Comparison of Mycobacterium avium complex (MAC) strains from pigs and humans in Sweden by random amplified polymorphic DNA (RAPD) using standardized reagents

Comparative genome analyses of Mycobacterium avium reveal genomic features of its subspecies and strains that cause progression of pulmonary disease

Pulmonary disease caused by nontuberculous mycobacteria (NTM) is increasing worldwide. Mycobacterium avium is the most clinically significant NTM species in humans and animals, and comprises four subspecies: M. avium subsp. avium (MAA), M. avium subsp. silvaticum (MAS), M. avium subsp. paratuberculosis (MAP), and M. avium subsp. hominissuis (MAH). To improve our understanding of the genetic landscape and diversity of M. avium and its role in disease, we performed a comparative genome analysis of 79 M. avium strains. Our analysis demonstrated that MAH is an open pan-genome species. Phylogenetic analysis based on single nucleotide variants showed that MAH had the highest degree of sequence variability among the subspecies, and MAH strains isolated in Japan and those isolated abroad possessed distinct phylogenetic features. Furthermore, MAP strains, MAS and MAA strains isolated from birds, and many MAH strains that cause the progression of pulmonary disease were grouped in each specific cluster. Comparative genome analysis revealed the presence of genetic elements specific to each lineage, which are thought to be acquired via horizontal gene transfer during the evolutionary process, and identified potential genetic determinants accounting for the pathogenic and host range characteristics of M. avium.

Mycobacterium avium Possesses Extracellular DNA that Contributes to Biofilm Formation, Structural Integrity, and Tolerance to Antibiotics

Mycobacterium avium subsp. hominissuis is an opportunistic pathogen that is associated with biofilm-related infections of the respiratory tract and is difficult to treat. In recent years, extracellular DNA (eDNA) has been found to be a major component of bacterial biofilms, including many pathogens involved in biofilm-associated infections. To date, eDNA has not been described as a component of mycobacterial biofilms. In this study, we identified and characterized eDNA in a high biofilm-producing strain of Mycobacterium avium subsp. hominissuis (MAH). In addition, we surveyed for presence of eDNA in various MAH strains and other nontuberculous mycobacteria. Biofilms of MAH A5 (high biofilm-producing strain) and MAH 104 (reference strain) were established at 22°C and 37°C on abiotic surfaces. Acellular biofilm matrix and supernatant from MAH A5 7 day-old biofilms both possess abundant eDNA, however very little eDNA was found in MAH 104 biofilms. A survey of MAH clinical isolates and other clinically relevant nontuberculous mycobacterial species revealed many species and strains that also produce eDNA. RAPD analysis demonstrated that eDNA resembles genomic DNA. Treatment with DNase I reduced the biomass of MAH A5 biofilms when added upon biofilm formation or to an already established biofilm both on abiotic surfaces and on top of human pharyngeal epithelial cells. Furthermore, co-treatment of an established biofilm with DNase 1 and either moxifloxacin or clarithromycin significantly increased the susceptibility of the bacteria within the biofilm to these clinically used antimicrobials. Collectively, our results describe an additional matrix component of mycobacterial biofilms and a potential new target to help treat biofilm-associated nontuberculous mycobacterial infections.

Characterization of a novel plasmid, pMAH135, from Mycobacterium avium subsp. hominissuis

Mycobacterium avium complex (MAC) causes mainly two types of disease. The first is disseminated disease in immunocompromised hosts, such as individuals infected by human immunodeficiency virus (HIV). The second is pulmonary disease in individuals without systemic immunosuppression, and the incidence of this type is increasing worldwide. M. avium subsp. hominissuis, a component of MAC, causes infection in pigs as well as in humans. Many aspects of the different modes of M. avium infection and its host specificity remain unclear. Here, we report the characteristics and complete sequence of a novel plasmid, designated pMAH135, derived from M. avium strain TH135 in an HIV-negative patient with pulmonary MAC disease. The pMAH135 plasmid consists of 194,711 nucleotides with an average G + C content of 66.5% and encodes 164 coding sequences (CDSs). This plasmid was unique in terms of its homology to other mycobacterial plasmids. Interestingly, it contains CDSs with sequence homology to mycobactin biosynthesis proteins and type VII secretion system-related proteins, which are involved in the pathogenicity of mycobacteria. It also contains putative conserved domains of the multidrug efflux transporter. Screening of isolates from humans and pigs for genes located on pMAH135 revealed that the detection rate of these genes was higher in clinical isolates from pulmonary MAC disease patients than in those from HIV-positive patients, whereas the genes were almost entirely absent in isolates from pigs. Moreover, variable number tandem repeats typing analysis showed that isolates carrying pMAH135 genes are grouped in a specific cluster. Collectively, the pMAH135 plasmid contains genes associated with M. avium's pathogenicity and resistance to antimicrobial agents. The results of this study suggest that pMAH135 influence not only the pathological manifestations of MAC disease, but also the host specificity of MAC infection.

First case of pulmonary disease caused by a Mycobacterium avium complex strain of presumed veterinary origin in an adult human patient

We report the first case of pulmonary disease caused by a strain of Mycobacterium avium complex of presumed veterinary origin in an elderly patient. All serial isolates were identified by multilocus sequence analysis based on rpoB, hsp65, and 16S rRNA fragments. Disease persisted despite macrolide-based combination antibiotic therapy.

Molecular epidemiology of mycobacteriosis in wildlife and pet animals

The ecology of mycobacteria is shifting in accordance with environmental change and new patterns of interaction between wildlife, humans, and nondomestic animals. Infection of vertebrate hosts throughout the world is greater now than ever and includes a growing prevalence in free ranging and captive wild animals. Molecular epidemiologic studies using standardized methods with high discriminatory power are useful for tracking individual cases and outbreaks, identifying reservoirs, and describing patterns of transmission and are used with increasing frequency to characterize disease wildlife. This review describes current features of mycobacteriosis in wildlife species based on traditional descriptive studies and recent molecular applications.

Occurrence of Mycobacterium spp. and other pathogens in lymph nodes of slaughtered swine and wild boars (Sus scrofa)

Mycobacterium spp. and other pathogens were investigated in 258 swine lymph nodes (129 with and 129 without apparent lesions), and 120 lymph nodes (60 with and 60 without lesions) from wild boars (Sus scrofa). A total of lymph nodes from swine and wild boars were collected of different animals. Submaxillar and mesenteric lymph nodes were submitted to microbiological examination and colonies suggestive of Mycobacterium spp. (alcohol-acid bacilli) were submitted to PCR Restriction Assay (PRA). In swine with lymphadenitis, Mycobacterium spp. (24.1%) and Rhodococcus equi (13.2%) were the most prevalent microorganisms, while in lymph nodes without lesions were identified a complex of microorganisms, including of environmental mycobacteria. In wild boars with lymphadenitis, ß-haemolytic Streptococcus (10.0%), Mycobacterium spp (8.4%) and R. equi (6.6%) were the most frequent. Among mycobacterias were identified predominantly Mycobacterium avium subspecies type 1 (48.3%) and M. avium subspecies type 2 (16.1%), followed by Mycobacterium intracellulare, Mycobacterium szulgai,Mycobacterium fortuitum, Mycobacterium gordonae, Mycobacterium simiae, Mycobacterium nonchromogenicum and Mycobacterium intracellulare type 2.

Comparison of variable-number tandem-repeat markers typing and IS1245 restriction fragment length polymorphism fingerprinting of Mycobacterium avium subsp. hominissuis from human and porcine origins

BACKGROUND

Animal mycobacterioses are regarded as a potential zoonotic risk and cause economical losses world wide. M. avium subsp. hominissuis is a slow-growing subspecies found in mycobacterial infected humans and pigs and therefore rapid and discriminatory typing methods are needed for epidemiological studies. The genetic similarity of M. avium subsp. hominissuis from human and porcine origins using two different typing methods have not been studied earlier. The objective of this study was to compare the IS1245 RFLP pattern and MIRU-VNTR typing to study the genetic relatedness of M. avium strains isolated from slaughter pigs and humans in Finland with regard to public health aspects.

METHODS

A novel PCR-based genotyping method, variable number tandem repeat (VNTR) typing of eight mycobacterial interspersed repetitive units (MIRUs), was evaluated for its ability to characterize Finnish Mycobacterium avium subsp. hominissuis strains isolated from pigs (n = 16) and humans (n = 13) and the results were compared with those obtained by the conventional IS1245 RFLP method.

RESULTS

The MIRU-VNTR results showed a discriminatory index (DI) of 0,92 and the IS1245 RFLP resulted in DI 0,98. The combined DI for both methods was 0,98. The MIRU-VNTR test has the advantages of being simple, reproducible, non-subjective, which makes it suitable for large-scale screening of M. avium strains.

CONCLUSIONS

Both typing methods demonstrated a high degree of similarity between the strains of human and porcine origin. The parallel application of the methods adds epidemiological value to the comparison of the strains and their origins. The present approach and results support the hypothesis that there is a common source of M. avium subsp. hominissuis infection for pigs and humans or alternatively one species may be the infective source to the other.

High genetic relatedness among Mycobacterium avium strains isolated from pigs and humans revealed by comparative IS1245 RFLP analysis

Members of the Mycobacterium avium complex cause pig mycobacteriosis and opportunistic human infections. Infections due to environmental mycobacteria are increasing in both industrial and developing countries. Mycobacterium-infected pig carcasses can pass for human consumption due to the poor specificity of meat control by visual detection at the slaughter houses. The genetic relatedness of porcine and human MAC isolates in Finland has been unknown. M. avium isolates isolated from pig organs (n=16) and clinical samples (n=13) were compared by IS1245 RFLP analysis to evaluate the similarity of the isolates obtained from human and porcine samples. Nearly identical multicopy M. avium subsp. hominissuis IS1245 RFLP fingerprints were obtained for isolates of porcine and human origin. IS1245 RFLP patterns of 38% of the porcine and human M. a. hominissuis isolates were >90% similar. The RFLP patterns of two porcine and two human isolates showed >95% similarity. The high similarity of the IS1245 RFLP patterns of the human and porcine M. a. hominissuis isolates indicates close genetic relatedness, suggesting that M. a. hominissuis is transmitted between pigs and humans, or that pigs and humans share common environmental sources of infection. Porcine and human isolates with RFLP patterns differing by only one or two bands were found, which shows that the same M. a. hominissuis strains may infect both humans and pigs.

Proliferation of mycobacteria in a piggery environment revealed by mycobacterium-specific real-time quantitative PCR and 16S rRNA sandwich hybridization

Pig mycobacteriosis is the most common animal mycobacterial disease in Finland with a long-term average prevalence of 0.34% and temporary peaks as high as 0.85%. In the current study Mycobacterium-specific real-time qPCR and 16S rRNA sandwich hybridization were utilized for culture-independent detection and measurement of potentially infectious mycobacteria in selected piggeries. Participating herds (n=5) were selected according to prevalence of tuberculous lesions (>4%) in slaughtered carcasses. When DNA extracted from piggery bedding materials was analyzed by Mycobacterium-targeted qPCR using the SYBR green I dye for detection of amplification products, 10(5) to 10(7) cell equivalents of mycobacterial DNA were detected in unused bedding materials and 10(8) to 10(10)g(-1) dry weight in used bedding materials. When Mycobacterium-specific hybridization probes were used for detection of amplification products, 10(5) to 10(7) cell equivalents of mycobacterial DNA g(-1) dry weight were detected in unused bedding materials in four out of the five piggeries studied and up to 10(8) cell equivalents in used bedding material. The results were confirmed by the Mycobacterium-specific 16S rRNA sandwich hybridization assay. The present results show, that mycobacteria occur in organic materials commonly used on pig farms, and may proliferate in bedding materials during use. We also show that DNA- and RNA-based methods may be utilized for detection of environmental reservoirs of mycobacteria causing porcine and human infection.

Disseminated Mycobacterium avium infection in young cats: overrepresentation of Abyssinian cats

Disseminated Mycobacterium avium-intracellulare complex (MAC) infection was diagnosed in 10 young cats (1-5 years of age) from Australia or North America between 1995 and 2004. A further two cats with disseminated mycobacteriosis (precise agent not identified) were recognised during this period. Of the 12, 10 were Abyssinian cats, one was a Somali cat and one was a domestic shorthair cat. None of the cats tested positive for either FeLV antigen or FIV antibody. The clinical course of these infections was indolent, with cats typically presenting for weight loss, initially in the face of polyphagia, with a chronicity of up to several months. Additional clinical features included lower respiratory tract signs and peripheral lymphadenomegaly. A marked diffuse interstitial pattern was evident in thoracic radiographs, even in cats without overt respiratory involvement. Hair clipped to perform diagnostic procedures tended to regrow slowly, if at all. Diagnosis was generally made by obtaining representative tissue specimens from mesenteric lymph nodes, liver or kidney at laparotomy, or from a popliteal lymph node. The primary antecedent event was most likely colonisation of either the alimentary or respiratory tract, followed by local invasion and eventual lymphatic and haematogenous dissemination. Nine cases were treated using combination therapy with agents effective for MAC infection in human patients. Two cats are still undergoing initial therapy and have responded. Of the remaining seven, all responded during long courses (5-14 months) of clarithromycin combined with either clofazimine or rifampicin, and a fluoroquinolone or doxycycline. Of these, three cats remain well (with durations between 2 months and 2 years following therapy); two developed recurrent disease (at 3 months and 2 years, respectively, following therapy) and have restarted therapy. The remaining two cats improved 1 year and 5 months, respectively, after diagnosis but ultimately succumbed. The two cats in which therapy was restarted have improved dramatically. Certain lines of Abyssinian and Somali cats likely suffer from a familial immunodeficiency that predisposes them to infection with slow-growing mycobacteria such as MAC.

Distribution of Mycobacterium avium complex isolates in tissue samples of pigs fed peat naturally contaminated with mycobacteria as a supplement

In early 1999, there was an increased incidence of tuberculous lesions in the lymph nodes of slaughtered pigs in the Czech Republic. In part 1 of this study, tuberculous lesions were detected in 140 (62%) tissue samples collected from pigs coming from 15 farms in 15 districts at routine veterinary meat inspections in abattoirs. Mycobacteria were isolated from 37 (16%) tissue samples: 34 Mycobacterium avium subsp. hominissuis isolates and three environmentally derived mycobacteria. In search of infection sources, M. avium subsp. hominissuis was isolated from 38 (79%) samples of peat used as a feed supplement. In part 2 of our study, the head, mesenteric, and inguinal lymph nodes of 117 randomly selected slaughtered pigs from one farm with young piglets fed peat as a supplement were investigated for mycobacterial infection. From 65 (56%) pigs, a total of 76 mycobacterial isolates were identified (56 M. avium subsp. hominissuis isolates, 5 M. avium subsp. avium isolates, 3 M. intracellulare isolates, and 12 environmentally derived mycobacterial isolates). IS1245 restriction fragment length polymorphism (RFLP) types with >20 bands of 45 distinct RFLP types were found in 49 M. avium subsp. hominissuis isolates from pigs (n = 31) and peat (n = 18). Identical RFLP types were found in only four pig isolates. Five randomly selected isolates from pigs and peat were subcultured to six independent clones or colonies. Among the IS1245 RFLP types of 30 clones, identical RFLP types obtained from pigs and peat were identified, which confirmed the hypothesis that peat contaminated with mycobacteria represents a significant source of mycobacterial infection for pigs.