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Jhaveri TA, Weiss ZF, Winkler ML, Pyden AD, Basu SS, Pecora ND. A decade of clinical microbiology: top 10 advances in 10 years: what every infection preventionist and antimicrobial steward should know. ANTIMICROBIAL STEWARDSHIP & HEALTHCARE EPIDEMIOLOGY : ASHE 2024; 4:e8. [PMID: 38415089 PMCID: PMC10897726 DOI: 10.1017/ash.2024.10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 12/22/2023] [Accepted: 12/28/2023] [Indexed: 02/29/2024]
Abstract
The past 10 years have brought paradigm-shifting changes to clinical microbiology. This paper explores the top 10 transformative innovations across the diagnostic spectrum, including not only state of the art technologies but also preanalytic and post-analytic advances. Clinical decision support tools have reshaped testing practices, curbing unnecessary tests. Innovations like broad-range polymerase chain reaction and metagenomic sequencing, whole genome sequencing, multiplex molecular panels, rapid phenotypic susceptibility testing, and matrix-assisted laser desorption ionization time-of-flight mass spectrometry have all expanded our diagnostic armamentarium. Rapid home-based testing has made diagnostic testing more accessible than ever. Enhancements to clinician-laboratory interfaces allow for automated stewardship interventions and education. Laboratory restructuring and consolidation efforts are reshaping the field of microbiology, presenting both opportunities and challenges for the future of clinical microbiology laboratories. Here, we review key innovations of the last decade.
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Affiliation(s)
- Tulip A. Jhaveri
- Division of Infectious Diseases, University of Mississippi Medical Center, Jackson, MS, USA
| | - Zoe Freeman Weiss
- Division of Pathology and Laboratory Medicine, Tufts Medical Center, Boston, MA, USA
- Division of Geographic Medicine & Infectious Disease, Tufts Medical Center, Boston, MA, USA
| | - Marisa L. Winkler
- Division of Infectious Diseases, Emory University School of Medicine, Atlanta, GA, USA
| | - Alexander D. Pyden
- Division of Pathology and Laboratory Medicine, Lahey Hospital and Medical Center, Burlington, MA, USA
- Department of Anatomic and Clinical Pathology, Tufts University School of Medicine, Boston, MA, USA
| | - Sankha S. Basu
- Division of Pathology and Laboratory Medicine, Tufts Medical Center, Boston, MA, USA
| | - Nicole D. Pecora
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA, USA
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Vecilla DF, Radigales JR, Vivanco CA, Llanos MIG, Arco JLDDTD. Lymphangitis caused by Nocardia brasiliensis after a mosquito bite. An Pediatr (Barc) 2023; 99:431-432. [PMID: 37598077 DOI: 10.1016/j.anpede.2023.08.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 05/30/2023] [Indexed: 08/21/2023] Open
Affiliation(s)
- Domingo Fernández Vecilla
- Servicio de Microbiología Clínica, Hospital Universitario de Basurto, Bilbao, Spain; Instituto de Investigación Sanitaria Biocruces, Barakaldo, Vizcaya, Spain.
| | | | - Cristina Aspichueta Vivanco
- Servicio de Microbiología Clínica, Hospital Universitario de Basurto, Bilbao, Spain; Instituto de Investigación Sanitaria Biocruces, Barakaldo, Vizcaya, Spain
| | | | - José Luis Díaz de Tuesta Del Arco
- Servicio de Microbiología Clínica, Hospital Universitario de Basurto, Bilbao, Spain; Instituto de Investigación Sanitaria Biocruces, Barakaldo, Vizcaya, Spain
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Fernández Vecilla D, Roche Matheus MP, Urrutikoetxea Gutiérrez MJ, Calvo Muro FE, Aspichueta Vivanco C, López Azkarreta I, Grau García M, Díaz de Tuesta Del Arco JL. Disseminated Nocardia farcinica infection associated with bacteraemia and osteomyelitis pubis in an elderly patient. Infect Dis (Lond) 2023; 55:738-743. [PMID: 37376969 DOI: 10.1080/23744235.2023.2229425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 06/17/2023] [Accepted: 06/20/2023] [Indexed: 06/29/2023] Open
Abstract
OBJECTIVE We describe a rare case of a disseminated Nocardia farcinica infection associated with hip osteomyelitis. METHODS A 91-year-old female patient was admitted with oedema of her right leg, fever of 38 °C and data consistent with ruptured Baker's cyst. A disseminated Nocardia farcinica infection including bloodstream infection, pneumonia and multiple abscesses along both lower limbs was observed. RESULTS After a four-week course of 320 mg/1600 mg/12 h of intravenous trimethoprim/sulfamethoxazole and multiple chirurgic drainages the patient was discharged with oral trimethoprim/sulfamethoxazole. Nevertheless, the patient expired done month after being discharged from the hospital. CONCLUSIONS The implementation of a combination of intravenous antibiotics and drainages resulted in an initial improvement in the patient's condition. However, despite these interventions, the patient ultimately passed away probably due to natural causes.
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Affiliation(s)
| | - Mary Paz Roche Matheus
- Clinical Microbiology Service, Basurto University Hospital, Bilbao, Biscay, Spain
- Biocruces Bizkaia Health Research Institute, Biscay, Spain
| | | | - Felicitas Elena Calvo Muro
- Clinical Microbiology Service, Basurto University Hospital, Bilbao, Biscay, Spain
- Biocruces Bizkaia Health Research Institute, Biscay, Spain
| | - Cristina Aspichueta Vivanco
- Clinical Microbiology Service, Basurto University Hospital, Bilbao, Biscay, Spain
- Biocruces Bizkaia Health Research Institute, Biscay, Spain
| | | | - Mikel Grau García
- Radiodiagnosis Service of Basurto University Hospital, Bilbao, Biscay, Spain
| | - José Luis Díaz de Tuesta Del Arco
- Clinical Microbiology Service, Basurto University Hospital, Bilbao, Biscay, Spain
- Biocruces Bizkaia Health Research Institute, Biscay, Spain
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Yang CH, Kuo SF, Chen FJ, Lee CH. Clinical manifestations and outcome of nocardiosis and antimicrobial susceptibility of Nocardia species in southern Taiwan, 2011-2021. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2023; 56:382-391. [PMID: 36456442 DOI: 10.1016/j.jmii.2022.11.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Revised: 10/15/2022] [Accepted: 11/12/2022] [Indexed: 11/18/2022]
Abstract
BACKGROUND/PURPOSE Nocardiosis is an uncommon infectious disease. This study aimed to assess the clinical outcome of patients with nocardiosis and examine the antimicrobial susceptibility profiles of Nocardia spp. isolated. METHODS We retrospectively reviewed the medical records of all inpatients diagnosed with nocardiosis between 2011 and 2021. The identification of Nocardia spp. at the species level was performed with the use of MALDI-TOF and 16S rRNA assays. The antimicrobial susceptibility of Nocardia spp. was performed using the microbroth dilution method. Factors associated with 90-day all-cause mortality were identified in multivariate logistic regression analysis. RESULTS Of 60 patients with nocardiosis in the 11-year study period, the lungs (55.0%) were the most common site of involvement, followed by the skin and soft tissue (45.0%). Twenty-two patients (36.7%) died within 90 days following the diagnosis. All of the Nocardia isolates were susceptible to trimethoprim-sulfamethoxazole, linezolid, and amikacin, whereas more than 70% of the isolates were not susceptible to ciprofloxacin, imipenem-cilastatin, moxifloxacin, cefepime, and clarithromycin. Nocardiosis involving the lungs (relative risk [RR], 9.99; 95% confidence interval [CI], 1.52-65.50; p = 0.02), nocardiosis involving the skin and soft tissue (RR, 0.15; 95% CI, 0.02-0.92; p = 0.04), and treatment with trimethoprim-sulfamethoxazole (RR, 0.14; 95% CI, 0.03-0.67; p = 0.01) were independently associated with 90-day all-cause mortality. CONCLUSIONS Nocardia spp. identified between 2011 and 2021 remained fully susceptible to trimethoprim-sulfamethoxazole, linezolid, and amikacin. Nocardiosis of the lungs, skin and soft tissue infection, and treatment with trimethoprim-sulfamethoxazole were independently associated with 90-day all-cause mortality.
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Affiliation(s)
- Chen-Hsun Yang
- Division of Infectious Diseases, Department of Internal Medicine, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung, Taiwan
| | - Shu-Fang Kuo
- Department of Laboratory Medicine, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung, Taiwan; Department of Laboratory Medicine, Chiayi Chang Gung Memorial Hospital, Chiayi, Taiwan; Department of Medical Biotechnology and Laboratory Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Fang-Ju Chen
- Division of Infectious Diseases, Department of Internal Medicine, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung, Taiwan
| | - Chen-Hsiang Lee
- Division of Infectious Diseases, Department of Internal Medicine, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung, Taiwan; Chang Gung University College of Medicine, Kaohsiung, Taiwan; Division of Infectious Diseases, Department of Internal Medicine, Chiayi Chang Gung Memorial Hospital, Chiayi, Taiwan.
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Rodríguez‐Temporal D, Zvezdánova ME, Benedí P, Marín M, Blázquez‐Sánchez M, Ruiz‐Serrano MJ, Muñoz P, Rodríguez‐Sánchez B. Identification of Nocardia and non-tuberculous Mycobacterium species by MALDI-TOF MS using the VITEK MS coupled to IVD and RUO databases. Microb Biotechnol 2023; 16:778-783. [PMID: 36541026 PMCID: PMC10034632 DOI: 10.1111/1751-7915.14146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 06/22/2022] [Accepted: 09/01/2022] [Indexed: 12/24/2022] Open
Abstract
Identification of Nocardia and Mycobacterium species by matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) is still a challenging task that requires both suitable protein extraction procedures and extensive databases. This study aimed to evaluate the VITEK MS Plus system coupled with updated RUO (v4.17) and IVD (v3.2) databases for the identification of Nocardia spp. and Mycobacterium spp. clinical isolates. Sample preparation was carried out using the VITEK MS Mycobacterium/Nocardia kit for protein extraction. From 90 Nocardia spp. isolates analysed, 86 (95.6%) were correctly identified at species or complex level using IVD and 78 (86.7%) using RUO. Only two strains were misidentified as other species pertaining to the same complex. Among the 106 non-tuberculous Mycobacterium clinical isolates tested from a liquid culture medium, VITEK MS identified correctly at species or complex level 96 (90.6%) isolates in the IVD mode and 89 (84.0%) isolates in the RUO mode. No misidentifications were detected. Although the IVD mode was unable to differentiate members of the M. fortuitum complex, the RUO mode correctly discriminated M. peregrinum and M. septicum. The robustness and accuracy showed by this system allow its implementation for routine identification of these microorganisms in clinical laboratories.
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Affiliation(s)
- David Rodríguez‐Temporal
- Clinical Microbiology and Infectious Diseases DepartmentHospital General Universitario Gregorio MarañónMadridSpain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM)MadridSpain
| | - Margarita Estreya Zvezdánova
- Clinical Microbiology and Infectious Diseases DepartmentHospital General Universitario Gregorio MarañónMadridSpain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM)MadridSpain
| | - Pablo Benedí
- Clinical Microbiology and Infectious Diseases DepartmentHospital General Universitario Gregorio MarañónMadridSpain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM)MadridSpain
| | - Mercedes Marín
- Clinical Microbiology and Infectious Diseases DepartmentHospital General Universitario Gregorio MarañónMadridSpain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM)MadridSpain
- CIBER de Enfermedades Respiratorias (CIBERES CB06/06/0058)MadridSpain
| | - Mario Blázquez‐Sánchez
- Clinical Microbiology and Infectious Diseases DepartmentHospital General Universitario Gregorio MarañónMadridSpain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM)MadridSpain
| | - María Jesús Ruiz‐Serrano
- Clinical Microbiology and Infectious Diseases DepartmentHospital General Universitario Gregorio MarañónMadridSpain
| | - Patricia Muñoz
- Clinical Microbiology and Infectious Diseases DepartmentHospital General Universitario Gregorio MarañónMadridSpain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM)MadridSpain
- CIBER de Enfermedades Respiratorias (CIBERES CB06/06/0058)MadridSpain
- Medicine Department, Faculty of MedicineUniversidad Complutense de MadridMadridSpain
| | - Belén Rodríguez‐Sánchez
- Clinical Microbiology and Infectious Diseases DepartmentHospital General Universitario Gregorio MarañónMadridSpain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM)MadridSpain
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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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Choquet E, Rodriguez-Nava V, Peltier F, Wankap-Mogo R, Bergeron E, Joseph C, Lemaitre N. Nocardia neocaledoniensis as Rare Cause of Spondylodiscitis. Emerg Infect Dis 2023; 29:444-446. [PMID: 36692867 PMCID: PMC9881783 DOI: 10.3201/eid2902.221389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Nocardia neocaledoniensis is a rare species of Nocardia bacteria, identified in 2004 in hypermagnesian ultramafic soil of New Caledonia. Culture of this opportunistic pathogen from spinal biopsy samples confirmed N. neocaledoniensis spondylodiscitis in an immunocompromised man. Isolation of this unusual species from spinal biopsy samples illustrates its underappreciated ability to cause invasive infection.
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Omori K, Kitagawa H, Nagaoka R, Naka Y, Kawamoto K, Horimasu Y, Nomura T, Shigemoto N, Yaguchi T, Hattori N, Ohge H. Lung and Cerebral Nocardiosis Caused by Nocardia elegans in a Lung Transplant Recipient: A Case Report and Literature Review. Intern Med 2023; 62:431-437. [PMID: 35831116 PMCID: PMC9970818 DOI: 10.2169/internalmedicine.9813-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Patients after lung transplantation are at risk for Nocardia infections. We herein report a case of lung and cerebral nocardiosis caused by Nocardia elegans, a rare species of Nocardia, in a lung transplant recipient. Antibiotic therapy, including sulfamethoxazole-trimethoprim (ST), and brain abscess drainage improved symptoms and imaging findings. A literature review of N. elegans infections showed that 12 of 14 cases (85.7%) were reported from East Asia, particularly Japan (9 cases, 64.2%). The lungs were the predominant site (12/14 cases, 85.7%), and most of the cases were susceptible to ST (9/10 cases, 90%).
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Affiliation(s)
- Keitaro Omori
- Department of Infectious Diseases, Hiroshima University Hospital, Japan
- Department of Molecular and Internal Medicine, Graduate School of Biomedical and Health Sciences, Hiroshima University, Japan
| | - Hiroki Kitagawa
- Department of Infectious Diseases, Hiroshima University Hospital, Japan
- Department of Surgery, Graduate School of Biomedical and Health Sciences, Hiroshima University, Japan
| | - Rie Nagaoka
- Section of Clinical Laboratory, Department of Clinical Support, Hiroshima University Hospital, Japan
- Division of Clinical Laboratory Medicine, Hiroshima University Hospital, Japan
| | - Yasuhiko Naka
- Department of Molecular and Internal Medicine, Graduate School of Biomedical and Health Sciences, Hiroshima University, Japan
| | - Kazuma Kawamoto
- Department of Molecular and Internal Medicine, Graduate School of Biomedical and Health Sciences, Hiroshima University, Japan
| | - Yasushi Horimasu
- Department of Molecular and Internal Medicine, Graduate School of Biomedical and Health Sciences, Hiroshima University, Japan
| | - Toshihito Nomura
- Department of Infectious Diseases, Hiroshima University Hospital, Japan
| | - Norifumi Shigemoto
- Department of Infectious Diseases, Hiroshima University Hospital, Japan
- Department of Surgery, Graduate School of Biomedical and Health Sciences, Hiroshima University, Japan
- Translational Research Center, Hiroshima University, Japan
| | | | - Noboru Hattori
- Department of Molecular and Internal Medicine, Graduate School of Biomedical and Health Sciences, Hiroshima University, Japan
| | - Hiroki Ohge
- Department of Infectious Diseases, Hiroshima University Hospital, Japan
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Zendri F, Richards-Rios P, Maciuca I, Ricci E, Timofte D. Disseminated Nocardiosis Caused by Nocardia farcinica in Two Puppy Siblings. Vet Sci 2022; 10:vetsci10010028. [PMID: 36669029 PMCID: PMC9860694 DOI: 10.3390/vetsci10010028] [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: 12/02/2022] [Revised: 12/27/2022] [Accepted: 12/28/2022] [Indexed: 01/04/2023] Open
Abstract
Systemic nocardiosis due to Nocardia farcinica has not been reported in canine outbreaks. Two 14-week-old female Dogue de Bordeaux siblings presented with fever and severe, acute onset limb lameness; traumatic lesions with evidence of infection were identified over the lame limbs of both dogs. The patients were euthanised owing to lack of therapeutic response and rapid escalation to systemic infection with central nervous system manifestations. The post-mortem changes consisted of multiple disseminated abscesses, mainly affecting the skin and subcutis at the limb traumatic injuries, local and hilar lymph nodes, lung, kidney and brain. Bacterial culture and identification via MALDI-TOF and 16S rRNA sequencing revealed Nocardia farcinica from several of these sites in both dogs. Clinical significance of the isolate was supported by cytology of the post-mortem organs' impression smears showing numerous branching filamentous bacteria associated with inflammation. The organism displayed marked multidrug-resistance. No history of immunosuppression was available, and immunohistochemistry ruled out viral pathogens as canine distemper and parvovirus. N. farcinica should be considered as a potential differential cause of sudden lameness and systemic infection in dogs with traumatic skin lesions over the limbs. This is the first reported small-scale outbreak of systemic nocardiosis in dogs due to N. farcinica.
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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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Salar-Vidal L, Martín-García M, Macías-Valcayo A, Ponz A, Esteban J. Epidemiology and in vitro antimicrobial susceptibility of aerobic Actinomycetales in a clinical setting. ENFERMEDADES INFECCIOSAS Y MICROBIOLOGIA CLINICA (ENGLISH ED.) 2022; 40:562-567. [PMID: 36464473 DOI: 10.1016/j.eimce.2021.02.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 02/22/2021] [Indexed: 06/17/2023]
Abstract
INTRODUCTION The incidence of infections caused by aerobic actinomycetes is increasing. Recent changes in taxonomy and the variability in susceptibility patterns among species make necessary a proper identification and antibiotic susceptibility testing. MATERIAL AND METHODS Fifty-three strains of aerobic actinomycetes were identified by MALDI-TOF MS using the VITEK MS Mycobacterium/Nocardia kit (bioMérieux, France) in a tertiary hospital in Spain during a six-year period. Antimicrobial susceptibility testing of the isolates was performed using the Sensititre Rapmycoi microdilution panel (Thermo Fisher Scientific, Massachusetts, USA). RESULTS Forty strains of Nocardia spp. were identified in the study, being N. farcinica and N. cyriacigeorgica the most prevalent ones. All isolates were susceptible to linezolid and the resistance to amikacin was only observed in one isolate of Gordonia sputi. Resistance to cotrimoxazole was only found in five isolates. CONCLUSIONS Routine identification and antimicrobial susceptibility testing of aerobic actinomycetes is advisable for an efficient identification of species and effective treatment.
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Affiliation(s)
- Llanos Salar-Vidal
- Department of Clinical Microbiology, IIS-Fundación Jiménez Díaz, UAM Madrid, Spain
| | - Marta Martín-García
- Department of Clinical Microbiology, IIS-Fundación Jiménez Díaz, UAM Madrid, Spain
| | | | - Ana Ponz
- Department of Clinical Microbiology, IIS-Fundación Jiménez Díaz, UAM Madrid, Spain
| | - Jaime Esteban
- Department of Clinical Microbiology, IIS-Fundación Jiménez Díaz, UAM Madrid, Spain.
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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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Lao CK, Tseng MC, Chiu CH, Chen NY, Chen CH, Chung WH, Liu TP, Lu JJ, Lai HC, Yang LY, Lee CH, Wu TS. Clinical manifestations and antimicrobial susceptibility of Nocardia species at a tertiary hospital in Taiwan, 2011-2020. J Formos Med Assoc 2022; 121:2109-2122. [PMID: 35811270 DOI: 10.1016/j.jfma.2022.06.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 06/21/2022] [Accepted: 06/22/2022] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND The study aimed to assess the clinical characteristics of patients with nocardiosis, to evaluate the in vitro susceptibility of antimicrobial agents against Nocardia species, and to explore changes in antimicrobial susceptibilities in this era of multidrug resistance. METHODS Nocardia isolates were identified to the species level using matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) and 16S rRNA, hsp65, and secA1 gene sequencing, and minimum inhibitory concentrations (MICs) of 15 antimicrobial agents were assessed with the broth microdilution method. RESULTS Eighty-nine isolates from 68 patients were identified to species level. The most common species were Nocardia brasiliensis (n = 28, 31.5%), followed by N. farcinica (n = 24, 27%) and N. cyriacigeorgica (n = 16, 18%). Skin and soft tissue were the most common sites of nocardiosis. In multivariate analysis, cutaneous infection (OR, 0.052; p = 0.009), immunosuppressant use (OR, 16.006; p = 0.013) and Charlson combidity index (OR, 1.522; p = 0.029) were significant predictors for death. In total, 98.9% isolates were susceptible to trimethoprim-sulfamethoxazole and linezolid. Further, the MIC range and resistance rate of all Nocardia species to ceftriaxone, imipenem, and amoxicillin-clavulanic acid were found to generally increase over time. CONCLUSIONS Considering that trimethoprim-sulfamethoxazole is effective against most Nocardia species, it is the antibiotic of choice in Taiwan. Besides, amikacin, tigecycline, and linezolid showed high activity against Nocardia species and are thus good alternatives or additional therapies to treat nocardiosis, depending on patient's underlying conditions and site of infection.
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Affiliation(s)
- Chong Kei Lao
- Division of Infectious Diseases, Department of Internal Medicine, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, 5, Fuxing Street, Guishan District, Taoyuan 33305, Taiwan
| | - Mei-Chueh Tseng
- Department of Medical Research and Development, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, 5, Fuxing Street, Guishan District, Taoyuan 33305, Taiwan
| | - Cheng-Hsun Chiu
- School of Medicine, Chang Gung University, 259, Wenhua 1st Road, Guishan District, Taoyuan 33302, Taiwan; Department of Pediatrics, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, 5, Fuxing Street, Guishan District, Taoyuan 33305, Taiwan; Infection Control Committee, Chang Gung Memorial Hospital, 5, Fuxing Street, Guishan District, Taoyuan 33305, Taiwan
| | - Nan-Yu Chen
- Division of Infectious Diseases, Department of Internal Medicine, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, 5, Fuxing Street, Guishan District, Taoyuan 33305, Taiwan; School of Medicine, Chang Gung University, 259, Wenhua 1st Road, Guishan District, Taoyuan 33302, Taiwan
| | - Chih-Hung Chen
- School of Medicine, Chang Gung University, 259, Wenhua 1st Road, Guishan District, Taoyuan 33302, Taiwan; Department of Thoracic Medicine, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, 5, Fuxing Street, Guishan District, Taoyuan 33305, Taiwan
| | - Wen-Hung Chung
- School of Medicine, Chang Gung University, 259, Wenhua 1st Road, Guishan District, Taoyuan 33302, Taiwan; Department of Dermatology, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, 5, Fuxing Street, Guishan District, Taoyuan 33305, Taiwan
| | - Tsui-Ping Liu
- Department of Laboratory Medicine, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, 5, Fuxing Street, Guishan District, Taoyuan 33305, Taiwan
| | - Jang-Jih Lu
- School of Medicine, Chang Gung University, 259, Wenhua 1st Road, Guishan District, Taoyuan 33302, Taiwan; Department of Laboratory Medicine, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, 5, Fuxing Street, Guishan District, Taoyuan 33305, Taiwan
| | - Hsin-Chih Lai
- Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, 259, Wenhua 1st Road, Gueishan District, Taoyuan 33302, Taiwan
| | - Lan-Yan Yang
- Biostatistics Unit of Clinical Trial Center, Chang Gung Memorial Hospital, 5, Fuxing Street, Guishan District, Taoyuan City 33305, Taiwan
| | - Chia-Hui Lee
- Biostatistics Unit of Clinical Trial Center, Chang Gung Memorial Hospital, 5, Fuxing Street, Guishan District, Taoyuan City 33305, Taiwan
| | - Ting-Shu Wu
- Division of Infectious Diseases, Department of Internal Medicine, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, 5, Fuxing Street, Guishan District, Taoyuan 33305, Taiwan; School of Medicine, Chang Gung University, 259, Wenhua 1st Road, Guishan District, Taoyuan 33302, Taiwan; Infection Control Committee, Chang Gung Memorial Hospital, 5, Fuxing Street, Guishan District, Taoyuan 33305, Taiwan.
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14
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The developed molecular biological identification tools for mycetoma causative agents: An update. Acta Trop 2022; 225:106205. [PMID: 34687643 DOI: 10.1016/j.actatropica.2021.106205] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 09/27/2021] [Accepted: 10/15/2021] [Indexed: 11/23/2022]
Abstract
Mycetoma is a chronic granulomatous inflammatory disease that is caused either by bacteria or fungi. Bacterial mycetoma (actinomycetoma) can be caused by various causative agents of the genera Nocardia, Streptomyces and Actinomadura. On the other hand, fungal mycetoma (eumycetoma) is most commonly caused by causative agents belonging to the genera Madurella, Scedosporium and Falciformispora. Early and accurate diagnosis of the causative organisms can guide proper patient management and treatment. To allow rapid and accurate species identification, different molecular techniques were developed over the past decades. These techniques can be protein based (MALDI-TOF MS) as well as DNA based (Sequencing, PCR and isothermal amplification methods). In this review, we provide an overview of the different molecular techniques currently in use and identify knowledge gaps, which need to be addressed before we can implement molecular diagnostics for mycetoma in different clinical settings.
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15
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Aydin F, Abay S, Kayman T, Karakaya E, Mustak HK, Mustak IB, Bilgen N, Goncuoglu M, Duzler A, Guran O, Sahin O, Saticioglu IB. Campylobacter anatolicus sp. nov., a novel member of the genus Campylobacter isolated from feces of Anatolian Ground Squirrel (Spermophilus xanthoprymnus) in Turkey. Syst Appl Microbiol 2021; 44:126265. [PMID: 34624709 DOI: 10.1016/j.syapm.2021.126265] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 09/10/2021] [Accepted: 09/16/2021] [Indexed: 10/20/2022]
Abstract
Seventy-four Gram-negative, motile, slightly curved rod-shaped, microaerophilic, oxidase-positive and catalase-negative isolates, recovered from fecal samples of the Anatolian ground squirrel (Spermophilus xanthoprymnus) in Kayseri, Turkey, were subjected to a polyphasic taxonomic study. Results of a genus-specific PCR indicated that all isolates belonged to the genus Campylobacter. 16S rRNA gene sequence analyses revealed the closest match as Campylobacter curvus DSM 6644T with identity levels of 96.41-96.70%. Based on the 16S rRNA gene phylogeny of the 74 isolates, six isolates (faydin-G24, faydin-G52, faydin-G105, faydin-G114, faydin-G129 and faydin-G140T) were chosen as representatives for further characterization. The overall genome relatedness indices for the strain faydin-G140T, compared to the most closely related type strain C. curvus ATCC 35224T, were calculated as 15.2%, 72.5%, and 83.7% for digital DNA-DNA hybridization (dDDH), and average nucleotide identity (ANIb and ANIm), respectively. The G+C content and genome size of the strains ranged between 35.2-35.4 mol% and 1.7-1.8 Mb, respectively. Based on data obtained from the polyphasic taxonomy approach, including phenotypic characterization as well as genomic and chemotaxonomic analyses, these strains are concluded to represent a novel species, for which the name Campylobacter anatolicus sp. nov. is proposed with faydin-G140T as the type strain (=DSM 112311T = LMG 32238T).
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Affiliation(s)
- Fuat Aydin
- Department of Microbiology, Faculty of Veterinary Medicine, Erciyes University, 38280 Kayseri, Turkey
| | - Secil Abay
- Department of Microbiology, Faculty of Veterinary Medicine, Erciyes University, 38280 Kayseri, Turkey
| | - Tuba Kayman
- Medical Microbiology Clinic, Şişli Hamidiye Etfal Training and Research Hospital, University of Health Sciences, 34371 Istanbul, Turkey
| | - Emre Karakaya
- Department of Microbiology, Faculty of Veterinary Medicine, Erciyes University, 38280 Kayseri, Turkey
| | - Hamit Kaan Mustak
- Department of Microbiology, Faculty of Veterinary Medicine, Ankara University, 06110 Ankara, Turkey
| | - Inci Basak Mustak
- Department of Microbiology, Faculty of Veterinary Medicine, Ankara University, 06110 Ankara, Turkey
| | - Nuket Bilgen
- Department of Genetics, Faculty of Veterinary Medicine, Ankara University, 06110 Ankara, Turkey
| | - Muammer Goncuoglu
- Department of Food Hygiene and Technology, Faculty of Veterinary Medicine, Ankara University, 06110 Ankara, Turkey
| | - Ayhan Duzler
- Department of Anatomy, Faculty of Veterinary Medicine, Erciyes University, 38280 Kayseri, Turkey
| | - Ozgur Guran
- Faculty of Veterinary Medicine, Ankara University, 06110 Ankara, Turkey
| | - Orhan Sahin
- Department of Veterinary Diagnostic & Production Animal Medicine, College of Veterinary Medicine, Iowa State University, 50011 Ames, Iowa, United States of America
| | - Izzet Burcin Saticioglu
- Department of Aquatic Animal Diseases, Faculty of Veterinary Medicine, Erciyes University, 38280 Kayseri, Turkey
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Chhatwal P, Woltemate S, Ziesing S, Welte T, Schlüter D, Vital M. Molecular characterization and improved diagnostics of Nocardia strains isolated over the last two decades at a German tertiary care center. EXCLI JOURNAL 2021; 20:851-862. [PMID: 34177407 PMCID: PMC8222631 DOI: 10.17179/excli2021-3787] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Accepted: 04/22/2021] [Indexed: 02/03/2023]
Abstract
Nocardiosis is a rare but life-threatening infection caused by aerobic Actinomycetes of the genus Nocardia particularly affecting immunocompromised hosts. The identification of Nocardia ssp. and antibiotic susceptibility testing by standard microbiological methods are incomplete and molecular techniques may improve diagnostics. We studied 39 Nocardia strains isolated from 33 patients between 2000 and 2018. Twenty-four patients (72.7 %) were immunocompromised. Whole genome sequencing (WGS) revealed a broad taxonomic range of those isolates spanning 13 different species, including four strains that belonged to three novel species based on average nucleotide identity (ANI < 95 % with currently available genome sequences). 16S rRNA gene analyses mirrored WGS results. Conventional MALDI-TOF analysis correctly identified 29 isolates at the species level (74.4 %). Our advanced protocol with formic acid and acetonitrile treatment increased identification to 35 isolates (89.7 %). Antibiotic resistance was tested using both a microdilution method and MIC strip testing. Results were in good concordance with an overall trimethoprim-sulfamethoxazole (SXT) resistance rate of 13.5 %. WGS of a SXT resistant N. farcinica isolate showed a deletion of several amino acids in a homolog of dihydropteroate synthase (FolP2) that was not seen in sensitive members of this species. Diversity of Nocardia isolates was high and involved many different species, suggesting that this taxon has broadly distributed mechanisms for infecting individuals. Widely applicable diagnostic methods including MALDI-TOF and 16S rRNA gene analyses correctly identified most strains. WGS additionally revealed molecular insights into SXT resistance mechanisms of clinical Nocardia isolates highlighting the potential application of (meta)genomic-based diagnostics in the future.
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Affiliation(s)
- Patrick Chhatwal
- Institute for Medical Microbiology and Hospital Epidemiology, Hannover Medical School (MHH), Hannover, Germany
| | - Sabrina Woltemate
- Institute for Medical Microbiology and Hospital Epidemiology, Hannover Medical School (MHH), Hannover, Germany
| | - Stefan Ziesing
- Institute for Medical Microbiology and Hospital Epidemiology, Hannover Medical School (MHH), Hannover, Germany
| | - Tobias Welte
- Department of Pneumology and German Center for Lung Research, Hannover Medical School (MHH), Hannover, Germany
| | - Dirk Schlüter
- Institute for Medical Microbiology and Hospital Epidemiology, Hannover Medical School (MHH), Hannover, Germany
| | - Marius Vital
- Institute for Medical Microbiology and Hospital Epidemiology, Hannover Medical School (MHH), Hannover, Germany
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17
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MALDI-TOF mass spectrometry in the 21st century clinical microbiology laboratory. Enferm Infecc Microbiol Clin 2021; 39:192-200. [DOI: 10.1016/j.eimc.2020.02.027] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 02/09/2020] [Accepted: 02/19/2020] [Indexed: 01/12/2023]
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18
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Salar-Vidal L, Martín-García M, Macías-Valcayo A, Ponz A, Esteban J. Epidemiology and in vitro antimicrobial susceptibility of aerobic Actinomycetales in a clinical setting. Enferm Infecc Microbiol Clin 2021; 40:S0213-005X(21)00075-6. [PMID: 33812738 DOI: 10.1016/j.eimc.2021.02.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 02/08/2021] [Accepted: 02/22/2021] [Indexed: 10/21/2022]
Abstract
INTRODUCTION The incidence of infections caused by aerobic actinomycetes is increasing. Recent changes in taxonomy and the variability in susceptibility patterns among species make necessary a proper identification and antibiotic susceptibility testing. MATERIAL AND METHODS Fifty-three strains of aerobic actinomycetes were identified by MALDI-TOF MS using the VITEK MS Mycobacterium/Nocardia kit (bioMérieux, France) in a tertiary hospital in Spain during a six-year period. Antimicrobial susceptibility testing of the isolates was performed using the Sensititre Rapmycoi microdilution panel (Thermo Fisher Scientific, Massachusetts, USA). RESULTS Forty strains of Nocardia spp. were identified in the study, being N. farcinica and N. cyriacigeorgica the most prevalent ones. All isolates were susceptible to linezolid and the resistance to amikacin was only observed in one isolate of Gordonia sputi. Resistance to cotrimoxazole was only found in five isolates. CONCLUSIONS Routine identification and antimicrobial susceptibility testing of aerobic actinomycetes is advisable for an efficient identification of species and effective treatment.
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Affiliation(s)
- Llanos Salar-Vidal
- Department of Clinical Microbiology, IIS-Fundación Jiménez Díaz, UAM Madrid, Spain
| | - Marta Martín-García
- Department of Clinical Microbiology, IIS-Fundación Jiménez Díaz, UAM Madrid, Spain
| | | | - Ana Ponz
- Department of Clinical Microbiology, IIS-Fundación Jiménez Díaz, UAM Madrid, Spain
| | - Jaime Esteban
- Department of Clinical Microbiology, IIS-Fundación Jiménez Díaz, UAM Madrid, Spain.
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19
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Bhandari M, Kathuria S, Khunger N, Sharma B. Mycetoma due to Nocardia Africana/Nova Treated Successfully with Cotrimoxazole and Moxifloxacin. Indian Dermatol Online J 2021; 12:298-301. [PMID: 33959529 PMCID: PMC8088171 DOI: 10.4103/idoj.idoj_533_20] [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: 07/07/2020] [Revised: 08/20/2020] [Accepted: 09/20/2020] [Indexed: 01/19/2023] Open
Abstract
Nocardia africana is a recently identified organism and has rarely been reported to cause mycetoma. Here we report the case of a 40-year-old woman who presented with discharging sinuses and nodules for the past 7 years along with few discrete axillary lymph nodes. Cultures and Maldi-TOF MS (Matrix-assisted laser desorption/ionization–time of flight mass spectrometry) method identified the causative organism as Nocardia africana/nova. The organism was acid-fast positive on modified Ziehl-Neelsen stain and Gram's stain revealed branched filamentous beaded gram-positive bacilli, while histopathology showed granulation tissue along with few ill-defined epithelioid cell granulomas, with giant cells. Based on the sensitivity report, the patient was started on tablet moxifloxacin and cotrimoxazole, and has shown considerable improvement at 2.5 months of follow-up.
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Affiliation(s)
- Molisha Bhandari
- Department of Dermatology and STD, Safdarjung Hospital and Vardhaman Mahavir Medical College, Ansari Nagar, New Delhi, India
| | - Sushruta Kathuria
- Department of Dermatology and STD, Safdarjung Hospital and Vardhaman Mahavir Medical College, Ansari Nagar, New Delhi, India
| | - Niti Khunger
- Department of Dermatology and STD, Safdarjung Hospital and Vardhaman Mahavir Medical College, Ansari Nagar, New Delhi, India
| | - Bhawna Sharma
- Department of Microbiology, Safdarjung Hospital and Vardhaman Mahavir Medical College, Ansari Nagar, New Delhi, India
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20
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In Vitro Susceptibility of Nocardia farcinica to the Antimycobacterial Drug Clofazimine. Antimicrob Agents Chemother 2020; 65:AAC.01849-20. [PMID: 33077650 DOI: 10.1128/aac.01849-20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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21
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Performance and Application of 16S rRNA Gene Cycle Sequencing for Routine Identification of Bacteria in the Clinical Microbiology Laboratory. Clin Microbiol Rev 2020; 33:33/4/e00053-19. [PMID: 32907806 DOI: 10.1128/cmr.00053-19] [Citation(s) in RCA: 119] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
This review provides a state-of-the-art description of the performance of Sanger cycle sequencing of the 16S rRNA gene for routine identification of bacteria in the clinical microbiology laboratory. A detailed description of the technology and current methodology is outlined with a major focus on proper data analyses and interpretation of sequences. The remainder of the article is focused on a comprehensive evaluation of the application of this method for identification of bacterial pathogens based on analyses of 16S multialignment sequences. In particular, the existing limitations of similarity within 16S for genus- and species-level differentiation of clinically relevant pathogens and the lack of sequence data currently available in public databases is highlighted. A multiyear experience is described of a large regional clinical microbiology service with direct 16S broad-range PCR followed by cycle sequencing for direct detection of pathogens in appropriate clinical samples. The ability of proteomics (matrix-assisted desorption ionization-time of flight) versus 16S sequencing for bacterial identification and genotyping is compared. Finally, the potential for whole-genome analysis by next-generation sequencing (NGS) to replace 16S sequencing for routine diagnostic use is presented for several applications, including the barriers that must be overcome to fully implement newer genomic methods in clinical microbiology. A future challenge for large clinical, reference, and research laboratories, as well as for industry, will be the translation of vast amounts of accrued NGS microbial data into convenient algorithm testing schemes for various applications (i.e., microbial identification, genotyping, and metagenomics and microbiome analyses) so that clinically relevant information can be reported to physicians in a format that is understood and actionable. These challenges will not be faced by clinical microbiologists alone but by every scientist involved in a domain where natural diversity of genes and gene sequences plays a critical role in disease, health, pathogenicity, epidemiology, and other aspects of life-forms. Overcoming these challenges will require global multidisciplinary efforts across fields that do not normally interact with the clinical arena to make vast amounts of sequencing data clinically interpretable and actionable at the bedside.
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22
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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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Fan Y, Xie T, Pang Y, Zhu L, Zhou S. Percutaneous transforaminal endoscopic discectomy for the treatment of lateral recess stenosis secondary occurred the discal fungus infection. BMC Musculoskelet Disord 2020; 21:175. [PMID: 32188432 PMCID: PMC7081584 DOI: 10.1186/s12891-020-03211-7] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Accepted: 03/12/2020] [Indexed: 02/04/2023] Open
Abstract
Background This is a case of lateral recess stenosis secondary occurred the discal fungus infection treated with percutaneous transforaminal endoscopic discectomy (PTED). There has been no relevant reports before. Case presentation A 49-year-old patient who had taken itraconazole for 13 months for lateral recess stenosis secondary occurred the discal fungus infection complained of gradually worsening radiating pain and numbness in the back and inguinal and inner thigh region of right side. In order to relieve the radiating neuralgia and reduce the damage to spinal stability, the minimally invasive PTED was performed.The patient’s prognosis was assessed using Oswestry Disability Index (ODI) and Visual Analogue Scale (VAS). During the follow-up, the patient’s ODI and VAS scores were decreased significantly. The radiating pain in the inguinal and inner thigh region of right side were significantly alleviated and the discomfort caused by lower back instability was improved by plaster vest. Discussion and conclusion PTED not only avoids further damage to the stability of the lumbar spine, but also effectively relieves the symptoms of leg neuroradialgia caused by lateral recess stenosis secondary occurred the discal fungus infection.
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Affiliation(s)
- Yunpeng Fan
- The Affiliated Hangzhou Hospital of Nanjing Medical University, Hangzhou, 310006, China
| | - Tao Xie
- The affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine Hangzhou, 261# huansha road, Shangcheng District, Hangzhou City, 310006, Zhejiang Province, China
| | - Yao Pang
- The Affiliated Hangzhou Hospital of Nanjing Medical University, Hangzhou, 310006, China
| | - Liulong Zhu
- The Affiliated Hangzhou Hospital of Nanjing Medical University, Hangzhou, 310006, China.,The affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine Hangzhou, 261# huansha road, Shangcheng District, Hangzhou City, 310006, Zhejiang Province, China
| | - Shaobo Zhou
- The affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine Hangzhou, 261# huansha road, Shangcheng District, Hangzhou City, 310006, Zhejiang Province, China.
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Li S, Xu X, Wu M, Zhu J, Cen P, Ding J, Wu S, Jin J. Lymphocutaneous nocardiosis caused by Nocardia brasiliensis in an immunocompetent patient: a case report. J Int Med Res 2020; 48:300060519897690. [PMID: 31948315 PMCID: PMC7113809 DOI: 10.1177/0300060519897690] [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: 11/18/2022] Open
Abstract
Nocardia usually manifests as opportunistic infections in immunocompromised hosts. Here, we report a rare case of an immunocompetent patient with lymphocutaneous nocardiosis. The patient was a 34-year-old man presenting with fever, multiple scattered pustules on both upper limbs and several subcutaneous nodules on the left elbow and forearm. Skin biopsy of the subcutaneous nodule revealed suppurative inflammation of the lymph nodes. Pus cultures were finally identified as Nocardia brasiliensis. The patient fully recovered without relapse after receiving optimized antimicrobial therapy consisting of linezolid combined with sulfonamides. Nocardiosis is a rare opportunistic disease which may be fatal and usually affects immunocompromised hosts, resulting in suppurative and granulomatous inflammation. Nocardia has a long culture cycle, is difficult to diagnose, and is more likely to be neglected in healthy young people. The present case suggests that physicians should be aware that nocardiosis is a differential diagnosis to consider in patients with suppurative infection, especially when anti-infective treatment is ineffective.
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Affiliation(s)
- Siying Li
- Division of Infectious Disease, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xiangfei Xu
- Division of Infectious Disease, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Min Wu
- Division of Infectious Disease, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jing Zhu
- Division of Infectious Disease, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Panpan Cen
- Division of Infectious Disease, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jiexia Ding
- Division of Infectious Disease, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Shenghai Wu
- Department of Laboratory Medicine, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jie Jin
- Division of Infectious Disease, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, China
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Durand T, Vautrin F, Bergeron E, Girard V, Polsinelli S, Monnin V, Durand G, Dauwalder O, Dumitrescu O, Laurent F, Rodríguez-Nava V. Assessment of VITEK® MS IVD database V3.0 for identification of Nocardia spp. using two culture media and comparing direct smear and protein extraction procedures. Eur J Clin Microbiol Infect Dis 2019; 39:559-567. [PMID: 31758438 DOI: 10.1007/s10096-019-03758-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 10/30/2019] [Indexed: 02/06/2023]
Abstract
We assessed the performance of the VITEK® MS IVD V3.0 matrix-assisted laser desorption ionization - time of flight mass spectrometry (MALDI-ToF MS) V3.0 database for the identification of Nocardia spp. as compared with targeted DNA sequencing. A collection of 222 DNA sequence-defined Nocardia spp. strains encompassing 18 different species present or not in the database was tested. Bromocresol purple agar (BCP) and Columbia agar +5% sheep's blood (COS) culture media were used together with two different preparation steps: direct smear and a "3 attempts" procedure that covered (1) spotting of an extract, (2) new spotting of the same extract, and (3) spotting of a new extract. The direct smear protocol yielded low correct identification rates (≤ 15% for both media) whereas protein extraction yielded correct identification results (> 67% regardless of the media used.). The use of 2 additional attempts using repeat or new extracts increased correct identification rates to 87% and 91% for BCP and COS, respectively. When using the 3 attempts procedure, the best identification results, independent of media types, were obtained for N. farcinica and N. cyriacigeorgica (100%). Identification attempts 2 and 3 allowed to increase the number of correct identifications (BCP, +20%; COS, +13%). The enhancement in performance during attempts 2 and 3 was remarkable for N. abscessus (81% for both media) and low prevalence species (BCP, 70%; COS, 85%). Up to 3.4% and 2.4% of the strains belonging to species present in the database were misidentified with BCP and COS media, respectively. In 1.9% of the cases for BCP and 1.4% for COS, these misidentifications concerned a species belonging to the same phylogenetic complex. Concerning strains that are not claimed in the V3.0 database, N. puris and N. goodfellowi generated "No identification" results and 100% of the strains belonging to N. arthritidis, N.cerradoensis, and N. altamirensis yielded a misidentification within the same phylogenetic complex. Vitek® MS IVD V3.0 is an accurate and useful tool for identification of Nocardia spp.
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Affiliation(s)
- T Durand
- Institut des Agents infectieux, Centre de Biologie et Pathologies Nord, Hôpital de la Croix Rousse, Lyon, France
| | - F Vautrin
- UMR CNRS 5557, Ecologie Microbienne - Groupe de Recherche "Pathogènes Opportunistes et Environnement" - ISPB-Faculté de Pharmacie, Université Lyon 1, Lyon, France
| | - E Bergeron
- UMR CNRS 5557, Ecologie Microbienne - Groupe de Recherche "Pathogènes Opportunistes et Environnement" - ISPB-Faculté de Pharmacie, Université Lyon 1, Lyon, France
| | - V Girard
- bioMérieux France, Microbiology R&D, La Balme-les-Grottes, France
| | - S Polsinelli
- bioMérieux France, Microbiology R&D, La Balme-les-Grottes, France
| | - V Monnin
- bioMérieux France, Microbiology R&D, La Balme-les-Grottes, France
| | - G Durand
- bioMérieux France, Microbiology R&D, La Balme-les-Grottes, France
| | - O Dauwalder
- Institut des Agents infectieux, Centre de Biologie et Pathologies Nord, Hôpital de la Croix Rousse, Lyon, France
| | - O Dumitrescu
- Institut des Agents infectieux, Centre de Biologie et Pathologies Nord, Hôpital de la Croix Rousse, Lyon, France
| | - F Laurent
- Institut des Agents infectieux, Centre de Biologie et Pathologies Nord, Hôpital de la Croix Rousse, Lyon, France
| | - V Rodríguez-Nava
- Institut des Agents infectieux, Centre de Biologie et Pathologies Nord, Hôpital de la Croix Rousse, Lyon, France. .,UMR CNRS 5557, Ecologie Microbienne - Groupe de Recherche "Pathogènes Opportunistes et Environnement" - ISPB-Faculté de Pharmacie, Université Lyon 1, Lyon, France.
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O'Connor C, Rodrigues C, Zheng C, Macallan DC, Riley P. Nocardiosis at a London teaching hospital: Be aware and beware of what is rare. CLINICAL INFECTION IN PRACTICE 2019. [DOI: 10.1016/j.clinpr.2019.100004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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Zheng SW. Disseminated nocardiosis due to Nocardia otitidiscaviarum: A case report and literature review. ASIAN PAC J TROP MED 2019. [DOI: 10.4103/1995-7645.257120] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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Ma F, Kang M, Liao YH, Lee GZ, Tang Q, Tang C, Ding YH, Zhong DJ. Nocardial spinal epidural abscess with lumbar disc herniation: A case report and review of literature. Medicine (Baltimore) 2018; 97:e13541. [PMID: 30544463 PMCID: PMC6310552 DOI: 10.1097/md.0000000000013541] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [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
RATIONALE Nocardial spinal epidural abscess is rare. The diagnosis is often difficult to make and, if delayed, poses a high risk of long-term disability. Nocardial spinal epidural abscess with severe lumbar disc herniation has not previously been reported. PATIENT CONCERNS A 50-year-old man presented with progressive lumbago and leg pain for 6 weeks after receiving acupuncture therapy, and then the patient suddenly occurred urine retention after walking. DIAGNOSES Clinical examination revealed sign of cauda equina syndrome. Magnetic resonance imaging (MRI) revealed a Lumbar(L)4 to L5 disc herniation, L3 to Sacrum(S)1 epidural abscess, and L2 to S1 paravertebral abscess. The causative organism was Nocardia farcinica. INTERVENTIONS An urgent paravertebral abscess debridement and right L4 to L5 laminectomy were performed. Simultaneously, the disc tissue protruding into the spinal canal was removed, as well as irrigation and drainage. And antimicrobial treatment was continued for 12 months. OUTCOMES Fortunately, the patient was able to walk with a cane and urinate autonomously without a catheter, although this remained difficult 7 days after surgery. After 1 year of treatment, the patient has recovered completely and returned to work. LESSONS Nocardial spinal epidural abscess with severe lumbar disc herniation is extremely rare. Pain from spinal degenerative diseases often masks the early symptoms of spinal infection. It's worth noting that invasive treatment of spine is a way of causing spinal nocardial infection.
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Affiliation(s)
- Fei Ma
- Department of Spine Surgery
| | | | | | | | | | | | - Yin Huan Ding
- Department of Medical laboratory, The Affiliated Hospital of Southwest Medical University, Luzhou City, China
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