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Duan Y, Zhang X, Deng W, Wang S, Hu J, Wang X, Li W, Chen B. The first reported pulmonary nocardiosis caused by Nocardia gipuzkoensis resisted to trimethoprim/sulfamethoxazol (TMP-SMZ) in an immunocompetent patient. J Glob Antimicrob Resist 2024; 37:214-218. [PMID: 38462073 DOI: 10.1016/j.jgar.2024.02.008] [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: 03/25/2023] [Revised: 01/21/2024] [Accepted: 02/06/2024] [Indexed: 03/12/2024] Open
Abstract
OBJECTIVES Nocardia gipuzkoensis was first described as a novel and distinct species in 2020 by Imen Nouioui and pulmonary nocardiosis associated with N. gipuzkoensis was once reported in two bronchiectasis patients. Noteworthy, both reported N. gipuzkoensis cases showed sensitivity to trimethoprim/sulfamethoxazol (TMP-SMZ), which are usually recommended for empirical therapy. METHODS We reported the third case of N. gipuzkoensis infection in a 16-year-old girl with chief complaints of cough and persistent chest and back pain. No underlying immuno-suppressive conditions and glucocorticoid use was revealed. Patchy lesions next to the spine and located in the posterior basal segment of the lower lobes of the left lung were seen in thorax computed tomography (CT), but no pathogenic bacteria were detected according to routine laboratory testings. RESULTS Metagenomic next-generation sequencing (mNGS) combined with whole-genome sequencing (WGS) was used to classified our isolate from bronchoalveolar lavage fluid (BALF) as N. gipuzkoensis. It is worth mentioning that drug susceptibility testing of our isolate showed resistance to TMP-SMZ, which was never reported before. The patient improved remarkably both clinically and radiographically according to the treatment with imipenem-cilastatin infusion alone. CONCLUSION mNGS and WGS showed excellent performance in identifying the Nocardia genus to the species level and improving the detection rate of N. gipuzkoensis ignored by traditional culture. Different from previously reported cases, the N. gipuzkoensis infection case showed resistance to TMP-SMZ, which is an unprecedented finding and a crucial addition to our understanding of the antibacterial spectrum of N. gipuzkoensis. The successful treatment with imipenem-cilastatin infusion alone in this case is a testament to the importance of precise identification and tailored antibiotic therapy.
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Affiliation(s)
- Yishan Duan
- Department of Respiratory and Critical Care Medicine, West China Hospital of Sichuan University, Chengdu, Sichuan Province, China
| | - Xiaoxia Zhang
- Center of Infectious Diseases, West China Hospital of Sichuan University, Chengdu, Sichuan Province, China
| | - Wen Deng
- Department of Respiratory and Critical Care Medicine, West China Hospital of Sichuan University, Chengdu, Sichuan Province, China
| | - Suyan Wang
- Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China
| | - Jinrui Hu
- Department of Respiratory and Critical Care Medicine, West China Hospital of Sichuan University, Chengdu, Sichuan Province, China
| | - Xiaohui Wang
- Center of Infectious Diseases, West China Hospital of Sichuan University, Chengdu, Sichuan Province, China; Center for Infectious Diseases, Ya'an People's Hospital, Ya'an, Sichuan Province, China
| | - Weimin Li
- Department of Respiratory and Critical Care Medicine, West China Hospital of Sichuan University, Chengdu, Sichuan Province, China; Precision Medicine Center, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China
| | - Bojiang Chen
- Department of Respiratory and Critical Care Medicine, West China Hospital of Sichuan University, Chengdu, Sichuan Province, China; Precision Medicine Center, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China.
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Nathar S, Rajmichael R, Jeyaraj Pandian C, Nagarajan H, Mathimaran A, Kingsley JD, Jeyaraman J. Exploring Nocardia's ecological spectrum and novel therapeutic frontiers through whole-genome sequencing: unraveling drug resistance and virulence factors. Arch Microbiol 2024; 206:76. [PMID: 38267747 DOI: 10.1007/s00203-023-03799-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 12/14/2023] [Accepted: 12/15/2023] [Indexed: 01/26/2024]
Abstract
Nocardia farcinica is the leading pathogen responsible for nocardiosis, a life-threatening infection primarily affecting immunocompromised patients. In this study, the genomic sequence of a clinically isolated N. farcinica sample was sequenced. Subsequently, the assembled genome was annotated to identify antimicrobial resistance and virulence genes, as well as plasmid and prophages. The analysis of the entire genome size was 6,021,225 bp, with a GC content of 70.78% and consists of 103 contigs and N50 values of 292,531 bp. The genome analysis revealed the presence of several antimicrobial resistance genes, including RbpA, mtrA, FAR-1, blaFAR-1, blaFAR-1_1, and rox. In addition, virulence genes such as relA, icl, and mbtH were also detected. The present study signifies that N. farcinica genome is pivotal for the understanding of antimicrobial resistance and virulence genes is crucial for comprehending resistance mechanism, and developing effective strategies to combat bacterial infections effectively, especially adhesins and toxins. This study aids in identifying crucial drug targets for combating multidrug-resistant N. farcinica in the future.
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Affiliation(s)
- Shaslinah Nathar
- Structural Biology and Bio-Computing Lab, Department of Bioinformatics, Alagappa University, Science Block, Karaikudi, 630 003, Tamil Nadu, India
| | - Raji Rajmichael
- Structural Biology and Bio-Computing Lab, Department of Bioinformatics, Alagappa University, Science Block, Karaikudi, 630 003, Tamil Nadu, India
| | - Chitra Jeyaraj Pandian
- Department of Biotechnology, Dr. Umayal Ramanathan College for Women, Karaikudi, 630 003, Tamil Nadu, India
| | - Hemavathy Nagarajan
- Structural Biology and Bio-Computing Lab, Department of Bioinformatics, Alagappa University, Science Block, Karaikudi, 630 003, Tamil Nadu, India
| | - Ahila Mathimaran
- Structural Biology and Bio-Computing Lab, Department of Bioinformatics, Alagappa University, Science Block, Karaikudi, 630 003, Tamil Nadu, India
| | - Jemima D Kingsley
- Orbito Asia Diagnostics Private Limited Coimbatore, Coimbatore, 641 045, Tamil Nadu, India
| | - Jeyakanthan Jeyaraman
- Structural Biology and Bio-Computing Lab, Department of Bioinformatics, Alagappa University, Science Block, Karaikudi, 630 003, Tamil Nadu, India.
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Li X, Feng Y, Li D, Chen L, Shen M, Li H, Li S, Wu X, Lu L. Cerebral Abscess Infected by Nocardia gipuzkoensis. Infect Drug Resist 2023; 16:7247-7253. [PMID: 38023399 PMCID: PMC10657549 DOI: 10.2147/idr.s428415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 10/31/2023] [Indexed: 12/01/2023] Open
Abstract
Purpose Nocardia gipuzkoensis is a novel species that solely identified in patients with pulmonary infections by far. Growing evidence showed the excellent performance of metagenomics next-generation sequencing (mNGS) on pathogenic identification, especially for new species. Here, we described the first case of an elderly female patient suddenly suffering from neurological disorders owing to N. gipuzkoensis infection. And linezolid could effectively treat N. gipuzkoensis infection. Patients and Methods The results of imaging, laboratory cultures, and mNGS, as well as therapeutic process are shared. Results An elderly female patient suddenly suffered from neurological disorders with dysphasia and right limb trembles under no obvious causes. Subsequently, she was diagnosed as intracranial space-occupying lesions by magnetic resonance imaging (MRI). The isolate from brain secretion was further identified as N. gipuzkoensis through mNGS. The targeted therapy with linezolid according to the antimicrobial susceptibility was used to treat cerebral abscess induced by N. gipuzkoensis. During the follow-up, no relapse was observed for the patient after surgery for 104 days. Conclusion Cerebral abscess induced by N. gipuzkoensis is rare disorder with high mortality. mNGS has been identified as a promising tool in pathogen diagnosis for timely therapy. Linezolid as one of the antimicrobial drugs could effectively treat N. gipuzkoensis infection and prevent adverse outcomes.
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Affiliation(s)
- Xiaosi Li
- Department of Clinical Laboratory, The Second Affiliated Hospital of Jiaxing University, Jiaxing, People’s Republic of China
| | - Yan Feng
- Department of Clinical Laboratory, Jiaxing Maternity and Child Health Care Hospital Affiliated to Jiaxing University, Jiaxing, People’s Republic of China
| | - Dan Li
- Key laboratory of Digital Technology in Medical Diagnostics of Zhejiang Province, Dian Diagnostics Group Co, Ltd, Hangzhou, People’s Republic of China
| | - Liyang Chen
- Department of Clinical Laboratory, The Second Affiliated Hospital of Jiaxing University, Jiaxing, People’s Republic of China
| | - Mengli Shen
- Department of Clinical Laboratory, The Second Affiliated Hospital of Jiaxing University, Jiaxing, People’s Republic of China
| | - Hongsheng Li
- Department of Clinical Laboratory, The Second Affiliated Hospital of Jiaxing University, Jiaxing, People’s Republic of China
| | - Shuo Li
- Key laboratory of Digital Technology in Medical Diagnostics of Zhejiang Province, Dian Diagnostics Group Co, Ltd, Hangzhou, People’s Republic of China
| | - Xiaoyan Wu
- Department of Clinical Laboratory, The Second Affiliated Hospital of Jiaxing University, Jiaxing, People’s Republic of China
| | - Lingling Lu
- Key laboratory of Digital Technology in Medical Diagnostics of Zhejiang Province, Dian Diagnostics Group Co, Ltd, Hangzhou, People’s Republic of China
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Xing F, Xia Y, Lu Q, Lo SKF, Lau SKP, Woo PCY. Rapid diagnosis of fatal Nocardia kroppenstedtii bacteremic pneumonia and empyema thoracis by next-generation sequencing: a case report. Front Med (Lausanne) 2023; 10:1226126. [PMID: 37534314 PMCID: PMC10392123 DOI: 10.3389/fmed.2023.1226126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Accepted: 06/27/2023] [Indexed: 08/04/2023] Open
Abstract
Nocardia species do not replicate as rapidly as other pyogenic bacteria and nocardial infections can be highly fatal, particularly in immunocompromised patients. Here, we present the first report of fatal Nocardia kroppenstedtii bacteremic pneumonia and empyema thoracis diagnosed by next-generation sequencing (NGS) using the Oxford Nanopore Technologies' MinION device. The bacterium was not identified by matrix-assisted laser desorption ionization-time of flight mass spectrometry. Due to its low equipment cost, short turn-around-time, and portable size, the Oxford Nanopore Technologies' MinION device is a useful platform for NGS in routine clinical microbiology laboratories.
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Affiliation(s)
- Fanfan Xing
- Department of Clinical Microbiology and Infection Control, The University of Hong Kong—Shenzhen Hospital, Shenzhen, China
| | - Yao Xia
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Qianyun Lu
- Department of Clinical Microbiology and Infection Control, The University of Hong Kong—Shenzhen Hospital, Shenzhen, China
| | - Simon K. F. Lo
- Department of Clinical Microbiology and Infection Control, The University of Hong Kong—Shenzhen Hospital, Shenzhen, China
| | - Susanna K. P. Lau
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Patrick C. Y. Woo
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
- Doctoral Program in Translational Medicine and Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan
- The iEGG and Animal Biotechnology Research Center, National Chung Hsing University, Taichung, Taiwan
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Hodille E, Prudhomme C, Dumitrescu O, Benito Y, Dauwalder O, Lina G. Rapid, Easy, and Reliable Identification of Nocardia sp. by MALDI-TOF Mass Spectrometry, VITEK®-MS IVD V3.2 Database, Using Direct Deposit. Int J Mol Sci 2023; 24:ijms24065469. [PMID: 36982540 PMCID: PMC10049377 DOI: 10.3390/ijms24065469] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 03/06/2023] [Accepted: 03/09/2023] [Indexed: 03/16/2023] Open
Abstract
The reference methods for Nocardia identification are based on gene sequencing. These methods are time-consuming and not accessible for all laboratories. Conversely, matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry is easy to use and widely available in clinical laboratories, but for Nocardia identification, the VITEK®-MS manufacturer recommends a tedious step of colony preparation that is difficult to integrate into a laboratory workflow. This study aimed to evaluate Nocardia identification by MALDI-TOF VITEK®-MS using direct deposit with the VITEK®-PICKMETM pen and a formic acid-based protein extraction directly onto the bacterial smear on a 134 isolates collection; this identification was compared to the results from molecular reference methods. For 81.3% of the isolates, VITEK®-MS delivered an interpretable result. The overall agreement with the reference method was 78.4%. Taking only the species included in the VITEK®-MS in vitro diagnostic V3.2 database into account, the overall agreement was significantly higher, 93.7%. VITEK®-MS rarely misidentified isolates (4/134, 3%). Among the 25 isolates that produced no result with the VITEK®-MS, 18 were expected, as Nocardia species were not included in the VITEK®-MS V3.2 database. A rapid and reliable Nocardia identification using direct deposit by VITEK®-MS is possible by combining the use of the VITEK®-PICKMETM pen and a formic acid-based protein extractiondirectly onto the bacterial smear.
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Update on Accepted Novel Bacterial Isolates Derived from Human Clinical Specimens and Taxonomic Revisions Published in 2020 and 2021. J Clin Microbiol 2023; 61:e0028222. [PMID: 36533910 PMCID: PMC9879126 DOI: 10.1128/jcm.00282-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
A number of factors, including microbiome analyses and the increased utilization of whole-genome sequencing in the clinical microbiology laboratory, has contributed to the explosion of novel prokaryotic species discovery, as well as bacterial taxonomy revision. This review attempts to summarize such changes relative to human clinical specimens that occurred in 2020 and 2021, per primary publication in the International Journal of Systematic and Evolutionary Microbiology or acceptance on Validation Lists published by the International Journal of Systematic and Evolutionary Microbiology. Of particular significance among valid and effectively published taxa within the past 2 years were novel Corynebacterium spp., coagulase-positive staphylococci, Pandoraea spp., and members of family Yersiniaceae. Noteworthy taxonomic revisions include those within the Bacillus and Lactobacillus genera, family Staphylococcaceae (including unifications of subspecies designations to species level taxa), Elizabethkingia spp., and former members of Clostridium spp. and Bacteroides spp. Revisions within the Brucella genus have the potential to cause deleterious effects unless the relevance of such changes is properly communicated by microbiologists to stakeholders in clinical practice, infection prevention, and public health.
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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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Cai Q, Huang Y, Zhou L, Hu N, Liu Y, Guo F, Liu Q, Huang X, Zhang Y, Zeng L. A Complete Genome of Nocardia terpenica NC_YFY_NT001 and Pan-Genomic Analysis Based on Different Sources of Nocardia spp. Isolates Reveal Possibly Host-Related Virulence Factors. Infect Drug Resist 2022; 15:7259-7270. [PMID: 36536862 PMCID: PMC9758982 DOI: 10.2147/idr.s384673] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 11/29/2022] [Indexed: 04/22/2024] Open
Abstract
OBJECTIVE We aimed to identify the possible virulence genes associated with Nocardia NC_YFY_NT001 isolated by ourselves and other Nocardia spp. METHODS The genome of Nocardia terpenica NC_YFY_NT001 was completed by using PacBio and Illumina platforms. A pan-genomic analysis was applied to selected complete Nocardia genomes. RESULTS Nocardia terpenica NC_YFY_NT001 can cause healthy mice death by tail intravenous injection. The genome of NT001 has one circular chromosome 8,850,000 bp and one circular plasmid 70,000 bp with ~68% GC content. The chromosome and plasmid encode 7914 and 80 proteins, respectively. Furthermore, a pan-genomic analysis showed a total of 45,825 gene clusters, then 304 core, 21,045 shell and 24,476 cloud gene clusters were classified using specific parameters. In addition, we found that catalases were more abundant in human isolates. Furthermore, we also found no significant differences in the MCE proteins between different strains from different sources. The pan-genomic analysis also showed that 67 genes could only be found in humoral isolates. ReX3 and DUF853 domain protein were found in all eight human isolates. The composition of unique genes in humoral isolate genomes indicated that the transcriptional regulators may be important when Nocardia invades the host, which allows them to survive in the new ecological system. CONCLUSION In this study, we confirmed that NT001 could cause infected animal death, and identified many possible virulence factors for our future studies. This study also provides new insight for our further study on Nocardia virulence mechanisms.
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Affiliation(s)
- Qinming Cai
- The First Affiliated Hospital of Nanchang University, School of Public Health, Nanchang University, Nanchang, People’s Republic of China
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, People’s Republic of China
| | - Yongcheng Huang
- The First Affiliated Hospital of Nanchang University, School of Public Health, Nanchang University, Nanchang, People’s Republic of China
| | - Li Zhou
- The First Affiliated Hospital of Nanchang University, School of Public Health, Nanchang University, Nanchang, People’s Republic of China
| | - Niya Hu
- The First Affiliated Hospital of Nanchang University, School of Public Health, Nanchang University, Nanchang, People’s Republic of China
| | - Yanling Liu
- The First Affiliated Hospital of Nanchang University, School of Public Health, Nanchang University, Nanchang, People’s Republic of China
| | - Fujia Guo
- The First Affiliated Hospital of Nanchang University, School of Public Health, Nanchang University, Nanchang, People’s Republic of China
| | - Qiong Liu
- Department of Medical Microbiology, School of Medicine, Nanchang University, Nanchang, People’s Republic of China
| | - Xiaotian Huang
- The First Affiliated Hospital of Nanchang University, School of Public Health, Nanchang University, Nanchang, People’s Republic of China
- Department of Medical Microbiology, School of Medicine, Nanchang University, Nanchang, People’s Republic of China
| | - Yunyi Zhang
- Department of Microbiology, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, 310051, People’s Republic of China
| | - Lingbing Zeng
- The First Affiliated Hospital of Nanchang University, School of Public Health, Nanchang University, Nanchang, People’s Republic of China
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Liu C, Yang J, Huang H, Zhan S, Xia X. Case report: Nocardia gipuzkoensis infection in an immunocompetent patient diagnosed by metagenomic next-generation sequencing and whole genome sequencing. Front Immunol 2022; 13:1053914. [PMID: 36569853 PMCID: PMC9780257 DOI: 10.3389/fimmu.2022.1053914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 11/21/2022] [Indexed: 12/13/2022] Open
Abstract
The infection of Nocardia gipuzkoensis is a relatively uncommon form of pulmonary nocardiosis seen in clinical patients. In general, nocardiosis tends to occur in patients with immune deficiency. Here, we report a 23-year-old female who was admitted to the hospital due to cough and sputum production over 10 years, diagnosed with bronchiectasis. The N. gipuzkoensis infection was identified by metagenomic next-generation sequencing and whole genome sequencing. Imipenem/cilastatin and compound sulfamethoxazole tablets were used to control the infection and the pulmonary inflammation subsided gradually.
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Affiliation(s)
- Chengxin Liu
- The First Clinical Medical School, Guangzhou University of Chinese Medicine, Guangzhou, China,The First Affiliated Hospital, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Juhua Yang
- Vision Medicals Co., Ltd., Guangzhou, China
| | - Huiting Huang
- The First Affiliated Hospital, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Shaofeng Zhan
- The First Affiliated Hospital, Guangzhou University of Chinese Medicine, Guangzhou, China,*Correspondence: Shaofeng Zhan, ; Xintian Xia,
| | - Xintian Xia
- The First Affiliated Hospital, Guangzhou University of Chinese Medicine, Guangzhou, China,*Correspondence: Shaofeng Zhan, ; Xintian Xia,
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Sun X, Chen Z, Kong T, Chen Z, Dong Y, Kolton M, Cao Z, Zhang X, Zhang H, Liu G, Gao P, Yang N, Lan L, Xu Y, Sun W. Mycobacteriaceae Mineralizes Micropolyethylene in Riverine Ecosystems. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:15705-15717. [PMID: 36288260 DOI: 10.1021/acs.est.2c05346] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Microplastic (MP) contamination is a serious global environmental problem. Plastic contamination has attracted extensive attention during the past decades. While physiochemical weathering may influence the properties of MPs, biodegradation by microorganisms could ultimately mineralize plastics into CO2. Compared to the well-studied marine ecosystems, the MP biodegradation process in riverine ecosystems, however, is less understood. The current study focuses on the MP biodegradation in one of the world's most plastic contaminated rivers, Pearl River, using micropolyethylene (mPE) as a model substrate. Mineralization of 13C-labeled mPE into 13CO2 provided direct evidence of mPE biodegradation by indigenous microorganisms. Several Actinobacteriota genera were identified as putative mPE degraders. Furthermore, two Mycobacteriaceae isolates related to the putative mPE degraders, Mycobacterium sp. mPE3 and Nocardia sp. mPE12, were retrieved, and their ability to mineralize 13C-mPE into 13CO2 was confirmed. Pangenomic analysis reveals that the genes related to the proposed mPE biodegradation pathway are shared by members of Mycobacteriaceae. While both Mycobacterium and Nocardia are known for their pathogenicity, these populations on the plastisphere in this study were likely nonpathogenic as they lacked virulence factors. The current study provided direct evidence for MP mineralization by indigenous biodegraders and predicted their biodegradation pathway, which may be harnessed to improve bioremediation of MPs in urban rivers.
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Affiliation(s)
- Xiaoxu Sun
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, P. R. China
- Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Zhenyu Chen
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, P. R. China
- Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
- School of Environment, Key Laboratory of Yellow River and Huai River Water Environment and Pollution Control, Ministry of Education, Henan Normal University, Xinxiang 453007, China
| | - Tianle Kong
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, P. R. China
- Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
- College of Environmental Science and Engineering, Donghua University, Shanghai 201620, China
| | - Zheng Chen
- Department of Health and Environmental Sciences, Xi'an Jiaotong-Liverpool University, Suzhou 215123, China
| | - Yiran Dong
- School of Environmental Studies, China University of Geosciences (Wuhan), Wuhan 430074, China
| | - Max Kolton
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, P. R. China
- Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
- French Associates Institute for Agriculture and Biotechnology of Drylands, Ben-Gurion University of the Negev, Beer Sheva 849900, Israel
| | - Zhiguo Cao
- School of Environment, Key Laboratory of Yellow River and Huai River Water Environment and Pollution Control, Ministry of Education, Henan Normal University, Xinxiang 453007, China
| | - Xin Zhang
- School of Environment, Key Laboratory of Yellow River and Huai River Water Environment and Pollution Control, Ministry of Education, Henan Normal University, Xinxiang 453007, China
| | - Haihan Zhang
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Guoqiang Liu
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou 511443, China
| | - Pin Gao
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, P. R. China
- Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
- College of Environmental Science and Engineering, Donghua University, Shanghai 201620, China
| | - Nie Yang
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, P. R. China
- Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
- College of Environmental Science and Engineering, Donghua University, Shanghai 201620, China
| | - Ling Lan
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, P. R. China
- Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Yating Xu
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, P. R. China
- Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Weimin Sun
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, P. R. China
- Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
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11
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Wang X, Wei M, Pu J, Huang Y, Zhang S, Zhou J, Wang L, Yang J, Li Z, Zhu X. Nocardia sputi sp. nov. isolated from the sputum of patients with pulmonary infection. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Two Gram-stain-positive, aerobic and rod-shaped actinomycetes (strains CY18T and CY8) were isolated from the sputum of two patients with pulmonary infections, and their taxonomic status was investigated. The 16S rRNA gene sequences and the results of phylogenetic analyses indicated that CY18T and CY8 were identical (100 %) and were most closely related to
Nocardia beijingensis
CGMCC 4.1521T (99.9 %) and
Nocardia araoensis
NBRC 100135T (99.5 %). The predominant cellular fatty acids of CY18T and CY8 were C16 : 0, C18 : 0, C18 : 1ω9c and summed feature 3 (comprising C16 : 1ɷ7c and/or C16 : 1ɷ6c), and the major menaquinone was MK-8(H4ω-cycl).The diagnostic diamino acid in the cell-wall peptidoglycan was meso-diaminopimelic acid. The whole-cell hydrolytic sugar pattern consisted of arabinose and glucose. The polar lipid profile contained diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositol mannoside, two unidentified phospholipids, three unidentified glycolipids and two unidentified lipids.The DNA G+C contents of CY18T and CY8 were 67.9 and 68.0 % respectively. The digital DNA–DNA hybridization and average nucleotide identity values between the two novel strains and closely related species were well under the 70 % and 95–96 % thresholds, respectively, but these values between the two novel strains were 95.5 % and 99.5 %, respectively. On the basis of morphological and chemotaxonomic characteristics and the results of phylogenetic analyses, strains CY18T and CY8 represent a novel species of the genus
Nocardia
, for which the name Nocardia sputi sp. nov. is proposed. The type strain is CY18T (=GDMCC 1.3318T = JCM 33932T).
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Affiliation(s)
- Xiaoxia Wang
- Central & Clinical Laboratory of Sanya People’s Hospital, Sanya, Hainan 572000, PR China
| | - Ming Wei
- Department of Infectious Diseases and Clinical Microbiology, Beijing Institute of Respiratory Medicine and Beijing Chao-Yang Hospital, Capital Medical University, Beijing 100020, PR China
| | - Ji Pu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, PR China
| | - Yuyuan Huang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, PR China
| | - Sihui Zhang
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing 100191, PR China
| | - Juan Zhou
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, PR China
| | - Licheng Wang
- Central & Clinical Laboratory of Sanya People’s Hospital, Sanya, Hainan 572000, PR China
| | - Jing Yang
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing 100730, PR China
- Shanghai Institute for Emerging and Re-emerging Infectious Diseases, Shanghai Public Health Clinical Center, Shanghai 201508, PR China
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, PR China
| | - Zhenjun Li
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, PR China
| | - Xiong Zhu
- Central & Clinical Laboratory of Sanya People’s Hospital, Sanya, Hainan 572000, PR China
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12
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Nouioui I, Pötter G, Jando M, Goodfellow M. Nocardia noduli sp. nov., a novel actinobacterium with biotechnological potential. Arch Microbiol 2022; 204:260. [PMID: 35419662 PMCID: PMC9007811 DOI: 10.1007/s00203-022-02878-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 03/23/2022] [Accepted: 03/25/2022] [Indexed: 11/25/2022]
Abstract
A genome-based polyphasic study was undertaken to establish the taxonomic status of an actinobacterium strain isolated from an actinorhizal root nodule. Strain ncl1T was found to have chemotaxonomic, cultural and morphological properties characteristic of members of the genus Nocardia. The strain was closely related to Nocardia aurea in the phylogenetic trees based on 16S rRNA gene and genome sequences. The draft genome of the strain is 8.9 Mbp in size, has a genomic DNA G + C content of 67.0% and was predicted to contain at least 19 biosynthetic gene clusters encoding for specialized metabolites. Strain ncl1T was distinguished from its closest neighbour, N. aurea DSM 103986T, by a broad range of phenotypic properties and by low average nucleotide identity and digital DNA-DNA hybridization scores. Consequently, the strain represents a novel Nocardia species for which the name Nocardia noduli sp. nov. is proposed. The type strain is ncl1T (CECT 30123T = DSM 110878T). The present study provides further evidence that actinorhizal nodules are a source of novel species of Nocardia.
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Affiliation(s)
- Imen Nouioui
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, 38124, Braunschweig, Germany.
| | - Gabriele Pötter
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, 38124, Braunschweig, Germany
| | - Marlen Jando
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, 38124, Braunschweig, Germany
| | - Michael Goodfellow
- School of Natural and Environmental Sciences, Newcastle University, Ridley Building 2, Newcastle upon Tyne, NE1 7RU, UK
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13
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Dumic I, Brown A, Magee K, Elwasila S, Kaljevic M, Antic M, Igandan O, Cardozo M, Rueda Prada L, Paulson M. Primary Lymphocutaneous Nocardia brasiliensis in an Immunocompetent Host: Case Report and Literature Review. Medicina (B Aires) 2022; 58:medicina58040488. [PMID: 35454327 PMCID: PMC9030709 DOI: 10.3390/medicina58040488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 03/19/2022] [Accepted: 03/21/2022] [Indexed: 11/16/2022] Open
Abstract
Nocardia spp. is a Gram-positive, partially acid-fast aerobic bacterium usually associated with infection in immunocompromised people. The most common sites of infection are the skin, lungs, and the brain, however disease can disseminate and affect every organ. Clinical manifestations of cutaneous disease are varied and frequently misdiagnosed. We present a case of an immunocompetent 66-year-old man who sustained a left finger injury while gardening. He was misdiagnosed on several occasions and treated with inappropriate antibiotics against Streptococcus spp. and Staphylococcus spp. When infection spread cutaneously, sporotrichoid (lymphocutaneous) nocardiosis was suspected and the patient was started on appropriate therapy with Bactrim which resulted in a cure. We also summarize the literature on lymphocutaneous infection by Nocardia brasiliensis. By reporting this case, we want to raise awareness among clinicians about unusual causes of cellulitis, the differential diagnosis of lymphocutaneous infection and the importance of obtaining a detailed exposure history to assist in the prompt diagnosis of nocardiosis.
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Affiliation(s)
- Igor Dumic
- Hospital Medicine, Mayo Clinic Health System, Eau Claire, WI 54703, USA; (O.I.); (M.C.); (L.R.P.); (M.P.)
- Mayo Clinic College of Medicine, 200 1st St SW, Rochester, MN 55905, USA
- Correspondence:
| | - Alethea Brown
- Hospital Medicine, Mayo Clinic, Jacksonville, FL 32224, USA;
| | - Kyle Magee
- Department of Microbiology, Mayo Clinic, Jacksonville, FL 32224, USA;
| | - Sammer Elwasila
- Department of Infectious Disease, Mayo Clinic, Jacksonville, FL 32224, USA;
| | - Marija Kaljevic
- Department of Hospital Medicine, University of Connecticut, Hartford, CT 06032, USA;
| | - Marina Antic
- Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Pl, New York, NY 10029, USA;
| | - Oladapo Igandan
- Hospital Medicine, Mayo Clinic Health System, Eau Claire, WI 54703, USA; (O.I.); (M.C.); (L.R.P.); (M.P.)
- Mayo Clinic College of Medicine, 200 1st St SW, Rochester, MN 55905, USA
| | - Milena Cardozo
- Hospital Medicine, Mayo Clinic Health System, Eau Claire, WI 54703, USA; (O.I.); (M.C.); (L.R.P.); (M.P.)
- Mayo Clinic College of Medicine, 200 1st St SW, Rochester, MN 55905, USA
| | - Libardo Rueda Prada
- Hospital Medicine, Mayo Clinic Health System, Eau Claire, WI 54703, USA; (O.I.); (M.C.); (L.R.P.); (M.P.)
- Mayo Clinic College of Medicine, 200 1st St SW, Rochester, MN 55905, USA
| | - Margaret Paulson
- Hospital Medicine, Mayo Clinic Health System, Eau Claire, WI 54703, USA; (O.I.); (M.C.); (L.R.P.); (M.P.)
- Mayo Clinic College of Medicine, 200 1st St SW, Rochester, MN 55905, USA
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14
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Nouioui I, Ha SM, Baek I, Chun J, Goodfellow M. Genome insights into the pharmaceutical and plant growth promoting features of the novel species Nocardia alni sp. nov. BMC Genomics 2022; 23:70. [PMID: 35062865 PMCID: PMC8783487 DOI: 10.1186/s12864-021-08257-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 12/14/2021] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Recent studies highlighted the biosynthetic potential of nocardiae to produce diverse novel natural products comparable to that of Streptomyces, thereby making them an attractive source of new drug leads. Many of the 119 Nocardia validly named species were isolated from natural habitats but little is known about the diversity and the potential of the endophytic nocardiae of root nodule of actinorhizal plants. RESULTS The taxonomic status of an actinobacterium strain, designated ncl2T, was established in a genome-based polyphasic study. The strain was Gram-stain-positive, produced substrate and aerial hyphae that fragmented into coccoid and rod-like elements and showed chemotaxonomic properties that were also typical of the genus Nocardia. It formed a distinct branch in the Nocardia 16S rRNA gene tree and was most closely related to the type strains of Nocardia nova (98.6%), Nocardia jiangxiensis (98.4%), Nocardia miyuensis (97.8%) and Nocardia vaccinii (97.7%). A comparison of the draft genome sequence generated for the isolate with the whole genome sequences of its closest phylogenetic neighbours showed that it was most closely related to the N. jiangxiensis, N. miyuensis and N. vaccinii strains, a result underpinned by average nucleotide identity and digital DNA-DNA hybridization data. Corresponding taxogenomic data, including those from a pan-genome sequence analysis showed that strain ncl2T was most closely related to N. vaccinii DSM 43285T. A combination of genomic, genotypic and phenotypic data distinguished these strains from one another. Consequently, it is proposed that strain ncl2T (= DSM 110931T = CECT 30122T) represents a new species within the genus Nocardia, namely Nocardia alni sp. nov. The genomes of the N. alni and N. vaccinii strains contained 36 and 29 natural product-biosynthetic gene clusters, respectively, many of which were predicted to encode for a broad range of novel specialised products, notably antibiotics. Genome mining of the N. alni strain and the type strains of its closest phylogenetic neighbours revealed the presence of genes associated with direct and indirect mechanisms that promote plant growth. The core genomes of these strains mainly consisted of genes involved in amino acid transport and metabolism, energy production and conversion and transcription. CONCLUSIONS Our genome-based taxonomic study showed that isolate ncl2T formed a new centre of evolutionary variation within the genus Nocardia. This novel endophytic strain contained natural product biosynthetic gene clusters predicted to synthesize novel specialised products, notably antibiotics and genes associated with the expression of plant growth promoting compounds.
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Affiliation(s)
- Imen Nouioui
- Department of Microorganisms, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, 38124, Braunschweig, Germany.
| | - Sung-Min Ha
- Department of Integrative Biology and Physiology, University of California Los Angeles, 610 Charles E. Young Drive East, Los Angeles, CA 90095, USA
| | - Inwoo Baek
- School of Biological Sciences & Institute of Molecular Biology and Genetics, Seoul National University, Seoul, Korea
| | - Jongsik Chun
- School of Biological Sciences & Institute of Molecular Biology and Genetics, Seoul National University, Seoul, Korea
- ChunLab, Inc, Seoul, Korea
| | - Michael Goodfellow
- School of Natural and Environmental Sciences, Newcastle University, Ridley Building 2, NE1 7RU, Newcastle upon Tyne, UK
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15
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Fatahi-Bafghi M. Role of Williamsia and Segniliparus in human infections with the approach taxonomy, cultivation, and identification methods. Ann Clin Microbiol Antimicrob 2021; 20:10. [PMID: 33485346 PMCID: PMC7825236 DOI: 10.1186/s12941-021-00416-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 01/12/2021] [Indexed: 02/01/2023] Open
Abstract
The genera Williamsia and Segniliparus are of aerobic actinomycetes and at the time of writing, they have 12 and 2 species, respectively. These genera cause various infections in humans. In this review, we surveyed their taxonomy, isolation, identification, as well as their role to cause human infections.
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Affiliation(s)
- Mehdi Fatahi-Bafghi
- Shahid Sadoughi University of Medical Sciences and Health Services, Yazd, Iran.
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16
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Oren A, Garrity GM. List of new names and new combinations that have appeared in effective publications outside of the IJSEM and are submitted for valid publication. Int J Syst Evol Microbiol 2019; 71. [PMID: 33787483 DOI: 10.1099/ijsem.0.004688] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Affiliation(s)
- Aharon Oren
- The Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond J. Safra Campus, 9190401 Jerusalem, Israel
| | - George M Garrity
- Department of Microbiology & Molecular Genetics, Biomedical Physical Sciences, Michigan State University, East Lansing, MI 48824-4320, USA
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