Non-tuberculous Mycobacteria have gained much clinical significance in the last couple of decades not only in immuno-compromised but also in immuno-competent patients. Their ubiquitous distribution in nature and man-made ecologies put them at an advantage of having their hosts close to their ecological niches. NTM cause a wide variety of infections. Two broad categories include pulmonary and extra-pulmonary NTM infections. Therapy of these infections depends on the NTM species isolated, site of infection and its drug susceptibility profile. Current guidelines recommend speciation of all clinically significant NTM isolates [9]. Published literature describes geographical variation in NTM species distribution. Present study is the first from Pakistan describing identification of NTM species and their clinical significance from clinical specimens submitted to a tertiary care hospital.
A total of 104 NTM isolates were included in this study. Among these, 68% (71/104) were RGM and 32% (33/104) were SGM. This is in contrast to an Indian study where 87% of the isolates were reported to be RGM over a period of 6 years [7]. A study from Taiwan reported 41.4% of NTM as RGM isolated from 1997–2003 [8]. In this Taiwanese study 39% of the NTM were Mycobacterium avium complex (MAC). A study from Karachi, Pakistan, described M. xenopi as the most common while M. fortuitum as relatively rare NTM species among isolates collected from four laboratories in Karachi [14]. These results are in contrast with the present study and need further studies to confirm the findings reported.
In our study, 70% of the NTM could be identified (54/71 from RGM and 19/33 from SGM). M. fortuitum group (21/71, 29.6%) and MAC (14/33, 42.4%) were the most common RGM and SGM species isolated respectively in our study. From India, 46% and 41% of the NTM were M. chelonae and M. fortuitum respectively among all the species included in the study [7]. A multi-country study involving 14 countries [5], reported M. fortuitum as the commonest species from Iran and Turkey and MAC as most frequent isolate from European countries and Brazil. Belgium had the highest rate for M. xenopi followed by M. gordonae. Czech Republic was reported to have M. gordonae and M. kansasii as the most frequent NTM species isolated. These findings highlight local and regional differences in NTM species distribution.
Association of NTM isolate and clinical presentation is difficult particularly for respiratory isolates owing to the ubiquitous nature of these organisms. Multiple factors increase the probability of clinical significance of NTM: “recovery from multiple specimens or sites, recovery of the organism in large quantities (AFB smear-positive specimens) or recovery of an NTM isolate from a normally sterile site” [9]. A total of 27 isolates from 17 patients were found to be clinically significant. Table 2 describes distribution of NTM isolates according to specimen type in cases where clinical information was available. This could be performed for a proportion of cases because clinical details were available for a limited number of patients. Finding of MAC as the commonest species associated with clinical disease (4 pulmonary and 2 extra-pulmonary cases) followed by RGM is in accordance with a study from Taiwan where most cases were caused by MAC and RGM [8].
Healthcare associated NTM infections are well documented in the literature [15, 16]. We were able to assess 3 such extra-pulmonary healthcare associated NTM infections. Medical instruments can easily become contaminated with NTM if these are washed with tap water containing NTM and/or failure to use mycobactericidal disinfectants [17]. Similarly, fluids used during surgical procedures or for irrigation of surgical wounds can become contaminated with NTM if adequate sterile practices are not adhered to, resulting in non-healing surgical wounds.
Apart from causing healthcare associated infections, NTM may also contaminate specimens during collection (e.g. specimen contamination by NTM contained in tap water used to rinse mouth before sputum collection) [18]. Similarly, laboratories may be reporting an increased number of NTM because of contamination of reagents used in processing of specimens [19]. Therefore, isolation of NTM from clinical specimens should be evaluated carefully in the light of clinical information to assess their significance.
Proper management of patients with a particular NTM infection depends on drug susceptibility testing performed by standard methodology. We performed DST of NTM isolates by broth microdilution which is a reference method as recommended by CLSI [10]. Because of limited information on pharmacokinetic data to inform decisions regarding therapeutic MICs, discrepancies exist between in vitro DST and in vivo treatment outcomes [20]. American Thoracic Society/Infectious Diseases Society of America (ATS/IDSA) guidelines generally recommend a combination of agents based on in vitro DST results. Amikacin was found to inhibit all our RGM isolates that were tested and similarly all RGM were susceptible to clarithromycin (except for M. fortuitum group where it is not recommended because of the presence of an inducible macrolide resistance ‘erm’ gene). Linezolid also seems to be a good option for RGM treatment. Quinolone susceptibility was found to be variable with 45% and 75% isolates susceptible to ciprofloxacin and moxifloxacin respectively suggesting that these agents may be used in treatment regimens. Imipenem results are not encouraging with only 20% RGM found susceptible. Therefore in our setting, treatment options for M. fortuitum infections would be a combination of two agents with in vitro activity and that may include amikacin with a quinolone, linezolid or cotrimoxazole or two oral agents if amikacin cannot be tolerated. Looking at the DST results, clarithromycin either with amikacin or linezolid appears to be an option for treating M. chelonae-abscessus infections. For MAC, all isolates were susceptible to clarithromycin and most (4/6, 66.7%) were susceptible to linezolid. Only one isolate was susceptible to moxifloxacin. Thus, clarithromycin which is the first line agent for the treatment of MAC infection in a multidrug regimen (including ethambutol, rifamycin and/or amikacin/streptomycin depending on the disease severity) appears a viable option. Though, rifampin, isoniazid, ethambutol, ethionamide, streptomycin and clarithromycin are inhibitory for M. kansasii isolates, but susceptibility breakpoints are not established for all of these drugs. Routine testing of rifampin and clarithromycin only is recommended for M. kansasii isolates. All our M. kansasii isolates were susceptible to clarithromycin and moxifloxacin and may be utilized for treatment in a multidrug regimen.
This study has certain limitations. Currently, molecular identification is used to identify related/newer NTM species. We could not perform molecular identification for our NTM isolates to show concordance. However, in resource limited settings where these newer technologies are not widely used either because of cost or lack of expertise, conventional test based NTM identification should be undertaken in an attempt to identify clinically significant isolates. Another limitation of this study is unavailability of clinical details for all the cases which limited our ability to assess their clinical significance.
