Extrapulmonary Nontuberculous Mycobacteria Infections in Hospitalized Patients

United States, 2009-2014

Emily E. Ricotta; Jennifer Adjemian; Rebekah A. Blakney; Yi Ling Lai; Sameer S. Kadri; D. Rebecca Prevots


Emerging Infectious Diseases. 2021;27(3):845-852. 

In This Article


Of 9,196,147 unique inpatients from 275 inpatient facilities reporting culture results throughout the United States, laboratory-confirmed extrapulmonary NTM was reported for 998 unique species/source isolates from 831 patients at 89 hospitals. Isolates represented 321 (39%) patients with SST infections, 269 (32%) with disseminated infections, and 337 (41%) with infection at other sites. Both disseminated and SST infections were reported for 23 (2.8%) patients. Most isolates identified to the species level were Mycobacterium avium complex (MAC) (50%), followed by M. fortuitum (10%), M. abscessus (9.4%), M. chelonae (5.3%), and M. chelonae/abscessus (4.3%). Other species were rapidly growing NTM (8.7%), non–rapidly growing NTM (3.7%), or not speciated (7.9%) (Table 3).

The overall 6-year prevalence of extrapulmonary NTM in hospitals reporting ≥1 inpatient with extrapulmonary NTM was 11 cases/100,000 inpatients. Site-specific infections were 4.4 SST infections/100,000 inpatients, 3.7 disseminated infections/100,000 inpatients, and 0.3 cases of both types of infection/100,000 inpatients. Annual prevalence of disseminated NTM remained stable over the study period, whereas SST infections increased 8.2% (95% CI 1%–15%) (Figure 1). Prevalence was highest in the Midwest (13 cases/100,000 inpatients), South (13 cases/100,000 inpatients), and Northeast (11 cases/100,000 inpatients) and lowest in the West (5.3 cases/100,000 inpatients).

Figure 1.

Annual prevalence of extrapulmonary nontuberculous mycobacteria cases by year and site of infection among hospitalized patients in the United States, 2009–2014. SST, skin and soft tissue.

Among patients, 49% were female, 58% were White, and 60% were >40 years of age; 32% were Black and 11% were <18 years of age. Relative to patients with SST infections, those with disseminated cases were more frequently male (60% vs. 45%; p<0.001), younger (mean age 40 vs. 50 years; p<0.001), and Black (56% vs. 13%; p<0.001). Among patients with both SST and disseminated infection, 61% were female, most (52%) were White, and mean age was 52 years (Table 4). Among patients with SST infections, 15% had undergone a surgical procedure (e.g., invasive, minimally invasive, surgical biopsy) compared with 4% of patients with disseminated infection. Among all patients, 20% had ever taken an immunosuppressive drug (Table 4); among these, 19% had SST infection, 23% had disseminated infection, and 22% had both. Crude overall mortality rate was 5% (11% among those with disseminated and 2% among those with SST infections); 1 patient with both types of infection died.

MAC accounted for more than half of disseminated (54%) and SST infections (52%), and rapidly growing NTM accounted for 34% of SST infections and 37% of disseminated infections. Distribution of cases by source and species varied by region (Table 4). SST infections were more common in the Midwest (30% vs. 18%; p = 0.002) and Northeast (32% vs. 18%; p<0.001), and disseminated infections were more common in the South (60% vs. 32%; p<0.001). MAC was found at a higher proportion than rapidly growing NTM in the Northeast (30% vs. 13%; p<0.001), and rapidly growing NTM were found at a higher proportion in the Midwest (32% vs. 23%; p = 0.004) and South (52% vs .40%; p = 0.001). When infections were broken down further by species and infection type, a significantly higher proportion of MAC was found in the Northeast for disseminated (62% vs. 29%; p = 0.002) and SST infections (72% vs. 12%; p<0.001) and in the South for disseminated infections (54% vs. 36%; p<0.001). Compared with MAC, the proportion of rapidly growing NTM causing SST infections was higher in the South (51% vs. 33%; p = 0.009) (Figure 2).

Figure 2.

Distribution of extrapulmonary NTM cases by species and infection type across regions among hospitalized patients in the United States, 2009–2014. DIS, disseminated; NTM, nontuberculous mycobacteria; MAC, Mycobacterium avium complex; SST, skin and soft tissue.

Underlying conditions included fungal co-infections (11%), HIV infection (13%), cancer (4%), and other immunodeficiencies (2%); 14 (2%) NTM patients had a history of invasive cardiac procedures (Table 4). A higher proportion of patients with MAC than with rapidly growing NTM had HIV infection (21% vs. 1.5%; p<0.001) and fungal infections (16% vs. 6.7%; p<0.001), and a higher proportion of patients with rapidly growing NTM had cancer (6.7% vs. 1.4%; p<0.001). Co-infections (including pulmonary pathogens) identified during the same hospitalization as NTM isolation were common; ≥1 concomitant pathogen of interest grew for 42% of patients (Appendix Table 4).

By extrapulmonary NTM infection type, co-infection was found for 37% of patients with SST, 47% with disseminated, and 61% with both. Among all persons with co-infection, 13% had Staphylococcus spp., 10% had Candida spp., 9.0% had Enterococcus spp., 7.0% had Streptococcus spp., 6.6% had Pseudomonas spp., 5.2% had Escherichia coli, 3.8% had Klebsiella spp., and 8.2% had M. tuberculosis complex (MTBC) (Table 5). Of patients with both SST and disseminated NTM, 36% were co-infected with Enterococcus spp., 26% with MTBC, and 29% with Staphylococcus spp. (Figure 3). Patients with disseminated NTM had a higher proportion of Acinetobacter spp., Bacillus spp., Candida spp., Clostridium spp., Coccidioides spp., Cryptococcus spp., Enterococcus spp., E. coli, Stenotrophomonas spp., and Streptococcus spp. infection; patients with SST NTM infection had a higher proportion of Aeromonas spp., Aspergillus spp., Corynebacterium spp., Enterobacter spp., Klebsiella spp., MTBC, Salmonella spp., and Staphylococcus spp., although the differences were not significant (Table 5; Figure 3).

Figure 3.

Distribution of laboratory-confirmed concomitant pathogens by infection type among hospitalized patients with extrapulmonary nontuberculous mycobacteria, United States, 2009–2014.