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Muigg V, Seth-Smith HMB, Adam KM, Weisser M, Hinić V, Blaich A, Roloff T, Heininger U, Schmid H, Kohler M, Graf L, Winterflood DM, Schlaepfer P, Goldenberger D. Novel Organism Verification and Analysis (NOVA) study: identification of 35 clinical isolates representing potentially novel bacterial taxa using a pipeline based on whole genome sequencing. BMC Microbiol 2024; 24:14. [PMID: 38178003 PMCID: PMC10768270 DOI: 10.1186/s12866-023-03163-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 12/15/2023] [Indexed: 01/06/2024] Open
Abstract
BACKGROUND Reliable species identification of cultured isolates is essential in clinical bacteriology. We established a new study algorithm named NOVA - Novel Organism Verification and Analysis to systematically analyze bacterial isolates that cannot be characterized by conventional identification procedures MALDI-TOF MS and partial 16 S rRNA gene sequencing using Whole Genome Sequencing (WGS). RESULTS We identified a total of 35 bacterial strains that represent potentially novel species. Corynebacterium sp. (n = 6) and Schaalia sp. (n = 5) were the predominant genera. Two strains each were identified within the genera Anaerococcus, Clostridium, Desulfovibrio, and Peptoniphilus, and one new species was detected within Citrobacter, Dermabacter, Helcococcus, Lancefieldella, Neisseria, Ochrobactrum (Brucella), Paenibacillus, Pantoea, Porphyromonas, Pseudoclavibacter, Pseudomonas, Psychrobacter, Pusillimonas, Rothia, Sneathia, and Tessaracoccus. Twenty-seven of 35 strains were isolated from deep tissue specimens or blood cultures. Seven out of 35 isolated strains identified were clinically relevant. In addition, 26 bacterial strains that could only be identified at the species level using WGS analysis, were mainly organisms that have been identified/classified very recently. CONCLUSION Our new algorithm proved to be a powerful tool for detection and identification of novel bacterial organisms. Publicly available clinical and genomic data may help to better understand their clinical and ecological role. Our identification of 35 novel strains, 7 of which appear to be clinically relevant, shows the wide range of undescribed pathogens yet to define.
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Affiliation(s)
- Veronika Muigg
- Clinical Bacteriology and Mycology, University Hospital Basel and University of Basel, Petersgraben 4, Basel, 4031, Switzerland
| | - Helena M B Seth-Smith
- Clinical Bacteriology and Mycology, University Hospital Basel and University of Basel, Petersgraben 4, Basel, 4031, Switzerland
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland
- Swiss Institute of Bioinformatics, Basel, Switzerland
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Kai-Manuel Adam
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Basel, Switzerland
| | - Maja Weisser
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Basel, Switzerland
| | - Vladimira Hinić
- Clinical Bacteriology and Mycology, University Hospital Basel and University of Basel, Petersgraben 4, Basel, 4031, Switzerland
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Annette Blaich
- Clinical Bacteriology and Mycology, University Hospital Basel and University of Basel, Petersgraben 4, Basel, 4031, Switzerland
| | - Tim Roloff
- Clinical Bacteriology and Mycology, University Hospital Basel and University of Basel, Petersgraben 4, Basel, 4031, Switzerland
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland
- Swiss Institute of Bioinformatics, Basel, Switzerland
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Ulrich Heininger
- Infectious Diseases and Vaccinology, University of Basel Children's Hospital, Basel, Switzerland
| | - Hanna Schmid
- Infectious Diseases and Vaccinology, University of Basel Children's Hospital, Basel, Switzerland
| | - Maurus Kohler
- Kantonsspital Baselland (Bruderholz, Liestal, Laufen), Bruderholz, Switzerland
| | - Lukas Graf
- Ear, Nose and Throat Department, University Hospital Basel, Basel, Switzerland
| | - Dylan M Winterflood
- Clinical Bacteriology and Mycology, University Hospital Basel and University of Basel, Petersgraben 4, Basel, 4031, Switzerland
| | - Pascal Schlaepfer
- Laboratory Medicine, University Hospital Basel and University of Basel, Basel, Switzerland
| | - Daniel Goldenberger
- Clinical Bacteriology and Mycology, University Hospital Basel and University of Basel, Petersgraben 4, Basel, 4031, Switzerland.
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Munson E, Carella A, Carroll KC. Valid and accepted novel bacterial taxa derived from human clinical specimens and taxonomic revisions published in 2022. J Clin Microbiol 2023; 61:e0083823. [PMID: 37889007 PMCID: PMC10662342 DOI: 10.1128/jcm.00838-23] [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: 10/28/2023] Open
Abstract
Although some nomenclature changes have caused consternation among clinical microbiologists, the discovery of novel taxa and improving classification of existing groups of organisms is exciting and adds to our understanding of microbial pathogenesis. In this mini-review, we present an in-depth summary of novel taxonomic designations and revisions to prokaryotic taxonomy that were published in 2022. Henceforth, these bacteriology taxonomic summaries will appear annually. Several of the novel Gram-positive organisms have been associated with disease, namely, the Corynebacterium kroppenstedtii-like organisms Corynebacterium parakroppenstedtii sp. nov. and Corynebacterium pseudokroppenstedtii sp. nov. A newly described Streptococcus species, Streptococcus toyakuensis sp. nov., is noteworthy for exhibiting multi-drug resistance. Among the novel Gram-negative pathogens, Vibrio paracholerae sp. nov. stands out as an organism associated with diarrhea and sepsis and has probably been co-circulating with pandemic Vibrio cholerae for decades. Many new anaerobic organisms have been described in this past year largely from genetic assessments of gastrointestinal microbiome collections. With respect to revised taxa, as discussed in previous reviews, the genus Bacillus continues to undergo further division into additional genera and reassignment of existing species into them. Reassignment of two subspecies of Fusobacterium nucleatum to species designations (Fusobacterium animalis sp. nov. and Fusobacterium vincentii sp. nov.) is also noteworthy. As was typical of previous reviews, literature updates for selected clinically relevant organisms discovered between 2017 and 2021 have been included.
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Affiliation(s)
- Erik Munson
- Department of Medical Laboratory Science, Marquette University, Milwaukee, Wisconsin, USA
| | - Arianna Carella
- Department of Medical Laboratory Science, Marquette University, Milwaukee, Wisconsin, USA
| | - Karen C. Carroll
- Division of Medical Microbiology, Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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Description of Pseudoclavibacter triregionum sp. nov. from human blood and Pseudoclavibacter albus comb. nov., and revised classification of the genus Pseudoclavibacter: proposal of Caespitibacter gen. nov., with Caespitibacter soli comb. nov. and Caespitibacter caeni comb. nov. Antonie Van Leeuwenhoek 2022; 115:461-472. [PMID: 35107701 DOI: 10.1007/s10482-022-01712-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 01/21/2022] [Indexed: 10/19/2022]
Abstract
We present polyphasic taxonomic data to demonstrate that strain 125703-2019T, a human blood isolate, represents a novel species within the genus Pseudoclavibacter, and to reclassify the illegitimate Zimmermannella alba Lin et al., 2004 as Pseudoclavibacter albus comb. nov. Upon primary isolation, strain 125703-2019T could not be identified reliably using MALDI-TOF mass spectrometry during routine diagnostic work, but partial 16S rRNA gene sequence analysis revealed that it belonged to the genus Pseudoclavibacter. Average nucleotide identity and digital DNA-DNA hybridisation analyses confirmed that it represented a novel species within this genus. A detailed physiological characterisation yielded differential tests between the novel species and its nearest neighbor taxa, which could also be differentiated using MALDI-TOF mass spectrometry. We propose to formally classify this strain into the novel species Pseudoclavibacter triregionum sp. nov., with strain 125703-2019T (= R-76471T, LMG 31777T, CCUG 74796T) as the type strain. The whole-genome assembly of strain 125703-2019T has a size of 2.4 Mb and a G + C content of 72.74%. A Pseudoclavibacter pangenome analysis revealed that 667 gene clusters were exclusively present in strain 125703-2019T. While these gene clusters were enriched in several COG functional categories, this analysis did not reveal functions that explained the occurrence of this species in human infection. Finally, several phylogenetic and phylogenomic analyses demonstrated that the genus Pseudoclavibacter is polyphyletic with Pseudoclavibacter soli and Pseudoclavibacter caeni representing a unique and deeply branching line of descent within the family Microbacteriaceae. We therefore also propose to reclassify both species into the novel genus Caespitibacter gen. nov. as Caespitibacter soli comb. nov. and Caespitibacter caeni comb. nov., respectively, and with C. soli comb. nov. as the type species.
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Oren A, Garrity GM. Valid publication of new names and new combinations effectively published outside the IJSEM. Validation List no. 203. Int J Syst Evol Microbiol 2022; 72. [PMID: 35108178 DOI: 10.1099/ijsem.0.005167] [Citation(s) in RCA: 275] [Impact Index Per Article: 137.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Affiliation(s)
- Aharon Oren
- The Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond J. Safra Campus, 9190401 Jerusalem, Israel
| | - George M Garrity
- Department of Microbiology & Molecular Genetics, Biomedical Physical Sciences, Michigan State University, East Lansing, MI 48824-4320, USA
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