Background
Methods
Collection and decontamination of clinical specimens
Culture and identification of the isolates
Biochemical identification
DNA extraction
PCR for 16S rRNA
PCR specific for hsp65 gene
Sequencing of 16S rRNA and hsp65 PCR product fragments
Ethical clearance
Results
Detection of Mycobacteria and Nocardia species
Profiles of isolates obtained by using the biomèrieux ID 32C yeast identification system
Isolate | Profile | Organism |
---|---|---|
1 | 37,735,522 |
Streptomyces cyanescens
|
2 | 37,735,522 |
Streptomyces cyanescens
|
3 | 37,516,506 |
S. griseus
|
4 | 75,112,246 |
A. madurae
|
5 | 71,414,140 |
N. brasiliensis
|
6 | 20,004,004 |
N. nova
|
7 | 26,420,142 |
N. asteroides
|
8 | 10,000,304 |
N. farcinica
|
9 | 61,400,304 |
N. farcinica
|
10 | 00000106 |
N. asteroides
|
11 | 00040100 |
N. asteroides
|
12 | 20,000,100 |
N. asteroides
|
13 | 00000104 |
N. asteroides
|
14 | 31,014,100 |
N. brasiliensis
|
15 | 31,414,100 |
N. brasiliensis
|
16 | 20,000,401 |
N. asteroides
|
17 | 20,000,100 |
N. asteroides
|
18 | 10,000,204 |
N. farcinica
|
19 | 71,414,140 |
N. brasiliensis
|
20 | 00040100 |
N. asteroides
|
Identification of Nocardia species by 16S rRNA and hsp65 gene sequencing
Smear microscopy | API profile | Biomèrieux ID 32C yeast identification system | 16S rRNA gene | Proximal cluster |
hsp65 gene | Identity (%) |
---|---|---|---|---|---|---|
Sm + ve | 37,735,522 |
Streptomyces cyanescens
|
N. farcinica
| NA* |
N.farcinica
| 99 |
Sm-ve | 71,414,140 |
N. brasiliensis
|
N. cyriacigeorgica
| TDQ659904 |
N. cyriacigeorgica
| 99 |
Sm-ve | 20,004,004 |
N. nova
|
N. jinanensis
| TDQ462650 |
N. testacea
| 100 |
Sm-ve | 26,420,142 |
N. asteroides
|
N. farcinica
| NA* |
N.farcinica
| 99 |
Sm-ve | 10,000,304 |
N. farcinica
|
N. flavorosea
| TAY756552 |
N. flavorosea
| 99 |
Sm-ve | 61,400,304 |
N. farcinica
|
N. farcinica
| TAY756551 |
N. farcinica
| 99 |
Sm-ve | 00000106 |
N. asteroides
|
N. cyriacigeorgica
| TDQ659904 |
N. cyriacigeorgica
| 99 |
Sm-ve | 00040100 |
N. asteroides
|
N. nova
| TGQ376190 |
N. nova
| 100 |
Sm + ve | 20,000,100 |
N. asteroides
|
N. carnea
| TZ36929b
|
N. sp./flavorosea
| 99 |
Sm + ve | 00000104 |
N. asteroides
|
N. farcinica
| NA* |
N. farcinica
| 99 |
Sm-ve | 31,014,100 |
N. brasiliensis
|
N. thailandica
| TGQ376186 |
N. cyriacigeorgica
| 99 |
Sm-ve | 31,414,100 |
N. brasiliensis
|
N. cyriacigeorgica
| TDQ659904 |
N. cyriacigeorgica
| 99 |
Sm + ve | 20,000,401 |
N. asteroides
|
N. testacea
| TAY903612 |
N. testacea
| 99 |
Sm-ve | 20,000,100 |
N. asteroides
|
N. testacea
| TAY903612 |
N. testacea
| 100 |
Sm-ve | 10,000,204 |
N. farcinica
|
N. brevicatena
| TAY756545 |
N. brevicatena
| 99 |
Sm-ve | 71,414,140 |
N. brasiliensis
|
N. flavorosea
| TAY756552 |
N.flavorosea
| 99 |
Sm-ve | 00040100 |
N. asteroides
|
N. cyriacigeorgica
| TDQ659904 |
N. cyriacigeorgica
| 99 |
N. cyriacigeorgica
(n = 4) |
N. farcinica
(n = 4) |
N. testacea
(n = 2) |
N. flavorosea
(n = 2) |
N. nova
(n = 1) |
N. jinanensis
(n = 1) |
N. thailandica
(n = 1) |
N. carnea
(n = 1) |
N. brevicatena
(n = 1) | Total N (%) | |
---|---|---|---|---|---|---|---|---|---|---|
Age (yrs): | ||||||||||
• ≤ 35 | 1 | 1 | 2 | 1 | 0 | 0 | 1 | 0 | 1 | 7 (41.2) |
• ≥ 35 | 3 | 3 | 0 | 1 | 1 | 1 | 0 | 1 | 0 | 10 (58.8) |
Sex | ||||||||||
• Male | 2 | 2 | 0 | 2 | 1 | 1 | 0 | 0 | 8 (47.1) | |
• Female | 2 | 2 | 2 | 0 | 0 | 0 | 1 | 1 | 1 | 9 (52.9) |
Clinical symptoms | ||||||||||
• Chronic cough ≥2 weeks | 4 | 4 | 2 | 2 | 1 | 1 | 1 | 1 | 1 | 17 (100) |
• Haemoptysis | 1 | 1 | 0 | 1 | 1 | 0 | 1 | 0 | 0 | 5 (29.4) |
• Dyspnoea | 3 | 3 | 0 | 1 | 0 | 1 | 0 | 1 | 1 | 10 (58.8) |
• Night sweat | 1 | 3 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 11 (64.7) |
• Fever | 4 | 3 | 2 | 2 | 0 | 1 | 0 | 1 | 1 | 14 (82.4) |
• Fatigue | 2 | 2 | 1 | 2 | 0 | 1 | 1 | 1 | 0 | 10 (58.8) |
• Weight loss | 1 | 2 | 0 | 1 | 0 | 1 | 0 | 1 | 1 | 7 (41.2) |
Concurrent conditions | ||||||||||
• Smoking | 2 | 2 | 0 | 0 | 1 | 0 | 1 | 0 | 0 | 6 (35.3) |
• TB- Coinfection | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 2 (11.8) |
• HIV- Coinfection | 1 | 1 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 3 (17.7) |
•
Nocardia alone | 4 | 2 | 2 | 1 | 1 | 1 | 1 | 0 | 1 | 13 (76.5) |
Smear Microscopy | ||||||||||
• AFB positive | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 2 (11.8) |
• AFB negative | 4 | 3 | 2 | 2 | 1 | 1 | 1 | 0 | 1 | 15 (88.2) |
Treatment initiated | ||||||||||
• Anti-TB drugs | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 2 (11.8) |
• Broad-spectrum antibiotics | 4 | 2 | 1 | 1 | 0 | 1 | 0 | 0 | 1 | 10 (58.8) |
• Not treated | 1 | 1 | 1 | 1 | 1 | 0 | 0 | 0 | 0 | 5 (29.4) |