Mycobacterium abscessus is an emerging rapidly growing mycobacterium (RGM) causing a pseudotuberculous lung disease to which patients with cystic fibrosis (CF) are particularly susceptible. We report here its complete genome sequence. The genome of M. abscessus (CIP 104536T) consists of a 5,067,172-bp circular chromosome including 4920 predicted coding sequences (CDS), an 81-kb full-length prophage and 5 IS elements, and a 23-kb mercury resistance plasmid almost identical to pMM23 from Mycobacterium marinum. The chromosome encodes many virulence proteins and virulence protein families absent or present in only small numbers in the model RGM species Mycobacterium smegmatis. Many of these proteins are encoded by genes belonging to a “mycobacterial” gene pool (e.g. PE and PPE proteins, MCE and YrbE proteins, lipoprotein LpqH precursors). However, many others (e.g. phospholipase C, MgtC, MsrA, ABC Fe(3+) transporter) appear to have been horizontally acquired from distantly related environmental bacteria with a high G+C content, mostly actinobacteria (e.g. Rhodococcus sp., Streptomyces sp.) and pseudomonads. We also identified several metabolic regions acquired from actinobacteria and pseudomonads (relating to phenazine biosynthesis, homogentisate catabolism, phenylacetic acid degradation, DNA degradation) not present in the M. smegmatis genome. Many of the “non mycobacterial” factors detected in M. abscessus are also present in two of the pathogens most frequently isolated from CF patients, Pseudomonas aeruginosa and Burkholderia cepacia. This study elucidates the genetic basis of the unique pathogenicity of M. abscessus among RGM, and raises the question of similar mechanisms of pathogenicity shared by unrelated organisms in CF patients.
We performed a multicenter prevalence study of nontuberculous mycobacteria (NTM) involving 1,582 patients (mean age, 18.9 years; male/female ratio, 1.06) with cystic fibrosis in France. The overall NTM prevalence (percentage of patients with at least one positive culture) was 6.6% (104/1,582 patients), with prevalences ranging from 3.7% (in the east of France) to 9.6% (in the greater Paris area). Mycobacterium abscessus complex (MABSC; 50 patients) and Mycobacterium avium complex (MAC; 23 patients) species were the most common NTM, and the only ones associated with fulfillment of the American Thoracic Society bacteriological criteria for NTM lung disease. The "new" species, Mycobacterium bolletii and Mycobacterium massiliense, accounted for 40% of MABSC isolates. MABSC species were isolated at all ages, with a prevalence peak between 11 and 15 years of age (5.8%), while MAC species reached their highest prevalence value among patients over 25 years of age (2.2%).Nontuberculous mycobacteria (NTM) have emerged as "new" pathogens in cystic fibrosis (CF) patients over the last 2 decades (10). CF centers worldwide have reported isolation of NTM from the respiratory tracts of CF patients, with prevalence values ranging from 5% to 20% (5,6,8,9,13,14,16,19,22,25). Mycobacterium avium complex (MAC) and Mycobacterium abscessus complex (MABSC) species are the most frequently isolated NTM and together account for Ͼ95% of NTM lung diseases affecting CF patients. The MAC, a member of the subgroup comprising slowly growing mycobacteria, ranks first in North America (22), whereas the MABSC, a member of the subgroup comprising rapidly growing mycobacteria, seems to predominate in Western Europe (15,23,25) and is also more prevalent than the MAC in Israel (19).Previous studies have reported isolation of NTM from 6.6 to 9.8% of French CF cohorts (9,23,25). These studies also reported a much higher isolation rate for MABSC than for MAC or other NTM species (23,25). However, these studies were done exclusively in pediatric CF centers in Paris. This may have distorted the results since MABSC species are more prevalent than MAC species in children (23). Moreover, the epidemiology of NTM in Paris does not necessarily reflect the situation in other regions of France. For example, studies involving non-CF patients have reported higher rates of NTM disease in urban areas (20). Moreover, previous French studies were performed before M. abscessus (now M. abscessus sensu lato, or the MABSC) was shown to include at least three distinct species, M. abscessus (sensu stricto) (hereafter referred to as M. abscessus), Mycobacterium massiliense, and Mycobacterium bolletii (1,3). The prevalences of these three species in CF patients in France were therefore unknown.We thus conducted a large, prospective, nationwide study addressing NTM prevalence in CF patients in France. This study shows relatively low prevalence figures for French CF centers. It also provides evidence that MABSC species are currently the most prevalent NTM in the French CF populat...
We report the case of a cystic fibrosis patient colonized with a smooth-morphotype form of Mycobacterium abscessus who developed acute respiratory failure with the emergence of an isogenic rough (R) variant while he was recovering from peritonitis-induced shock. This report emphasizes the role of R forms in severe M. abscessus infections. (Fig. 1). CASE REPORTIn December 2003, the patient was admitted to the emergency unit of Hôpital Cochin, Assistance Publique-Hôpitaux de Paris, Paris, France, with a colic perforation and diffuse peritonitis secondary to a stercolith. Septic shock with severe hypoxemia occurred on day 1, requiring mechanical ventilation, inotropic adrenaline support, and treatment with combined antibiotics (ceftazidime, vancomycin, tobramycin, and ornidazole), hydrocortisone hemisuccinate, and drotrecogin alpha. Laboratory parameters showed lymphopenia (absolute lymphocyte count, 1,060/mm 3 ) and raised serum transaminase levels (alanine aminotransferase level, 80 IU/liter, three times the upper limit of the normal range). The patient's clinical status slowly improved. Bronchial aspiration performed on day 6 yielded A. fumigatus and a rough (R) variant of M. abscessus (M. abscessus CF01-R). Positive A. fumigatus antigenemia results led to the initiation of antifungal therapy on day 9.Unexpectedly, septic shock recurred on day 11. Severe respiratory failure was present (ratio of the partial pressure of oxygen in arterial blood to the fraction of inspired oxygen [PaO 2 /FiO 2 index], 190), associated with patchy alveolar consolidation (Fig. 2). A surgical lung biopsy (right thoracotomy) was performed on day 12: the biopsy specimen culture was positive for an R-morphotype isolate of M. abscessus as the sole pathogen, with concordant histology showing a granulomatous epithelioid reaction with giant cells in areas of peribronchovascular fibrosis and multiple microabscesses. Antibiotic therapy was shifted empirically to imipenem-cilastin, amikacin, and clarithromycin on day 13. Bronchial aspiration performed on day 13 yielded results similar to those from the lung biopsy, thus confirming the diagnosis of M. abscessus respiratory infection (7). Antibiotic susceptibility testing performed on several isolated strains (Institut Pasteur, Centre National de Références, Paris, France) showed the strains to be susceptible to the prescribed regimen. Bronchoalveolar lavage on day 32 still yielded an R-morphotype isolate of M. abscessus. Nebulized amikacin was added to the systemic anti-M. abscessus therapy on day 56. The patient became apyrexial on day 77, and mechanical ventilation was stopped on day 83. The patient was discharged on day 128 (April 2004) under a regimen of clarithromycin monotherapy, which was maintained until April 2005. Sputum samples remained repeatedly positive for M. abscessus (R form) throughout treatment (Fig. 1) (24) and multilocus sequence typing (data not shown) confirmed the clonal nature of the isolates of different morphotypes (Fig. 3). These results established the persistence ...
Mycobacterium abscessus, Mycobacterium bolletii, and Mycobacterium massiliense (Mycobacterium abscessus sensu lato) are closely related species that currently are identified by the sequencing of the rpoB gene. However, recent studies show that rpoB sequencing alone is insufficient to discriminate between these species, and some authors have questioned their current taxonomic classification. We studied here a large collection of M. abscessus (sensu lato) strains by partial rpoB sequencing (752 bp) and multilocus sequence analysis (MLSA). The final MLSA scheme developed was based on the partial sequences of eight housekeeping genes: argH, cya, glpK, gnd, murC, pgm, pta, and purH. The strains studied included the three type strains (M. abscessus CIP 104536 T , M. massiliense CIP 108297 T , and M. bolletii CIP 108541 T ) and 120 isolates recovered between 1997 and 2007 in France, Germany, Switzerland, and Brazil. The rpoB phylogenetic tree confirmed the existence of three main clusters, each comprising the type strain of one species. However, divergence values between the M. massiliense and M. bolletii clusters all were below 3% and between the M. abscessus and M. massiliense clusters were from 2.66 to 3.59%. The tree produced using the concatenated MLSA gene sequences (4,071 bp) also showed three main clusters, each comprising the type strain of one species. The M. abscessus cluster had a bootstrap value of 100% and was mostly compact. Bootstrap values for the M. massiliense and M. bolletii branches were much lower (71 and 61%, respectively), with the M. massiliense cluster having a fuzzy aspect. Mean (range) divergence values were 2.17% (1.13 to 2.58%) between the M. abscessus and M. massiliense clusters, 2.37% (1.5 to 2.85%) between the M. abscessus and M. bolletii clusters, and 2.28% (0.86 to 2.68%) between the M. massiliense and M. bolletii clusters. Adding the rpoB sequence to the MLSA-concatenated sequence (total sequence, 4,823 bp) had little effect on the clustering of strains. We found 10/120 (8.3%) isolates for which the concatenated MLSA gene sequence and rpoB sequence were discordant (e.g., M. massiliense MLSA sequence and M. abscessus rpoB sequence), suggesting the intergroup lateral transfers of rpoB. In conclusion, our study strongly supports the recent proposal that M. abscessus, M. massiliense, and M. bolletii should constitute a single species. Our findings also indicate that there has been a horizontal transfer of rpoB sequences between these subgroups, precluding the use of rpoB sequencing alone for the accurate identification of the two proposed M. abscessus subspecies.
We determined nucleotide sequences of rpoB, hsp65, and sodA in 59 clinical isolates (from 58 patients) of the Mycobacterium abscessus group. Identification to the species level, based on three target genes, was concordant for 44 isolates (25 M. abscessus, 13 Mycobacterium massiliense, and 6 Mycobacterium bolletii isolates) and discordant for 15 isolates which had "interspecific composite patterns." Sequence analysis of five housekeeping genes also showed composite patterns in 8 of these 15 isolates.Mycobacterium abscessus is a rapidly growing mycobacterium (RGM) causing a wide spectrum of disease in humans, including pulmonary disease, skin and soft tissue disease, and disseminated disease (8). It is a major pathogen in patients with cystic fibrosis (CF) (15,23,25,29), in which case it is responsible for severe lung disease and may cause disseminated infection following transplantation (10). M. abscessus has undergone many taxonomic changes since its first description by Moore and Frerichs in 1953, in We recently isolated an RGM strain which was identified as M. abscessus sensu stricto (for reasons of simplicity, M. abscessus sensu stricto will hereinafter be referred to as M. abscessus) on the basis of the rpoB sequence but as M. massiliense on the basis of the hsp65 sequence (strain AP3). This suggested the existence of isolates with "interspecific composite patterns" (e.g., isolates with an M. abscessus rpoB sequence and an M. massiliense hsp65 sequence) within the M. abscessus group, potentially leading to inaccuracy for diagnostic approaches based on single-target sequencing. We investigated this issue by determining the sequences of rpoB, hsp65, and another widely used molecular target, sodA (3, 18), in a large panel of M. abscessus sensu lato strains.The studied panel included 59 clinical isolates of M. abscessus sensu lato obtained from 58 CF patients in France between 1997 and 2007. Strains were grown on sheep blood agar at 37°C for 4 days to obtain visible colonies. Smooth (S) and rough (R) phenotypes were determined as described previously (9). A loopful of colonies was used for DNA extraction by using Tris-EDTA, lysozyme, and proteinase K, in the presence of thiourea to avoid DNA degradation (37). [3]) were amplified by PCR using AmpliTaq Gold polymerase (Applied Biosystems, Courtaboeuf, France). Dideoxy sequencing was carried out on both strands with the BigDye Terminator cycle sequencing kit (Applied Biosystems). Sequencing products were purified by gel filtration (Bio-Gel P-100; Bio-Rad, Marnes-la-Coquette, France) and were run on a 3700 DNA analyzer (Applied Biosystems).Species identification based on rpoB, hsp65, and sodA sequencing was concordant for 44 isolates (25 M. abscessus [16 S and 9 R], 13 M. massiliense [8 S and 5 R], and 6 M. bolletii [4 S and 2 R] isolates) and discordant for 15 isolates (8 S and 7 R). In 8 of these 15 isolates (see Table 2), both rpoB and hsp65 were 100% identical to the M. abscessus type strain sequence, whereas sodA shared the highest identity with the M. bolle...
Mycobacterium abscessus is a species of rapidly growing mycobacteria (RGM). This species can cause skin and soft tissue infections after trauma or surgical procedures, pulmonary infections and disseminated diseases in immunocompromised patients. It has been rarely documented after tattoo procedures. Herein we describe the case of a 51-year- old man who presented with erythematous papules over a tattoo on the back 10 days after a tattoo session. Culture revealed M. abscessus. Tattoo infections, clinical features and treatment options due to RGM are reviewed.
e Nonpigmented and late-pigmenting rapidly growing mycobacteria (RGM) have been reported to commonly colonize water production and distribution systems. However, there is little information about the nature and distribution of RGM species within the different parts of such complex networks or about their clustering into specific RGM species communities. We conducted a large-scale survey between 2007 and 2009 in the Parisian urban tap water production and distribution system. We analyzed 1,418 water samples from 36 sites, covering all production units, water storage tanks, and distribution units; RGM isolates were identified by using rpoB gene sequencing. We detected 18 RGM species and putative new species, with most isolates being Mycobacterium chelonae and Mycobacterium llatzerense. Using hierarchical clustering and principal-component analysis, we found that RGM were organized into various communities correlating with water origin (groundwater or surface water) and location within the distribution network. Water treatment plants were more specifically associated with species of the Mycobacterium septicum group. On average, M. chelonae dominated network sites fed by surface water, and M. llatzerense dominated those fed by groundwater. Overall, the M. chelonae prevalence index increased along the distribution network and was associated with a correlative decrease in the prevalence index of M. llatzerense, suggesting competitive or niche exclusion between these two dominant species. Our data describe the great diversity and complexity of RGM species living in the interconnected environments that constitute the water production and distribution system of a large city and highlight the prevalence index of the potentially pathogenic species M. chelonae in the distribution network. N onpigmented and late-pigmenting rapidly growing mycobacteria (RGM) are ubiquitous in soil and water environments (1-6). Most are harmless saprophytes, but some, such as Mycobacterium chelonae and Mycobacterium abscessus, are opportunistic pathogens that are causing increasing concern (7-9). Potentially pathogenic RGM are associated with a wide spectrum of diseases in humans, including pulmonary tract, skin, soft tissue, and disseminated infections (10-14), mostly in patients with predisposing conditions (e.g., lung diseases, chronic obstructive pulmonary disease, cystic fibrosis, genetic predisposition, or immunosuppressive therapy). Contamination and hypersensitive reactions are often due to environmental exposure (associated with, for example, hot tubs, metalworking fluids, or contaminated dust) (15-19), and many outbreaks following invasive medical procedures have been reported over the last decade (20-25). Tap water may be an important source of contamination in urban environments (13,18,(26)(27)(28)(29)(30).RGM are commonly recovered from water treatment and distribution systems (31-38), probably because they can form biofilms (2, 39-41) and resist chlorination and oligotrophic conditions (42,43). Mycobacterium chelonae and Mycobact...
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