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Azad MA, Patel R. Practical Guidance for Clinical Microbiology Laboratories: Microbiologic diagnosis of implant-associated infections. Clin Microbiol Rev 2024; 37:e0010423. [PMID: 38506553 PMCID: PMC11237642 DOI: 10.1128/cmr.00104-23] [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] [Indexed: 03/21/2024] Open
Abstract
SUMMARYImplant-associated infections (IAIs) pose serious threats to patients and can be associated with significant morbidity and mortality. These infections may be difficult to diagnose due, in part, to biofilm formation on device surfaces, and because even when microbes are found, their clinical significance may be unclear. Despite recent advances in laboratory testing, IAIs remain a diagnostic challenge. From a therapeutic standpoint, many IAIs currently require device removal and prolonged courses of antimicrobial therapy to effect a cure. Therefore, making an accurate diagnosis, defining both the presence of infection and the involved microorganisms, is paramount. The sensitivity of standard microbial culture for IAI diagnosis varies depending on the type of IAI, the specimen analyzed, and the culture technique(s) used. Although IAI-specific culture-based diagnostics have been described, the challenge of culture-negative IAIs remains. Given this, molecular assays, including both nucleic acid amplification tests and next-generation sequencing-based assays, have been used. In this review, an overview of these challenging infections is presented, as well as an approach to their diagnosis from a microbiologic perspective.
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Affiliation(s)
- Marisa Ann Azad
- Division of Infectious Diseases, Department of Medicine, The Ottawa Hospital, Ottawa, Canada
- Ottawa Hospital Research Institute, Ottawa, Canada
| | - Robin Patel
- Division of Public Health, Infectious Diseases, and Occupational Medicine, Department of Medicine, Mayo Clinic, Rochester, Minnesota, USA
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
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Jin W, Liu Y, Ning Q, Wu S, Su S, Zheng D, Ma S, Zou J, Yang M, Hu D, Ding H. A case of chronic wounds caused by Sporothrix schenckii infection was rapidly detected by metagenomic next generation sequencing. Heliyon 2024; 10:e24420. [PMID: 38298647 PMCID: PMC10827762 DOI: 10.1016/j.heliyon.2024.e24420] [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: 07/17/2023] [Revised: 12/12/2023] [Accepted: 01/09/2024] [Indexed: 02/02/2024] Open
Abstract
The dimorphic fungus Sporothrix schenckii is widely distributed in soil, vegetation, and decaying organic matter, and can cause sporotrichosis when the patient's skin trauma was exposed to contaminated material with Sporothrix spp. The cases of Sporothrix schenckii infection in chronic wounds are rarely reported. Here we reported a 53-year-old male construction worker who was admitted to our hospital on July 9, 2022, without underlying disease presented with a painless subcutaneous hard nodule on his right calf, which later ulcerated and oozed, with an enlarged wound and no fever during the course of the disease. His procalcitonin, C-reactive protein, erythrocyte sedimentation rate increased, and necrotic histopathology suggested chronic granulomatous inflammation. Then his necrotic tissue and pus were sent for metagenomic next generation sequencing(mNGS), the result reported Sporothrix schenckii after 43 hours, which was consistent with the result of culture after 18 days. mNGS might be more useful and valuable in diseases such as sporotrichosis where it is difficult to see the yeast cells in the tissues.
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Affiliation(s)
- Wenxiang Jin
- Department of Infectious Diseases, KingMed Diagnostics, Guangzhou, Guangdong, 510005, China
| | - Yong Liu
- Department of Infectious Diseases, KingMed Diagnostics, Guangzhou, Guangdong, 510005, China
| | - Qiuyue Ning
- Department of Infectious Diseases, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, 530021, China
| | - Shuwen Wu
- Department of Infectious Diseases, KingMed Diagnostics, Guangzhou, Guangdong, 510005, China
| | - Sibiao Su
- Department of Gastroenterology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, 530021, China
| | - Dongyan Zheng
- Department of Dermatology and Venereology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, 530021, China
| | - Shasha Ma
- Department of Infectious Diseases, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, 530021, China
| | - Jun Zou
- Department of Infectious Diseases, The Fourth People's Hospital of Nanning, Nanning, Guangxi, 530023, China
| | - Min Yang
- Department of Infectious Diseases, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, 530021, China
| | - Diefei Hu
- Department of Infectious Diseases, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, 530021, China
| | - Huarong Ding
- Department of Burns and Plastic Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, 530021, China
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Klose SM, Legione AR, Monotti I, Bushell RN, Sugiyama T, Browning GF, Vaz PK. Genomic characterization of Mycoplasma edwardii isolated from a dog bite induced cat wound reveals multiple horizontal gene transfer events and loss of the CRISPR/Cas system. J Med Microbiol 2024; 73. [PMID: 38167305 DOI: 10.1099/jmm.0.001788] [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] [Indexed: 01/05/2024] Open
Abstract
A domestic short hair cat (Felis catus) suffering from a purulent wound infection resulting from a dog bite was sampled for bacterial culture and isolation as the wound had been unresponsive to prolonged antimicrobial treatment. A mycoplasma was isolated from the wound. Whole genome sequencing of the isolate was performed using short-read Illumina and long-read Oxford Nanopore chemistry, and the organism was identified as Mycoplasma edwardii. Comparison of the genome sequence of the isolate to a reference M. edwardii genome sequence (canid isolate) identified the loss of several key bacterial factors involved in genome editing, as well the insertion of several novel ORFs most closely related to those found in other canine mycoplasmas, specifically Mycoplasma canis, M. cynos, M. molare and M. maculosa. This is only the second known report of disease caused by M. edwardii in a non-canid species, and the first report of it infecting and causing clinical disease in a cat.
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Affiliation(s)
- Sara M Klose
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, University of Melbourne, VIC, Australia
- Institute of Molecular Medicine and Experimental Immunology, Faculty of Medicine, University of Bonn, NRW, Germany
| | - Alistair R Legione
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, University of Melbourne, VIC, Australia
| | - Isobel Monotti
- U-Vet, Department of Veterinary Clinical Sciences, Melbourne Veterinary School, University of Melbourne, VIC, Australia
| | - Rhys N Bushell
- U-Vet, Department of Veterinary Clinical Sciences, Melbourne Veterinary School, University of Melbourne, VIC, Australia
| | - Takanori Sugiyama
- U-Vet, Department of Veterinary Clinical Sciences, Melbourne Veterinary School, University of Melbourne, VIC, Australia
- Present address: Animalius Vet, WA, Australia
| | - Glenn F Browning
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, University of Melbourne, VIC, Australia
| | - Paola K Vaz
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, University of Melbourne, VIC, Australia
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Yang Y, Shi Q, Jin Q, Yang Z, Li W, Han J, Mao J, Zheng B. Case Report: Metagenomic Next-Generation Sequencing Clinches the Diagnosis of Acute Q Fever and Verified by Indirect Immunofluorescence Assay. Front Med (Lausanne) 2022; 9:846526. [PMID: 35721056 PMCID: PMC9204269 DOI: 10.3389/fmed.2022.846526] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Accepted: 05/04/2022] [Indexed: 11/13/2022] Open
Abstract
Q fever is a zoonotic infectious disease caused by Coxiella burnetii. The clinical symptoms of acute Q fever are usually atypical, and routine serological tests of C. burnetii are not readily available, making the diagnosis of Q fever a challenge. In this case, we report a male patient who had repeated fevers and was administered empirical anti-infective treatment, but the effect was poor. After conducting relevant laboratory and imagological examinations, the etiology has not yet been confirmed. Subsequently, metagenomic next-generation sequencing (mNGS) identified the sequence reads of C. burnetii from the patient's peripheral blood within 48 h, and then the diagnosis of acute Q fever was established. Moreover, the serological test of indirect immunofluorescence assay (IFA) of the C. burnetii antibody was further performed in the Centers for Disease Control, certifying the result of mNGS. The patient was ultimately treated with doxycycline and recovered well. mNGS is an unbiased and comprehensive method in infrequent or culture-negative pathogen identification. To our knowledge, this is the first case of acute Q fever identified by mNGS and confirmed by IFA in Taizhou, China. A further large-scale prospective clinical cohort study is worth carrying out to compare the diagnostic efficiency of mNGS with traditional serological methods and PCR in acute Q fever.
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Affiliation(s)
- Yide Yang
- Department of Infectious Diseases, Taizhou Municipal Hospital, Taizhou, China
| | - Qingmiao Shi
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan, China.,State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Qian Jin
- Department of Infectious Diseases, Taizhou Municipal Hospital, Taizhou, China
| | - Zhangnv Yang
- Department of Microbiology, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | | | - Jianfeng Han
- Sansure Biotech Inc. Medical Affairs Department, National Joint Local Engineering Research Center for Genetic Diagnosis of Infection Diseases and Tumours, Beijing, China
| | - Juanjuan Mao
- Department of Infectious Diseases, Taizhou Municipal Hospital, Taizhou, China
| | - Beiwen Zheng
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan, China.,State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
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