Identification and antimicrobial susceptibility of referred Nocardia isolates in Victoria, Australia 2009-2019

Nocardia sichangensis sp. nov., isolated from rocky soil of Sichang Island

A novel actinobacterium, designated strain SC052T, was isolated from rocky soil collected from Sichang Island, Chonburi Province, Thailand. Morphological and chemotaxonomic analyses indicated that strain SC052T belongs to the genus Nocardia. The strain exhibited extensively branched substrate mycelia and produced short chains of four to six spores on the aerial mycelia. The cell wall contained meso-diaminopimelic acid, while ribose, arabinose, glucose and galactose were detected in the whole-cell hydrolysate. The identified polar lipids included diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannoside, one unidentified glycolipid, two unidentified lipids and three unidentified phospholipids. The menaquinone was MK-8 (H4ω-cycl). The major cellular fatty acids included C16:0, C17:0, C18:0, 10-methyl C18:0 tuberculostearic acid, C18:1  ω9c, summed feature 3 and summed feature 6. Mycolic acids were also detected. A blast search of the 16S rRNA gene sequence revealed that strain SC052T exhibited the highest similarity (99.7%) to Nocardia araoensis NBRC 100135T. Phylogenetic analysis based on the gyrB gene and phylogenomic tree construction further supported that N. araoensis NBRC 100135T is the closest phylogenetic neighbour of strain SC052T. Comparative genomic analyses between strain SC052T and N. araoensis NBRC 100135T revealed digital DNA-DNA hybridization values of 47.9% and average nucleotide identity values of 91.5% (ANIb) and 92.8% (ANIm), all of which fall below the threshold used to delineate strains of the same species. Based on phenotypic and genomic analyses, strain SC052T is proposed as a novel species within the genus Nocardia, for which the name Nocardia sichangensis sp. nov. is proposed (=TBRC 14541T, =NBRC 115195T).

Nocardia arseniciresistens sp. nov., isolated from lead-zinc mine tailing

A strain with aerial hyphae presented, designated KC 131T, was isolated from lead-zinc mine tailings, Lanping, Yunnan province, Southwest China. The strain was Gram-stain-positive, acid-alcohol-fast, aerobic and non-motile. Based on 16S rRNA gene sequence and phylogeny analysis, strains Nocardia ninae NBRC 108245T (98.4%), Nocardia alba YIM 30243T (98.4%) and Nocardia colli CICC 11023T (98.2%) were the most closely related species of strain KC 131T, and the four strains were in one cluster. The meso-diaminopimelic acid, arabinose and galactose were detected in the whole-cell hydrolysates. The mycolic acids were presented, and the major fatty acids (>5%) were C16:0 (30.0%), C18:1 ω9c (12.5%), C18:0 (7.5%), 10-methyl C18:0 (27.3%) and summed feature 3 (C16:1 ω7c and/or C16:1 ω6c; 12.4%). The menaquinone was MK-8 (H4, ω-cyclo), and the major polar lipids were diphosphatidylglycerol and phosphatidylethanolamine. All these features were consistent with the genus Nocardia. Digital DNA-DNA hybridization values between strain KC 131T and N. ninae NBRC 108245T, N. alba DSM 44684T and N. colli CICC 11023T were 23.8%, 20.9% and 23.5%, respectively. The average nucleotide identity values between strain KC 131T and the three strains were 80.0%, 76.5% and 80.0%, respectively. In addition, some physiological and biochemical characteristics were also different. Thus, strain KC 131T represents a novel species of the genus Nocardia, for which the name Nocardia arseniciresistens sp. nov. is proposed. The type strain is KC 131T (=CGMCC 1.19493T=JCM 35916T).

Trimethoprim-sulfamethoxazole dosing and outcomes of pulmonary nocardiosis

BACKGROUND

Nocardia often causes pulmonary infection among those with chronic pulmonary disease or immunocompromising conditions. Trimethoprim-sulfamethoxazole (TMP-SMX) is recommended as first-line treatment, though little data exists regarding outcomes of different dosing regimens.

METHODS

We performed a multicenter retrospective cohort study of adult patients with non-disseminated pulmonary nocardiosis initially treated with TMP-SMX monotherapy. Patients' initial TMP-SMX dosing was categorized as high- (> 10 mg/kg/day), intermediate- (5-10 mg/kg/day) or low-dose (< 5 mg/kg/day). Outcomes included one-year mortality, post-treatment recurrence, and dose adjustment or early discontinuation of TMP-SMX. SMX serum concentrations and their effect on management were also assessed. Inverse probability of treatment weighting was applied to Cox regression analyses.

RESULTS

Ninety-one patients were included with 24 (26.4%), 37 (40.7%), and 30 (33.0%) treated with high-, intermediate-, and low-dose TMP-SMX, respectively. Patients who initially received low-dose (HR 0.07, 95% CI 0.01-0.68) and intermediate-dose TMP-SMX (HR 0.27, 95% CI 0.07-1.04) had lower risk of one-year mortality than the high-dose group. Risk of recurrence was similar between groups. Nineteen patients had peak SMX serum concentrations measured which resulted in 7 (36.8%) dose changes and was not associated with one-year mortality or recurrence. However, 66.7% of the high-dose group required TMP-SMX dose adjustment/discontinuation compared to 24.3% of the intermediate-dose and 26.7% of the low-dose groups (p = 0.001).

CONCLUSIONS

Low- and intermediate-dose TMP-SMX for non-disseminated pulmonary nocardiosis were not associated with poor outcomes compared to high-dose therapy, which had a higher rate of dose adjustment/early discontinuation. Historically used high-dose TMP-SMX may not be necessary for management of isolated pulmonary nocardiosis.

Triple-drug antibiotic therapy for disseminated nocardial abscess in the mediastinum and brain of an immunocompetent patient: a case report

BACKGROUND

Nocardia are widely present in nature and considered opportunistic pathogens. They can result in hematogenous spread infection through the ruptured skin or respiratory tract when the host's immune system is compromised. Currently, 119 species of Nocardia have been identified, with 54 capable of causing infections in humans. Nocardial brain abscesses are a rare intracranial lesion that accounts for only 2% of all brain abscesses, but have a mortality rate of 20-55%. This article reports a successfully cured case of mediastinal Nocardia infection with disseminated brain abscess.

CASE PRESENTATION

The patient presented with intermittent chills, shivering, and fever, with the highest temperature of 39˚C, accompanied by shoulder and back pain, dizziness, and headaches. A chest-enhanced computed tomography (CT) revealed multiple enhanced nodulars in the bilateral hilum and mediastinum. A head-enhanced CT revealed scattered multiple ring-enhanced nodules in both cerebral hemispheres and the left cerebrum, accompanied by extensive surrounding edema. The mediastinal puncture tissue culture confirmed the growth of Nocardia. After twice discussions with multidisciplinary team (MDT) to rule out the possibility of mediastinal and intracranial metastatic tumors, we promptly initiated treatment with a triple-drug antibiotic regimen consisting of imipenem/cilastatin sodium, linezolid dextrose, and Trimethoprim-sulfamethoxazole (TMP-SMX). The patient ultimately achieved complete remission.

CONCLUSIONS

Mediastinal nocardiosis with disseminated brain abscesses is a rare condition that can be difficult to differentiate from brain metastases caused by lung cancer. Bacterial culture results, imaging features, and MDT discussions are crucial for accurate diagnosis and treatment. A triple-drug antibiotic regimen has been found to be effective in treatment with acceptable levels of toxicity.

Discovery of Novel Diagnostic Biomarkers for Common Pathogenic Nocardia Through Pan-Genome and Comparative Genome Analysis, with Preliminary Validation

The aim of this study was to reveal diagnostic biomarkers of considerable importance for common pathogenic Nocardia, utilizing pan-genomic and comparative genome analysis to accurately characterize clinical Nocardia infections. In this study, complete or assembled genome sequences of common pathogenic Nocardia and closely related species were obtained from NCBI as discovery and validation sets, respectively. Genome annotation was performed using Prokka software, and pan-genomic analysis and extraction of Nocardia core genes were performed using BPGA software. Comparative genome analysis of these core genes with the validation-set gene sequences was then performed using BLAT, with a threshold of 30% amino acid coverage and identity, in order to distinguish specific core genes. Finally, candidate gene-specific primers were designed using Snapgene software and DNA samples were obtained from clinical Nocardia strains and closely related species for validation. The analysis identified eighteen core genes specific to Nocardia spp., four core genes specific to N. farcinica, and forty-six core genes specific to N. cyriacigeorgica. After rigorous clinical validation, one gene from Nocardia spp. and five genes from N. cyriacigeorgica were confirmed to have high specificity and therefore can be used as reliable biomarkers for accurate diagnosis of Nocardia infection. This pioneering research reveals diagnostic biomarkers of considerable significance, with the potential to substantially enhance the precise diagnosis of common pathogenic Nocardia infections, thereby laying the groundwork for innovative diagnostic methodologies in subsequent studies.

Selenomethionine Mitigates Effects of Nocardia cyriacigeorgica-Induced Inflammation, Oxidative Stress, and Apoptosis in Bovine Mammary Epithelial Cells

Nocardia cyriacigeorgica causes bovine mastitis, reduces milk quantity and quality, and is often resistant to antimicrobials. Selenomethionine (SeMet) is a form of selenium, which reduces reactive oxygen species (ROS)-mediated apoptosis and intramammary infections. However, the protective effects of SeMet on N. cyriacigeorgica-infected bovine mammary epithelial cells (bMECs) are unclear. The objective of this study was to evaluate whether SeMet mitigated N. cyriacigeorgica-induced inflammatory injury, oxidative damage and apoptosis in bMECs. Cells were cultured with or without being pretreated with 40 µM of SeMet for 12 h, then challenged with N. cyriacigeorgica (multiplicity of infection = 5:1) for 6 h. Although N. cyriacigeorgica was resistant to lincomycin, erythromycin, enrofloxacin, penicillin, amoxicillin, cephalonium, cephalexin, and ceftriaxone, 40 μM SeMet increased cell viability and inhibited lactate dehydrogenase release in infected bMECs. Furthermore, N. cyriacigeorgica significantly induced mRNA production and protein expression of TNF-α, IL-1β, IL-6, and IL-8 at 6 h. Cell membrane rupture, cristae degeneration and mitochondria swelling were evident with transmission electron microscopy. Superoxide dismutase (SOD) and glutathione peroxidase (GSH-px) activities were down-regulated after 3, 6, or 12 h, whereas malondialdehyde (MDA) and ROS contents were significantly upregulated, with cell damage and apoptosis rapidly evident (the latter increased significantly in a time-dependent manner). In contrast, bMECs pretreated with 40 μM SeMet before infection, SOD, and GSH-px activities were upregulated (p < 0.05); MDA and ROS concentrations were downregulated (p < 0.05), and apoptosis was reduced (p < 0.05). In conclusion, 40 μM SeMet alleviated inflammation, oxidative stress and apoptosis induced by N. cyriacigeorgica in bMECs cultured in vitro.

Epidemiology, Timing, and Secondary Prophylaxis of Recurrent Nocardiosis

Background

Nocardia tends to cause infection in immunocompromised patients or those with chronic pulmonary disease. Nocardia is known to recur, prompting the practice of secondary prophylaxis in patients perceived at high risk. However, few data exist regarding the epidemiology of recurrent nocardiosis or the effectiveness of secondary prophylaxis.

Methods

We performed a multicenter, retrospective cohort study of adults diagnosed with nocardiosis from November 2011 to April 2022, including patients who completed primary treatment and had at least 30 days of posttreatment follow-up. Propensity score matching was used to analyze the effect of secondary prophylaxis on Nocardia recurrence.

Results

Fifteen of 303 (5.0%) patients developed recurrent nocardiosis after primary treatment. Most recurrences were diagnosed either within 60 days (N = 6/15, 40.0%) or between 2 to 3 years (N = 4/15, 26.7%). Patients with primary disseminated infection tended to recur within 1 year, whereas later recurrences were often nondisseminated pulmonary infection. Seventy-eight (25.7%) patients were prescribed secondary prophylaxis, mostly trimethoprim-sulfamethoxazole (N = 67/78). After propensity-matching, secondary prophylaxis was not associated with reduced risk of recurrence (hazard ratio, 0.96; 95% confidence interval, .24-3.83), including in multiple subgroups. Eight (53.3%) patients with recurrent nocardiosis required hospitalization and no patients died from recurrent infection.

Conclusions

Recurrent nocardiosis tends to occur either within months because of the same Nocardia species or after several years with a new species. Although we did not find evidence for the effectiveness of secondary prophylaxis, the confidence intervals were wide. However, outcomes of recurrent nocardiosis are generally favorable and may not justify long-term antibiotic prophylaxis for this indication alone.

Nocardia species distribution and antimicrobial susceptibility within Australia

BACKGROUND

Nocardia is a ubiquitous saprophyte capable of causing human disease. Disease is primarily respiratory or cutaneous, usually acquired via inhalation or inoculation. Under the influence of environmental and host factors, Nocardia incidence and species distribution demonstrate geographical variation.

AIMS

To examine for differences in Nocardia incidence within Western Australia (WA) and analyse species distribution in the context of prior published studies. To analyse antibiogram data from a nationwide passive antimicrobial resistance surveillance program.

METHODS

Retrospective extraction of laboratory data for Western Australian Nocardia isolates over a 21-year period. Analysis of Nocardia antimicrobial susceptibility testing data submitted to the Australian Passive Antimicrobial Resistance Surveillance (APAS) program between 2005 and 2022.

RESULTS

Nine hundred sixty WA isolates were identified, giving an annual incidence of 3.03 per 100 000 population with apparent latitudinal variation. The four most common species identified within WA and amongst APAS isolates were N. nova, N. cyriacigeorgica, N. brasiliensis and N. farcinica. APAS data demonstrated that all species exhibited high rates of susceptibility to linezolid (100%) and trimethoprim-sulfamethoxazole (98%). Amikacin (>90% susceptibility for all species except N. transvalensis) was the next most active parenteral agent, superior to both carbapenems and third-generation cephalosporins. Susceptibility to oral antimicrobials (other than linezolid) demonstrated significant interspecies variation.

CONCLUSIONS

We demonstrate geographical variation in the distribution of Nocardia incidence. Four species predominate in the Australian setting, and nationwide data confirm a high in vitro susceptibility to trimethoprim-sulphamethoxazole and linezolid, justifying their ongoing role as part of first-line empiric therapy.

Discovery and Biosynthesis of the Cytotoxic Polyene Terpenomycin in Human Pathogenic Nocardia

Nocardia are opportunistic human pathogens that can cause a range of debilitating and difficult to treat infections of the lungs, brain, skin, and soft tissues. Despite their close relationship to the well-known secondary metabolite-producing genus, Streptomyces, comparatively few natural products are known from the Nocardia, and even less is known about their involvement in the pathogenesis. Here, we combine chemistry, genomics, and molecular microbiology to reveal the production of terpenomycin, a new cytotoxic and antifungal polyene from a human pathogenic Nocardia terpenica isolate. We unveil the polyketide synthase (PKS) responsible for terpenomycin biosynthesis and show that it combines several unusual features, including "split", skipped, and iteratively used modules, and the use of the unusual extender unit methoxymalonate as a starter unit. To link genes to molecules, we constructed a transposon mutant library in N. terpenica, identifying a terpenomycin-null mutant with an inactivated terpenomycin PKS. Our findings show that the neglected actinomycetes have an unappreciated capacity for the production of bioactive molecules with unique biosynthetic pathways waiting to be uncovered and highlights these organisms as producers of diverse natural products.

Mortality After Nocardiosis: Risk Factors and Evaluation of Disseminated Infection

Background

Nocardia primarily infects patients who are immunocompromised or those with chronic lung disease. Although disseminated infection is widely recognized as an important prognostic factor, studies have been mixed on its impact on outcomes of nocardiosis.

Methods

We performed a retrospective cohort study of adults with culture-confirmed nocardiosis. Advanced infection was defined as disseminated infection, cavitary pulmonary infection, or pleural infection. The primary outcome was 1-year mortality, as analyzed by multivariable Cox regression.

Results

Of 511 patients with culture growth of Nocardia, 374 (73.2%) who had clinical infection were included. The most common infection sites were pulmonary (82.6%), skin (17.9%), and central nervous system (14.2%). In total, 117 (31.3%) patients had advanced infection, including 74 (19.8%) with disseminated infection, 50 (13.4%) with cavitary infection, and 18 (4.8%) with pleural infection. Fifty-nine (15.8%) patients died within 1 year. In multivariable models, disseminated infection was not associated with mortality (hazard ratio, 1.16; 95% CI, .62-2.16; P = .650) while advanced infection was (hazard ratio, 2.48; 95% CI, 1.37-4.49; P = .003). N. farcinica, higher Charlson Comorbidity Index, and culture-confirmed pleural infection were also associated with mortality. Immunocompromised status and combination therapy were not associated with mortality.

Conclusions

Advanced infection, rather than dissemination alone, predicted worse 1-year mortality after nocardiosis. N. farcinica was associated with mortality, even after adjusting for extent of infection. While patients who were immunocompromised had high rates of disseminated and advanced infection, immunocompromised status did not predict mortality after adjustment. Future studies should account for high-risk characteristics and specific infection sites rather than dissemination alone.

The species distribution and antimicrobial resistance profiles of Nocardia species in China: A systematic review and meta-analysis

BACKGROUND

Nocardia species can cause local or disseminated infection. Prompt diagnosis and appropriate treatment of nocardiosis are required, because it can cause significant morbidity and mortality. Knowledge of local species distribution and susceptibility patterns is important to appropriate empiric therapy. However, knowledge on the epidemiology and antimicrobial susceptibility profiles of clinical Nocardia species remains limited in China.

METHODS

The data of isolation of Nocardia species were collected from databases such as Pubmed, Web of Science, Embase as well as Chinese databases (CNKI, Wanfang and VIP). Meta-analysis was performed using RevMan 5.3 software. Random effect models were used and tested with Cochran's Q and I2 statistics taking into account the possibility of heterogeneity between studies.

RESULTS

In total, 791 Nocardia isolates were identified to 19 species levels among all the recruited studies. The most common species were N. farcinica (29.1%, 230/791), followed by N. cyriacigeorgica (25.3%, 200/791), N. brasiliensis (11.8%, 93/791) and N. otitidiscaviarum (7.8%, 62/791). N. farcinica and N. cyriacigeorgica are widely distributed, N. brasiliensis mainly prevalent in the Southern, N. otitidiscaviarum mainly distributed in the east coastal provinces of China. Totally, 70.4% (223/317) Nocardia were cultured from respiratory tract specimens, 16.4% (52/317) from extra-pulmonary specimens, and 13.3% (42/317) from disseminated infection. The proportion of susceptible isolates as follows: linezolid 99.5% (197/198), amikacin 96.0% (190/198), trimethoprim-sulfamethoxazole 92.9% (184/198), imipenem 64.7% (128/198). Susceptibility varied by species of Nocardia.

CONCLUSIONS

N. farcinica and N. cyriacigeorgica are the most frequently isolated species, which are widely distributed in China. Pulmonary nocardiosis is the most common type of infection. Trimethoprim-sulfamethoxazole can still be the preferred agent for initial Nocardia infection therapy due to the low resistance rate, linezolid and amikacin could be an alternative to treat nocardiosis or a choice in a combination regimen.

Pathogenic Nocardia amamiensis infection: A rare case report and literature review

Background

To date, only six cases of Nocardia amamiensis infection have been reported, including two ocular cases, three pulmonary cases, and one disseminated case. However, no Nocardia amamiensis pulmonary infection cases have been reported in immunocompetent patients without structural pulmonary disease. This study describes a rare case and provides a detailed review of all previous cases.

Methods

A pulmonary infection caused by Nocardia amamiensis in a 64-year-old man with low-grade fever, night sweats, and weight loss was reported. All previously reported cases of Nocardia amamiensis infection were searched and reviewed.

Results

The pathogen was identified as Nocardia amamiensis using bronchoalveolar lavage fluid (BALF) mNGS, and the current case was successfully treated with trimethoprim-sulfamethoxazole (ST) monotherapy. mNGS and 16S rRNA PCR are standard tests to identify Nocardia.Conclusion: mNGS has high diagnostic performance for Nocardia amamiensis. Further studies are needed to clarify the clinical characteristics and explore more effective treatment protocols for this rare pathogen.