Extra-Pulmonary Nontuberculous Mycobacterial Infections: 16 Year Retrospective Analysis at an Academic Institution in Cincinnati, Ohio

Extra-pulmonary Nontuberculous Mycobacterial Infections: 16 year retrospective analysis at an academic institution in Cincinnati, Ohio.

A thesis submitted to the

Graduate School

of the University of Cincinnati

in partial fulfillment of the

requirements for the degree of

Master of Science

in Clinical & Translational Research

In the Department of Environmental Health

Division of Epidemiology

of the College of Medicine

July, 2017

Kiran Afshan

MBBS, University of Karachi, Pakistan, August, 2006

Committee Chair: Erin Haynes, DrPH

Abstract

Title: Extra-pulmonary Nontuberculous Mycobacterial Infections: 16 year retrospective analysis at an academic institution in Cincinnati, Ohio.

Authors: Afshan K, Smulian AG, Jandarov RA, Haglund L.

Background: Nontuberculous mycobacterial infections (NTM), once considered a rare cause of human disease, are now increasingly recognized in clinical practice. We have sought to identify clinical and demographic characteristics of the extra-pulmonary NTM infections presenting at our institution during 2000-2015.

Methods: Records of patient with culture proven extra-pulmonary NTM infections were reviewed. Demographic information, clinical and microbiologic characteristics and treatment outcomes were captured.

Results: 58 cases of extra-pulmonary NTM infections identified were classified into cutaneous 9

(15.52%), soft tissue 38 (65.52%), osteo-articular 9 (15.52%) and disseminated infections 2

(3.45%). 52% of the cases were male. Median age at diagnosis was 52years. All cases were diagnosed based on culture positivity. Among identified mycobacterial species, rapid growing mycobacteria constituted 79% of all cases with following distribution: Mycobacterium fortuitum complex 28 (48.28%), Mycobacterium abscessus/chelonae complex 15 (25.86%),

Mycobacterium avium intracellulare complex 3 (5.17%), Mycobacterium marinum 3 (5.17%),

Mycobacterium gordonae 2 (3.45%), and one case each of Mycobacterium arupense,

Mycobacterium goodii, Mycobacterium haemophilum, Mycobacterium kansasii, Mycobacterium mageritense, Mycobacterium simiae and Mycobacterium wolinskyi, [combined 7(12.04%)].

Overall cure rate was 84.6%.

Conclusion: Health care professionals should be aware of increasing significance of the extra- pulmonary NTM infections and should utilize appropriate diagnostic modalities to ensure proper identification and improve treatment outcomes.

Key Words: Nontuberculous mycobacteria, extra-pulmonary infections, M fortuitum, M abscessus/chelonae, immunocompromised conditions, treatment outcome.

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Table of Contents

Introduction------1

Methods------2

Results------3-5

Discussion------5-7

References------8-10

Tables and Figures------11-14

List of Tables & Figures

Table 1: Baseline characteristics of the patients with extra-pulmonary nontuberculous

Mycobacterial infections during 2000-2015 (n=58).

Table 2: Distribution of mycobacterial species causing extra-pulmonary NTM infections (n=58).

Figure 1: Antimicrobial susceptibility profile for the extra-pulmonary M. fortuitum isolates.

Figure 2: Temporal trends of extra-pulmonary NTM infections, 2000-2015.

Introduction

Nontuberculous mycobacteria (NTM) are ubiquitous environmental agents which are widely distributed in nature1. Belonging to the genus mycobacteria, NTM are acid fast bacilli which exclude Mycobacterium tuberculosis complex and Mycobacterium leprae. There are more than

180 known species of NTM (http://www.bacterio.net/mycobacterium.html) which are traditionally described as rapid growing (RGM) or slow growing (SGM) based on their growth characteristics in the culture media. NTM cause disease states in humans with varied clinical presentation.

Nontuberculous mycobacteria, once considered a rare cause of human disease1, have lately emerged as pathogen with increasing clinical significance2, 3, 4. The incidence of NTM infections is on a rise worldwide5-8. NTM have increasingly been implicated in health care related outbreaks9, notably the outbreak of Mycobacterium chimera infections in cardiothoracic surgery patients in centers across Europe and United States10, 11. Nontuberculous mycobacteria are now considered serious pathogen in patients with predisposing conditions such as cystic fibrosis12, 13 and with advanced immunosuppression14-17.

NTM cause three major clinical syndromes; pulmonary, extra-pulmonary and disseminated disease18. The majority of pulmonary infections occur in immunocompetent patients19. The disseminated infections are mostly encountered in patients with immunodeficiency states like

AIDS, transplant recipients and patients with cancer19-21. The spectrum of extra-pulmonary NTM infections is varied and include skin and soft tissue infections, osteo-articular infections, catheter related and device related infections22. In this retrospective study, we aim to report the clinical features and treatment outcomes of extra-pulmonary NTM infections encountered in our institution over a span of 16 years.

Methods

We reviewed medical records of the patients with nontuberculous mycobacterial infections at the University of Cincinnati Medical Center (UCMC), Cincinnati Veterans Affairs Medical Center

(VAMC) and West Chester Hospital between 2000 and 2015. We utilized mycobacterial culture data from three sources; the microbiology laboratory at the UCMC, VAMC, and a database maintained at the Hamilton County Public Health Tuberculosis Control Unit. The Hamilton

County Public Health Department has set up a laboratory surveillance system whereby all laboratories report positive mycobacterial culture results to the Health Department to capture potential tuberculosis cases. We screened these sources to identify patients with positive culture data and performed a retrospective chart review to identify cases of extra-pulmonary

NTM infections at our institution.

We defined a case of extra-pulmonary NTM infection as a patient demonstrating clinical signs and symptoms of infection, along with a positive culture result for nontuberculous mycobacteria.

We excluded all cases of pulmonary NTM infections, cases of active tuberculosis or disseminated mycobacterium avium complex (MAC) infections in patients with HIV. We abstracted data including patients’ demographic information, clinical characteristics, microbiologic data, histopathology findings and radiographic abnormalities. We recorded information pertaining to the treatment modalities utilized, the length of antimicrobial therapy and eventual outcome as defined by clinical cure of infection. We applied descriptive statistics to analyze results using statistical software R. We analyzed categorical variables using Chi-square test and continuous variables using student-T test. This study has been approved by the institutional review board of the University of Cincinnati.

Results

We identified 58 cases of extra-pulmonary NTM infections, which were classified as cutaneous

9 (15.52%), soft tissue 38 (65.52%), osteo-articular 9 (15.52%) and disseminated infections 2

(3.45%). There were 30 male (52%) and 28 female (48%) cases. Mean age at diagnosis was

51.26 years (median 52.90, range 24.83-84.93). There were 38 Caucasians (66%) and 17

African Americans (29%).

The clinical and demographic characteristics of the extra-pulmonary NTM infections are summarized in Table 1. Among comorbid conditions, 11 cases (18.97%) had diabetes mellitus,

8 (13.79%) had cardiovascular disease and 13 (22.41%) had chronic kidney disease. 25 cases

(43.1%) reported history of smoking and 14 cases (24.14%) reported alcohol dependence.

There were 22 (37.93%) immunocompromised (IC) patients in our study with extra-pulmonary

NTM infections. Among these patients, 5 had HIV infection with median CD4 count of 13 cells/µL. There were 4 transplant recipients on immunosuppressive regimen. Rest of the 13 IC cases were on immunosuppressive medications such as corticosteroids and biologics for variety of reasons including Rheumatoid arthritis, Sjogren’s syndrome and Sarcoidosis.

The predisposing conditions for the extra-pulmonary NTM infections identified in our study include open trauma in 10 cases (17.24%) and penetrating injuries in 5 cases (8.62%). Injection drug use was identified in 2 cases (3.45%), while another case diagnosed with nasal and maxillary sinusitis had history of intranasal cocaine use. 9 cases (15.52%) occurred post- surgery. Device related infections were identified in 8 cases (13.79%), among which 6 had infected peritoneal dialysis catheters, one patient had ventriculo-peritoneal shunt infection and one with gastric lap band associated abdominal wall infection and intra-abdominal abscess. 6 cases (10.34%) reported history of administration of injectable medications at the infection site prior to acquisition of infections, among which 4 cases received steroid injections and one case received epidural and estrogen injection each. There were 5 (8.62%) extra-pulmonary NTM

3 infections associated with breast augmentation procedures due to infected breast implants.

There was a history of animal bite in 4 cases (6.90%). Tattooing was identified as a risk factor in

3 cases (5.17%) of extra-pulmonary NTM infections in our study.

The diagnosis of extra-pulmonary NTM infections was based on presence of clinical and microbiologic criteria. All 58 patients met both of these criteria (100%), 33 patients (56.9%) additionally had positive histopathologic findings. Diagnosis was further supported by presence of radiographic abnormalities detected on imaging performed at the time of presentation in 35 cases (60.3%). Pain was the most common presenting symptom, detected in 53 cases

(25.86%). Fever was present in 15 cases (25.86%) and elevated leukocyte count in 13 cases

(28.89%). Erythrocyte sedimentation rate (ESR) was elevated in 16 cases (88.89%) and C reactive protein (CRP) in 13 cases (81.25%). The mean duration of symptoms prior to the clinical presentation was 66.53 days (median 18, Interquartile range, IQR 7-88, n=53). The mean time to diagnosis after clinical presentation was 54.17 days (median 15, IQR 6-50, n=53).

The distribution of the NTM species causing extra-pulmonary NTM infections is depicted in

Table 2 and noted as follows: Mycobacterium fortuitum complex 28 (48.28%), Mycobacterium abscessus/chelonae complex 15 (25.86%), Mycobacterium avium intracellulare complex 3

(5.17%), Mycobacterium marinum 3 (5.17%), Mycobacterium gordonae 2 (3.45%), and one case each of Mycobacterium arupense, Mycobacterium goodii, Mycobacterium haemophilum,

Mycobacterium kansasii, Mycobacterium mageritense, Mycobacterium simiae and

Mycobacterium wolinskyi, [combined 7(12.04%)]. The macrolide susceptibility was known for 43 isolates. Overall, 23 NTM isolates (53.48%) were noted to be susceptible to clarithromycin, while 13 isolates (30.23%) were resistant. The antimicrobial susceptibility profile of 28 M fortuitum isolates is presented in figure 1.

The majority of the extra-pulmonary NTM cases in our study were treated with a combination of medical and surgery therapy (36, 63.16%, n=57). 6 cases only received surgical treatment,

4 while 2 cases received no treatment at all. 75.5% of those treated medically received a combination of empiric treatment followed by susceptibility directed antimicrobial therapy.

Combination of two or more antimicrobials was utilized in the treatment regimen in 81.6% of the cases, as opposed to single antimicrobial agent used in 12.2% of the cases. The median duration of antimicrobial regimen received was 168 days (IQR 116-321). We recorded an overall cure rate of 84.6% in our study. The median time to cure was 132.50 days (IQR 86.50-233.25).

There was no statistically significant difference in cure rate based on age, gender, ethnicity or immune status.

Discussion

This study has identified rapid growing mycobacteria, RGM (Mycobacterium fortuitum,

Mycobacterium abscessus/chelonae complex) as the predominant cause of extra-pulmonary

NTM infection as they comprise 75% of all the isolates in our study. This result is in keeping with the prior published studies whereby RGM are increasingly recognized as a cause of extra- pulmonary NTM22, 23, 24. Our study also confirms the traditional risk factors for the acquisition of extra-pulmonary NTM infections25. NTMs are widely prevalent in water and soil and are believed to be acquired through contamination or inoculation from environmental sources, traumatic or iatrogenic. In our study, about 50% of all NTM infections have a known predisposing condition pointing to environmental inoculation as a likely etiology. 38% of the cases in our study are either post-surgical or device related, which might underlie an iatrogenic source of contamination in health related setting, although we were not able to capture any health related outbreak in our study owing to retrospective study design.

We observed that Mycobacterium fortuitum tends to cause infections in immunocompetent patients while infections in the immunocompromised patients were predominantly caused by

Mycobacterium abscessus/chelonae complex. In this study 60% of all M abscessus/chelonae infections occurred in immunocompromised patients as opposed to 21% of Mycobacterium

5 fortuitum infections. This result is in accordance with a similar study on NTM SSTI conducted in

Taiwan which noted that M. fortuitum is more likely associated with previous invasive procedure, while M. abscessus is more likely associated with concomitant immunosuppression22. Other

NTM species causing infections in the IC hosts in our study include Mycobacterium hemophilum which caused disseminated skin nodules in a patient with cardiac transplant. We observed three cases of Mycobacterium avium intracellulare complex (MAC) in non-HIV immunocompromised patients; one case of tenosynovitis of the wrist and two cases of skin nodules. Among patients with HIV, we observed three cases of Mycobacterium fortuitum, while one case each of

Mycobacterium marinum and Mycobacterium kansasii causing tenosynovitis of the hand and septic arthritis respectively. This finding underscores the importance of consideration of non-

MAC NTM infections in the differential diagnosis when encountering patients with advanced immunosuppression including HIV.

Our study identified two cases of Mycobacterium gordonae infections. M. gordonae is usually considered a contaminant when found in clinical specimen1, 26. However, in our study, we found both cases meeting clinical and microbiologic criteria for infection as delineated in our study.

One case of M. gordonae caused peritoneal dialysis catheter associated peritonitis in an immunocompetent patient, who was treated with a combination of antimicrobials with eventual cure. The other case of M. gordonae caused olecranon bursitis in a severely immunocompromised patient with rheumatoid arthritis and plaque psoriasis, who was receiving an immunosuppressive regimen comprising of prednisone, methotrexate, hydroxychloroquine and infliximab. This patient underwent resection of the olecranon bursa but did not receive any antimicrobial therapy. The outcome was initial cure following surgery, with subsequent two relapses culminating in permanent disability.

The incidence of the nontuberculous mycobacterial infections is increasing worldwide5. This increase is also attributed to an increase in the incidence of extra-pulmonary NTM infections23.

In our study, we have observed an overall upward trend in the number of cases of extra- pulmonary NTM infections as depicted in Figure 2. The reason for this increase could be multifactorial including, but not limited to, availability of newer diagnostic modalities such as 16S rRNA sequencing27, 28 and MALDI-TOF29, an increase in the number of susceptible hosts such as patients with advanced immunosuppression30, and heightened awareness among health care professionals leading to increase in surveillance efforts9. We presume that the number of cases of NTM infections identified in our study only constitute a fraction of the actual cases owing to the stringent inclusion criteria applied in our study. Many more cases could have been included in the study if culture data were known, and as such, a number of cases were missed since culture data were not obtained. Thus, the actual burden of the extra-pulmonary NTM infections might be underreported and underrepresented in this study.

Our study has several limitation, including small sample size, retrospective study design and reliance on the medical records to abstract data. To mitigate this problem we applied strict inclusion and exclusion criteria and utilized three different sets of data sources to ensure the integrity of our results. We included only definitive, culture proven cases of extra-pulmonary

NTM infections. We assume that the number of cases identified in our study is an underrepresentation of the actual disease burden. We recommend that health care professionals be aware of this increasing significance of the extra-pulmonary NTM infections and utilize appropriate diagnostic modalities to maximize their identification. Further prospective studies are needed to enhance our knowledge and understanding of the extra-pulmonary NTM infections.

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Tables and Figures

Table 1: Baseline characteristics of the patients with extra-pulmonary nontuberculous Mycobacterial infections during 2000-2015 (n=58). Age at diagnosis, mean (median; range) 51.26 years (52.90; 24.83-84.93)

Gender Male 30 (52%) Female 28 (48%) Race Caucasian 38 (66%) African Americans 17 (29%) Others 2 (3%) Unknown 1 (2%) State Ohio 54 (93%) Kentucky 3 (5%) Illinois 1 (2%) Infection type Soft tissue 38 (65.52) Cutaneous 9 (15.52) Osteo-articular 9 (15.52) Disseminated 2 (3.45) Co-morbid Conditions Diabetes mellitus 11 (18.97%) Chronic kidney disease 13 (22.41%) Cardiovascular disease 8 (13.79%) Autoimmune diseases 8 (13.79%) Predisposing conditions Trauma 10 (17.24) Penetrating injury 5 (8.62) Post-surgery 9 (15.52) Device related 8 (13.79) Breast augmentation procedures 5 (8.62) Injectable medication use at the infection site 6 (10.34) Illicit Injection Drug Use 2 (3.45%) Animal bites 4 (6.90) Tattoos 3 (5.17) Immunocompromising HIV infection 5 (8.62) Conditions Transplant recipients 4 (6.90)* Corticosteroids 15 (25.86)* Biologic agents 3 (5.17)*

Diagnosis Culture positivity 58 (100%) Presence of Clinical features 58 (100%) Histopathologic findings 33 (56.89%) Imaging findings 35 (60.34%)

Treatment (n=57) Medical 13 (22.81%) Surgical 6 (10.53%) Combined medical and surgical 36 (63.16%) No treatment received 2 (3.51%) Cure rate 84.6% All values are presented as number and percentages unless otherwise indicated *Numbers and percentages overlap, total 22 immunocompromised patients.

Table 2: Distribution of mycobacterial species causing extra-pulmonary NTM infections (n=58).

Mycobacterial species Number (Percentage) Rapidly Growing Mycobacteria (RGM): 46 (79.3%) Mycobacterium fortuitum complex 28 (48.3) Mycobacterium abscessus/chelonae complex 15 (25.9) Mycobacterium goodii 1 (1.7) Mycobacterium mageritense 1 (1.7) Mycobacterium wolinskyi 1 (1.7) Intermediately or Slowly Growing Mycobacteria (SGM): 12 (20.7%) Mycobacterium avium intracellulare complex 3 (5.2) Mycobacterium marinum 3 (5.2) Mycobacterium gordonae 2 (3.5) Mycobacterium haemophilum 1 (1.7) Mycobacterium kansasii 1 (1.7) Mycobacterium simiae 1 (1.7) Mycobacterium arupense 1 (1.7)

Antimicrobial Susceptibility profile of extra-pulmonary M. fortuitum isolates (N=28)

6666 6 7 8

0 11 1 0 1 0 1 2 8 21 12

20 21 7 21 0 19 18

1 0 10 7 6

1 Amikacin Cefoxitin Clarithromycin Ciprofloxacin Doxycycline TMP/SMX Linezolid Imipenem

Susceptible Intermediate Resistant Not Available

Figure 1: Antimicrobial susceptibility profile for the extra-pulmonary M. fortuitum isolates.

Extra-pulmonary NTM Infections, temporal trends over 2000-2015

12 12

10 10 Infections 8 8 NTM 7 of

6 Cases 5 of

4 4 33 Number 2 2 111 1

0 2000 2003 2005 2006 2007 2008 2009 2010 2011 2012 2013 2014 2015 Time in Years

Figure 2: Temporal trends of extra-pulmonary NTM infections, 2000-2015.