrophs, able to grow at low carbon levels [>50 microg assimilable organic carbon (AOC) l(-1)], making them effective competitors in low nutrient, and disinfected environments (drinking water). Biofilm formation and oligotrophy lead to survival, persistence, and growth in drinking water distribution systems. In addition to their role as human and animal pathogens, the widespread distribution of NTM in the environment, coupled with their ability to degrade and metabolize a variety of complex hydrocarbons including pollutants, suggests that NTM may be agents of nutrient cycling.

Evaluation of the INNO-LiPA mycobacteria v2 assay for identification of aquatic mycobacteria

Fifty-seven isolates of mycobacteria comprising 10 reference strains, 47 field isolates and one non-Mycobacterium isolate were screened using commercial INNO-LiPA v2 assay kits. All mycobacteria isolates tested hybridized with the Mycobacterium genus probe on the LiPA strip. All M. marinum, M. fortuitum and M. chelonae reference and field strains and three out of the four M. gordonae isolates hybridized to their corresponding species- or complex-specific probes. Two cultures (a type strain and a field isolate) yielded mixed growth of two mycobacterial species, i.e. M. chelonae and M. fortuitum. A Mycobacterium isolate from one of these cultures was subsequently purified and correctly identified with the kit. However, sequence analysis of the 16S-23S rRNA internal transcribed spacer (ITS) region of various mycobacteria isolates revealed a misidentification of M. shottsii and M. pseudoshottsii with the kit because these isolates reacted with the M. marinum/M. ulcerans probe. Moreover, nine of the 13 field isolates presumed to be M. fortuitum from the results of the kit had closer ITS sequence homology with M. conceptionense, a species which, to our knowledge, has never been reported in fish. These findings highlight the need to redesign the M. fortuitum-M. peregrinum probe included in the INNO-LiPA assay and to introduce additional complex-specific probes into the kit. Nevertheless, the kit proved to be a rapid and reliable method for identifying mycobacteria in the aquatic environment and would be particularly useful in laboratories without sequencing facilities.

Assessment of cross-reactivity between Mycobacterium bovis and M. kansasii ESAT-6 and CFP-10 at the T-cell epitope level

Cross-reactivity between Mycobacterium kansasii ESAT-6 and CFP-10 homologues and their M. bovis counterparts can confound the interpretation of immunodiagnostic tests for tuberculosis. M. kansasii is a nontuberculous mycobacterial species cultured from skin test-positive cattle in Great Britain. Using peptides derived from M. bovis and M. kansasii ESAT-6 and CFP-10 regions that differ between these species, we investigated the species specificity and cross-reactivity at the level of individual bovine T-cell epitopes. Our results demonstrated that all peptides tested are fully cross-reactive, with the exception of one ESAT-6-derived peptide that harbored an M. bovis-specific epitope(s) when it was recognized in the context of bovine leukocyte antigen (BoLA)-DQ but that was cross-reactive with its M. kansasii homologues when it was restricted by BoLA-DR. This observation further highlights that prediction of species specificity by comparing sequence identity/homology alone is not sufficient and that individuals with diverse major histocompatibility complex constellations need to be tested to characterize the cross-reactivity or species specificity of peptide-based reagents.

Application of the hsp65 PRA method for the rapid identification of mycobacteria isolated from clinical samples in Belgium

Biochemical identification of mycobacteria is slow and many times fail to produce correct results. We compared PCR-restriction fragment length polymorphism analysis (PRA) of hsp65 and biochemical methods for the identification of mycobacteria from human samples in Belgium. PRA was found useful in the identification of mycobacteria and simple to implement as a quick method in the laboratory.

The Neff strain of Acanthamoeba castellanii, a tool for testing the virulence of Mycobacterium kansasii

Virulent Mycobacterium kansasii (mainly subtype 1) may cause lung infections, whereas certain other strains (essentially subtype 3) are commonly non-pathogenic mycobacteria colonizing the human lower respiratory tract of patients. Determining the clinical significance of a strain isolated from a respiratory sample represents a major challenge for clinicians. Since some mycobacteria may use free-living amoebae as a training ground to select virulence traits, we wondered whether the Acanthamoeba castellanii amoeba could be used to determine the virulence of these intracellular bacteria. We investigated whether the growth and cytopathic effect of M. kansasii in A. castellanii correlate with the virulence of M. kansasii determined clinically and by subtyping. Pathogenic subtype 1 M. kansasii strains grew better in A. castellanii than non-pathogenic subtype 3 strains when considering both the number of bacteria per amoeba and the percentage of infected amoebae. Moreover, a subtype 3 M. kansasii strain isolated from blood culture, and thus considered pathogenic, was revealed to grow in A. castellanii similarly to pathogenic subtype 1 strains. These results suggest that amoebae may represent useful tools for testing the virulence of intracellular mycobacteria and other amoeba-resisting bacteria. This is important, since identification of novel bacterial virulence factors relies largely on in vitro assessment of virulence.

[New methods for mycobacteria identification]

Currently, the genus Mycobacterium comprises more than 100 different species, many of which cause significant clinical infections with high morbidity and mortality. Mycobacteria identification by conventional methods (rate and optimal temperature of growth, pigment production, colony morphology, and biochemical characteristics) has been the standard in most clinical microbiology laboratories. However, this phenotypic approach has considerable limitations, since numerous species cannot be differentiated. Moreover, because of the slow growth of these microorganisms, the results may not be available until 2-4 weeks after the initial isolation. Therefore, one of the most important challenges for clinical mycobacteriology laboratories is rapid and accurate identification of this variety of microorganism. This review aims to briefly describe several alternative procedures for mycobacterial identification. Although analysis of cell wall lipids (mycolic acids) by high-performance liquid chromatography is an interesting and well-known option, the most promising innovation for mycobacteria identification is the use of rapid molecular methods such as nucleic acid probes and, especially, genomic amplification methods.

Evaluation of the GenoType Mycobacterium Assay for identification of mycobacterial species from cultures

A new commercially available DNA strip assay (GenoType Mycobacterium CM/AS; Hain Lifescience, Nehren, Germany) was evaluated for the ability to differentiate mycobacterial species. The test is based on a PCR technique targeting a 23S rRNA gene region, followed by reverse hybridization and line probe technology. The GenoType CM is capable of identifying 23, the GenoType AS a further 14, species either alone or in combination with one or more species. Both tests were evaluated with 156 mycobacterial strains composed of 61 validly published species including different subspecies, 6 not validly published species, and 3 strains other than mycobacterial species. All strains were precharacterized by sequencing of the 5' region of the 16S rRNA gene and biochemical tests. In total, results for 151 strains were interpretable. Concordant results were obtained for 137 (92.6%) of 148 mycobacterial strains with the CM assay and 133 (89.9%) of 148 mycobacterial strains with the AS assay, and all three non-Mycobacterium species were identified.

Immune responses to defined antigens of Mycobacterium bovis in cattle experimentally infected with Mycobacterium kansasii

Cross-reactive responses elicited by exposure to nontuberculous mycobacteria often confound the interpretation of antemortem tests for Mycobacterium bovis infection of cattle. The use of specific proteins (e.g., ESAT-6, CFP-10, and MPB83), however, generally enhances the specificity of bovine tuberculosis tests. While genes for these proteins are absent from many nontuberculous mycobacteria, they are present in M. kansasii. Instillation of M. kansasii into the tonsillar crypts of calves elicited delayed-type hypersensitivity and in vitro gamma interferon and nitrite concentration responses of leukocytes to M. avium and M. bovis purified protein derivatives (PPDs). While the responses of M. kansasii-inoculated calves to M. avium and M. bovis PPDs were approximately equivalent, the responses of M. bovis-inoculated calves to M. bovis PPD exceeded their respective responses to M. avium PPD. The gamma interferon and nitrite responses of M. kansasii-inoculated calves to recombinant ESAT-6-CFP-10 (rESAT-6-CFP-10) exceeded corresponding responses of noninoculated calves as early as 15 and 30 days after inoculation, respectively, and persisted throughout the study. The gamma interferon and nitrite responses of M. bovis-inoculated calves to rESAT-6-CFP-10 exceeded the corresponding responses of M. kansasii-inoculated calves beginning 30 days after inoculation. By using a lipoarabinomannan-based enzyme-linked immunosorbent assay, specific serum antibodies were detected as early as 50 days after challenge with M. kansasii. By a multiantigen print immunoassay and immunoblotting, serum antibodies to MPB83, but not ESAT-6 or CFP-10, were detected in M. kansasii-inoculated calves; however, responses to MPB83 were notably weaker than those elicited by M. bovis infection. These findings indicate that M. kansasii infection of calves elicits specific responses that may confound the interpretation of bovine tuberculosis tests.

Evaluation of the new GenoType Mycobacterium assay for identification of mycobacterial species

The new commercial assay GenoType Mycobacterium, intended for the identification of mycobacteria, was evaluated with a panel of 197 strains belonging to 86 different taxa. The system, which relies on solid-phase reverse hybridization, is composed of two different kits: GenoType CM for the identification of more frequently detected mycobacterial species and GenoType AS for less common species. The sensitivity and specificity were 97.9% and 92.4% for the CM kit and 99.3% and 99.4% for the AS kit. Our results show that the system may represent a useful tool to substantially enlarge the number of mycobacteria that can be reliably identified in clinical laboratories.

Comparative study of two typing methods, hsp65 PRA and ITS sequencing, revealed a possible evolutionary link between Mycobacterium kansasii type I and II isolates

One hundred and ninety-eight clinical isolates of Mycobacterium kansasii collected between 2003 and 2004 in Japan were genotyped by PCR and restriction enzyme analysis (PRA) and 16S-23S internal transcribed spacer (ITS) sequencing. The results demonstrated that clinical isolates of M. kansasii in Japan are almost exclusively of the type I PRA genotype, as is the case in other countries. Although the results of subtyping using the 16S-23S ITS sequence were generally consistent with subtyping using hsp65 PRA, four strains showed a discrepancy between the two methods. Sequence analysis of the hsp65, gyrB and 16S rRNA genes and the ITS sequence of the four strains suggests that they branched from type II and could be considered an ancestral strain of the type I strain. The newly recognized strains were designated as intermediate type I.

Identification of Mycobacterium species by comparative analysis of the dnaA gene

For the establishment of a diagnostic tool for mycobacterial species, a part of the dnaA gene was amplified and sequenced from clinically relevant 27 mycobacterial species as well as 49 clinical isolates. Sequence variability in the amplified segment of the dnaA gene allowed the differentiation of all species except for Mycobacterium tuberculosis, Mycobacterium africanum and Mycobacterium microti, which had identical sequences. Partial sequences of dnaA from clinical isolates belonging to three frequently isolated species revealed a very high intraspecies similarity, with a range of 96.0–100%. Based on the dnaA sequences, a species-specific primer set for Mycobacterium kansasii and Mycobacterium gastri was successfully designed for a simple loop-mediated isothermal amplification method. These results demonstrate that the variable sequences in the dnaA gene were species specific and were sufficient for the development of an accurate and rapid diagnosis of Mycobacterium species.

Pulmonary Mycobacterium kansasii Infection in Israel, 1999–2004

BACKGROUND

Mycobacterium kansasii infection is one of the most common causes of nontuberculous mycobacterial lung disease in world. However, little is known about its background characteristics or drug sensitivity in nonendemic areas.

DESIGN

We assessed the clinical features, radiologic findings, and drug sensitivity associated with M kansasii infection in Israel.

METHODS

Patients with a culture-positive diagnosis of M kansasii infection between April 1999 and April 2004 were identified from a clinic database of tuberculosis centers. Mycobacterial cultures were performed with standard methods. Data on patient background and clinical features were collected from the medical files.

RESULTS

Mean age (+/- SD) of the 56 patients was 58 +/- 18 years, and 64% were men; 59% had associated lung disease. Fifteen percent were receiving immunosuppressive medications. None had HIV infection. Systemic comorbid diseases were noted in 27%. The most common clinical presentations were chest pain, cough, hemoptysis, fever, and night sweats. Cavitation was noted only in 54%. Older patients had more noncavitary disease than younger patients (p = 0.01, r = 0.35). Lower-lobe predominance was very rare (4%). None of the patients presented with pleural effusion or lymphadenopathy. Only seven patients (11%) underwent bronchoscopy for diagnosis. M kansasii isolates showed the highest sensitivity to rifampin, ethambutol, clarithromycin, and ofloxacin, and the highest resistance to ciprofloxacin and capreomycin. The mean duration of treatment was 21 +/- 7.2 months. There were no disease-related deaths.

CONCLUSIONS

M kansasii disease in Israel has no association with HIV, more systemic comorbid diseases and associated lung disease, and fewer cavitations. Following appropriate treatment, patients with M kansasii disease have an excellent prognosis.

Mycobacterium kansasii: antibiotic susceptibility and PCR-restriction analysis of clinical isolates

Mycobacterium kansasii is the second most common cause of non-tuberculosis mycobacterial diseases in Sao Paulo, Brazil. An important component of the management of infections caused by this organism is antibiotic susceptibility testing. The objective of this study was to determine the drug susceptibility profiles and genotypes of clinical isolates of M. kansasii obtained from patients with or without an infection that met the American Thoracic Society's case definition criteria of M. kansasii disease. One hundred and sixty-nine clinical isolates of M. kansasii collected between 1993 and 1998 in Sao Paulo, Brazil, were tested consecutively. The isolates were genotyped by PCR restriction-enzyme pattern analysis (PRA). Most of the M. kansasii strains were susceptible to isoniazid, streptomycin, rifabutin, rifampicin, clarithromycin, ethionamide, amikacin, clofazimine and cycloserine, and resistant to ethambutol, ciprofloxacin and doxycycline. Of 169 isolates, 167 belonged to the type I PRA genotype and one each belonged to type II and III genotypes. There was no correlation between PRA subtype and M. kansasii disease according to the American Thoracic Society case definition. Clinical trials may be needed to better correlate MIC values with treatment outcomes to identify appropriate parameters for drug-resistance testing of M. kansasii.

Intra- and interpatient variability of the hsp65 and 16S-23S intergenic gene region in Mycobacterium abscessus strains from patients with cystic fibrosis

To establish the exact pathogenic role of Mycobacterium abscessus in cystic fibrosis (CF), molecular tests are required for accurate identification. Forty-eight M. abscessus isolates from seven patients with CF were analyzed by sequence analysis for sequence variants within the hsp65 gene and the 16S-23S intergenic sequence (ITS). We detected two different hsp65 genes and correspondingly two ITS sequevars belonging to M. abscessus type I and type II.

PCR restriction fragment length polymorphism analysis (PRA)-algorithm targeting 644 bp Heat Shock Protein 65 (hsp65) gene for differentiation of Mycobacterium spp

A method based on PCR-restriction fragment length polymorphism analysis (PRA) using a novel region of the hsp65 gene was developed for the rapid and exact identification of mycobacteria to the species level. A 644 bp region of hsp65 in 62 mycobacteria reference strains, and 4 related bacterial strains were amplified, and the amplified DNAs were subsequently digested with restriction enzymes, namely, AvaII, HphI, and HpaII. Most of the mycobacteria species were easily differentiated at the species level by the developed method. In particular, the method enabled the separation of M. avium, M. intracellulare and M. tuberculosis to the species level by AvaII digestion alone. An algorithm was constructed based on the results and a blind test was successfully performed on 251 clinical isolates, which had been characterized by conventional biochemical testing. Our results suggest that this novel PRA offers a simple, rapid, and accurate method for the identification of mycobacteria culture isolates at the species level.

Use of the INNO-LiPA-MYCOBACTERIA assay (version 2) for identification of Mycobacterium avium-Mycobacterium intracellulare-Mycobacterium scrofulaceum complex isolates

Using INNO-LiPA-MYCOBACTERIA (Lipav1; Innogenetics) and the AccuProbe (Gen-Probe Inc./bioMérieux) techniques, 35 Mycobacterium avium-Mycobacterium intracellulare-Mycobacterium scrofulaceum (MAC/MAIS) complex strains were identified between January 2000 and December 2002. Thirty-four of 35 isolates were positive only for the MAIS complex probe by Lipav1 and were further analyzed by INNO-LiPA-MYCOBACTERIA version 2 (Lipav2), hsp65 PCR restriction pattern analysis (PRA), and ribosomal internal transcribed spacer (ITS), hsp65, and 16S rRNA sequences. Lipav2 identified 14 of 34 strains at the species level, including 11 isolates positive for the newly specific MAC sequevar Mac-A probe (MIN-2 probe). Ten of these 11 isolates corresponded to sequevar Mac-A, which was recently defined as Mycobacterium chimerae sp. nov. Among the last 20 of the 34 MAIS isolates, 17 (by hsp65 PRA) and 18 (by hsp65 sequence) were characterized as M. avium. Ten of the 20 were identified as Mac-U sequevar. All these 20 isolates were identified as M. intracellulare by 16S rRNA sequence except one isolate identified as Mycobacterium paraffinicum by 16S rRNA and ITS sequencing. One isolate out of 35 isolates that was positive for M. avium by AccuProbe and that was Mycobacterium genus probe positive and MAIS probe negative by Lipav1 and Lipav2 might be considered a new species. In conclusion, the new INNO-LiPA-MYCOBACTERIA allowed the identification of 40% of the previously unidentified MAIS isolates at the species level. The results of the Lipav2 assay on the MAIS isolates confirm the great heterogeneity of this group and suggest the use of hsp65 or ITS sequencing for precise identification of such isolates.

[Phenotypic and genotypic characteristics of Mycobacterium kansasii strains isolated in Spain (2000-2003)]

INTRODUCTION

Mycobacterium kansasii is an opportunistic pathogen that mainly causes pulmonary infections. This species accounted for 9.7% of Mycobacteria other than tuberculosis complex identified in the reference laboratory of the Spanish Centro Nacional de Microbiologia during the period of 2000-2003.

METHODS

In this study we analyzed the phenotypic and genotypic characteristics of 298 M. kansasii strains isolated over this 4-year period. The phenotypic characteristics were determined by conventional methods: biochemical testing, culture and morphological study. Genotypic characteristics were studied using PCR restriction fragment analysis of a fragment of the hsp65 gene and digestion with BstEII and HaeIII, according to the method of Telenti.

RESULTS

Among the total of tested strains, 57.4% had the typical phenotypic characteristics described for M. kansasii. The rest had atypical patterns that we grouped into 17 biotypes. Strains belonging to six of the seven described genotypes were identified, with 86.6% of the strains falling into genotype I.

CONCLUSION

Analysis of the phenotypic characteristics of M. kansasii showed a higher discrimination index for intraspecific differentiation than genotypic methods. Nevertheless, the high variability of phenotypic characteristics, some of which were very specific for the species (e.g., photochromogenicity), could complicate their identification. Hence both conventional and molecular methods should be used to accurately identify the atypical isolates.

Molecular analyses of mycobacteria other than the M. tuberculosis complex isolated from Northern Ireland cattle

Mycobacteria other than the Mycobacterium tuberculosis complex (MOTT), isolated from Northern Ireland cattle, were identified by PCR amplification of the 16S rRNA gene, and subsequent reverse cross blot hybridisation and sequence analyses. Elucidation of the MOTT species was to facilitate specificity testing of new and existing diagnostic test reagents for bovine tuberculosis. The presence of the genes for potential diagnostic antigens: MPB70, MPB64, ESAT-6 and CFP-10 in the isolated MOTT species was investigated. Molecular analyses of cultured isolates from bovine lymph node specimens of 48 cattle identified a wide variety of mycobacterial species including Mycobacterium nonchromogenicum, Mycobacterium malmoense, Mycobacterium bohemicum, Mycobacterium paratuberculosis, Mycobacterium avium, Mycobacterium kansasii, Mycobacterium holsaticum, Mycobacterium palustre, Mycobacterium sp. IWGMT 90210, Mycobacterium sp. LIV-2129, a potentially novel mycobacterial species (EMBL/GenBank/DDBJ Accession Number AJ617495) and Rhodococcus equi. Apart from M. kansasii, the results of traditional (standard phenotypic and biochemical) and molecular identification methods did not correlate well, with traditional methods identifying fewer species. Most of the species identified were either recognised pathogenic or potential pathogenic species. The genes for ESAT-6, CFP-10 and, unusually, MPB64 were detected in M. kansasii only. The MPB70 gene was not detected in any of the species. This study supported restricted species distribution of these genes as well as identifying a different range of MOTT species that could be included in specificity testing of new diagnostic reagents for bovine tuberculosis.

Comparative evaluation of polymerase chain reaction and restriction enzyme analysis: two amplified targets, hsp65 and rpoB, for identification of cultured mycobacteria

The increasing incidence of tuberculosis and other mycobacterial infections due to AIDS epidemic resulted in the need of rapid and accurate identification of isolated mycobacteria. The correct identification result leads to the selection of an appropriate therapeutic regimen. Polymerase chain reaction and restriction enzyme analysis (PCR-REA) has been developed since 1992 and used as the rapid method for identifying mycobacteria. Several genes or sequences have been used as an amplified target for PCR-REA. The present study aims to evaluate the potential use of PCR-REA of gene-encoding heat shock protein 65 kDa (hsp65) and beta-subunit RNA polymerase (rpoB) for the identification of mycobacteria compared with conventional biochemical identification. Two hundreds clinical isolates, consisting of 50 isolates of Mycobacterium tuberculosis and 150 isolates of nontuberculous mycobacteria (NTM), were submitted for identification using PCR-REA and biochemical method. The results demonstrated that PCR-REA identified 188 isolates of both M. tuberculosis and NTM concordantly with biochemical identification. Discordant identification results obtained from 12 isolates, comprised of 8 M. scrofulaceum, 1 M. avium complex, 1 M. malmoense, 1 M. terrae complex, and 1 M. chelonae/abscessus. Overall, the concordant percentage of results obtained from PCR-REA compared with biochemical method was 100%, 98.8%, and 83.3% for M. tuberculosis complex, rapidly growing, and slowly growing mycobacteria, respectively, and the results of hsp65 PCR-REA was in agreement with those obtained from rpoB PCR-REA. From this study, PCR-REA appears to be a simple, rapid, and reliable method for identifying mycobacteria in a routine microbiology laboratory.

Clinical and Epidemiological Study of Disease Caused by Mycobacterium kansasii in the Metropolitan Area of Bilbao, Spain

OBJECTIVE

Epidemiological description of individuals from whom Mycobacterium kansasii isolates were obtained in respiratory samples, and analysis of the isolates using molecular biological techniques.

MATERIAL AND METHODS

A descriptive retrospective/ prospective study was carried out from January 1994 to April 2002 in Basurto Hospital and Santa Marina Hospital and from January 2000 to April 2002 in Cruces Hospital, Galdakao Hospital, and San Eloy Hospital. Diagnosis of the disease was performed according to American Thoracic Society criteria; other definitions were also applied to allow inclusion of all cases. Disease caused by M. kansasii in patients who were not infected with the human immunodeficiency virus (HIV) was compared with disease caused by Mycobacterium tuberculosis in a control group. Polymerase chain reaction was applied with analysis of restriction fragment length polymorphisms to differentiate between species of mycobacteria and classify them into genotypes. Amplified fragment length polymorphisms were used to recognize clones within each genotype.

RESULTS

The patient charts of 334 patients in which an isolate of M. kansasii had been recorded were reviewed. We considered 220 patients to be suffering from disease caused by M. kansasii (American Thoracic Society criteria along with probable disease according to established definitions). The disease was more frequent in male patients (n=185; 84.1%) and in individuals who were not HIV positive (n=184; 83.6%). The highest incidence of disease in the Bizkaia region was found in Margen Izquierda-Encartaciones, where the rate was 8.05 per 100 000 inhabitants. In the Bilbao area, the highest rate was found in the districts lying on the outskirts. The underlying diseases were tuberculosis (20.5%), chronic obstructive pulmonary disease (25.9%), pulmonary neoplasia (7.7%), silicosis (0.9%), chronic liver disease (11.4%), and duodenal ulcer (8.6%). The most frequent constitutional symptoms were fever (39.1%), loss of appetite (23.2%), and weight loss (33.3%). Among the respiratory symptoms, the most outstanding were cough (70.9%) and expectoration (62.3%). The most frequent radiographic patterns were cavitation and pulmonary infiltration. The most common treatment regimen was rifampicin, isoniazid, and ethambutol (43.4%), and the average duration was 12 months in patients who were HIV negative. Analysis of antibiotic sensitivity, performed on 56 strains, revealed that 100% were resistant to isoniazid, while none displayed rifampicin resistance. Thirty-four cases of disease caused by M. kansasii were compared with 68 cases of tuberculosis, all of them without HIV infection. The comparison revealed a predominance of smokers, respiratory symptoms, and cavitation in patients with disease caused by M. kansasii. The majority of the isolates (98.5%) corresponded to genotype I. A total of 8 clones were obtained; the clones designated 1 and 3 were more common in HIV-positive and HIV-negative individuals respectively.

CONCLUSIONS

In recent years, there has been an increase in the number of patients with disease caused by M. kansasii in the province of Bizkaia. The disease is more frequent in male patients, individuals who are HIV negative, and in urban areas. In addition, more respiratory symptoms and a higher incidence of cavitation were found in patients with disease caused by M. kansasii than in those with tuberculosis. Genotype I is the most common isolate, and clones 1 and 3 affect 80% of patients suffering from the disease.