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...