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Shokrpoor S, Darabian Aghdas R, Ziafati Kafi Z, Abdollahi M, Ashrafi Tamai I. Lumpy jaw caused by Nocardia farcinica in a Holstein cow. Vet Med Sci 2024; 10:e1433. [PMID: 38520249 PMCID: PMC10981914 DOI: 10.1002/vms3.1433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 03/03/2024] [Accepted: 03/10/2024] [Indexed: 03/25/2024] Open
Abstract
A 3-year-old Holstein cow was examined in an intensive system due to unilateral swelling in the mandible. A right mandibular mass was associated with painful mastication and Ptyalism. In palpation, the mass was raised, ulcerated, attached to the mandible bone and firm, approximately 17 × 12 × 10 cm3 in size. The lesion was sampled, and after routine bacteriology and histopathology procedures, the occurrence of lumpy jaw caused by Nocardia farcinica was confirmed. The bacterium was analysed using genome sequencing and new strain called Najm 114. Due to the risk of zoonosis of the isolated agent, the cow was euthanized. This is the first report of lumpy jaw caused by N. farcinica in a cow. This study showed that N. farcinica should be considered a possible etiological agent for lumpy jaw in cattle.
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Affiliation(s)
- Sara Shokrpoor
- Department of Pathology, Faculty of Veterinary MedicineUniversity of TehranTehranIran
| | | | - Zahra Ziafati Kafi
- Department of Microbiology and Immunology, Faculty of Veterinary MedicineUniversity of TehranTehranIran
| | - Mostafa Abdollahi
- Department of Clinical Sciences, Faculty of Veterinary MedicineSemnan UniversitySemnanIran
| | - Iradj Ashrafi Tamai
- Department of Microbiology and Immunology, Faculty of Veterinary MedicineUniversity of TehranTehranIran
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2
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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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3
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Frantsuzova E, Bogun A, Vetrova A, Delegan Y. Methods of Identifying Gordonia Strains in Clinical Samples. Pathogens 2022; 11:pathogens11121496. [PMID: 36558832 PMCID: PMC9786905 DOI: 10.3390/pathogens11121496] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 12/04/2022] [Accepted: 12/06/2022] [Indexed: 12/13/2022] Open
Abstract
Gordonia spp. are members of the family Gordoniacea in the suborder Corynebacteriales; their habitat, in most cases, is soil. Many representatives of this genus are human or veterinary pathogens. The main cause of the lack of a standardized approach to dealing with infections caused by Gordonia is their erroneous identification and little information regarding their susceptibility to antimicrobial drugs. This review presents the most common methods for identifying Gordonia strains, including modern approaches for identifying a species. The main prospects and future directions of this field of knowledge are briefly presented.
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Affiliation(s)
- Ekaterina Frantsuzova
- Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center “Pushchino Scientific Center for Biological Research of Russian Academy of Sciences” (FRC PSCBR RAS), 142290 Pushchino, Moscow Region, Russia
| | - Alexander Bogun
- Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center “Pushchino Scientific Center for Biological Research of Russian Academy of Sciences” (FRC PSCBR RAS), 142290 Pushchino, Moscow Region, Russia
- State Research Center for Applied Microbiology and Biotechnology, 142279 Obolensk, Moscow Region, Russia
| | - Anna Vetrova
- Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center “Pushchino Scientific Center for Biological Research of Russian Academy of Sciences” (FRC PSCBR RAS), 142290 Pushchino, Moscow Region, Russia
| | - Yanina Delegan
- Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center “Pushchino Scientific Center for Biological Research of Russian Academy of Sciences” (FRC PSCBR RAS), 142290 Pushchino, Moscow Region, Russia
- Correspondence:
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Epidemiology of Nocardia Species at a Tertiary Hospital in Southern Taiwan, 2012 to 2020: MLSA Phylogeny and Antimicrobial Susceptibility. Antibiotics (Basel) 2022; 11:antibiotics11101438. [PMID: 36290097 PMCID: PMC9598236 DOI: 10.3390/antibiotics11101438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 10/13/2022] [Accepted: 10/17/2022] [Indexed: 11/23/2022] Open
Abstract
The identification and antimicrobial susceptibility of Nocardia spp. are essential for guiding antibiotic treatment. We investigated the species distribution and evaluated the antimicrobial susceptibility of Nocardia species collected in southern Taiwan from 2012 to 2020. A total of 77 Nocardia isolates were collected and identified to the species level using multi-locus sequence analysis (MLSA). The susceptibilities to 15 antibiotics for Nocardia isolates were determined by the broth microdilution method, and the MIC50 and MIC90 for each antibiotic against different species were analyzed. N. cyriacigeorgica was the leading isolate, accounting for 32.5% of all Nocardia isolates, and the prevalence of Nocardia isolates decreased in summer. All of the isolates were susceptible to trimethoprim/sulfamethoxazole, amikacin, and linezolid, whereas 90.9% were non-susceptible to cefepime and imipenem. The phylogenic tree by MLSA showed that the similarity between N. beijingensis and N. asiatica was as high as 99%, 73% between N. niigatensis and N. crassostreae, and 86% between N. cerradoensis and N. cyriacigeorgica. While trimethoprim/sulfamethoxazole, amikacin, and linezolid remained fully active against all of the Nocardia isolates tested, 90.9% of the isolates were non-susceptible to cefepime and imipenem.
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Buresova‐Faitova A, Kopecky J, Sagova‐Mareckova M, Alonso L, Vautrin F, Moënne‐Loccoz Y, Rodriguez‐Nava V. Comparison of
Actinobacteria
communities from human‐impacted and pristine karst caves. Microbiologyopen 2022; 11:e1276. [PMID: 35478281 PMCID: PMC8988830 DOI: 10.1002/mbo3.1276] [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: 06/24/2021] [Revised: 03/10/2022] [Accepted: 03/10/2022] [Indexed: 11/07/2022] Open
Abstract
Actinobacteria are important cave inhabitants, but knowledge of how anthropization and anthropization‐related visual marks affect this community on cave walls is lacking. We compared Actinobacteria communities among four French limestone caves (Mouflon, Reille, Rouffignac, and Lascaux) ranging from pristine to anthropized, and within Lascaux Cave between marked (wall visual marks) and unmarked areas in different rooms (Sas‐1, Passage, Apse, and Diaclase). In addition to the 16S rRNA gene marker, 441 bp fragments of the hsp65 gene were used and an hsp65‐related taxonomic database was constructed for the identification of Actinobacteria to the species level by Illumina‐MiSeq analysis. The hsp65 marker revealed higher resolution for species and higher richness (99% operational taxonomic units cutoff) versus the 16S rRNA gene; however, more taxa were identified at higher taxonomic ranks. Actinobacteria communities varied between Mouflon and Reille caves (both pristine), and Rouffignac and Lascaux (both anthropized). Rouffignac displayed high diversity of Nocardia, suggesting human inputs, and Lascaux exhibited high Mycobacterium relative abundance, whereas Gaiellales were typical in pristine caves and the Diaclase (least affected area of Lascaux Cave). Within Lascaux, Pseudonocardiaceae dominated on unmarked walls and Streptomycetaceae (especially Streptomyces mirabilis) on marked walls, indicating a possible role in mark formation. A new taxonomic database was developed. Although not all Actinobacteria species were represented, the use of the hsp65 marker enabled species‐level variations of the Actinobacteria community to be documented based on the extent of anthropogenic pressure. This approach proved effective when comparing different limestone caves or specific conditions within one cave.
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Affiliation(s)
- Andrea Buresova‐Faitova
- CNRS, INRAe, VetAgro Sup, UMR 5557 Ecologie MicrobienneUniversité de Lyon, Université Claude Bernard Lyon 1VilleurbanneFrance
- Department of Ecology, Faculty of ScienceCharles University in PraguePrague 2PragueCzech Republic
- Laboratory for Epidemiology and Ecology of MicroorganismsCrop Research InstitutePrahaCzech Republic
| | - Jan Kopecky
- Laboratory for Epidemiology and Ecology of MicroorganismsCrop Research InstitutePrahaCzech Republic
| | - Marketa Sagova‐Mareckova
- Laboratory for Epidemiology and Ecology of MicroorganismsCrop Research InstitutePrahaCzech Republic
| | - Lise Alonso
- CNRS, INRAe, VetAgro Sup, UMR 5557 Ecologie MicrobienneUniversité de Lyon, Université Claude Bernard Lyon 1VilleurbanneFrance
| | - Florian Vautrin
- CNRS, INRAe, VetAgro Sup, UMR 5557 Ecologie MicrobienneUniversité de Lyon, Université Claude Bernard Lyon 1VilleurbanneFrance
| | - Yvan Moënne‐Loccoz
- CNRS, INRAe, VetAgro Sup, UMR 5557 Ecologie MicrobienneUniversité de Lyon, Université Claude Bernard Lyon 1VilleurbanneFrance
| | - Veronica Rodriguez‐Nava
- CNRS, INRAe, VetAgro Sup, UMR 5557 Ecologie MicrobienneUniversité de Lyon, Université Claude Bernard Lyon 1VilleurbanneFrance
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Gephyromycinifex aptenodytis gen. nov., sp. nov., isolated from gut of Antarctic emperor penguin Aptenodytes forsteri. Antonie van Leeuwenhoek 2021; 114:2003-2017. [PMID: 34532778 DOI: 10.1007/s10482-021-01657-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 09/09/2021] [Indexed: 12/15/2022]
Abstract
A novel actinobacterium NJES-13T was isolated from the gut of Antarctic emperor penguin Aptenodytes forsteri. The new isolate produces bioactive gephyromycin metabolites and exopolysaccharides (EPS). Cells were Gram-negative, motile with the peritrichous flagella, and with a faint layer of extracellular slime. Colonies were yellow when grown on marine agar, ISP1, 2, 4 and TSA media. The strain developed clusters of coccoid, and divided by binary fission in the early phase of growth. The cell clusters were gradually disrupted during the stationary phase and formed short rod-shape cells which were interconnected by viscous EPS showing a three-dimensional net-like morphology, and contained polyhydroxyalkanoates (PHA) granules inside the cells. Growth of strain NJES-13T was observed at 15-45 °C, at pH 6.0-9.0 with 0.5-9.0% (w/v) NaCl. The complete genomic size of strain NJES-13T was 3.45 Mb with a DNA G + C content of 67.0 mol%. The combined polyphasic taxonomic characterizations presented in this study unequivocally separated strain NJES-13T from all known genera in the family Dermatophilaceae. Thus, strain NJES-13T represents a novel species of a new genus, for which the name Gephyromycinifex aptenodytis gen. nov., and sp. nov. is proposed. The type strain is NJES-13T (= CCTCC 2019007T = KCTC 49281T). Genetic prediction of secondary metabolite biosynthesis revealed a 44.5 kb-long biosynthetic gene cluster (BGC) of type III polyketide synthase (PKS) as well as four other BGCs, indicating its great potential to produce novel bioactive metabolites derived from the gut microbiota of animals living in the extreme habitats in the Antarctica.
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Kanchanasin P, Yuki M, Kudo T, Ohkuma M, Phongsopitanun W, Tanasupawat S. Nocardia aurantiaca sp. nov., isolated from soil in Thailand. Int J Syst Evol Microbiol 2020; 70:5432-5438. [DOI: 10.1099/ijsem.0.004432] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel actinomycete strain, CT2-14T, belonging to the genus
Nocardia
, was isolated from a soil sample collected from Phichit Province, Thailand. The taxonomic position of the strain was characterized using a polyphasic approach. The strain grew at 15–40 °C (optimum, 28–37 °C), pH 6–11 (optimum, pH 6–8) and on an International
Streptomyces
Project 2 with 4 % (w/v) NaCl agar plate. Meso-diaminopimelic acid was detected in the cell-wall peptidoglycan. Ribose, arabinose and galactose were detected in its whole-cell hydrolysates. Mycolic acids were present. The strain contained C16 : 0, summed feature 3, C17 : 0 10-methyl and C18 : 1
ω9c as the major fatty acids and MK-8(H4ω-cycl) as the major menaquinone. The major polar lipids were phosphatidylethanolamine, diphosphatidylglycerol and phosphatidylinositol mannosides. Strain CT2-14T showed the highest 16S rRNA gene similarity to
Nocardia veterana
JCM 11307T (98.4 %),
Nocardia africana
JCM 11438T (98.2 %) and
Nocardia kruczakiae
JCM 13032T (98.0 %). The draft genome of strain CT2-14T was 7.37 Mb with 6685 coding sequences with an average G+C content of 67.9 mol %. Based on the phylogenomic tree analysis, the strain was closely related to
Nocardia niigatensis
NBRC 100131T. On the basis of polyphasic and genome analyses, strain CT2-14T represented a novel species of the genus
Nocardia
for which the name Nocardia aurantiaca sp. nov. is proposed. The type strain is CT2-14T (=JCM 33775T=TISTR 2838T).
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Affiliation(s)
- Pawina Kanchanasin
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand
| | - Masahiro Yuki
- Japan Collection of Microorganisms, RIKEN BioResource Center, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | - Takuji Kudo
- Japan Collection of Microorganisms, RIKEN BioResource Center, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | - Moriya Ohkuma
- Japan Collection of Microorganisms, RIKEN BioResource Center, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | - Wongsakorn Phongsopitanun
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand
| | - Somboon Tanasupawat
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand
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Zhou T, Wang XY, Deng DQ, Xu LH, Li XL, Guo Y, Li WH, Xie H, Zhang PL, Zhou XH. Nocardia colli sp. nov., a new pathogen isolated from a patient with primary cutaneous nocardiosis. Int J Syst Evol Microbiol 2020; 70:2981-2987. [PMID: 32375925 PMCID: PMC7395626 DOI: 10.1099/ijsem.0.003856] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
A novel nocardioform strain, CICC 11023T, was isolated from a tissue biopsy of neck lesions of a patient with primary cutaneous nocardiosis and characterized to establish its taxonomic position. The morphological, biochemical, physiological and chemotaxonomic properties of strain CICC 11023T were consistent with classification in the genus Nocardia. Whole-cell hydrolysates were rich in meso-diaminopimelic acid, galactose, arabinose and fructose. Mycolic acids were present. The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, one unidentified phospholipid and two unidentified lipids, and the predominant menaquinone was cyclo MK-8 (H4, ω-cyclo). The main fatty acids (>5 %) were C18 : 0 10-methyl (TBSA), C16 : 0, summed feature 4 (C16 : 1 trans 9/C15 : 0 iso 2OH), C15 : 0 and C17 : 0 10-methyl. Phylogenetic analyses based on 16S rRNA gene sequences revealed that the isolate is most closely related (>98 % similarity) to the type strains Nocardia ninae OFN 02.72T, Nocardia iowensis UI 122540T and Nocardia alba YIM 30243T, and phylogenetic analysis of gyrB gene sequences showed similarity (89.1–92.2 %) to Nocardia vulneris NBRC 108936T, Nocardia brasiliensis IFM 0236T and Nocardia exalbida IFM 0803T. DNA–DNA hybridization results for strain CICC 11023T compared to Nocardia type strains ranged from 20.4 to 35.4 %. The genome of strain CICC 11023T was 8.78 Mbp with a G+C content of 67.4 mol% overall. The average nucleotide identity (ANI) values between strain CICC 11023T and N. alba YIM 30243T were low (OrthoANIu=77.47 %), and the ANI values between strain CICC 11023T and N. vulneris NBRC 108936 T were low (OrthoANIu=83.75 %). Consequently, strain CICC 11023T represents a novel Nocardia species on the basis of this polyphasic study, for which the name Nocardia colli sp. nov. is proposed. The type strain is CICC 11023T (=KCTC 39837T).
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Affiliation(s)
- Tao Zhou
- Department of Clinical Laboratory Medicine, Second Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650101, PR China
| | - Xiao-Yun Wang
- Department of Dermatology, Second Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650101, PR China
- *Correspondence: Xiao-Yun Wang,
| | - Dan-Qi Deng
- Department of Dermatology, Second Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650101, PR China
| | - Li-Hua Xu
- The Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education and Laboratory for Conservation and Utilization of Bio-resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan 650091, PR China
| | - Xiao-Lan Li
- Department of Dermatology, Second Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650101, PR China
| | - Yun Guo
- Department of Dermatology, Second Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650101, PR China
| | - Wen-Hua Li
- Department of Dermatology, Second Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650101, PR China
| | - Hong Xie
- Department of Dermatology, Second Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650101, PR China
| | - Pei-Lian Zhang
- Department of Dermatology, Second Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650101, PR China
| | - Xiao-Hong Zhou
- Department of Dermatology, Second Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650101, PR China
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Molecular Characterization and Antimicrobial Susceptibilities of Nocardia Species Isolated from the Soil; A Comparison with Species Isolated from Humans. Microorganisms 2020; 8:microorganisms8060900. [PMID: 32549367 PMCID: PMC7355893 DOI: 10.3390/microorganisms8060900] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 06/05/2020] [Accepted: 06/11/2020] [Indexed: 01/08/2023] Open
Abstract
Nocardia species, one of the most predominant Actinobacteria of the soil microbiota, cause infection in humans following traumatic inoculation or inhalation. The identification, typing, phylogenetic relationship and antimicrobial susceptibilities of 38 soil Nocardia strains from Lara State, Venezuela, were studied by 16S rRNA and gyrB (subunit B of topoisomerase II) genes, multilocus sequence analysis (MLSA), whole-genome sequencing (WGS), and microdilution. The results were compared with those for human strains. Just seven Nocardia species with one or two strains each, except for Nocardia cyriacigeorgica with 29, were identified. MLSA confirmed the species assignments made by 16S rRNA and gyrB analyses (89.5% and 71.0% respectively), and grouped each soil strain with its corresponding reference and clinical strains, except for 19 N. cyriacigeorgica strains found at five locations which grouped into a soil-only cluster. The soil strains of N. cyriacigeorgica showed fewer gyrB haplotypes than the examined human strains (13 vs. 17) but did show a larger number of gyrB SNPs (212 vs. 77). Their susceptibilities to antimicrobials were similar except for beta-lactams, fluoroquinolones, minocycline, and clarithromycin, with the soil strains more susceptible to the first three (p ≤ 0.05). WGS was performed on four strains belonging to the soil-only cluster and on two outside it, and the results compared with public N. cyriacigeorgica genomes. The average nucleotide/amino acid identity, in silico genome-to-genome hybridization similarity, and the difference in the genomic GC content, suggest that some strains of the soil-only cluster may belong to a novel subspecies or even a new species (proposed name Nocardia venezuelensis).
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Xu S, Hou X, Li D, Sun L, Li M, Ji X, Wang X, Li Z. Efficient differentiation of Nocardia farcinica, Nocardia cyriacigeorgica and Nocardia beijingensis by high-resolution melting analysis using a novel locus. J Med Microbiol 2020; 69:1367-1372. [PMID: 32478652 PMCID: PMC7819362 DOI: 10.1099/jmm.0.001205] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Accurate identification of Nocardia species remains a challenge due to the complexities of taxonomy and insufficient discriminatory power of traditional techniques. We report the development of a molecular technique that utilizes real-time PCR-based high-resolution melting (HRM) analysis for differentiation of the most common Nocardia species. Based on a novel fusA-tuf intergenic region sequence, Nocardia farcinica, Nocardia cyriacigeorgica and Nocardia beijingensis were clearly distinguished from one another by HRM analysis. The limit of detection of the HRM assay for purified Nocardia spp. DNA was at least 10 fg. No false positives were observed for specificity testing of 20 non-target clinical samples. In comparison to established matrix-assisted laser desorption/ionization-time of flight MS, the HRM assay improved the identification of N. beijingensis. Additionally, all the products of PCR were verified by direct sequencing. In conclusion, the developed molecular assay allows simultaneous detection and differentiation of N. farcinica, N. cyriacigeorgica and N. beijingensis with high sensitivity and specificity.
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Affiliation(s)
- Shuai Xu
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, PR China
| | - Xuexin Hou
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, PR China
| | - Dan Li
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, PR China
| | - Lina Sun
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, PR China
| | - Minghui Li
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, PR China
| | - Xingzhao Ji
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, PR China
| | - Xuebing Wang
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, PR China
| | - Zhenjun Li
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, PR China
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11
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Gnanam H, Rajapandian SGK, Gunasekaran R, Roshni Prithiviraj S, Ravindran RS, Sen S, Prajna L. Molecular identification of Nocardia species causing endophthalmitis using multilocus sequence analysis (MLSA): a 10-year perspective. J Med Microbiol 2020; 69:728-738. [PMID: 32310744 DOI: 10.1099/jmm.0.001180] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Introduction. Nocardia spp. can cause several ocular infections, such as keratitis, endophthalmitis and scleral abscesses. Molecular identification of Nocardia spp. by 16S rDNA sequencing is the gold standard method at present for species identification, but closely related species can only be identified by multilocus sequence analysis (MLSA) of housekeeping genes.Aim. The major objective was to profile Nocardia species, antibiotic susceptibility patterns and clinical outcomes in endophthalmitis patients.Methodology. Between January 2009 and December 2018, endophthalmitis patients who were diagnosed with Nocardia infection based on microscopic and culture characteristics were selected. Antibacterial susceptibility tests were performed and Nocardia speciation was performed using MLSA and phylogenetic tree analysis of the 16 s rRNA gene and the gyrB, hsp65 and secA1 genes.Results. A total of 43 culture-proven patients were identified during the study period. All isolates were 100 % sensitive to amikacin and 98 % resistant to ceftazidime. Fluoroquinolone sensitivity was observed in the range of 58 to 72 %. Year-wise analysis of antibiotic resistance patterns revealed there was a significant increase in resistance to fluoroquinolones. Twenty-two isolates were stored and six different species were identified. Nocardia farcinica (n=10) was found to be the most predominant, followed by Nocardia cyriacigeorgica (n=4), Nocardia otitidiscaviarum (n=3), Nocardia amikacinitolerans (n=2), Nocardia puris (n=2) and Nocardia higoensis (n=1).Conclusions. N. farcinica is the major pathogen, and this is the first report to identify N. otitidiscaviarum, N. amikacinitolerans and N. higoensis as causing endophthalmitis. Overall, visual outcomes were mostly poor even after aggressive management.
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Affiliation(s)
- Hariharan Gnanam
- Department of Biotechnology, Alagappa University, Karaikudi, India
| | | | | | | | | | - Sagnik Sen
- Department of Vitreoretinal Services, Aravind Eye Hospital, Madurai, India
| | - Lalitha Prajna
- Department of Ocular Microbiology, Aravind Eye Hospital, Madurai, India
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12
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Huang L, Sun L, Yan Y. Characteristics of nocardiosis patients with different immune status from a Chinese tertiary general hospital during 8-year period: A STROBE-compliment observational study. Medicine (Baltimore) 2019; 98:e17913. [PMID: 31702669 PMCID: PMC6855654 DOI: 10.1097/md.0000000000017913] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Nocardia is an opportunistic pathogen from environment, which is generally thought to infect immunosuppressed patients (ISPs), but recent studies showed it could also cause infections in immunocompetent patients (ICPs).The aim of this study was to compare the clinical characteristics, patients' outcome, Nocardia species' identification, and antibiotic susceptibility profiles of nocardiosis between ICPs and ISPs.The detailed clinical data were collected from all the nonrepetitive nocardiosis patients during 2011 and 2018, from a tertiary general hospital in Beijing, China. Then each Nocardia isolate was identified to species level by DNA sequencing. The antibiotic susceptibility testing was performed by E test method, and interpreted following CLSI M24 document. The clinical and microbiological characteristics between ICPs and ISPs were compared statistically.A total of 23 nonrepetitive nocardiosis patients with detailed clinical data were enrolled in this study. Among them, 9 were ICPs and 14 were ISPs. All the skin and soft tissue infections occurred in ICPs (33.3% vs 0%, P < .05). Bronchiectasis occurred more frequently in ICPs (44.4% vs 21.4%), whereas chronic kidney diseases and coinfection with aspergillosis occurred more frequently in ISPs (35.7% vs 0%, 35.7% vs 0%, respectively), although they did not reach the statistical significance. There were no significant differences in other clinical characteristics, Nocardia species' identification, and antibiotic susceptibility between ISPs and ICPs (P > .05).Nocardiosis could occur in both ISPs and ICPs. Skin and soft tissue infection and bronchiectasis occurred more frequently in ICPs. Chronic kidney diseases and co-infection with aspergillosis occurred more frequently in ISPs. These characteristics should be noticed by physicians in diagnosis of nocardiosis.
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13
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Huang L, Chen X, Xu H, Sun L, Li C, Guo W, Xiang L, Luo G, Cui Y, Lu B. Clinical features, identification, antimicrobial resistance patterns of Nocardia species in China: 2009-2017. Diagn Microbiol Infect Dis 2018; 94:165-172. [PMID: 30679058 DOI: 10.1016/j.diagmicrobio.2018.12.007] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2018] [Revised: 12/04/2018] [Accepted: 12/14/2018] [Indexed: 02/06/2023]
Abstract
Nocardia spp. is a pathogen responsible for a variety of clinical infections, ranging from skin and soft tissue infections, to the respiratory tract and central nervous system infections. Its epidemiological characteristics, including species distribution, clinical features, and antimicrobial susceptibility profiles, should be under surveillance for the prevention and treatment of nocardiosis. In the present study, over a 9-year period (from 2009 to 2017), 53 non-repetitive Nocardia isolates were collected from 8 tertiary general hospitals of 7 cities in China. These isolates were identified to species level by multilocus sequence analysis(MLSA). The clinical data were also reviewed. The susceptibilities to 10 commonly-used antibiotics for Nocardia were determined by E-test stripes, and the resistance rates, MIC50 and MIC90 to each antibiotic by different species were analyzed. Of 53 Nocardia isolates, N. farcinica was the most common species (24.5%, 13/53), followed by N. cyriacigeorgica (20.8%, 11/53), N. terpenica (15.1%, 8/53), N. abscessus (9.43%, 5/53), N. otitidiscaviarum (7.55%, 4/53), respectively. Furthermore, 31 Nocardia (58.5%) isolates were recovered from lower respiratory tract (sputum and BALF), 15 (28.3%) from superficial Infection, 3 (5.7%) from pleural effusion, 2 (3.8%) from CSF, and 1 from bone marrow and 1 from synovial fluid, respectively. The antibiotic resistance profiles varied between different Nocardia species. All Nocardia isolates were susceptible to linezolid, followed by imipenem and amikacin (both 92.5% susceptibility rate). N. terpenica, rarely documented elsewhere, showed a different antimicrobial susceptibility profile. In summary, herein, the clinical and antibiotic resistance features of Nocardia species reported would be helpful for understanding the diversity of Nocardia species circulating in China and for decision making in the context of empiric therapy.
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Affiliation(s)
- Lei Huang
- Department of Clinical Laboratory, Peking University First Hospital, Beijing, China
| | - Xingchun Chen
- Department of Laboratory Medicine, People's Hospital of Guangxi Zhuang Autonomous Region, Nanning, Guangxi Zhuang Autonomous Region, China
| | - Heping Xu
- Department of Clinical Laboratory, First Hospital Affiliated to Xiamen University, Xiamen, China
| | - Liying Sun
- Department of Clinical Laboratory, Peking University First Hospital, Beijing, China
| | - Chen Li
- Department of Laboratory Medicine, Liuyang city traditional Chinese medicine hospital, Liuyang City, Changsha, Hunan, China
| | - Wenchen Guo
- Department of Laboratory Medicine, Weifang People's Hospital, Weifang,Shandong, China
| | - Lili Xiang
- Department of Laboratory Medicine, Affiliated Hospital of Chongqing Medical and Pharmaceutical College, Shapingba District, Chongqing, China
| | - Guolan Luo
- Medical Science Laboratory, the Fourth Affiliated Hospital of Guangxi Medical University, Liuzhou, Guangxi, China
| | - Yancao Cui
- Department of Laboratory Medicine, Civil Aviation General Hospital, Beijing, China
| | - Binghuai Lu
- Laboratory of Clinical Microbiology and Infectious Diseases, Department of Pulmonary and Critical Care Medicine, China-Japan Friendship Hospital, Beijing, China.
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14
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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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15
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Ding P, Bai JL, Wang TT, Sun Y, Cao CL, Jiang JH, Qin S. Nocardia rhizosphaerihabitans sp. nov., a novel actinomycete isolated from a coastal soil. Int J Syst Evol Microbiol 2017; 68:192-197. [PMID: 29125460 DOI: 10.1099/ijsem.0.002481] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An actinomycete strain, designated KLBMP S0039T, was isolated from the rhizosphere soil of Lycium Linn., collected from the coastal region in Lianyungang, Jiangsu Province, eastern PR China, and was studied to determine its taxonomic position. The isolate showed a combination of morphological and chemotaxonomic properties typical of the members of the genus Nocardia. The cell wall contained meso-diaminopimelic acid as the diagnostic diamino acid and the whole-cell sugars were galactose, arabinose, glucose and ribose. The predominant menaquinone was identified as MK-8(H4ω-cycl). The diagnostic phospholipids were found to be diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and unknown lipids. The predominant cellular fatty acids were identified as C16 : 0, C18 : 0, C18 : 1ω9c, and 10-methyl C18 : 0 [tuberculostearic acid (TBSA)]. The G+C content of the genomic DNA was determined to be 68.2 mol%. The 16S rRNA gene sequence similarity indicated that KLBMP S0039T was most closely related to Nocardia neocaledoniensis NBRC 108232T (99.4 % 16S rRNA gene sequence similarity) and Nocardia asteroides NBRC 15531T (99.2 %), similarities to other type strains of species of the genus Nocardia were found to be less than 98.6 %. However, DNA-DNA relatedness values and phenotypic data indicated that KLBMP S0039T could be clearly distinguished from the closely related species of the genus Nocardia. On the basis of polyphasic taxonomic data, it is concluded that KLBMP S0039T represents a novel species of the genus Nocardia, for which the name Nocardiarhizosphaerihabitans sp. nov. is proposed. The type strain is KLBMP S0039T (=KCTC 39693T=CGMCC 4.7329T).
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Affiliation(s)
- Peng Ding
- School of Life Science, The Key Laboratory of Biotechnology for Medicinal Plants of Jiangsu Province, Jiangsu Normal University, Xuzhou, Jiangsu 221116, PR China
| | - Juan-Luan Bai
- School of Life Science, The Key Laboratory of Biotechnology for Medicinal Plants of Jiangsu Province, Jiangsu Normal University, Xuzhou, Jiangsu 221116, PR China
| | - Tian-Tian Wang
- School of Life Science, The Key Laboratory of Biotechnology for Medicinal Plants of Jiangsu Province, Jiangsu Normal University, Xuzhou, Jiangsu 221116, PR China
| | - Yong Sun
- School of Life Science, The Key Laboratory of Biotechnology for Medicinal Plants of Jiangsu Province, Jiangsu Normal University, Xuzhou, Jiangsu 221116, PR China
| | - Cheng-Liang Cao
- School of Life Science, The Key Laboratory of Biotechnology for Medicinal Plants of Jiangsu Province, Jiangsu Normal University, Xuzhou, Jiangsu 221116, PR China
| | - Ji-Hong Jiang
- School of Life Science, The Key Laboratory of Biotechnology for Medicinal Plants of Jiangsu Province, Jiangsu Normal University, Xuzhou, Jiangsu 221116, PR China
| | - Sheng Qin
- School of Life Science, The Key Laboratory of Biotechnology for Medicinal Plants of Jiangsu Province, Jiangsu Normal University, Xuzhou, Jiangsu 221116, PR China
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16
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Valdezate S, Garrido N, Carrasco G, Medina-Pascual MJ, Villalón P, Navarro AM, Saéz-Nieto JA. Epidemiology and susceptibility to antimicrobial agents of the main Nocardia species in Spain. J Antimicrob Chemother 2017; 72:754-761. [PMID: 27999029 DOI: 10.1093/jac/dkw489] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 10/12/2016] [Indexed: 12/14/2022] Open
Abstract
Objectives The aims of this study were to explore the clinical distribution, by species, of the genus Nocardia and to assess the antimicrobial susceptibilities of the 10 most prevalent species identified in Spain. Methods Over a 10 year period (2005-14), 1119 Nocardia strains were molecularly identified and subjected to the Etest. The distribution and resistance trends over the sub-periods 2005-09 and 2010-14 were also examined. Results Of the strains examined, 82.9% belonged to the following species: Nocardia cyriacigeorgica (25.3%), Nocardia nova (15.0%), Nocardia abscessus (12.7%), Nocardia farcinica (11.4%), Nocardia carnea (4.3%), Nocardia brasiliensis (3.5%), Nocardia otitidiscaviarum (3.1%), Nocardia flavorosea (2.6%), Nocardia rhamnosiphila (2.6%) and Nocardia transvalensis (2.4%). Their prevalence values were similar during 2005-09 and 2010-14, except for those of N. abscessus , N. farcinica and N. transvalensis , which fell significantly in the second sub-period ( P ≤ 0.05). The major location of isolation was the respiratory tract (∼86%). Half (13/27) of all strains from the CNS were N. farcinica . Significant differences in MIC results were recorded for some species between the two sub-periods. According to the CLSI's breakpoints, low resistance rates (≤15%) were recorded for seven species with respect to cefotaxime, imipenem and tobramycin; five species showed similar rates with respect to trimethoprim/sulfamethoxazole. Linezolid and amikacin were the most frequently active agents. Conclusion The accurate identification of the infecting species and the determination of its susceptibility to antimicrobial agents, given the large number of strains with atypical patterns, are crucial if patients with nocardiosis are to be successfully treated.
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17
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Thawai C, Rungjindamai N, Klanbut K, Tanasupawat S. Nocardia xestospongiae sp. nov., isolated from a marine sponge in the Andaman Sea. Int J Syst Evol Microbiol 2017; 67:1451-1456. [DOI: 10.1099/ijsem.0.001736] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Affiliation(s)
- Chitti Thawai
- Department of Biology, Faculty of Science, King Mongkut’s Institute of Technology Ladkrabang, Bangkok 10520, Thailand
- Actinobacterial Research Unit, Faculty of Science, King Mongkut’s Institute of Technology Ladkrabang, Bangkok 10520, Thailand
| | - Nattawut Rungjindamai
- Department of Biology, Faculty of Science, King Mongkut’s Institute of Technology Ladkrabang, Bangkok 10520, Thailand
- Actinobacterial Research Unit, Faculty of Science, King Mongkut’s Institute of Technology Ladkrabang, Bangkok 10520, Thailand
| | - Khanungkan Klanbut
- Department of Biology, Faculty of Science, King Mongkut’s Institute of Technology Ladkrabang, Bangkok 10520, Thailand
- Actinobacterial Research Unit, Faculty of Science, King Mongkut’s Institute of Technology Ladkrabang, Bangkok 10520, Thailand
| | - Somboon Tanasupawat
- Departments of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand
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18
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Molecular identification of Nocardia species using the sodA gene: Identificación molecular de especies de Nocardia utilizando el gen sodA. New Microbes New Infect 2017; 19:96-116. [PMID: 28794885 PMCID: PMC5547243 DOI: 10.1016/j.nmni.2017.03.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Revised: 03/08/2017] [Accepted: 03/21/2017] [Indexed: 11/21/2022] Open
Abstract
Currently for bacterial identification and classification the rrs gene encoding 16S rRNA is used as a reference method for the analysis of strains of the genus Nocardia. However, it does not have enough polymorphism to differentiate them at the species level. This fact makes it necessary to search for molecular targets that can provide better identification. The sodA gene (encoding the enzyme superoxide dismutase) has had good results in identifying species of other Actinomycetes. In this study the sodA gene is proposed for the identification and differentiation at the species level of the genus Nocardia. We used 41 type species of various collections; a 386 bp fragment of the sodA gene was amplified and sequenced, and a phylogenetic analysis was performed comparing the genes rrs (1171 bp), hsp65 (401 bp), secA1 (494 bp), gyrB (1195 bp) and rpoB (401 bp). The sequences were aligned using the Clustal X program. Evolutionary trees according to the neighbour-joining method were created with the programs Phylo_win and MEGA 6. The specific variability of the sodA genus of the genus Nocardia was analysed. A high phylogenetic resolution, significant genetic variability, and specificity and reliability were observed for the differentiation of the isolates at the species level. The polymorphism observed in the sodA gene sequence contains variable regions that allow the discrimination of closely related Nocardia species. The clear specificity, despite its small size, proves to be of great advantage for use in taxonomic studies and clinical diagnosis of the genus Nocardia.
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19
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Bai JL, Wang Y, Qin S, Ding P, Xing K, Yuan B, Cao CL, Huang Y, Zhang YQ, Jiang JH. Nocardia
jiangsuensis sp. nov., an actinomycete isolated from coastal soil. Int J Syst Evol Microbiol 2016; 66:4633-4638. [DOI: 10.1099/ijsem.0.001402] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Juan-Luan Bai
- School of Life Science, The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, Jiangsu Normal University, Xuzhou, Jiangsu 221116, PR China
| | - Yu Wang
- School of Life Science, The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, Jiangsu Normal University, Xuzhou, Jiangsu 221116, PR China
| | - Sheng Qin
- School of Life Science, The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, Jiangsu Normal University, Xuzhou, Jiangsu 221116, PR China
| | - Peng Ding
- School of Life Science, The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, Jiangsu Normal University, Xuzhou, Jiangsu 221116, PR China
| | - Ke Xing
- School of Life Science, The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, Jiangsu Normal University, Xuzhou, Jiangsu 221116, PR China
| | - Bo Yuan
- School of Life Science, The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, Jiangsu Normal University, Xuzhou, Jiangsu 221116, PR China
| | - Cheng-Liang Cao
- School of Life Science, The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, Jiangsu Normal University, Xuzhou, Jiangsu 221116, PR China
| | - Ying Huang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Yu-Qin Zhang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, PR China
| | - Ji-Hong Jiang
- School of Life Science, The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, Jiangsu Normal University, Xuzhou, Jiangsu 221116, PR China
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20
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Comparison of restriction enzyme pattern analysis and full gene sequencing of 16S rRNA gene for Nocardia species identification, the first report of Nocardia transvalensis isolated of sputum from Iran, and review of the literature. Antonie Van Leeuwenhoek 2016; 109:1285-98. [DOI: 10.1007/s10482-016-0746-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Accepted: 06/29/2016] [Indexed: 10/21/2022]
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21
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Kuchibiro T, Ikeda T, Nakanishi H, Morishita Y, Houdai K, Ito J, Gonoi T. First case report of pulmonary nocardiosis caused by Nocardia mexicana. JMM Case Rep 2016; 3:e005054. [PMID: 28348776 PMCID: PMC5330244 DOI: 10.1099/jmmcr.0.005054] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Accepted: 06/10/2016] [Indexed: 11/25/2022] Open
Abstract
Introduction: Nocardia species usually cause opportunistic infections, and the frequency of these infections is increasing owing to the growing population of immunocompromised hosts. However, Nocardia species may sometimes cause an infection disease in immunocompetent hosts. Nocardia mexicana infections are the least common and are very rare. Case presentation: Herein, we report the first case of a pulmonary infection with N. mexicana in a 61-year-old Japanese woman with a history of hyperlipidaemia and bronchiectasis and a 6-month history of non-productive hacking cough. A sample of bronchial lavage fluid obtained by bronchofiberscopy showed filamentous branching gram-positive rods and acid-fast filamentous branching rods, and a colony of suspected Nocardia was cultured. Based on 16S rRNA, gyrB, rpoB, secA1 and hsp65 gene sequence analyses and biochemical and physiological properties, the strain was identified as N. mexicana. The strain was resistant to the antimicrobial agents amoxicillin-clavulanic acid, clarithromycin, minocycline, gentamycin, tobramycin, ciprofloxacin and trimethoprim-sulfamethoxazole. The patient was treated with biapenem followed by intravenous amikacin and oral linezolid. Conclusion: Despite its rarity, the species require attention owing to the existence of multidrug-resistant strains.
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Affiliation(s)
- Tomokazu Kuchibiro
- Department of Clinical Laboratory, Naga Municipal Hospital, 1282 Uchita, Kinokawa, Wakayama, 649-6414, Japan
| | - Takeshi Ikeda
- Department of Respiratory Medicine, Naga Municipal Hospital, 1282 Uchita, Kinokawa, Wakayama, 649-6414, Japan
| | - Hirotaka Nakanishi
- Department of Respiratory Medicine, Naga Municipal Hospital, 1282 Uchita, Kinokawa, Wakayama, 649-6414, Japan
| | - Yukiko Morishita
- Department of Respiratory Medicine, Naga Municipal Hospital, 1282 Uchita, Kinokawa, Wakayama, 649-6414, Japan
| | - Katsuyuki Houdai
- Department of Clinical Laboratory, Naga Municipal Hospital, 1282 Uchita, Kinokawa, Wakayama, 649-6414, Japan
| | - Junko Ito
- Medical Mycology Research Center, Chiba University, 1-8-1 Inohana, Chuoku, Chiba City, Chiba, 260-8673, Japan
| | - Tohru Gonoi
- Medical Mycology Research Center, Chiba University, 1-8-1 Inohana, Chuoku, Chiba City, Chiba, 260-8673, Japan
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22
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Tanasupawat S, Phongsopitanun W, Suwanborirux K, Ohkuma M, Kudo T. Nocardia rayongensis sp. nov., isolated from Thai peat swamp forest soil. Int J Syst Evol Microbiol 2016; 66:1950-1955. [DOI: 10.1099/ijsem.0.000971] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Somboon Tanasupawat
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand
| | - Wongsakorn Phongsopitanun
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand
| | - Khanit Suwanborirux
- Department of Pharmacognosy and Pharmaceutical Botany, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand
| | - Moriya Ohkuma
- Japan Collection of Microorganisms, RIKEN BioResource Center, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | - Takuji Kudo
- Japan Collection of Microorganisms, RIKEN BioResource Center, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
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23
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Compte RB, Martínez-Osorio H, Carrasco G, Lorente B, Elizalde J, Valdezate S, Lorente R, Iglesias E, Saez-Nieto JA. Traumatic endophthalmitis caused by Nocardia kruczakiae in a patient with traumatic eye injury. J Ophthalmic Inflamm Infect 2015; 5:36. [PMID: 26604206 PMCID: PMC4658342 DOI: 10.1186/s12348-015-0067-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Accepted: 11/16/2015] [Indexed: 11/21/2022] Open
Abstract
Background We describe a case of traumatic ocular endophthalmitis caused by Nocardia kruczakiae after vegetable trauma in an immunocompetent child. Findings A 5-year-old boy suffered from a trauma with a palm tree leaflet. Two months later, he was diagnosed with traumatic infectious uveitis and intumescent cataract with anterior capsule rupture. Intensive treatment with systemic and topical vancomycin, ceftazidime and methylprednisolone began. After 1 month, he underwent phacoemulsification with intraocular lens implantation (IOL). After some episodes of reactivation, he was diagnosed with traumatic nocardial endophthalmitis from aqueous humour samples. Several operations and specific antibiotic therapy resolved the infection. Conclusions In cases of traumatic endophthalmitis and several recurrences, it is extremely useful to make an etiologic diagnosis in order to treat the patient with specific antibiotics.
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Affiliation(s)
- Rafael Barraquer Compte
- Centro de Oftalmología Barraquer, Muntaner 314, 08021, Barcelona, Spain. .,Institut universitari Barraquer, Barcelona, Spain.
| | - Hernán Martínez-Osorio
- Centro de Oftalmología Barraquer, Muntaner 314, 08021, Barcelona, Spain. .,Institut universitari Barraquer, Barcelona, Spain.
| | - Gema Carrasco
- Servicio de Bacteriología, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain.
| | - Betty Lorente
- Centro de Oftalmología Barraquer, Muntaner 314, 08021, Barcelona, Spain. .,Institut universitari Barraquer, Barcelona, Spain.
| | - Javier Elizalde
- Centro de Oftalmología Barraquer, Muntaner 314, 08021, Barcelona, Spain. .,Institut universitari Barraquer, Barcelona, Spain.
| | - Sylvia Valdezate
- Servicio de Bacteriología, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain.
| | - Ramón Lorente
- Servicio de Oftalmología, Complexo Hospitalario Universitario, Ourense, Spain.
| | - Emilio Iglesias
- Servicio de Oftalmología, Complexo Hospitalario Universitario, Ourense, Spain.
| | - Juan Antonio Saez-Nieto
- Servicio de Bacteriología, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain.
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24
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Nocardia zapadnayensis sp. nov., isolated from soil. Antonie van Leeuwenhoek 2015; 109:95-103. [DOI: 10.1007/s10482-015-0612-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Accepted: 10/24/2015] [Indexed: 10/22/2022]
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25
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Intra-Genomic Heterogeneity in 16S rRNA Genes in Strictly Anaerobic Clinical Isolates from Periodontal Abscesses. PLoS One 2015; 10:e0130265. [PMID: 26103050 PMCID: PMC4477887 DOI: 10.1371/journal.pone.0130265] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Accepted: 05/18/2015] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Members of the genera Prevotella, Veillonella and Fusobacterium are the predominant culturable obligate anaerobic bacteria isolated from periodontal abscesses. When determining the cumulative number of clinical anaerobic isolates from periodontal abscesses, ambiguous or overlapping signals were frequently encountered in 16S rRNA gene sequencing chromatograms, resulting in ambiguous identifications. With the exception of the genus Veillonella, the high intra-chromosomal heterogeneity of rrs genes has not been reported. METHODS The 16S rRNA genes of 138 clinical, strictly anaerobic isolates and one reference strain were directly sequenced, and the chromatograms were carefully examined. Gene cloning was performed for 22 typical isolates with doublet sequencing signals for the 16S rRNA genes, and four copies of the rrs-ITS genes of 9 Prevotella intermedia isolates were separately amplified by PCR, sequenced and compared. Five conserved housekeeping genes, hsp60, recA, dnaJ, gyrB1 and rpoB from 89 clinical isolates of Prevotella were also amplified by PCR and sequenced for identification and phylogenetic analysis along with 18 Prevotella reference strains. RESULTS Heterogeneity of 16S rRNA genes was apparent in clinical, strictly anaerobic oral bacteria, particularly in the genera Prevotella and Veillonella. One hundred out of 138 anaerobic strains (72%) had intragenomic nucleotide polymorphisms (SNPs) in multiple locations, and 13 strains (9.4%) had intragenomic insertions or deletions in the 16S rRNA gene. In the genera Prevotella and Veillonella, 75% (67/89) and 100% (19/19) of the strains had SNPs in the 16S rRNA gene, respectively. Gene cloning and separate amplifications of four copies of the rrs-ITS genes confirmed that 2 to 4 heterogeneous 16S rRNA copies existed. CONCLUSION Sequence alignment of five housekeeping genes revealed that intra-species nucleotide similarities were very high in the genera Prevotella, ranging from 94.3-100%. However, the inter-species similarities were relatively low, ranging from 68.7-97.9%. The housekeeping genes rpoB and gyrB1 were demonstrated to be alternative classification markers to the species level based on intra- and inter-species comparisons, whereas based on phylogenetic tree rpoB proved to be reliable phylogenetic marker for the genus Prevotella.
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Brown-Elliott BA, Conville P, Wallace RJ. Current Status of Nocardia Taxonomy and Recommended Identification Methods. ACTA ACUST UNITED AC 2015. [DOI: 10.1016/j.clinmicnews.2015.01.007] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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First case of disseminated infection with Nocardia cerradoensis in a human. J Clin Microbiol 2015; 53:1034-7. [PMID: 25568436 DOI: 10.1128/jcm.02979-14] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Here we report in a human, a renal transplant patient, the first disseminated infection with Nocardia cerradoensis, isolated after a brain biopsy. Species identification was based on 16S rRNA, gyrB, and hsp65 gene analyses. Antibiotic treatment was successful by combining carbapenems and aminoglycosides and then switching to oral trimethoprim-sulfamethoxazole.
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gyrB analysis as a tool for identifying Nocardia species and exploring their phylogeny. J Clin Microbiol 2014; 53:997-1001. [PMID: 25540402 DOI: 10.1128/jcm.03072-14] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
gyrB is used to improve the identification of the Nocardia species N. brasiliensis, N. higoensis, N. ignorata, N. otitidiscaviarum, N. paucivorans, N. pneumoniae, N. puris, N. takedensis, N. veterana, and N. vinacea, but it does not improve the identification of another 12 Nocardia studied species. gyrB provides typing and phylogenetic markers for N. carnea, N. transvalensis, N. brasiliensis, and N. otitidiscaviarum.
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Hu Y, Wang L, Huang X, Liang Y, Zhang J. Systemic Nocardia brasiliensis infection in a patient with systemic lupus erythematosus: successful diagnosis and therapy. Int J Dermatol 2014; 55:453-9. [PMID: 25311703 DOI: 10.1111/ijd.12712] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Revised: 01/11/2014] [Accepted: 03/08/2014] [Indexed: 11/30/2022]
Affiliation(s)
- Yongxuan Hu
- Department of Dermatology and Venereology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China.,Department of Dermatology and Venereology, The 3rd Affiliated Hospital of Southern Medical University, Guangzhou, China
| | - Li Wang
- Department of Dermatology and Venereology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China.,Department of Dermatology and Venereology, The People's Hospital of Taiping, Dongguan, China
| | - Xiao Huang
- Department of Dermatology and Venereology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Yuheng Liang
- Department of Dermatology and Venereology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Junmin Zhang
- Department of Dermatology and Venereology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
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Camas M, Veyisoglu A, Sahin N. Nocardia sungurluensis sp. nov., isolated from soil. Int J Syst Evol Microbiol 2014; 64:1629-1634. [DOI: 10.1099/ijs.0.051334-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel Gram-reaction-positive, rod-shaped, non-motile and mycolic acid-containing strain, CR3272T, isolated from soil, was studied using a polyphasic approach. The organism showed a combination of chemotaxonomic and morphological properties typical of the genus
Nocardia
. The cell wall contained meso-diaminopimelic acid (type IV) and whole-cell sugars were galactose, glucose, arabinose and xylose. The predominant menaquinone was MK-8(H4cyc). The major phospholipids were diphosphatidylglycerol and phosphatidylinositol mannosides. Major fatty acids were C16 : 0, C18 : 1
cis9, C18 : 0 10-methyl (TBSA) and C16 : 1
cis9. The novel strain formed distinct phyletic line in the
Nocardia
16S rRNA gene tree and was closely associated with
Nocardia goodfellowii
A2012T (98.6 % 16S rRNA gene sequence similarity),
Nocardia alba
YIM 30243T (98.5 %) and
Nocardia caishijiensis
F829T (97.9 %). However, DNA–DNA relatedness values and phenotypic data demonstrated that strain CR3272T was clearly distinguished from all closely related species of the genus
Nocardia
. It is concluded that the organism be classified as representing a novel species of the genus
Nocardia
, for which the name Nocardia sungurluensis is proposed. The type strain is CR3272T ( = DSM 45714T = KCTC 29094T).
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Affiliation(s)
- Mustafa Camas
- Department of Biology, Faculty of Art and Science, Ondokuz Mayis University, 55139 Kurupelit-Samsun, Turkey
| | - Aysel Veyisoglu
- Department of Biology, Faculty of Art and Science, Ondokuz Mayis University, 55139 Kurupelit-Samsun, Turkey
| | - Nevzat Sahin
- Department of Biology, Faculty of Art and Science, Ondokuz Mayis University, 55139 Kurupelit-Samsun, Turkey
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Gyrase subunit B amino acid signatures for the actinobacterial family Streptosporangiaceae. Syst Appl Microbiol 2014; 37:252-60. [PMID: 24423454 DOI: 10.1016/j.syapm.2013.12.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2013] [Revised: 12/03/2013] [Accepted: 12/13/2013] [Indexed: 11/24/2022]
Abstract
Higher order taxonomic assignments (family level and above) in the phylum Actinobacteria are currently based only on 16S-rRNA gene sequence analyses. Additional molecular markers need to be identified to increase the number of reference points for defining actinobacterial families and other higher taxa. Furthermore, since most novel actinobacterial taxa are defined at the level of species and genera, it is necessary to define molecular signatures at the genus level to enhance the robustness of genus descriptions. The current use of chemotaxonomic markers to define genera could be improved by the identification of genus-specific molecular signatures. In this study, GyrB amino acid sequences for members of the family Streptosporangiaceae were analysed for molecular signatures. Phylogenetic analyses showed that the gyrB gene tree supported the composition of the currently recognised genera in this family. The catalytically important amino acids were identified in the GyrB sequences, as were the GHKL superfamily motifs. Examination of GyrB protein sequence alignments revealed that there are genus-specific sequences for most of the multi-species genera and genus-defining amino acid insertions for the genera Herbidospora and Microbispora. Furthermore, there are GyrB signature amino acids which distinguish the family Streptosporangiaceae from the family Nocardiopsaceae.
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Baio PVP, Ramos JN, dos Santos LS, Soriano MF, Ladeira EM, Souza MC, Camello TCF, Ribeiro MG, Hirata Junior R, Vieira VV, Mattos-Guaraldi AL. Molecular identification of nocardia isolates from clinical samples and an overview of human nocardiosis in Brazil. PLoS Negl Trop Dis 2013; 7:e2573. [PMID: 24340116 PMCID: PMC3854972 DOI: 10.1371/journal.pntd.0002573] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2013] [Accepted: 10/21/2013] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Nocardia sp. causes a variety of clinical presentations. The incidence of nocardiosis varies geographically according to several factors, such as the prevalence of HIV infections, transplants, neoplastic and rheumatic diseases, as well as climate, socio-economic conditions and laboratory procedures for Nocardia detection and identification. In Brazil the paucity of clinical reports of Nocardia infections suggests that this genus may be underestimated as a cause of human diseases and/or either neglected or misidentified in laboratory specimens. Accurate identification of Nocardia species has become increasingly important for clinical and epidemiological investigations. In this study, seven clinical Nocardia isolates were identified by multilocus sequence analysis (MLSA) and their antimicrobial susceptibility was also determined. Most Nocardia isolates were associated to pulmonary disease. METHODOLOGY/PRINCIPAL FINDINGS The majority of Brazilian human isolates in cases reported in literature were identified as Nocardia sp. Molecular characterization was used for species identification of Nocardia nova, Nocardia cyriacigeorgica, Nocardia asiatica and Nocardia exalbida/gamkensis. Data indicated that molecular analysis provided a different Nocardia speciation than the initial biochemical identification for most Brazilian isolates. All Nocardia isolates showed susceptibility to trimethoprim-sulfamethoxazole, the antimicrobial of choice in the treatment nocardiosis. N. nova isolated from different clinical specimens from one patient showed identical antimicrobial susceptibility patterns and two distinct clones. CONCLUSIONS/SIGNIFICANCE Although Brazil is the world's fifth-largest country in terms of land mass and population, pulmonary, extrapulmonary and systemic forms of nocardiosis were reported in only 6 of the 26 Brazilian states from 1970 to 2013. A least 33.8% of these 46 cases of nocardiosis proved fatal. Interestingly, coinfection by two clones may occur in patients presenting nocardiosis. Nocardia infection may be more common throughout the Brazilian territory and in other developing tropical countries than is currently recognized and MLSA should be used more extensively as an effective method for Nocardia identification.
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Affiliation(s)
- Paulo Victor Pereira Baio
- Universidade do Estado do Rio de Janeiro – UERJ, Faculdade de Ciências Médicas, Departamento de Microbiologia, Imunologia e Patologia, Laboratório de Difteria e Corinebactérias de Importância Clínica-LDCIC, Centro Colaborador para Difteria da CGLAB/SVS/MS, Rio de Janeiro, Rio de Janeiro, Brazil
- Fundação Oswaldo Cruz, Instituto Nacional de Controle de Qualidade em Saúde (INCQS), Instituto Oswaldo Cruz, Rio de Janeiro, Rio de Janeiro, Brazil
- Ministério da Defesa, Laboratório Químico Farmacêutico do Exército, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Juliana Nunes Ramos
- Universidade do Estado do Rio de Janeiro – UERJ, Faculdade de Ciências Médicas, Departamento de Microbiologia, Imunologia e Patologia, Laboratório de Difteria e Corinebactérias de Importância Clínica-LDCIC, Centro Colaborador para Difteria da CGLAB/SVS/MS, Rio de Janeiro, Rio de Janeiro, Brazil
- Fundação Oswaldo Cruz, Instituto Nacional de Controle de Qualidade em Saúde (INCQS), Instituto Oswaldo Cruz, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Louisy Sanches dos Santos
- Universidade do Estado do Rio de Janeiro – UERJ, Faculdade de Ciências Médicas, Departamento de Microbiologia, Imunologia e Patologia, Laboratório de Difteria e Corinebactérias de Importância Clínica-LDCIC, Centro Colaborador para Difteria da CGLAB/SVS/MS, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Morgana Fonseca Soriano
- Universidade do Estado do Rio de Janeiro – UERJ, Faculdade de Ciências Médicas, Departamento de Microbiologia, Imunologia e Patologia, Laboratório de Difteria e Corinebactérias de Importância Clínica-LDCIC, Centro Colaborador para Difteria da CGLAB/SVS/MS, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Elisa Martins Ladeira
- Fundação Oswaldo Cruz, Instituto Nacional de Controle de Qualidade em Saúde (INCQS), Instituto Oswaldo Cruz, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Mônica Cristina Souza
- Universidade do Estado do Rio de Janeiro – UERJ, Faculdade de Ciências Médicas, Departamento de Microbiologia, Imunologia e Patologia, Laboratório de Difteria e Corinebactérias de Importância Clínica-LDCIC, Centro Colaborador para Difteria da CGLAB/SVS/MS, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Thereza Cristina Ferreira Camello
- Universidade do Estado do Rio de Janeiro – UERJ, Faculdade de Ciências Médicas, Departamento de Microbiologia, Imunologia e Patologia, Laboratório de Difteria e Corinebactérias de Importância Clínica-LDCIC, Centro Colaborador para Difteria da CGLAB/SVS/MS, Rio de Janeiro, Rio de Janeiro, Brazil
- Universidade do Estado do Rio de Janeiro – UERJ, Hospital Universitário Pedro Ernesto, Laboratório de Bacteriologia, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Marcio Garcia Ribeiro
- Universidade Estadual Paulista – UNESP, Faculdade de Medicina Veterinária e Zootecnia, Botucatu, São Paulo, Brazil
| | - Raphael Hirata Junior
- Universidade do Estado do Rio de Janeiro – UERJ, Faculdade de Ciências Médicas, Departamento de Microbiologia, Imunologia e Patologia, Laboratório de Difteria e Corinebactérias de Importância Clínica-LDCIC, Centro Colaborador para Difteria da CGLAB/SVS/MS, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Verônica Viana Vieira
- Fundação Oswaldo Cruz, Instituto Nacional de Controle de Qualidade em Saúde (INCQS), Instituto Oswaldo Cruz, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Ana Luíza Mattos-Guaraldi
- Universidade do Estado do Rio de Janeiro – UERJ, Faculdade de Ciências Médicas, Departamento de Microbiologia, Imunologia e Patologia, Laboratório de Difteria e Corinebactérias de Importância Clínica-LDCIC, Centro Colaborador para Difteria da CGLAB/SVS/MS, Rio de Janeiro, Rio de Janeiro, Brazil
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Development of a real-time PCR for detection of the oyster pathogen Nocardia crassostreae based on its homogeneous 16S–23S rRNA intergenic spacer region. J Invertebr Pathol 2013; 114:120-7. [DOI: 10.1016/j.jip.2013.07.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Revised: 07/09/2013] [Accepted: 07/11/2013] [Indexed: 11/17/2022]
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Chen KW, Lu CW, Huang TC, Lu CF, Liau YL, Lin JF, Li SY. Cutaneous manifestations of Nocardia brasiliensis infection in Taiwan during 2002–2012—clinical studies and molecular typing of pathogen by gyrB and 16S gene sequencing. Diagn Microbiol Infect Dis 2013; 77:74-8. [DOI: 10.1016/j.diagmicrobio.2013.05.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2013] [Revised: 05/08/2013] [Accepted: 05/14/2013] [Indexed: 11/16/2022]
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Identification, typing, and phylogenetic relationships of the main clinical Nocardia species in spain according to their gyrB and rpoB genes. J Clin Microbiol 2013; 51:3602-8. [PMID: 23966490 DOI: 10.1128/jcm.00515-13] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
This study compares the identification, typing, and phylogenetic relationships of the most prevalent clinical Nocardia species in Spain, as determined via sequence analysis of their housekeeping genes gyrB and rpoB, with the results returned by the gold standard 16S rRNA method. gyrB and rpoB analyses identified Nocardia abscessus, N. cyriacigeorgica, N. farcinica, and the N. nova complex, species that together account for more than half of the human nocardiosis cases recorded in Spain. The individual discriminatory power of gyrB and rpoB with respect to intraspecies typing, calculated using the Hunter-Gaston discriminatory index (HGDI), was generally high (HGDI, 0.85 to 1), except for rpoB with respect to N. farcinica (HGDI, 0.71). Phylogenetically, different degrees of intra- and interspecies microheterogeneity were observed for gyrB and rpoB in a group of 119 clinical strains. A single 16S haplotype was obtained for each species, except for the N. nova complex (8 types), while gyrB and rpoB were more polymorphic: N. abscessus had 14 and 18 haplotypes, N. cyriacigeorgica had 17 and 12, N. farcinica had 11 and 5, and the N. nova complex had 26 and 29 haplotypes, respectively. A diversity gradient was therefore seen, with N. farcinica at the bottom followed by N. abscessus and N. cyriacigeorgica in the middle and N. nova complex at the top. The complexity of the N. nova complex is highlighted by its six variations in the GyrB (126)AAAPEH motif. gyrB sequencing (with or without rpoB sequencing) offers a simple means for identifying the most prevalent Nocardia species in Spanish medical laboratories and for determining the intraspecific diversity among their strains.
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Wang X, Zhu D, Wang M, Cheng A, Jia R, Chen S, Chen X, Tang T. Development and application of specific polymerase chain reaction assay targeting the gyrB gene for rapid detection of Riemerella anatipestifer. Poult Sci 2012; 91:2450-3. [DOI: 10.3382/ps.2012-02375] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Kobayashi N, Sueoka-Aragane N, Naganobu N, Umeguchi H, Kusaba K, Nagasawa Z, Yazawa K, Gonoi T, Kimura S, Hayashi S. Disseminated Nocardiosis caused by Nocardia concava with acute respiratory failure and central nervous system involvement treated with linezolid. Intern Med 2012. [PMID: 23207125 DOI: 10.2169/internalmedicine.51.7733] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Nocardia concava was identified as a new species in 2005; however, the clinical manifestations of Nocardia concava infection have yet to be clarified. We herein present the case of an immunosuppressed patient who developed disseminated nocardiosis caused by N. concava with multiple abscesses in the lungs, cutis, subcutaneous tissue, skeletal muscles and kidneys accompanied by central nervous system involvement, including meningitis and ventriculitis. The patient was cured with appropriate treatment including linezolid after testing for susceptibility. Linezolid should be considered as an alternative agent for treating disseminated nocardiosis because of its effective distribution to multiple sites.
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Affiliation(s)
- Naomi Kobayashi
- Division of Hematology, Respiratory Medicine and Oncology, Department of Internal Medicine, Faculty of Medicine, Saga University, Japan
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Improved identification of Gordonia, Rhodococcus and Tsukamurella species by 5'-end 16S rRNA gene sequencing. Pathology 2011; 43:58-63. [PMID: 21240067 DOI: 10.1097/pat.0b013e328340e431] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
OBJECTIVES The identification of fastidious aerobic Actinomycetes such as Gordonia, Rhodococcus, and Tsukamurella has remained a challenge leading to clinically significant misclassifications. This study is intended to examine the feasibility of partial 5'-end 16S rRNA gene sequencing for the identification of Gordonia, Rhodococcus, and Tsukamurella, and defined potential reference sequences for species from each of these genera. METHODS The 16S rRNA gene sequence based identification algorithm for species identification was used and enhanced by aligning test sequences with reference sequences from the List of Prokaryotic Names with Standing in Nomenclature. RESULTS Conventional PCR based 16S rRNA gene sequencing and the alignment of the isolate 16S rRNA gene sequence with reference sequences accurately identified 100% of clinical strains of aerobic Actinomycetes. While partial 16S rRNA gene sequences of reference type strains matched with the 16S rRNA gene sequences of 19 isolates in our data set, another 13 strains demonstrated a degree of polymorphism with a 1-4 bp difference in the regions of difference. CONCLUSIONS 5'-end 606 bp 16S rRNA gene sequencing, coupled with the assignment of well defined reference sequences to clinically relevant species of bacteria, can be a useful strategy for improving the identification of clinically relevant aerobic Actinomycetes.
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Hu Y, Zheng D, Takizawa K, Mikami Y, Dai L, Yazawa K, Fukushima K, Lu C, Xi L. Systemic nocardiosis caused by Nocardia concava in China. Med Mycol 2011; 49:662-6. [PMID: 21284569 DOI: 10.3109/13693786.2011.555849] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
A 42-year-old man with polychondritis and a 2-year history of using low-dose prednisone and other immunosuppressive drugs was admitted to our hospital due to persistent high fever of 10 days duration. A strain of Nocardia was twice isolated from his blood and subsequently identified to be N. concava. The patient was initially treated with sulphadiazine sodium, vancomycin and imipenema for 7 days but the symptoms persisted. Consequently, the regimen was changed to sulphadiazine sodium, ciprofloxacin and amikacin sulfate based on the antibiotic susceptibility tests of the Nocardia isolate. The fever disappeared and the patient's condition improved after 10 days of this treatment to the extent that he was discharged. However, 7 days later, the patient's condition deteriorated and he died due to multiple organ failure. This is the first report of N. concava causing systemic nocardiosis in China.
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Affiliation(s)
- Yongxuan Hu
- Department of Dermatology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
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Phylogeny and identification of Nocardia species on the basis of multilocus sequence analysis. J Clin Microbiol 2010; 48:4525-33. [PMID: 20844218 DOI: 10.1128/jcm.00883-10] [Citation(s) in RCA: 104] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Nocardia species identification is difficult due to a complex and rapidly changing taxonomy, the failure of 16S rRNA and cellular fatty acid analysis to discriminate many species, and the unreliability of biochemical testing. Here, Nocardia species identification was achieved through multilocus sequence analysis (MLSA) of gyrase B of the β subunit of DNA topoisomerase (gyrB), 16S rRNA (16S), subunit A of SecA preprotein translocase (secA1), the 65-kDa heat shock protein (hsp65), and RNA polymerase (rpoB) applied to 190 clinical, 36 type, and 11 reference strains. Phylogenetic analysis resolved 30 sequence clusters with high (>85%) bootstrap support. Since most clusters contained a single type strain and the analysis corroborated current knowledge of Nocardia taxonomy, the sequence clusters were equated with species clusters and MLSA was deemed appropriate for species identification. By comparison, single-locus analysis was inadequate because it failed to resolve species clusters, partly due to the presence of foreign alleles in 22.1% of isolates. While MLSA identified the species of the majority (71.3%) of strains, it also identified clusters that may correspond to new species. The correlation of the identities by MLSA with those determined on the basis of microscopic examination, biochemical testing, and fatty acid analysis was 95%; however, MLSA was more discriminatory. Nocardia cyriacigeorgica (21.58%) and N. farcinica (14.74%) were the most frequently encountered species among clinical isolates. In summary, five-locus MLSA is a reliable method of elucidating taxonomic data to inform Nocardia species identification; however, three-locus (gyrB-16S-secA1) or four-locus (gyrB-16S-secA1-hsp65) MLSA was nearly as reliable, correctly identifying 98.5% and 99.5% of isolates, respectively, and would be more feasible for routine use in a clinical reference microbiology laboratory.
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secA1 gene sequence polymorphisms for species identification of Nocardia species and recognition of intraspecies genetic diversity. J Clin Microbiol 2010; 48:3928-34. [PMID: 20810768 DOI: 10.1128/jcm.01113-10] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Sequence analysis of the Nocardia essential secretory protein SecA1 gene (secA1) for species identification of 120 American Type Culture Collection (ATCC) and clinical isolates of Nocardia (16 species) was studied in comparison with 5'-end 606-bp 16S rRNA gene sequencing. Species determination by both methods was concordant for all 10 ATCC strains. secA1 gene sequencing provided the same species identification as 16S rRNA gene analysis for 94/110 (85.5%) clinical isolates. However, 40 (42.6%) isolates had sequences with <99.0% similarity to archived secA1 sequences for the species, including 29 Nocardia cyriacigeorgica (96.6 to 98.9% similarity) and 4 Nocardia veterana (91.5 to 98.9% similarity) strains. Discrepant species identification was obtained for 16 (14.5%) clinical isolates, including 13/23 Nocardia nova strains (identified as various Nocardia species by secA1 sequencing) and 1 isolate each of Nocardia abscessus (identified as Nocardia asiatica), Nocardia elegans (Nocardia africana), and Nocardia transvalensis (Nocardia blacklockiae); both secA1 gene sequence analysis and deduced amino acid sequence analysis determined the species to be different from those assigned by 16S rRNA gene sequencing. The secA1 locus showed high sequence diversity (66 sequence or genetic types versus 40 16S rRNA gene sequence types), which was highest for N. nova (14 secA1 sequence types), followed by Nocardia farcinica and N. veterana (n = 7 each); there was only a single sequence type among eight Nocardia paucivorans strains. The secA1 locus has potential for species identification as an adjunct to 16S rRNA gene sequencing but requires additional deduced amino acid sequence analysis. It may be a suitable marker for phylogenetic/subtyping studies.
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Wang X, Xiao M, Kong F, Sintchenko V, Wang H, Wang B, Lian S, Sorrell T, Chen S. Reverse line blot hybridization and DNA sequencing studies of the 16S-23S rRNA gene intergenic spacer regions of five emerging pathogenic Nocardia species. J Med Microbiol 2010; 59:548-555. [PMID: 20110385 DOI: 10.1099/jmm.0.017921-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The objective of this study was to examine DNA sequence polymorphisms in the 16S-23S rRNA gene intergenic spacer (ITS) regions of five emerging pathogenic Nocardia species: Nocardia beijingensis, Nocardia blacklockiae, Nocardia thailandica, Nocardia elegans and Nocardia vinacea. A set of six isolates belonging to the species of interest and 135 isolates belonging to other Nocardia species was studied. A PCR-based reverse line blot (RLB) hybridization assay incorporating species- or intraspecies ITS rRNA gene operon-specific probes was then developed for species identification. Substantial intraspecies sequence variation among different ITS operons was identified. Four sequence types of N. thailandica, eight sequence types of N. beijingensis (four types for each of two strains) and five sequence types of N. blacklockiae, N. elegans and N. vinacea were found. The results represent the first evidence of ITS sequence heterogeneity in emerging species of Nocardia. By incorporating species/operon-specific probes into a RLB assay, unique RLB patterns were identified for each of the species and every sequence type. The PCR/RLB assay demonstrated high specificity and showed promise in both the identification and genotyping of Nocardia species. More detailed studies of the polymorphism within the ITS locus may further advance our capacity to reliably identify and subtype medically important Nocardia species.
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Affiliation(s)
- Xiaoyan Wang
- Centre for Infectious Diseases and Microbiology, The University of Sydney, Westmead Hospital, Westmead, New South Wales, Australia.,Department of Dermatology and Venerology, Xuan Wu Hospital, Capital Medical University, Beijing, PR China.,Department of Dermatology and Venerology, The Affiliated Hospital of Inner Mongolia Medical College, Hohhot, PR China
| | - Meng Xiao
- Life Science College, Peking University, Beijing, PR China
| | - Fanrong Kong
- Centre for Infectious Diseases and Microbiology, The University of Sydney, Westmead Hospital, Westmead, New South Wales, Australia
| | - Vitali Sintchenko
- Centre for Infectious Diseases and Microbiology, The University of Sydney, Westmead Hospital, Westmead, New South Wales, Australia
| | - Huiping Wang
- Department of Dermatology, Tianjin Medical University General Hospital, Tianjin, PR China
| | - Bin Wang
- Retroviral Genetics Laboratory, Centre for Virus Research, Westmead Millennium Institute, The University of Sydney, Westmead, New South Wales, Australia
| | - Shi Lian
- Department of Dermatology and Venerology, Xuan Wu Hospital, Capital Medical University, Beijing, PR China
| | - Tania Sorrell
- Centre for Infectious Diseases and Microbiology, The University of Sydney, Westmead Hospital, Westmead, New South Wales, Australia
| | - Sharon Chen
- Centre for Infectious Diseases and Microbiology, The University of Sydney, Westmead Hospital, Westmead, New South Wales, Australia
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Mikami Y. Recent Progress of Taxonomic Studies on Pathogenic Nocardia and Usefulness of the Bacteria for the Studies on Secondary Metabolites and Antibiotic Resistant Mechanisms. ACTA ACUST UNITED AC 2010; 51:179-92. [DOI: 10.3314/jjmm.51.179] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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