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Loop-mediated Isothermal Amplification Test for Rapid Identification of Clinical Nocardia Isolates. Jundishapur J Microbiol 2023. [DOI: 10.5812/jjm-132432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/14/2023] Open
Abstract
Background: Nocardia is a Gram-positive and partially acid-fast bacterium. The species are widely distributed in the environment and cause severe human infections. Nocardiosis is not easily identifiable due to the lack of pathognomonic clinical signs. Objectives: The present study was designed to develop and evaluate a simple and quick method based on a loop-mediated isothermal amplification (LAMP) assay for detecting Nocardia spp isolated from bronchoalveolar lavage (BAL) samples. Methods: In this cross-sectional study, 357 BAL samples were collected from two teaching hospitals. The polymerase chain reaction (PCR) was performed using a set of species-specific primers for the 16S rRNA gene. Kinyoun acid-fast staining and culture were done on the Sabouraud dextrose plate. The optimal LAMP reaction condition was set at 65°C for 45 min, with the recognition limit as 1 pg DNA/tube and 100 CFU/reaction. In addition to calcein and manganous ions, agarose gel electrophoresis was used to visualize the amplified LAMP products. Results: Out of 357 BAL samples, 0 (0.0%), 4 (1.1%), 9 (2.5%), and 10 (2.8%) Nocardia strains were identified by direct staining of partial acid-fast, streak culture plate, PCR, and LAMP methods, respectively. Conclusions: We developed a new LAMP technique for the recognition of Nocardia, which is fast, very precise, simple, and low-cost. According to our knowledge, this is the first report of the LAMP method to detect Nocardia in clinical samples.
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Gao L, Yang T, Zhang X, Lei W, Huang JA. Rapid detection of pulmonary nocardiosis by metagenomic next generation sequencing. Diagn Microbiol Infect Dis 2023; 106:115928. [PMID: 37001227 DOI: 10.1016/j.diagmicrobio.2023.115928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 02/01/2023] [Accepted: 02/24/2023] [Indexed: 03/05/2023]
Abstract
We retrospectively analyzed 3 cases of pulmonary nocardiosis. Patients were identified by metagenomic next generation sequencing (mNGS) in the First Affiliated Hospital of Soochow University, from January 2019 to April 2022. All patients had underlying diseases, and were in immunocompromised state, with membranous nephropathy, acute lymphoblastic leukemia (ALL), and systemic lupus erythematosus (SLE), respectively. Symptoms common to all cases included fever, cough and expectoration. Chest computed tomography (CT) presented patchy shadows or nodules, with or without cavitation lesions, or pleural effusion. mNGS detected Nocardia spp. via bronchoalveolar lavage fluid (BALF) or blood samples from patients. All the patients were discharged with recovery after using the trimethoprim-sulfamethoxazole (TMP-SMX) and remained without evidence of disease during regular follow-ups. mNGS may be a tool for rapid and accurate detection and identification of pulmonary nocardiosis, but interpreting the mNGS results should be more cautious because the mNGS assay can also detect colonization.
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Zhu F, Tan C, Li C, Ma S, Wen H, Yang H, Rao M, Zhang P, Peng W, Cui Y, Chen J, Pan P. Design of a multi-epitope vaccine against six Nocardia species based on reverse vaccinology combined with immunoinformatics. Front Immunol 2023; 14:1100188. [PMID: 36845087 PMCID: PMC9952739 DOI: 10.3389/fimmu.2023.1100188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 01/13/2023] [Indexed: 02/12/2023] Open
Abstract
Background Nocardia genus, a complex group of species classified to be aerobic actinomycete, can lead to severe concurrent infection as well as disseminated infection, typically in immunocompromised patients. With the expansion of the susceptible population, the incidence of Nocardia has been gradually growing, accompanied by increased resistance of the pathogen to existing therapeutics. However, there is no effective vaccine against this pathogen yet. In this study, a multi-epitope vaccine was designed against the Nocardia infection using reverse vaccinology combined with immunoinformatics approaches. Methods First, the proteomes of 6 Nocardia subspecies Nocardia subspecies (Nocardia farcinica, Nocardia cyriacigeorgica, Nocardia abscessus, Nocardia otitidiscaviarum, Nocardia brasiliensis and Nocardia nova) were download NCBI (National Center for Biotechnology Information) database on May 1st, 2022 for the target proteins selection. The essential, virulent-associated or resistant-associated, surface-exposed, antigenic, non-toxic, and non-homologous with the human proteome proteins were selected for epitope identification. The shortlisted T-cell and B-cell epitopes were fused with appropriate adjuvants and linkers to construct vaccines. The physicochemical properties of the designed vaccine were predicted using multiple online servers. The Molecular docking and molecular dynamics (MD) simulation were performed to understand the binding pattern and binding stability between the vaccine candidate and Toll-like receptors (TLRs). The immunogenicity of the designed vaccines was evaluated via immune simulation. Results 3 proteins that are essential, virulent-associated or resistant-associated, surface-exposed, antigenic, non-toxic, and non-homologous with the human proteome were selected from 218 complete proteome sequences of the 6 Nocardia subspecies epitope identification. After screening, only 4 cytotoxic T lymphocyte (CTL) epitopes, 6 helper T lymphocyte (HTL) epitopes, and 8 B cell epitopes that were antigenic, non-allergenic, and non-toxic were included in the final vaccine construct. The results of molecular docking and MD simulation showed that the vaccine candidate has a strong affinity for TLR2 and TLR4 of the host and the vaccine-TLR complexes were dynamically stable in the natural environment. The results of the immune simulation indicated that the designed vaccine had the potential to induce strong protective immune responses in the host. The codon optimization and cloned analysis showed that the vaccine was available for mass production. Conclusion The designed vaccine has the potential to stimulate long-lasting immunity in the host, but further studies are required to validate its safety and efficacy.
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Affiliation(s)
- Fei Zhu
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, Hunan, China,Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, China,Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, Hunan, China,Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Changsha, Hunan, China,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan, China
| | - Caixia Tan
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan, China,Department of Infection Control Center of Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Chunhui Li
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan, China,Department of Infection Control Center of Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Shiyang Ma
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, Hunan, China,Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, China,Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, Hunan, China,Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Changsha, Hunan, China,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan, China
| | - Haicheng Wen
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan, China
| | - Hang Yang
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, Hunan, China,Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, China,Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, Hunan, China,Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Changsha, Hunan, China,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan, China
| | - Mingjun Rao
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, Hunan, China,Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, China,Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, Hunan, China,Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Changsha, Hunan, China,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan, China
| | - Peipei Zhang
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, Hunan, China,Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, China,Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, Hunan, China,Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Changsha, Hunan, China,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan, China
| | - Wenzhong Peng
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, Hunan, China,Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, China,Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, Hunan, China,Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Changsha, Hunan, China,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan, China
| | - Yanhui Cui
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, Hunan, China,Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, China,Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, Hunan, China,Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Changsha, Hunan, China,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan, China
| | - Jie Chen
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, Hunan, China,Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, China,Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, Hunan, China,Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Changsha, Hunan, China,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan, China,*Correspondence: Jie Chen, ; Pinhua Pan,
| | - Pinhua Pan
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, Hunan, China,Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, China,Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, Hunan, China,Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Changsha, Hunan, China,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan, China,*Correspondence: Jie Chen, ; Pinhua Pan,
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Rahdar HA, Heidari H, Karami-Zarandi M, Soori T, Asadollahi P, Kazemian H. Brain Abscess Caused by Nocardia asteroides in a Diabetic Patient: A Rare Case Report. THE YALE JOURNAL OF BIOLOGY AND MEDICINE 2022; 95:407-411. [PMID: 36568837 PMCID: PMC9765341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Nocardial brain abscess is usually associated with immunodeficiency, but can sometimes emerge in healthy individuals. This infection can be acquired through inhalation or direct inoculation of the bacteria, followed by dissemination to various organs, including the brain, through blood circulation. Mortality rate due to nocardial cerebral abscess is three times higher than that associated with cerebral abscess caused by other types of bacteria. Moreover, patients with Nocardia asteroides-associated brain abscess show poorer prognosis compared to patients with brain abscess caused by other Nocardia species, which is probably due to the high tendency of N. asteroides to become resistant to numerous antibiotics. It is, therefore, of paramount importance to diagnose and treat N. asteroides cerebral abscess in patients as soon as possible. The current paper is a rare report of a brain abscess caused by N. asteroides in a diabetic patient who failed to respond to multiple antibiotics (trimethoprim/sulfamethoxazole and amikacin), but improved by receiving imipenem and linezolid, and was finally successfully treated by surgical operation and long-term antibiotic therapy (imipenem and linezolid).
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Affiliation(s)
- Hossein Ali Rahdar
- Department of Microbiology, School of Medicine, Iranshahr University of Medical
Sciences, Iranshahr, Iran
| | - Hamid Heidari
- Department of Microbiology, Faculty of Medicine, Shahid
Sadoughi University of Medical Sciences, Yazd, Iran
| | - Morteza Karami-Zarandi
- Department of Microbiology,
Faculty of Medicine, Zanjan University of Medical Sciences, Zanjan, Iran
| | - Tahereh Soori
- Autoimmune Bullous Diseases Research Center, Department of Dermatology, Tehran
University of Medical Sciences, Tehran, Iran
| | - Parisa Asadollahi
- Clinical Microbiology Research
Center, Ilam University of Medical Sciences, Ilam, Iran
| | - Hossein Kazemian
- Clinical Microbiology Research
Center, Ilam University of Medical Sciences, Ilam, Iran,To whom all correspondence should be addressed: Hossein Kazemian, PhD, Clinical
Microbiology Research Center, Ilam University of Medical Sciences, Ilam, Iran;
; ORCID: https://www.orcid.org/0000-0003-4590-396X
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Traxler RM, Bell ME, Lasker B, Headd B, Shieh WJ, McQuiston JR. Updated Review on Nocardia Species: 2006-2021. Clin Microbiol Rev 2022; 35:e0002721. [PMID: 36314911 PMCID: PMC9769612 DOI: 10.1128/cmr.00027-21] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
This review serves as an update to the previous Nocardia review by Brown-Elliott et al. published in 2006 (B. A. Brown-Elliott, J. M. Brown, P. S. Conville, and R. J. Wallace. Jr., Clin Microbiol Rev 19:259-282, 2006, https://doi.org/10.1128/CMR.19.2.259-282.2006). Included is a discussion on the taxonomic expansion of the genus, current identification methods, and the impact of new technology (including matrix-assisted laser desorption ionization-time of flight [MALDI-TOF] and whole genome sequencing) on diagnosis and treatment. Clinical manifestations, the epidemiology, and geographic distribution are briefly discussed. An additional section on actinomycotic mycetoma is added to address this often-neglected disease.
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Affiliation(s)
- Rita M. Traxler
- Bacterial Special Pathogens Branch (BSPB), Division of High-Consequence Pathogens and Pathology (DHCPP), National Center for Emerging and Zoonotic Infectious Diseases (NCEZID), Centers for Disease Control and Prevention (CDC), Atlanta, Georgia, USA
| | - Melissa E. Bell
- Bacterial Special Pathogens Branch (BSPB), Division of High-Consequence Pathogens and Pathology (DHCPP), National Center for Emerging and Zoonotic Infectious Diseases (NCEZID), Centers for Disease Control and Prevention (CDC), Atlanta, Georgia, USA
| | - Brent Lasker
- Bacterial Special Pathogens Branch (BSPB), Division of High-Consequence Pathogens and Pathology (DHCPP), National Center for Emerging and Zoonotic Infectious Diseases (NCEZID), Centers for Disease Control and Prevention (CDC), Atlanta, Georgia, USA
| | - Brendan Headd
- Bacterial Special Pathogens Branch (BSPB), Division of High-Consequence Pathogens and Pathology (DHCPP), National Center for Emerging and Zoonotic Infectious Diseases (NCEZID), Centers for Disease Control and Prevention (CDC), Atlanta, Georgia, USA
| | - Wun-Ju Shieh
- Infectious Diseases Pathology Branch (IDPB), Division of High-Consequence Pathogens and Pathology (DHCPP), National Center for Emerging and Zoonotic Infectious Diseases (NCEZID), Centers for Disease Control and Prevention (CDC), Atlanta, Georgia, USA
| | - John R. McQuiston
- Bacterial Special Pathogens Branch (BSPB), Division of High-Consequence Pathogens and Pathology (DHCPP), National Center for Emerging and Zoonotic Infectious Diseases (NCEZID), Centers for Disease Control and Prevention (CDC), Atlanta, Georgia, USA
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Whole genome sequencing reveals the genomic diversity, taxonomic classification, and evolutionary relationships of the genus Nocardia. PLoS Negl Trop Dis 2021; 15:e0009665. [PMID: 34437546 PMCID: PMC8437295 DOI: 10.1371/journal.pntd.0009665] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 09/13/2021] [Accepted: 07/19/2021] [Indexed: 01/23/2023] Open
Abstract
Nocardia is a complex and diverse genus of aerobic actinomycetes that cause complex clinical presentations, which are difficult to diagnose due to being misunderstood. To date, the genetic diversity, evolution, and taxonomic structure of the genus Nocardia are still unclear. In this study, we investigated the pan-genome of 86 Nocardia type strains to clarify their genetic diversity. Our study revealed an open pan-genome for Nocardia containing 265,836 gene families, with about 99.7% of the pan-genome being variable. Horizontal gene transfer appears to have been an important evolutionary driver of genetic diversity shaping the Nocardia genome and may have caused historical taxonomic confusion from other taxa (primarily Rhodococcus, Skermania, Aldersonia, and Mycobacterium). Based on single-copy gene families, we established a high-accuracy phylogenomic approach for Nocardia using 229 genome sequences. Furthermore, we found 28 potentially new species and reclassified 16 strains. Finally, by comparing the topology between a phylogenomic tree and 384 phylogenetic trees (from 384 single-copy genes from the core genome), we identified a novel locus for inferring the phylogeny of this genus. The dapb1 gene, which encodes dipeptidyl aminopeptidase BI, was far superior to commonly used markers for Nocardia and yielded a topology almost identical to that of genome-based phylogeny. In conclusion, the present study provides insights into the genetic diversity, contributes a robust framework for the taxonomic classification, and elucidates the evolutionary relationships of Nocardia. This framework should facilitate the development of rapid tests for the species identification of highly variable species and has given new insight into the behavior of this genus. Nocardia species can be responsible for opportunistic infections in humans, causing a variety of clinical presentations. They can also cause mycetoma in a normal host through direct inoculation. Although these species are often overlooked and misunderstood by modern medicine, they can cause life-threatening infections. However, most of our knowledge about Nocardia is based upon case reports and a few small studies of limited scope. This study provides an overview of the taxonomic and evolutionary structure of the genus Nocardia through extensive analysis of genome sequences. Our work aids the field by dissecting the genetic diversity of this species and improving the identification scheme for Nocardia species.
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Hashemzadeh M, Dezfuli AAZ, Khosravi AD, Savari M, Jahangirimehr F. Genotypic and phenotypic prevalence of Nocardia species in Iran: First systematic review and meta-analysis of data accumulated over years 1992-2021. PLoS One 2021; 16:e0254840. [PMID: 34292995 PMCID: PMC8297923 DOI: 10.1371/journal.pone.0254840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 07/02/2021] [Indexed: 12/01/2022] Open
Abstract
Background Nocardia species belong to the aerobic actinomycetes group of bacteria which are gram-positive and partially acid-fast Bacilli. These bacteria may sometimes be associated with nosocomial infections. Nocardia diseases are not required to be reported to public health authorities in Iran. Hence, the present study was designed to determine the prevalence of human Nocardia spp. in Iran by using a systematic review and meta-analysis according to the preferred reporting items for systematic reviews and meta-Analyses statement. Methods The data of the prevalence of Nocardia species were collected from databases such as Embase, PubMed/MEDLINE via Ovid, Web of Science, Scopus and Google Scholar as well as national Iranian databases, including SID, Magiran. Analyses were conducted by STATA 14.0. Results The meta-analyses showed that the proportion of Nocardia spp. in Iranian studies varied from 1.71(1.17, 2.24) to 0.46(0.09, 0.83). N. asteroides (21% [95% CI 1.17, 2.24]), N. cyriacigeorgica (17% [95% CI 0.99, 1.77]), N. facanica (10% [95% CI 0.75, 1.00]) were considered to be common causative agents. Conclusions Our study presents that despite the fact that Nocardia spp. are normally are saprophytic organisms, are currently accounts as emerging pathogens due to an increase in immunocompromised patients among Iranian populations. Considering our results, the establishment of advanced diagnostic facilities for the rapid detection of Nocardia infections are required for optimal therapeutic strategies of Nocardia spp. in Iran. Our findings could help the programmatic management of the disease within the context of Nocardia control programs.
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Affiliation(s)
- Mohammad Hashemzadeh
- Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
- Department of Microbiology, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Aram Asareh Zadegan Dezfuli
- Department of Microbiology, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Azar Dokht Khosravi
- Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
- Department of Microbiology, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
- * E-mail:
| | - Mohammad Savari
- Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
- Department of Microbiology, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
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Lutfor AB, Afroz S, Mahmud AM, Selim T, Akhter T, Sultana T, Taskeen S. Nocardia infection causing non-healing surgical wounds: A case series from Bangladesh. Int J Infect Dis 2021; 110:272-278. [PMID: 34274509 DOI: 10.1016/j.ijid.2021.07.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 07/07/2021] [Accepted: 07/09/2021] [Indexed: 01/19/2023] Open
Abstract
OBJECTIVE Nocardia can be introduced accidentally causing non-healing surgical wounds. METHOD From February 2017 to January 2021 samples from wounds were collected. Nocardia identification and susceptibility testing were carried out by standard procedure. RESULTS Seventeen (35.4 %) Nocardia spp. and 20 other pathogens (41.7%) were recovered by culture. Drug susceptibility among Nocardia was >70% to amikacin, amoxicillin-clavulanic acid, levofloxacin, linezolid, and imipenem, 47% to cephalosporins and 41% to trimethoprim/sulfamethoxazole. CONCLUSIONS Infections with Nocardia spp. should be considered in non-healing surgical wounds.
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Affiliation(s)
| | - Samira Afroz
- Ad-Din Women's Medical College, 2 BoroMoghbazar, Dhaka-1217, Bangladesh.
| | - Asif Mujtaba Mahmud
- Asgar Ali Hospital, 111/1/A Distillery Road, Gandaria, Dhaka-1204, Bangladesh.
| | - Tasmiah Selim
- BRAC James P. Grant School of Public Health, BRAC University, 68 Shahid Tajuddin Ahmed Sharani, icddr,b Building, Mohakhali, Dhaka 1212, Bangladesh.
| | - Taskina Akhter
- Ad-Din Women's Medical College, 2 BoroMoghbazar, Dhaka-1217, Bangladesh.
| | - Tamanna Sultana
- Ad-Din Women's Medical College, 2 BoroMoghbazar, Dhaka-1217, Bangladesh.
| | - Sadia Taskeen
- Dhaka Medical College Hospital, Dhaka-1000, Bangladesh.
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Chhatwal P, Woltemate S, Ziesing S, Welte T, Schlüter D, Vital M. Molecular characterization and improved diagnostics of Nocardia strains isolated over the last two decades at a German tertiary care center. EXCLI JOURNAL 2021; 20:851-862. [PMID: 34177407 PMCID: PMC8222631 DOI: 10.17179/excli2021-3787] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Accepted: 04/22/2021] [Indexed: 02/03/2023]
Abstract
Nocardiosis is a rare but life-threatening infection caused by aerobic Actinomycetes of the genus Nocardia particularly affecting immunocompromised hosts. The identification of Nocardia ssp. and antibiotic susceptibility testing by standard microbiological methods are incomplete and molecular techniques may improve diagnostics. We studied 39 Nocardia strains isolated from 33 patients between 2000 and 2018. Twenty-four patients (72.7 %) were immunocompromised. Whole genome sequencing (WGS) revealed a broad taxonomic range of those isolates spanning 13 different species, including four strains that belonged to three novel species based on average nucleotide identity (ANI < 95 % with currently available genome sequences). 16S rRNA gene analyses mirrored WGS results. Conventional MALDI-TOF analysis correctly identified 29 isolates at the species level (74.4 %). Our advanced protocol with formic acid and acetonitrile treatment increased identification to 35 isolates (89.7 %). Antibiotic resistance was tested using both a microdilution method and MIC strip testing. Results were in good concordance with an overall trimethoprim-sulfamethoxazole (SXT) resistance rate of 13.5 %. WGS of a SXT resistant N. farcinica isolate showed a deletion of several amino acids in a homolog of dihydropteroate synthase (FolP2) that was not seen in sensitive members of this species. Diversity of Nocardia isolates was high and involved many different species, suggesting that this taxon has broadly distributed mechanisms for infecting individuals. Widely applicable diagnostic methods including MALDI-TOF and 16S rRNA gene analyses correctly identified most strains. WGS additionally revealed molecular insights into SXT resistance mechanisms of clinical Nocardia isolates highlighting the potential application of (meta)genomic-based diagnostics in the future.
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Affiliation(s)
- Patrick Chhatwal
- Institute for Medical Microbiology and Hospital Epidemiology, Hannover Medical School (MHH), Hannover, Germany
| | - Sabrina Woltemate
- Institute for Medical Microbiology and Hospital Epidemiology, Hannover Medical School (MHH), Hannover, Germany
| | - Stefan Ziesing
- Institute for Medical Microbiology and Hospital Epidemiology, Hannover Medical School (MHH), Hannover, Germany
| | - Tobias Welte
- Department of Pneumology and German Center for Lung Research, Hannover Medical School (MHH), Hannover, Germany
| | - Dirk Schlüter
- Institute for Medical Microbiology and Hospital Epidemiology, Hannover Medical School (MHH), Hannover, Germany
| | - Marius Vital
- Institute for Medical Microbiology and Hospital Epidemiology, Hannover Medical School (MHH), Hannover, Germany
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Lenskaya V, DeChavez V, Kaufman B, Caplivski D. Primary cutaneous nocardiosis caused by Nocardia nova with possible Apremilast contribution. IDCases 2021; 24:e01078. [PMID: 33850720 PMCID: PMC8024659 DOI: 10.1016/j.idcr.2021.e01078] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 03/15/2021] [Accepted: 03/16/2021] [Indexed: 11/17/2022] Open
Abstract
Primary cutaneous nocardiosis accounts for 5-8 % of all nocardiosis cases and represents a diagnostic dilemma among immunocompetent and immunocompromised hosts. Herein, we present a case of a 30-year-old male with history of psoriasis with recent addition of Apremilast. Patient received intralesional triamcinolone injections for psoriatic plaques on the hands and abdomen prior to traveling to warm climate vacation. While on vacation, patient developed hand swelling and painful, red nodules on the dorsal hands and abdomen, sites where he received intralesional injections. Patient was empirically given doxycycline, but continued to develop new nodules. An abdominal lesion was biopsied for H&E and tissue culture. Tissue culture revealed beaded gram-positive rods identified as Nocardia nova by MALDI-TOF. Patient was switched to trimethoprim-sulfamethoxazole with significant improvement. This case represents an atypical primary cutaneous nocardiosis with Nocardia nova most likely in the setting of intralesional steroid injections and possible contribution of Apremilast.
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Affiliation(s)
- Volha Lenskaya
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, 10129, NY, United States
- Corresponding author at: 1468 Madison Ave, Annenberg, 15th floor, New York, NY, 10029, United States.
| | - Vincent DeChavez
- Division of Infectious Disease, Icahn School of Medicine at Mount Sinai, New York, 10129, NY, United States
| | - Bridget Kaufman
- Department of Dermatopathology, Icahn School of Medicine at Mount Sinai, New York, 10129, NY, United States
| | - Daniel Caplivski
- Division of Infectious Disease, Icahn School of Medicine at Mount Sinai, New York, 10129, NY, United States
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11
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Mehta HH, Shamoo Y. Pathogenic Nocardia: A diverse genus of emerging pathogens or just poorly recognized? PLoS Pathog 2020; 16:e1008280. [PMID: 32134995 PMCID: PMC7058287 DOI: 10.1371/journal.ppat.1008280] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Affiliation(s)
- Heer H. Mehta
- Department of BioSciences, Rice University, Houston, Texas, United States of America
- * E-mail:
| | - Yousif Shamoo
- Department of BioSciences, Rice University, Houston, Texas, United States of America
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12
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Mu YZ, Liu Y, Wang YJ, Zhang ZZ. A case report and review of lymphocutaneous nocardiosis caused by Nocardia brasiliensis reported in China. Dermatol Ther 2019; 32:e13001. [PMID: 31216085 DOI: 10.1111/dth.13001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 06/06/2019] [Accepted: 06/17/2019] [Indexed: 12/14/2022]
Abstract
Primary cutaneous nocardiosis caused by Nocardia brasiliensis is an uncommon disease. The present authors report a Chinese woman presented with lymphocutaneous nocardiosis caused by N. brasiliensis. The lesion begin with her right hand after an unknown insect sting and evolved rapidly and formed painful erythema and two subcutaneous nodules and abscesses on her right forearm in 5 days. N. brasiliensis was isolated from pustule and identified by gene sequencing. The patient received 2 weeks of combination therapy contained infusion of amoxilin potassioum clavinet and oral TMP/SMX and followed by a single therapy of oral TMP/SMX for 1 month and got a marked improvement. The present authors reviewed a case of lymphocutaneous nocardiosis caused by N. brasiliensis reported in China.
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Affiliation(s)
- Yun-Zhu Mu
- Department of Dermatology, Affiliated Hospital of North Sichuan Medical College, Nanchong, China
| | - Ying- Liu
- Department of Dermatology, Affiliated Hospital of North Sichuan Medical College, Nanchong, China
| | - Yu-Juan Wang
- Department of Dermatology, Affiliated Hospital of North Sichuan Medical College, Nanchong, China
| | - Zheng-Zhong Zhang
- Department of Dermatology, Affiliated Hospital of North Sichuan Medical College, Nanchong, China
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13
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Townell N, Locke T, Gibbons M, Murphy D, Francis J, Nourse C. Mycetoma in Timor-Leste and first report of nocardiosis. Infect Dis Rep 2018; 10:7804. [PMID: 30662693 PMCID: PMC6315302 DOI: 10.4081/idr.2018.7804] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/29/2018] [Accepted: 10/19/2018] [Indexed: 11/30/2022] Open
Abstract
Mycetoma is a neglected tropical disease with an unknown global burden. Although considered endemic to South-east Asia, it has not previously been reported from Timor-Lest. We describe two cases in Timor-Leste, highlighting the challenges surrounding microbiological diagnosis and management shared by many low to middle-income countries. As characteristically described, both patients lived rurally and presented late with marked soft tissue involvement and multiple draining sinuses following a prolonged period of high morbidity. Nocardia brasiliensis, a beadedbranched, modified acid-fast, gram-positive bacilli, was isolated and confirmed by molecular testing in the first case. The causative organism in the second case could not be confirmed due to limited microbiological capabilities. Due to limited local laboratory capabilities, Nocardia spp. infection cannot be routinely confirmed in Timor- Leste. However, the microbiology laboratory is essential for the successful diagnosis and management of Mycetoma. In both cases, medical therapy alone resulted in cure and favorable outcomes, although supply of antibiotic remains an ongoing resource issue.
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Affiliation(s)
- Nicola Townell
- Infectious Disease Department, Sunshine Coast University Hospital, Queensland, Australia
| | - Thomas Locke
- Department of Infection, Sheffield Teaching Hospitals, United Kingdom
| | | | - Dan Murphy
- Bairo-Pite Clinic, Bairo-Pite, Timor-Leste
| | - Joshua Francis
- Infectious Disease Department, Royal Darwin Hospital, Northern Territories, Australia.,Maluk Timor, Dili, Timor- Leste.,Menzies School of Health Research (Global & Tropical Health Division), Australia
| | - Clare Nourse
- Maluk Timor, Dili, Timor- Leste.,Lady Cilento Children's Hospital, Brisbane, Australia
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14
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Abstract
RATIONALE Nocardia is a genus of pathogens that most commonly afflict immunocompromised hosts but may be an emerging infection among persons with bronchiectasis. OBJECTIVES To examine the epidemiology and clinical presentation of adult patients with Nocardia and bronchiectasis relative to other patient groups. METHODS We examined a retrospectively assembled cohort of adults at Duke University Hospital in Durham, North Carolina with at least one positive culture from a bodily fluid or tissue specimen for Nocardia between January 1996 and December 2013. Denominator data for key populations (e.g., bronchiectasis, transplant) were obtained using International Classification of Diseases, Ninth Revision codes. In addition, we performed a case-control analysis to examine the relationship between inhaled corticosteroid use and Nocardia lung infection among otherwise immunocompetent patients with bronchiectasis. MEASUREMENTS AND MAIN RESULTS We identified 183 patients with one or more cultures positive for Nocardia: 44 from 1996 to 2001, 64 from 2002 to 2007, and 75 from 2008 to 2013. Immune compromise was common (56%), particularly solid organ or hematopoietic cell transplant (30%). Infection usually was confined to the lungs (62%), followed by skin (10%), other sites (6%), brain (2%), and multiple sites (17%). Non-cystic fibrosis bronchiectasis was common among both immunocompetent (38%) and immunocompromised (10%) patients. Nocardia incidence in patients with bronchiectasis increased significantly over time, but there was no significant change in Nocardia incidence in hematopoietic cell or solid organ transplant recipients (our largest immunocompromised population). Among patients with bronchiectasis, Nocardia was positively but nonsignificantly associated with use of inhaled corticosteroids (odds ratio, 1.8; 95% confidence interval, 0.7-4.4). CONCLUSIONS The increasing incidence of Nocardia infections at our medical center appears to be driven by increased incidence in patients with bronchiectasis rather than increases in immunocompromised populations. It is unclear whether increased environmental exposures, microbiologic surveillance, or other factors account for the increased incidence of Nocardia in our patients with bronchiectasis.
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15
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Fatahi-Bafghi M. Nocardiosis from 1888 to 2017. Microb Pathog 2017; 114:369-384. [PMID: 29146497 DOI: 10.1016/j.micpath.2017.11.012] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2017] [Revised: 11/06/2017] [Accepted: 11/09/2017] [Indexed: 01/11/2023]
Abstract
The genus Nocardia is an aerobic bacterium, Gram-positive and catalase positive that is in Nocardiaceae family. This bacterium first described by Edmond Nocard in 1888 and is not in human commensal bacteria. To date, nocardiosis incidence is increasing due to increase population growth rate, increase in patients with immune disorder diseases and immunocompromised patients. We surveyed taxonomic position, isolation methods, phenotypic and molecular identification at the genus and species levels, antibiogram, treatment and epidemiology in the world from 1888 to 2017.
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Affiliation(s)
- Mehdi Fatahi-Bafghi
- Department of Microbiology, Faculty of Medicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran.
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16
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Camozzota C, Goldman A, Tchernev G, Lotti T, Wollina U. A Primary Cutaneous Nocardiosis of the Hand. Open Access Maced J Med Sci 2017; 5:470-472. [PMID: 28785335 PMCID: PMC5535660 DOI: 10.3889/oamjms.2017.106] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2017] [Revised: 04/10/2017] [Accepted: 04/11/2017] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Nocardiosis is caused by an aerobic actinomycete, most commonly introduced through the respiratory tract. The Nocardiae are gram-positive, partially acid-fast bacteria. Primary cutaneous nocardiosis infections are rare and caused by the traumatic introduction of organisms percutaneously. The manifestation is usually an opportunistic infection. Cutaneous involvement may develop as one of four types: mycetoma, lymphocutaneous infection, superficial skin infection, or systemic disease with cutaneous involvement. Diagnosis and evaluation of appropriate specimens are principally by culture. CASE PRESENTATION A 55-year-old female patient with diabetes type II presented with chronic skin lesions on the hand. Otherwise, her medical history was unremarkable. There were no signs of systemic disease. Direct examination of swabs demonstrated gramme bacteria and culture on Sabouraud agar was positive for Nocardia spp. The specimen of nocardiae was not identified. The patient was treated during nine months with sulfamethoxazole plus trimethoprim. There was an important clinical improvement of the cutaneous aspect of the lesions in hand. Some scars and fibrosis remained after nocardiosis. CONCLUSIONS Primary cutaneous nocardiosis of the hand is a rare condition. The clinical diagnosis is difficult, and culture is mandatory.
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Affiliation(s)
- Camilla Camozzota
- Santa Casa de Misericórdia Hospital, Porto Alegre, Porto Alegre, RS, Brazil
| | | | - Georgi Tchernev
- Department of Dermatology, Venereology and Dermatologic Surgery, Medical Institute of Ministry of Interior, and Onkoderma Policlinic for Dermatology and Dermatologic Surgery, Sofia, Bulgaria
| | - Torello Lotti
- Department of Dermatology, University of Rome "G. Marconi", Rome, Italy; Department of Biotechnology, Delft University of Technology, 2628 BC, Delft, The Netherlands
| | - Uwe Wollina
- Department of Dermatology and Allergology, Academic Teaching Hospital Dresden-Friedrichstadt, Friedrichstrasse 41, 01067, Dresden, Germany
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17
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Hoza AS, Mfinanga SG, Moser I, König B. Isolation, biochemical and molecular identification of Nocardia species among TB suspects in northeastern, Tanzania; a forgotten or neglected threat? BMC Infect Dis 2017; 17:407. [PMID: 28595598 PMCID: PMC5463502 DOI: 10.1186/s12879-017-2520-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Accepted: 06/01/2017] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Pulmonary nocardiosis mimic pulmonary tuberculosis in most clinical and radiological manifestations. In Tanzania, where tuberculosis is one of the major public health threat clinical impact of nocardiosis as the cause of the human disease remains unknown. The objective of the present study was to isolate and identify Nocardia isolates recovered from TB suspects in Northeastern, Tanzania by using biochemical and molecular methods. METHODS The study involved 744 sputum samples collected from 372 TB suspects from four periphery diagnostic centers in Northeastern, Tanzania. Twenty patients were diagnosed as having presumptively Nocardia infections based on microscopic, cultural characteristics and biomèrieux ID 32C Yeast Identification system and confirmed using 16S rRNA and hsp65 gene specific primers for Nocardia species and sequencing. RESULTS Biochemically, the majority of the isolates were N. asteroides (n = 8/20, 40%), N. brasiliensis (n = 4/20, 20%), N. farcinica (n = 3/20, 15%), N. nova (n = 1/20, 5%). Other aerobic actinomycetales included Streptomyces cyanescens (n = 2/20, 10%), Streptomyces griseus, Actinomadura madurae each (n = 1/20, 5%). Results of 16S rRNA and hsp65 sequencing were concordant in 15/17 (88. 2%) isolates and discordant in 2/17 (11.8%) isolates. Majority of the isolates belonged to N. cyriacigeorgica and N. farcinica, four (23.5%) each. CONCLUSIONS Our findings suggest that Nocardia species may be an important cause of pulmonary nocardiosis that is underdiagnosed or ignored. This underscores needs to consider pulmonary nocardiosis as a differential diagnosis when there is a failure of anti-TB therapy and as a possible cause of human infections.
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Affiliation(s)
- Abubakar S. Hoza
- Department of Medical Microbiology and Epidemiology of Infectious Diseases, Faculty of Medicine, University of Leipzig, Liebig Str. 21, 04103 Leipzig, Germany
- Department of Microbiology, Parasitology and Immunology, College of Veterinary and Medical Sciences, Sokoine University of Agriculture, P. O. Box, 3019 Morogoro, Tanzania
| | - Sayoki G.S. Mfinanga
- National Institute for Medical Research, Muhimbili Medical Research Centre, P. O. Box, 3436 Dar es Salaam, Tanzania
| | - Irmgard Moser
- Friedrich Loeffler Institut, Institute of Molecular Pathogenesis, Naumburger Str. 96a, 07743 Jena, Germany
| | - Brigitte König
- Department of Medical Microbiology and Epidemiology of Infectious Diseases, Faculty of Medicine, University of Leipzig, Liebig Str. 21, 04103 Leipzig, Germany
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18
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Girard V, Mailler S, Welker M, Arsac M, Cellière B, Cotte-Pattat PJ, Chatellier S, Durand G, Béni AM, Schrenzel J, Miller E, Dussoulier R, Dunne WM, Butler-Wu S, Saubolle MA, Sussland D, Bell M, van Belkum A, Deol P. Identification of mycobacterium spp. and nocardia spp. from solid and liquid cultures by matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). Diagn Microbiol Infect Dis 2016; 86:277-283. [PMID: 27567285 DOI: 10.1016/j.diagmicrobio.2016.07.027] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Revised: 06/20/2016] [Accepted: 07/26/2016] [Indexed: 01/15/2023]
Abstract
Identification of microorganisms by MALDI-TOF MS has been widely accepted in clinical microbiology. However, for Mycobacterium spp. and Nocardia spp. such identification has not yet reached the optimal level of routine testing. Here we describe the development of an identification tool for 49 and 15 species of Mycobacterium spp. and Nocardia spp., respectively. During database construction, a number of ambiguous reference identifications were revealed and corrected via molecular analyses. Eventually, more than 2000 individual mass spectra acquired from 494 strains were included in a reference database and subjected to bio-statistical analyses. This led to correct species identification and correct combination of species into several complexes or groups, such as the Mycobacterium tuberculosis complex. With the Advanced Spectrum Classifier algorithm, class-specific bin weights were determined and tested by cross-validation experiments with good results. When challenged with independent isolates, overall identification performance was 90% for identification of Mycobacterium spp. and 88% for Nocardia spp. However, for a number of Mycobacterium sp. isolates, no identification could be achieved and in most cases, this could be attributed to the production of polymers that masked the species-specific protein peak patterns. For the species where >20 isolates were tested, correct identification reached 95% or higher. With the current spectral database, the identification of Mycobacterium spp. and Nocardia spp. by MALDI-TOF MS can be performed in routine clinical diagnostics although in some complicated cases verification by sequencing remains mandatory.
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Affiliation(s)
- Victoria Girard
- bioMérieux, Microbiology R&D, Route de Port Michaud, 38390, La Balme, Les Grottes, France
| | - Sandrine Mailler
- bioMérieux, Microbiology R&D, Route de Port Michaud, 38390, La Balme, Les Grottes, France
| | - Martin Welker
- bioMérieux, Microbiology R&D, Route de Port Michaud, 38390, La Balme, Les Grottes, France
| | - Maud Arsac
- bioMérieux, Microbiology R&D, Route de Port Michaud, 38390, La Balme, Les Grottes, France
| | - Béatrice Cellière
- bioMérieux, Microbiology R&D, Route de Port Michaud, 38390, La Balme, Les Grottes, France
| | | | - Sonia Chatellier
- bioMérieux, Microbiology R&D, Route de Port Michaud, 38390, La Balme, Les Grottes, France
| | - Géraldine Durand
- bioMérieux, Microbiology R&D, Route de Port Michaud, 38390, La Balme, Les Grottes, France
| | - Anne-Marie Béni
- Hôpitaux Universitaires de Genève, Laboratoire de Bactériologie, Rue Gabrielle Perret Gentil 4, 1211, Geneva 14, Switzerland
| | - Jacques Schrenzel
- Hôpitaux Universitaires de Genève, Laboratoire de Bactériologie, Rue Gabrielle Perret Gentil 4, 1211, Geneva 14, Switzerland
| | - Elizabeth Miller
- bioMérieux Inc., Microbiology R&D, 100 Rodolphe St, Durham, NC, 27712, USA
| | - Rahima Dussoulier
- bioMérieux Inc., Microbiology R&D, 100 Rodolphe St, Durham, NC, 27712, USA
| | - W Michael Dunne
- bioMérieux Inc., Microbiology R&D, 100 Rodolphe St, Durham, NC, 27712, USA
| | - Susan Butler-Wu
- Clinical Microbiology Laboratory, University of Washington, 1959 NE Pacific Street, Seattle, WA 98195, USA; Keck School of Medicine, University of Southern California, 1975 Zonal Avenue, Los Angeles, CA, 90033, USA
| | - Michael A Saubolle
- Banner University Medical Center, 1111 E. McDowell Rd., Phoenix, AZ, 85006, USA
| | - Den Sussland
- Banner University Medical Center, 1111 E. McDowell Rd., Phoenix, AZ, 85006, USA
| | - Melissa Bell
- Centers for Disease Control and Prevention, 1600 Clifton Road, Atlanta, GA, 30329-4027, USA
| | - Alex van Belkum
- bioMérieux, Microbiology R&D, Route de Port Michaud, 38390, La Balme, Les Grottes, France.
| | - Parampal Deol
- bioMérieux Inc., Microbiology R&D, 100 Rodolphe St, Durham, NC, 27712, USA
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19
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Xiao M, Pang L, Chen SCA, Fan X, Zhang L, Li HX, Hou X, Cheng JW, Kong F, Zhao YP, Xu YC. Accurate Identification of Common Pathogenic Nocardia Species: Evaluation of a Multilocus Sequence Analysis Platform and Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry. PLoS One 2016; 11:e0147487. [PMID: 26808813 PMCID: PMC4726625 DOI: 10.1371/journal.pone.0147487] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2015] [Accepted: 01/05/2016] [Indexed: 12/12/2022] Open
Abstract
Species identification of Nocardia is not straightforward due to rapidly evolving taxonomy, insufficient discriminatory power of conventional phenotypic methods and also of single gene locus analysis including 16S rRNA gene sequencing. Here we evaluated the ability of a 5-locus (16S rRNA, gyrB, secA1, hsp65 and rpoB) multilocus sequence analysis (MLSA) approach as well as that of matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) in comparison with sequencing of the 5'-end 606 bp partial 16S rRNA gene to provide identification of 25 clinical isolates of Nocardia. The 5'-end 606 bp 16S rRNA gene sequencing successfully assigned 24 of 25 (96%) clinical isolates to species level, namely Nocardia cyriacigeorgica (n = 12, 48%), N. farcinica (n = 9, 36%), N. abscessus (n = 2, 8%) and N. otitidiscaviarum (n = 1, 4%). MLSA showed concordance with 16S rRNA gene sequencing results for the same 24 isolates. However, MLSA was able to identify the remaining isolate as N. wallacei, and clustered N. cyriacigeorgica into three subgroups. None of the clinical isolates were correctly identified to the species level by MALDI-TOF MS analysis using the manufacturer-provided database. A small "in-house" spectral database was established incorporating spectra of five clinical isolates representing the five species identified in this study. After complementation with the "in-house" database, of the remaining 20 isolates, 19 (95%) were correctly identified to species level (score ≥ 2.00) and one (an N. abscessus strain) to genus level (score ≥ 1.70 and < 2.00). In summary, MLSA showed superior discriminatory power compared with the 5'-end 606 bp partial 16S rRNA gene sequencing for species identification of Nocardia. MALDI-TOF MS can provide rapid and accurate identification but is reliant on a robust mass spectra database.
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Affiliation(s)
- Meng Xiao
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Lu Pang
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
- Department of Clinical Laboratory, Peking University First Hospital, Beijing, China
| | - Sharon C-A. Chen
- Centre for Infectious Diseases and Microbiology Laboratory Services, ICPMR–Pathology West, Westmead Hospital, University of Sydney, Westmead, New South Wales, Australia
| | - Xin Fan
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Li Zhang
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Hai-Xia Li
- Department of Clinical Laboratory, Peking University First Hospital, Beijing, China
| | - Xin Hou
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Jing-Wei Cheng
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Fanrong Kong
- Centre for Infectious Diseases and Microbiology Laboratory Services, ICPMR–Pathology West, Westmead Hospital, University of Sydney, Westmead, New South Wales, Australia
| | - Yu-Pei Zhao
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Ying-Chun Xu
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
- * E-mail:
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20
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Rudramurthy SM, Honnavar P, Kaur H, Samanta P, Ray P, Ghosh A, Chakrabarti A. Molecular identification of clinical Nocardia isolates from India. J Med Microbiol 2015. [DOI: 10.1099/jmm.0.000143] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Affiliation(s)
- Shivaprakash M. Rudramurthy
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Prasanna Honnavar
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Harsimran Kaur
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Palash Samanta
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Pallab Ray
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Anup Ghosh
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Arunaloke Chakrabarti
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
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21
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CONDAS LAZ, RIBEIRO MG, MURO MD, de VARGAS APC, MATSUZAWA T, YAZAWA K, SIQUEIRA AK, SALERNO T, LARA GHB, RISSETI RM, FERREIRA KS, GONOI T. MOLECULAR IDENTIFICATION AND ANTIMICROBIAL RESISTANCE PATTERN OF SEVEN CLINICAL ISOLATES OF Nocardia spp. IN BRAZIL. Rev Inst Med Trop Sao Paulo 2015; 57:251-6. [PMID: 26200967 PMCID: PMC4544251 DOI: 10.1590/s0036-46652015000300012] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2014] [Accepted: 09/23/2014] [Indexed: 11/29/2022] Open
Abstract
Nocardia is a ubiquitous microorganism related to pyogranulomatous infection, which is difficult to treat in humans and animals. The occurrence of the disease is on the rise in many countries due to an increase in immunosuppressive diseases and treatments. This report of cases from Brazil presents the genotypic characterization and the antimicrobial susceptibility pattern using the disk-diffusion method and inhibitory minimal concentration with E-test® strips. In summary, this report focuses on infections in young adult men, of which three cases were cutaneous, two pulmonary, one neurological and one systemic. The pulmonary, neurological and systemic cases were attributed to immunosuppressive diseases or treatments. Sequencing analysis of the 16S rRNA segments (1491 bp) identified four isolates of Nocardia farcinica, two isolates of Nocardia nova and one isolate of Nocardia asiatica. N. farcinica was involved in two cutaneous, one systemic and other pulmonary cases; N. nova was involved in one neurological and one pulmonary case; and Nocardia asiatica in one cutaneous case. The disk-diffusion antimicrobial susceptibility test showed that the most effective antimicrobials were amikacin (100%), amoxicillin/clavulanate (100%), cephalexin (100%) and ceftiofur (100%), while isolates had presented most resistance to gentamicin (43%), sulfamethoxazole/trimethoprim (43%) and ampicillin (29%). However, on the inhibitory minimal concentration test (MIC test), only one of the four isolates of Nocardia farcinica was resistant to sulfamethoxazole/trimethoprim.
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Affiliation(s)
- Larissa Anuska Zeni CONDAS
- Department Veterinary Hygiene and Public Health, Universidade Estadual
Paulista “Júlio de Mesquita Filho”, FMVZ/UNESP Botucatu, Sao Paulo, Brazil
| | - Márcio Garcia RIBEIRO
- Department Veterinary Hygiene and Public Health, Universidade Estadual
Paulista “Júlio de Mesquita Filho”, FMVZ/UNESP Botucatu, Sao Paulo, Brazil
| | | | | | | | - Katsukiyo YAZAWA
- Medical Mycology Research Centre of Chiba University, Chiba,
Japan
| | - Amanda Keller SIQUEIRA
- Department Veterinary Hygiene and Public Health, Universidade Estadual
Paulista “Júlio de Mesquita Filho”, FMVZ/UNESP Botucatu, Sao Paulo, Brazil
| | - Tatiana SALERNO
- Department Veterinary Hygiene and Public Health, Universidade Estadual
Paulista “Júlio de Mesquita Filho”, FMVZ/UNESP Botucatu, Sao Paulo, Brazil
| | - Gustavo Henrique Batista LARA
- Department Veterinary Hygiene and Public Health, Universidade Estadual
Paulista “Júlio de Mesquita Filho”, FMVZ/UNESP Botucatu, Sao Paulo, Brazil
| | - Rafaela Mastrangelo RISSETI
- Department Veterinary Hygiene and Public Health, Universidade Estadual
Paulista “Júlio de Mesquita Filho”, FMVZ/UNESP Botucatu, Sao Paulo, Brazil
| | - Karen Spadari FERREIRA
- Department of Biological Science, Microbiology, Immunology and
Parasitology Sector, Universidade Federal de São Paulo, UNIFESP, São Paulo, SP,
Brazil
| | - Tohru GONOI
- Medical Mycology Research Centre of Chiba University, Chiba,
Japan
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22
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Muricy ECM, Lemes RA, Bombarda S, Ferrazoli L, Chimara E. Differentiation between Nocardia spp. and Mycobacterium spp.: Critical aspects for bacteriological diagnosis. Rev Inst Med Trop Sao Paulo 2015; 56:397-401. [PMID: 25229219 PMCID: PMC4172110 DOI: 10.1590/s0036-46652014000500005] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2013] [Accepted: 03/07/2014] [Indexed: 11/22/2022] Open
Abstract
New methodologies were developed for the identification of Nocardia but the initial diagnosis still requires a fast and accurate method, mainly due to the similarity to Mycobacterium, both clinical and bacteriologically. Growth on Löwenstein-Jensen (LJ) medium, presence of acid-fast bacilli through Ziehl-Neelsen staining, and colony morphology can be confusing aspects between Nocardia and Mycobacterium. This study describes the occurrence of Nocardia spp. in a mycobacterial-reference laboratory, observing the main difficulties in differentiating Nocardia spp. from Mycobacterium spp., and correlating isolates with nocardiosis cases. Laboratory records for the period between 2008 and 2012 were analyzed, and the isolates identified as Nocardia sp. or as non-acid-fast filamentous bacilli were selected. Epidemiological and bacteriological data were analyzed as well. Thirty-three isolates identified as Nocardia sp. and 22 as non-acid-fast bacilli were selected for this study, and represented 0.12% of isolates during the study period. The presumptive identification was based on macroscopic and microscopic morphology, resistance to lysozyme and restriction profiles using the PRA-hsp65 method. Nocardia spp. can grow on media for mycobacteria isolation (LJ and BBL MGIT™) and microscopy and colony morphology are very similar to some mycobacteria species. Seventeen patients (54.8%) were reported and treated for tuberculosis, but presented signs and symptoms of nocardiosis. It was concluded that the occurrence of Nocardia sp. during the study period was 0.12%. Isolates with characteristics of filamentous bacilli, forming aerial hyphae, with colonies that may be pigmented, rough and without the BstEII digestion pattern in PRA-hsp65 method are suggestive of Nocardia spp. For a mycobacterial routine laboratory, a flow for the presumptive identification of Nocardia is essential, allowing the use of more accurate techniques for the correct identification, proper treatment and better quality of life for patients.
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Affiliation(s)
| | | | - Sidney Bombarda
- Epidemiological Surveillance Center Prof. Alexandre Vranjac, São Paulo, SP, Brazil
| | - Lucilaine Ferrazoli
- Tuberculosis and Mycobacteriosis Branch, Instituto Adolfo Lutz, São Paulo, SP, Brazil
| | - Erica Chimara
- Tuberculosis and Mycobacteriosis Branch, Instituto Adolfo Lutz, São Paulo, SP, Brazil
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Armas YD, Fernández CM, Díaz R, Stefano NB, Wissmann G, Calderón EJ. PCR-RFLP Methodology to Identify <i>Nocardia</i> Isolates in Cuba. ACTA ACUST UNITED AC 2015. [DOI: 10.4236/aim.2015.510076] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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