Rapid Detection of Nocardia by Next-Generation Sequencing

Weng, Shanshan; Zhang, Han‐Yue; Ai, Jingwen; Gao, Yan; Liu, Yuan-Yuan; Xu, Bin; Zhang, Wenhong

doi:10.3389/fcimb.2020.00013

Cited by 36 publications

(28 citation statements)

References 9 publications

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“…More than 50 species can cause infections both in immunocompetent and immunocompromised individuals [ 4 ]. Due to the inexperience of the clinical laboratory technicians in primary hospitals in China, the particular characteristics of Nocardia growth, the unspecific pulmonary symptoms, as well as the low sensitivity of the culture-based method for diagnosis of nocardiosis [ 5 – 7 ], it is easy to miss detection of Nocardia in clinical practice. Partially, as a result, Nocardia infection is underestimated in China.…”

Section: Introductionmentioning

confidence: 99%

MLSA phylogeny and antimicrobial susceptibility of clinical Nocardia isolates: a multicenter retrospective study in China

Wei

Yang

et al. 2021

BMC Microbiol

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Background With the increase of detection rate and long treatment period, nocardiosis has become a noticeable problem in China. However, there are limited large-scale studies on the epidemiology and antimicrobial susceptibility profiles of clinical Nocardia spp. in China. The present study aimed to explore the species distribution and drug susceptibility pattern of 82 clinical Nocardia isolates from three tertiary hospitals in China by multilocus sequence analysis (MLSA) and broth microdilution (BMD) method. Results Pulmonary nocardiosis (90.2%) was the most common clinical presentation of infection. N. cyriacigeorgica (n = 33; 40.2%) and N. farcinica (n = 20; 24.4%) were the most frequently encountered Nocardia species, followed by N. otitidiscaviarum (n = 7; 8.5%), N. abscessus (n = 5; 6.1%), N. asiatica (n = 4; 4.9%), and N. wallacei (n = 4; 4.9%). Trimethoprim/sulfamethoxazole (SXT) remained high activity against all Nocardia isolates (susceptibility rate: 98.8%). Linezolid and amikacin were also highly active; 100 and 95.1% of all isolates demonstrated susceptibility, respectively. Except for N. otitidiscaviarum, all the Nocardia isolates exhibited high susceptibility rates to imipenem. The resistance rates of all isolates to clarithromycin and ciprofloxacin were 92.7 and 73.2%, respectively, but the resistance rate of N. farcinica to ciprofloxacin was only 25%. Conclusions The clinically isolated Nocardia spp. had diverse antimicrobial susceptibility patterns, which were similar to the reports by other groups elsewhere, but some differences were also observed, mainly including imipenem and ciprofloxacin. According to this study, SXT still can be the first choice for empirical therapy due to the low resistance rate. Linezolid can be chosen when a patient is allergic to SXT, and amikacin and imipenem can be the choice in a combination regimen.

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Section: Introductionmentioning

confidence: 99%

MLSA phylogeny and antimicrobial susceptibility of clinical Nocardia isolates: a multicenter retrospective study in China

Wei

Yang

et al. 2021

BMC Microbiol

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“…According to a previous retrospective study, 14 samples from the patients diagnosed with nocardiosis were tested by both mNGS and culture. All 14 samples were positive for Nocardia by mNGS, but only 5 samples had positive culture results [ 16 ]. Another research reported a brain abscess caused by Nocardia diagnosed by Ziehl–Neelsen stain and mNGS, while the blood culture was negative [ 17 ].…”

Section: Discussionmentioning

confidence: 99%

Overlapping infection of Nocardia farcinica and Aspergillus fumigatus in a child with X-linked chronic granulomatous disease: a case report

et al. 2022

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Background Chronic granulomatous disease (CGD) is a rare inherited primary immunodeficiency syndrome, manifested as recurrent infections and inflammatory complications. Although prophylactic treatment with antibiotics and antifungals improved the outcome of CGD patients, infections remain the major cause of mortality. Case presentation A boy aged 3 years and 8 months was admitted to hospital complaining of lip swelling with fever for half a month and neck abscess for 11 days. After a thorough examination, severe pneumonia, respiratory failure, oral and maxillofacial space infection, and perianal abscess were confirmed. However, his condition didn’t improve after initial comprehensive therapy. Subsequently, overlapping infections of Nocardia farcinica and Aspergillus fumigatus were identified by metagenomic next-generation sequencing. He was treated with imipenem, linezolid, and voriconazole intravenously, plus taking oral compound sulfamethoxazole. Later, his condition improved. Through whole-exome sequencing, the child was ultimately diagnosed as X-linked chronic granulomatous disease (X-CGD) caused by CYBB gene mutation. Allogeneic hematopoietic stem cell transplantation was the potential sanative approach but there were no available human leukocyte antigen compatible donors for the child. The family requested to transfer to a superior hospital for further treatment. Two months later, we followed up the child’s family. Unfortunately, the child had expired due to severe infection. Conclusion To our knowledge, this is the first case of overlapping infection of Nocardia farcinica and Aspergillus fumigatus identified by metagenomic next-generation sequencing in a child with X-CGD from China. For infectious pathogens that are hard to diagnosis by traditional detection methods, metagenomic next-generation sequencing is recommended as an adminicle or indispensable approach for microbial identification. Patients with X-CGD have poor prognosis, early diagnosis and intervention of X-CGD may reduce the mortality.

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“…At present, isolation of Nocardia on common or selective media usually takes 2-7 days, which causes a delay in diagnosis 22,23 . Some Nocardia strains even need between 1-4 weeks to generate available results, because they require strict culture conditions and have a slow growth rate at 35°C in standard culture medium; the presence of normal ora or treatment with antimicrobial therapy would also affect Nocardia culture 11,13,14,24,25 . In our study, the average time for microbial detection was 4.8 days, and 11 specimens required more than 7 days, which exceeded the conventional culture time (≥ 2 days).…”

Section: Discussionmentioning

confidence: 99%

The Clinical Characteristic and Management of patients with nocardiosis in a tertiary hospital in China

Liu

Wang

Jian

et al. 2022

Preprint

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Background: Nocardiosis is an uncommon opportunistic bacterial infection caused by Nocardia spp., and its incidence has increased significantly in recent years. This study aimed to summarize the clinical characteristics and management of nocardiosis to provide a reference for clinical diagnosis and treatment.Methods : This retrospective study was conducted based on the medical records of nocardiosis patients between January 2015 and December 2021 in a tertiary hospital in China.Results: Overall, 44 patients with nocardiosis were included in this analysis including 26 males and 18 females with a mean age of 50.4 ± 13.2 years. Connective tissue disease (CTD) was the most common underlying disease (16/44). Twenty-six patients were given immunosuppressive therapy. The most frequent infection sites were the lungs (17/44) and skin and soft tissue (8/44). Common symptoms included cough (23/44), expectoration (18/44), fever (15/44), and subcutaneous abscesses (15/44). Average microbiology laboratory detection time was 4.8 days. Twenty-nine patients were managed only with antimicrobial treatment, and 14 patients received both antimicrobial and surgical therapies. Trimethoprim-sulfamethoxazole (TMP-SMX) was the most commonly used antibiotic (31/44). Thirty-five patients were cured or improved, 6 patients were discharged from the hospital due to poor prognosis, and 1 patient died.Conclusion : Clinicians should be alert to immunocompromised patients, especially those with CTD, and tend to pulmonary or cutaneous infections. Smear microscopic examination and prolonged culture time may aid Nocardia identification. Patients with nocardiosis can be treated with antimicrobials or surgical therapy. TMP-SMX remains the mainstay treatment, and its early and prompt use may improve nocardiosis outcome.

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Rapid Detection of Nocardia by Next-Generation Sequencing

Cited by 36 publications

References 9 publications

MLSA phylogeny and antimicrobial susceptibility of clinical Nocardia isolates: a multicenter retrospective study in China

MLSA phylogeny and antimicrobial susceptibility of clinical Nocardia isolates: a multicenter retrospective study in China

Overlapping infection of Nocardia farcinica and Aspergillus fumigatus in a child with X-linked chronic granulomatous disease: a case report

The Clinical Characteristic and Management of patients with nocardiosis in a tertiary hospital in China

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