Species distribution and susceptibility of Nocardia isolates in New Zealand 2002-2021

The aim was to record the distribution and susceptibility of Nocardia species in New Zealand. Local and referred isolates were identified by an evolving approach over the study period including conventional phenotypic methods, susceptibility profiles, matrix-assisted laser desorption ionisation-time of flight mass spectrometry (MALDI-TOF) and molecular sequencing. Isolates previously identified as a Nocardia sp. or part of the N. asteroides complex were reidentified by MALDI-TOF and/or molecular methods. Antimicrobial susceptibility to eight antibiotics was performed by standard microbroth dilution. The site of isolation, susceptibility profiles and species distribution were analysed. A total of 383 isolates were tested: N. brasiliensis 23 (6%), N. cyriacigeorgica 42 (11%), N. farcinica 41 (11%), N. nova complex 226 (59%), and 51 (13%) other species/complexes. The respiratory tract was the most common site of infection (244, 64%), with skin and soft tissue the second most common site (104, 27%). All 23 N. brasiliensis isolates were from skin and soft tissue specimens. Almost all isolates (≥98%) were susceptible to amikacin, linezolid and trimethoprim-sulfamethoxazole; 35% and 77% were resistant to clarithromycin and quinolones, respectively. The expected susceptibility profiles of the four common species and complex were observed for most agent-organism parings. Multi-drug resistance was uncommon (3.4%). The spectrum of Nocardia species in New Zealand is similar to overseas reports and our most common group is the N. nova complex. While amikacin, linezolid and trimethoprim-sulfamethoxazole remain good empiric treatment choices, other agents should have their activity confirmed before use.

Efficient differentiation of Nocardia farcinica, Nocardia cyriacigeorgica and Nocardia beijingensis by high-resolution melting analysis using a novel locus

Accurate identification of Nocardia species remains a challenge due to the complexities of taxonomy and insufficient discriminatory power of traditional techniques. We report the development of a molecular technique that utilizes real-time PCR-based high-resolution melting (HRM) analysis for differentiation of the most common Nocardia species. Based on a novel fusA-tuf intergenic region sequence, Nocardia farcinica, Nocardia cyriacigeorgica and Nocardia beijingensis were clearly distinguished from one another by HRM analysis. The limit of detection of the HRM assay for purified Nocardia spp. DNA was at least 10 fg. No false positives were observed for specificity testing of 20 non-target clinical samples. In comparison to established matrix-assisted laser desorption/ionization-time of flight MS, the HRM assay improved the identification of N. beijingensis. Additionally, all the products of PCR were verified by direct sequencing. In conclusion, the developed molecular assay allows simultaneous detection and differentiation of N. farcinica, N. cyriacigeorgica and N. beijingensis with high sensitivity and specificity.

When reporting Nocardia spp is not enough. Brain abscess caused by Nocardia farcinica

Abscesses caused by the genus Nocardia spp are relatively rare, accounting for approximately 2 % of all brain abscesses, but with a significantly higher mortality. Special stains of brain abscess material from a 60-year-old man showed Gram-positive branching bacilli and the presence of long, acid-fast branching filamentous bacilli suggesting Nocardia infection. Presented here is a case of multidisciplinary management of a patient who developed cerebral abscesses by Nocardia farcinica, confirmed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), that was susceptible to trimethoprim/sulfamethoxazole, linezolid, imipenem and not susceptible to minocycline. This case highlights the importance of performing subtyping and antimicrobial testing in order to improve clinical and treatment outcomes due to patterns of antibiotics resistance among Nocardia species.

Resistance gene pool to co-trimoxazole in non-susceptible Nocardia strains

The soil-borne pathogen Nocardia sp. causes severe cutaneous, pulmonary, and central nervous system infections. Against them, co-trimoxazole (SXT) constitutes the mainstay of antimicrobial therapy. However, some Nocardia strains show resistance to SXT, but the underlying genetic basis is unknown. We investigated the presence of genetic resistance determinants and class 1–3 integrons in 76 SXT-resistant Nocardia strains by PCR and sequencing. By E test, these clinical strains showed SXT minimum inhibitory concentrations of ≥32:608 mg/L (ratio of 1:19 for trimethoprim: sulfamethoxazole). They belonged to 12 species, being the main representatives Nocardia farcinica (32%), followed by N. flavorosea (6.5%), N. nova (11.8%), N. carnea (10.5%), N. transvalensis (10.5%), and Nocardia sp. (6.5%). The prevalence of resistance genes in the SXT-resistant strains was as follows: sul1 and sul2 93.4 and 78.9%, respectively, dfrA(S1) 14.7%, blaTEM-1 and blaZ 2.6 and 2.6%, respectively, VIM-2 1.3%, aph(3′)-IIIa 40.8%, ermA, ermB, mefA, and msrD 2.6, 77.6, 14.4, and 5.2%, respectively, and tet(O), tet(M), and tet(L) 48.6, 25.0, and 3.9%, respectively. Detected amino acid changes in GyrA were not related to fluoroquinolone resistance, but probably linked to species polymorphism. Class 1 and 3 integrons were found in 93.42 and 56.57% strains, respectively. Class 2 integrons and sul3 genes were not detected. Other mechanisms, different than dfrA(S1), dfrD, dfrF, dfrG, and dfrK, could explain the strong trimethoprim resistance shown by the other 64 strains. For first time, resistance determinants commonly found in clinically important bacteria were detected in Nocardia sp. sul1, sul2, erm(B), and tet(O) were the most prevalent in the SXT-resistant strains. The similarity in their resistome could be due to a common genetic platform, in which these determinants are co-transferred.

Pulmonary nocardiosis in southern Taiwan

BACKGROUND/PURPOSE

Nocardiosis mainly affects immunocompromised patients. The objectives of this study were to better understand the epidemiologic, demographic, clinical, and laboratory information in patients with pulmonary nocardiosis in southern Taiwan.

METHODS

Retrospective analyzing patients aged ≥18 years with culture-proven pulmonary nocardiosis received treatment at KCGMH between January 2004 and June 2010. Nocardiae were identified by 16S rRNA gene sequence analysis. Patients with pulmonary nocardiosis caused by the mostly commonly encountered Nocardia sp. were compared with those with pulmonary nocardiosis due to other Nocardia spp.

RESULTS

Among the 20 patients included, cough (80%) and fever (50%) were the 2 leading symptoms/signs, while lobar consolidation (50%) and pleural effusion (40%) were the most frequent radiographic manifestations. Eighteen patients (90%) had at least one underlying disease/condition. Nocardia cyriacigeorgica was most commonly found. Compared with those whose pathogens were other Nocardia spp., patients with pulmonary nocardiosis caused by N cyriacigeorgica experienced higher clinical severity as measured by APACHE II score (19.8 ± 7.0 vs. 12.8 ± 6.7; p = 0.04) and ICU admission rate (100% vs. 25%; p < 0.01). Thirteen patients (65%) turned out to be fatal. The severity (APACHE II score, 18 ± 6 vs. 10 ± 8; p = 0.02) and the proportion of acute and subacute pulmonary nocardiosis (76% vs. 0%, p = 0.03) between fatal and survived patients differed significantly.

CONCLUSIONS

N cyriacigeorgica was the most common pathogen in southern Taiwan. Higher mortality rate in patients with pulmonary nocardiosis was related to disease severity and acute and subacute infection.