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Munson E, Lawhon SD, Burbick CR, Zapp A, Villaflor M, Thelen E. An Update on Novel Taxa and Revised Taxonomic Status of Bacteria Isolated from Domestic Animals Described in 2018 to 2021. J Clin Microbiol 2023; 61:e0028122. [PMID: 36533907 DOI: 10.1128/jcm.00281-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Novel bacterial taxonomy and nomenclature revisions can have significant impacts on clinical practice, disease epidemiology, and veterinary microbiology laboratory operations. Expansion of research on the microbiota of humans, animals, and insects has significant potential impacts on the taxonomy of organisms of clinical interest. Implications of taxonomic changes may be especially important when considering zoonotic diseases. Here, we address novel taxonomy and nomenclature revisions of veterinary significance. Noteworthy discussion centers around descriptions of novel mastitis pathogens in Streptococcaceae, Staphylococcaceae, and Actinomycetaceae; bovine reproductive tract pathogens in Corynebacteriaceae; novel members of Mannheimia spp., Leptospira spp., and Mycobacterium spp.; the transfer of Ochrobactrum spp. to Brucella spp.; and revisions to the genus Mycoplasma.
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Chow SK. Uncommon Things Being Common: Gram Variability of Brucella as a Cause of Laboratory Exposure. J Clin Microbiol 2022;:e0050722. [PMID: 35531666 DOI: 10.1128/jcm.00507-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Inal N, Hazırolan G. Misidentification of Brucella melitensis as Octrobactrum deajoenense with MALDI-TOF MS: A report of three cases. Enferm Infecc Microbiol Clin (Engl Ed) 2022; 40:210-212. [PMID: 35473994 DOI: 10.1016/j.eimce.2021.03.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Accepted: 03/05/2021] [Indexed: 06/14/2023]
Affiliation(s)
- Neşe Inal
- Faculty of Medicine, Department of Medical Microbiology, Hacettepe University, Ankara, Turkey.
| | - Gülşen Hazırolan
- Faculty of Medicine, Department of Medical Microbiology, Hacettepe University, Ankara, Turkey
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Jeyaraman M, Muthu S, Sarangan P, Jeyaraman N, Packkyarathinam RP. Ochrobactrum anthropi - An Emerging Opportunistic Pathogen in Musculoskeletal Disorders - A Case Report and Review of Literature. J Orthop Case Rep 2022; 12:85-90. [PMID: 36199934 PMCID: PMC9499045 DOI: 10.13107/jocr.2022.v12.i03.2730] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Revised: 01/20/2022] [Indexed: 02/08/2023] Open
Abstract
INTRODUCTION Ochrobactrum anthropi is an opportunistic and rare human pathogen, which is seen widely in the environment. O. anthropi infections have been reported in both immunocompetent and immunocompromised individuals. There is no proper consensus on the diagnosis and management of O. anthropi related infections. CASE REPORT We report a case of O. anthropi related left distal clavicular osteomyelitis in an immunocompetent individual with an elaborative diagnostic and treatment algorithm for its effective management. CONCLUSION A comprehensive management strategy with a combination of implant removal (if present) with extensive surgical debridement of bone and soft tissue and intravenous antibiotics results in successful eradication of O. anthropi infection.
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Affiliation(s)
- Madhan Jeyaraman
- Department of Orthopaedics, Faculty of Medicine, Sri Lalithambigai Medical College and Hospital, Dr. MGR Educational and Research Institute, Chennai, Tamil Nadu, India
- Address of Correspondence: Dr. Madhan Jeyaraman, Department of Orthopaedics, Faculty of Medicine - Sri Lalithambigai Medical College and Hospital, Chennai, Tamil Nadu, India. E-mail:
| | - Sathish Muthu
- Department of Orthopaedics, Government Medical College and Hospital, Dindigul, Tamil Nadu, India
| | - Prasanna Sarangan
- Department of Microbiology, Shri Sathya Sai Medical College and Research Institute, Chengalpattu, Tamil Nadu, India
| | - Naveen Jeyaraman
- Department of Orthopaedics, Atlas Hospitals, Tiruchirappalli, Tamil Nadu, India
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Gopalsamy SN, Ramakrishnan A, Shariff MM, Gabel J, Brennan S, Drenzek C, Farley MM, Gaynes RP, Cartwright EJ. Brucellosis Initially Misidentified as Ochrobactrum anthropi Bacteremia: A Case Report and Review of the Literature. Open Forum Infect Dis 2021; 8:ofab473. [PMID: 34660837 PMCID: PMC8514177 DOI: 10.1093/ofid/ofab473] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 09/23/2021] [Indexed: 11/20/2022] Open
Abstract
Automated identification systems may misidentify Brucella, the causative agent of brucellosis, which may be re-emerging in the United States as the result of an expanding feral swine population. We present a case of Brucella suis likely associated with feral swine exposure that was misidentified as Ochrobactrum anthropi, a phylogenetic relative.
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Affiliation(s)
| | - Aditi Ramakrishnan
- Division of Infectious Diseases, Department of Medicine, Emory University, Atlanta, Georgia, USA
| | - Mustaf M Shariff
- Department of Medicine, Northside Hospital Gwinnett, Lawrenceville, Georgia, USA
| | - Julie Gabel
- Georgia Department of Public Health, Atlanta, Georgia, USA
| | - Skyler Brennan
- Georgia Department of Public Health, Atlanta, Georgia, USA
| | - Cherie Drenzek
- Georgia Department of Public Health, Atlanta, Georgia, USA
| | - Monica M Farley
- Division of Infectious Diseases, Department of Medicine, Emory University, Atlanta, Georgia, USA.,Atlanta VA Medical Center, Decatur, Georgia, USA
| | - Robert P Gaynes
- Division of Infectious Diseases, Department of Medicine, Emory University, Atlanta, Georgia, USA.,Atlanta VA Medical Center, Decatur, Georgia, USA
| | - Emily J Cartwright
- Division of Infectious Diseases, Department of Medicine, Emory University, Atlanta, Georgia, USA.,Atlanta VA Medical Center, Decatur, Georgia, USA
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Inal N, Hazırolan G. Misidentification of Brucella melitensis as Octrobactrum deajoenense with MALDI-TOF MS: A report of three cases. Enferm Infecc Microbiol Clin 2021; 40:S0213-005X(21)00069-0. [PMID: 33836909 DOI: 10.1016/j.eimc.2021.03.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Revised: 03/03/2021] [Accepted: 03/05/2021] [Indexed: 11/03/2022]
Affiliation(s)
- Neşe Inal
- Faculty of Medicine, Department of Medical Microbiology, Hacettepe University, Ankara, Turkey.
| | - Gülşen Hazırolan
- Faculty of Medicine, Department of Medical Microbiology, Hacettepe University, Ankara, Turkey
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Abstract
Ochrobactrum species are non-enteric, Gram-negative organisms that are closely related to the genus Brucella. Since the designation of the genus in 1988, several distinct species have now been characterised and implicated as opportunistic pathogens in multiple outbreaks. Here, we examine the genus, its members, diagnostic tools used for identification, data from recent Ochrobactrum whole genome sequencing and the pathogenicity associated with reported Ochrobactrum infections. This review identified 128 instances of Ochrobactrum spp. infections that have been discussed in the literature. These findings indicate that infection review programs should consider investigation of possible Ochrobactrum spp. outbreaks if these bacteria are clinically isolated in more than one patient and that Ochrobactrum spp. are more important pathogens than previously thought.
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Affiliation(s)
- Michael P. Ryan
- Department of Applied Sciences, Limerick Institute of Technology, Moylish V94 EC5T, Limerick, Ireland;
- Molecular Biochemistry Laboratory, Department of Chemical Sciences, School of Natural Sciences, Bernal Institute, University of Limerick, Limerick V94 T9PX2, Ireland
| | - J. Tony Pembroke
- Molecular Biochemistry Laboratory, Department of Chemical Sciences, School of Natural Sciences, Bernal Institute, University of Limerick, Limerick V94 T9PX2, Ireland
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Church DL, Cerutti L, Gürtler A, Griener T, Zelazny A, Emler S. Performance and Application of 16S rRNA Gene Cycle Sequencing for Routine Identification of Bacteria in the Clinical Microbiology Laboratory. Clin Microbiol Rev 2020; 33:e00053-19. [PMID: 32907806 DOI: 10.1128/CMR.00053-19] [Citation(s) in RCA: 103] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [What about the content of this article? (0)] [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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Yagel Y, Sestito S, Motro Y, Shnaiderman-Torban A, Khalfin B, Sagi O, Navon-Venezia S, Steinman A, Moran-Gilad J. Genomic Characterization of Antimicrobial Resistance, Virulence, and Phylogeny of the Genus Ochrobactrum. Antibiotics (Basel) 2020; 9:E177. [PMID: 32294990 DOI: 10.3390/antibiotics9040177] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 04/04/2020] [Accepted: 04/09/2020] [Indexed: 01/27/2023] Open
Abstract
Ochrobactrum is a ubiquitous Gram-negative microorganism, mostly found in the environment, which can cause opportunistic infections in humans. It is almost uniformly resistant to penicillins and cephalosporins through an AmpC-like β-lactamase enzyme class (OCH). We studied 130 assembled genomes, of which 5 were animal-derived isolates recovered in Israel, and 125 publicly available genomes. Our analysis focused on antimicrobial resistance (AMR) genes, virulence genes, and whole-genome phylogeny. We found that 76% of Ochrobactrum genomes harbored a blaOCH β-lactamase gene variant, while 7% harbored another AmpC-like gene. No virulence genes other than lipopolysaccharide-associated genes were found. Core genome multilocus sequence typing clustered most samples to known species, but neither geographical clustering nor isolation source clustering were evident. When analyzing the distribution of different blaOCH variants as well as of the blaOCH-deficient samples, a clear phylogenomic clustering was apparent for specific species. The current analysis of the largest collection to date of Ochrobactrum genomes sheds light on the resistome, virulome, phylogeny, and species classification of this increasingly reported human pathogen. Our findings also suggest that Ochrobactrum deserves further characterization to underpin its evolution, taxonomy, and antimicrobial resistance.
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