Genetic characterization of Mycobacterium avium isolates recovered from humans and animals in Australia

Differential Genotyping of Mycobacterium avium Complex and Its Implications in Clinical and Environmental Epidemiology

In recent decades, the incidence and prevalence of nontuberculous mycobacteria (NTM) have greatly increased, becoming a major worldwide public health problem. Among numerous NTM species, the Mycobacterium avium complex (MAC) is the most predominant species, causing disease in humans. MAC is recognized as a ubiquitous microorganism, with contaminated water and soil being established sources of infection. However, the reason for the recent increase in MAC-associated disease has not yet been fully elucidated. Furthermore, human MAC infections are associated with a variety of infection sources. To improve the determination of infection sources and epidemiology of MAC, feasible and reliable genotyping methods are required to allow for the characterization of the epidemiology and biology of MAC. In this review, we discuss genotyping methods, such as pulsed-field gel electrophoresis, a variable number of tandem repeats, mycobacterial interspersed repetitive-unit-variable number of tandem repeats, and repetitive element sequence-based PCR that have been applied to elucidate the association between the MAC genotypes and epidemiological dominance, clinical phenotypes, evolutionary process, and control measures of infection. Characterizing the association between infection sources and the epidemiology of MAC will allow for the development of novel preventive strategies for the effective control of MAC infection.

Marker genes of fecal indicator bacteria and potential pathogens in animal feces in subtropical catchments

We investigated the abundance of marker genes of two fecal indicator bacteria (FIB) and eight potential pathogens in fecal samples of humans (n = 14) and 10 domestic and native wild animals (n = 134). For each target animal, between 10 and 14 individual fecal samples were collected (n = 148 individual fecal samples in total). The abundance of FIB and potential pathogens within each sample was determined using quantitative PCR (qPCR) assays. All animals tested were positive for Escherichia coli (EC) and the concentrations ranged from 6.13 (flying fox) to 8.87 (chicken) log₁₀ GC/g of feces. These values for Enterococcus spp. (ENT) were 5.25 log₁₀ GC/g for flying fox and 8.12 log₁₀ GC/g of feces for chicken. Moderate correlations were observed between EC with P. aeruginosa, EC O157 and Cryptosporidium parvum, whereas weak correlations were observed between EC and Salmonella spp. and Giardia lamblia, Mycobacterium avium complex (MAC) and Campylobacter spp. The prevalence of MAC and P. aeruginosa were low in dog (14.3% each) and moderate (57.2%, MAC; 42.9% P. aeruginosa) in Eastern grey kangaroo fecal samples. Cryptosporidium parvum was detected in one cattle and one human fecal sample, while G. lamblia was detected in one dog, one flying fox, and one pig fecal samples. Among the eight potential pathogens tested, five pathogens were detected in chicken and dog fecal samples. The remaining animal species contained up to three potential pathogens in their feces. The data generated in this study may aid in the calculation of pathogen loads in the environment, and hence to assess the risks from human and animal fecal contamination of source waters.

Methodological and Clinical Aspects of the Molecular Epidemiology of Mycobacterium tuberculosis and Other Mycobacteria

Molecular typing has revolutionized epidemiological studies of infectious diseases, including those of a mycobacterial etiology. With the advent of fingerprinting techniques, many traditional concepts regarding transmission, infectivity, or pathogenicity of mycobacterial bacilli have been revisited, and their conventional interpretations have been challenged. Since the mid-1990s, when the first typing methods were introduced, a plethora of other modalities have been proposed. So-called molecular epidemiology has become an essential subdiscipline of modern mycobacteriology. It serves as a resource for understanding the key issues in the epidemiology of tuberculosis and other mycobacterial diseases. Among these issues are disclosing sources of infection, quantifying recent transmission, identifying transmission links, discerning reinfection from relapse, tracking the geographic distribution and clonal expansion of specific strains, and exploring the genetic mechanisms underlying specific phenotypic traits, including virulence, organ tropism, transmissibility, or drug resistance. Since genotyping continues to unravel the biology of mycobacteria, it offers enormous promise in the fight against and prevention of the diseases caused by these pathogens. In this review, molecular typing methods for Mycobacterium tuberculosis and nontuberculous mycobacteria elaborated over the last 2 decades are summarized. The relevance of these methods to the epidemiological investigation, diagnosis, evolution, and control of mycobacterial diseases is discussed.

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.

Phylogeny of Mycobacterium avium strains inferred from glycopeptidolipid biosynthesis pathway genes

The Mycobacterium avium complex (MAC) encompasses two species, M. avium and Mycobacterium intracellulare, which are opportunistic pathogens of humans and animals. The standard method of MAC strain differentiation is serotyping based on a variation in the antigenic glycopeptidolipid (GPL) composition. To elucidate the relationships among M. avium serotypes a phylogenetic analysis of 13 reference and clinical M. avium strains from 8 serotypes was performed using as markers two genomic regions (890 bp of the gtfB gene and 2150 bp spanning the rtfA-mtfC genes) which are associated with the strains' serological properties. Strains belonging to three other known M. avium serotypes were not included in the phylogeny inference due to apparent lack of the marker sequences in their genomes, as revealed by PCR and Southern blot analysis. These studies suggest that serotypes prevalent in AIDS patients have multiple origins. In trees inferred from both markers, serotype 1 strains, known to have the simplest and shortest GPLs among all other serotypes, were polyphyletic. Likewise, comparisons of the inferred phylogenies with the molecular typing results imply that the existing tools used in epidemiological studies may be poor estimators of M. avium strain relatedness. Additionally, trees inferred from each marker had significantly incongruent topologies due to a well supported alternative placement of strain 2151, suggesting a complex evolutionary history of this genomic region.

Epidemiology of Mycobacterium bovis infections of pigs and wild boars using a molecular approach

A molecular epidemiological approach was applied to establishing a possible role for the wild boar as a natural reservoir of Mycobacterium bovis in Sierra de Villuercas, Western Spain; an area free of farmed cattle and wild deer populations. Spoligo and VNTR typing were used over a three year period to study the epidemiological relationship between the occurrence of bovine tuberculosis (TB) in extensively bred Iberian pigs and indigenous wild boar. The 37 sampled wild boar showed different degree of calcified granulomatous lesions in retropharyngeal, mediastinal and pulmonary lymph nodes. The 25 sampled Iberian pigs showed calcified lesions, mainly in the respiratory tract. Lesions located in the mesenteric lymph nodes appeared secondarily. M. bovis was isolated from all affected animals. Twenty-five and 37 isolates of M. bovis were obtained from domestic pigs and wild boar, respectively. Our findings provide evidence that supports the possibility of cross infection between wild boar and domestic pig populations. This is contrary to the generally held belief that swine represent an epidemiological dead end host and play no role in the epidemiology of M. bovis.

Improved preparation of high molecular weight DNA for pulsed-field gel electrophoresis from mycobacteria

Molecular typing is now widely used to aid and supplement conventional epidemiological studies of mycobacterial diseases. Pulsed-field gel electrophoresis (PFGE), in which the entire genome can be represented as a distinct pattern of DNA restriction fragments, is a particularly powerful tool in epidemiology for the determination of clonal identity of bacteria providing information for understanding and controlling the spread of disease. Application of PFGE to the study of mycobacterial diseases has been limited because isolation of high-quality genomic DNA from mycobacterial sources has proved problematic. Here we report a simple, highly effective method for the preparation of high molecular weight DNA from a range of mycobacterial species. Cultures are continuously stirred and are homogeneous. This enables accurate quantification. The presence of detergent in buffers keeps the cells in suspension throughout preparation enabling efficient lysis. In addition, it is compatible with heat-inactivation of pathogenic mycobacteria and all of the preparation procedures can be carried out with a category III facility. This standardised method of preparation of DNA from mycobacteria means that PFGE should now be evaluated as a method for typing these organisms and it may be particularly important as a means of typing less well-characterised mycobacteria for which other techniques are not available.

Evaluation of the accuracy and reproducibility of a practical PCR panel assay for rapid detection and differentiation of Mycobacterium avium subspecies

The Mycobacterium avium subspecies (MAs) include the closely related MAs avium and MAs paratuberculosis. This study was conducted to evaluate the performance of a PCR panel assay as a diagnostic tool to detect and differentiate MAs avium and MAs paratuberculosis infection. Specific oligonucleotides primers derived from the 16 S rRNA (MAs) sequence, insertion elements IS 901 (MAs avium), IS 1245 Mycobacterium avium complex (MAC), IS 900 (MAs paratuberculosis), and the hspX (MAs paratuberculosis) gene sequences were synthesized and used in preassembled PCR reaction mixtures. These five primer sets made up the PCR panel assay. To determine the accuracy of the PCR panel assay for MAs avium and MAs paratuberculosis strain detection and differentiation, lysates of mycobacterial DNA from 120 (n=120) strains were tested with the PCR panel assay by one laboratory (#1). The PCR panel assay specifically detected and differentiated 91/91 (100%) of MAs avium and MAs paratuberculosis strains tested in this study. The PCR panel assay also specifically differentiated all MAs avium and MAs paratuberculosis strains from all but one (M. intracellulare, serovar 23) of the other mycobacterial strains tested. To confirm the accuracy and evaluate the reproducibility of the PCR panel assay, samples were numbered and given to a different laboratory (#2) as 'unknowns' for identification by the PCR panel assay. In this study, the overall accuracy for strain identification using the PCR panel assay was 99.2% (119/120). The reproducibility of the PCR panel assay when comparing data from laboratory #1 with laboratory #2 was found to be 100% (120/120). These results indicate that this 'easy-to-use', rapid PCR method can accurately and reliably detect and differentiate closely related MAs avium and MAs paratuberculosis from each other and from other mycobacterial species. The PCR panel assay can also differentiate mixed cultures of MAs. The simplicity of this PCR method could be beneficial to laboratories that test for members of MA.

Genetic diversity of mycobacterium avium recovered from AIDS patients in the caribbean as studied by a consensus IS1245-RFLP method and pulsed-field gel electrophoresis

A total of 45 strains of Mycobacterium avium from 31 human immunodeficiency virus (HIV)-positive patients in the French Caribbean islands and Guiana were subjected to DNA fingerprinting using a recently described consensus IS1245 restriction fragment length polymorphism (RFLP) method, and pulsed-field gel electrophoresis (PFGE). The IS1245-RFLP resulted in three distinct clusters composed of three 27-banded isolates from two patients (cluster A), nine two-banded isolates from six patients (cluster B), and three 20-banded isolates from three patients (cluster C). PFGE results obtained after XbaI and DraI digestions gave similar clustering results irrespective of the enzyme used, and confirmed the molecular clonality for high IS1245 copy number isolates (clusters A and C). However, PFGE further discriminated the low IS1245 copy number cluster B into two distinct subclusters: subcluster I containing six isolates from four patients during the same time period from a single hospital in Guadeloupe, and subcluster IV composed of four isolates from two patients, out of which three isolates were from a single patient (patient 19). Interestingly, in the latter case, PFGE grouped together all three isolates from patient 19 despite the fact that IS1245 fingerprinting permitted grouping only two of the three isolates (the remaining unclustered isolate contained two additional bands of 3.5 and 5 kbp, and was initially considered as evidence of polyclonal infection). A combined numerical analysis of the IS1245-RFLP and PFGE results corroborated the existence of four instead of three clusters. A comparison of IS1245-RFLP versus PFGE results suggested that the standardized RFLP procedure is compatible with PFGE only for M. avium isolates containing > or = 5 copies of IS1245. Consequently, the typing results for low IS1245 copy number isolates (31% of isolates in this study) should be reconsidered for secondary typing using PFGE. Lastly, the absence of a predominant genotype of M. avium infecting HIV-positive patients over a 5-year period in this tropical region argues in favor of a lack of a privileged ecological niche for M. avium, and instead suggests that microepidemics of M. avium may prevail during limited periods of time.

Population structure and diversity of avian isolates of Pasteurella multocida from Australia

A total of 110 isolates of Pasteurella multocida from Australian poultry and reference strains for the 16 somatic serovars plus the three subspecies (gallicida, multocida, septica) were analysed to examine their population structure and diversity. The 81 field isolates examined by multilocus enzyme electrophoresis (MLEE) were diverse, being divided into 56 electrophoretic types (ETs), with the 19 reference strains in another 15 ETs. The population was clonal and somatic serotyping was not particularly useful in establishing relationships between isolates. The 71 ETs formed three distinct subclusters (A, B and C) at a genetic distance of 0.36. Biovars tended to be associated with these subclusters: A with biovars 1, 3, 4, 5 and 8 and B with biovars 2, 6, 7, 9 and 10. Ribotyping, performed on all 110 isolates using Hpall, recognized 21 ribotypes forming nine clusters (R1-R9). The isolates in ribotype cluster R1 were almost identical to those in MLEE cluster B. Using both MLEE and ribotyping, the 19 non-Australian reference strains were found to be distributed over the full diversity of the Australian isolates of P. multocida. This study has shown that a range of P. multocida clones are associated with fowl cholera in Australia and that many of the Australian isolates are similar to non-Australian reference strains. Both the MLEE results and the ribotyping data identified a previously unrecognized subset of P. multocida strains.

Differentiation of Australian isolates of Mycobacterium paratuberculosis using pulsed-field gel electrophoresis

OBJECTIVES

To examine strain variation amongst Australian isolates of Mycobacterium paratuberculosis.

DESIGN

Pulsed field gel electrophoresis was optimised for differentiation of M paratuberculosis strains, and this typing technique was then applied to a collection of Australian isolates.

PROCEDURE

DNAs from 35 Australian isolates of M paratuberculosis and a UK reference strain were digested with one or other of three restriction endonucleases. The banding patterns obtained after pulsed field gel electrophoresis of the DNA fragments were compared.

RESULTS

The Australian isolates were divided into two groups on the basis of their DNA banding pattern. Both were different from the UK reference strain. Seven isolates from cattle in Victoria and the Northern Territory had the same pattern as five isolates from alpacas in Victoria and Western Australia. Another 20 isolates from cattle in Victoria, Western Australia and the Northern Territory had the same pattern as isolates from two sheep and a goat in New South Wales.

CONCLUSION

Pulsed field gel electrophoresis was a useful tool for strain typing of M paratuberculosis, and could be used to study the transmission of strains in Australia.

Use of four DNA insertion sequences to characterize strains of the Mycobacterium avium complex isolated from animals

The Mycobacterium avium complex (MAC) includes the closely related species M. avium, M. intracellulare and M. paratuberculosis. The insertion elements IS900, IS901, IS1245 and IS1311 were used as DNA probes to characterize by restriction fragment polymorphisms (RFLPs) eight reference strains, three animal isolates of M. paratuberculosis from outside New Zealand and 61 selected New Zealand MAC isolates from cattle, deer, pigs, sheep and humans. IS900 was found only in strains of M. paratuberculosis. All MAC strains contained IS1311 and the RFLPs associated with this insertion element divided M. paratuberculosis strains into the same groups as IS900 RFLPs. Except for M. paratuberculosis, all MAC strains contained IS1245 and the majority of those from lesions in cattle, deer and pigs also contained IS901. All animal strains containing IS901 had the same RFLPs with IS901, IS1245 and IS1311. In three cases, these apparently identical strains could be differentiated by restriction fragment analysis with BstEII. IS901 was not present in four human isolates or in isolates from deer without lesions. These results indicate that a very closely related group of strains causes the majority of non-paratuberculosis MAC lesions in animals in New Zealand.

Use of multilocus enzyme electrophoresis to examine genetic relationships amongst isolates of Mycobacterium intracellulare and related species

As part of a larger study investigating diversity and distribution of Mycobacterium spp. in Australia, multilocus enzyme electrophoresis was used to assess genetic relationships at 17 enzyme loci amongst a collection of reference strains and isolates initially identified on biochemical and other grounds as M. intracellulare (70), "X' mycobacteria (10), M. scrofulaceum (7), M. avium (8) and M. avium subsp. paratuberculosis (2). Two of the isolates initially identified as M. intracellulare were shown to be quite distinct from the others. Both gave negative results in a species-specific DNA probe test, whilst one was positive by PCR. These results emphasize the uncertainties involved in identifying members of this group. The other M. intracellulare isolates formed a cohesive but diverse group, being divided into 48 electrophoretic types (ETs), with a mean genetic diversity of 0.38. Forty-three of these ETs contained only single isolates. There was no clear relationship between the serovar and ET designation. The index of association calculated for M. intracellulare was significantly different from zero, suggesting that it is a clonal species. PFGE was also applied to selected isolates from the ETs containing multiple isolates, and some of these could be differentiated further. The strains of M. scrofulaceum and "X' mycobacteria were distinct from M. intracellulare, but themselves were highly heterogeneous, with mean genetic diversities of 0.66 and 0.65, respectively. Each of these groups may represent more than one species. M. avium strains were distinct from the two M. avium subsp. paratuberculosis strains, as well as from the other mycobacteria studied.