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Breyer GM, Rocha Jacques da Silva ME, Slaviero M, Albuquerque de Almeida B, Machado Sousa da Silva E, de Queiroz Schmidt VR, Alievi M, Maboni G, Petinatti Pavarini S, Maboni Siqueira F. Genotypic characterization of Streptococcus didelphis causative of fatal infection in white-eared opossums. Lett Appl Microbiol 2023; 76:ovad131. [PMID: 37968138 DOI: 10.1093/lambio/ovad131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 10/25/2023] [Accepted: 11/14/2023] [Indexed: 11/17/2023]
Abstract
Streptococcus didelphis was once reported as related to severe infections in opossums. Thus, we present the first comprehensive whole-genome characterization of clinical S. didelphis strains isolated from white-eared opossums (Didelphis albiventris). Long-read whole-genome sequencing was performed using the MinION platform, which allowed the prediction of several genomic features. We observed that S. didelphis genomes harbor a cluster for streptolysin biosynthesis and a conserved genomic island with genes involved in transcriptional regulation (arlR) and transmembrane transport (bcrA). Antimicrobial resistance genes for several drug classes were found, including beta-lactam, which is the main antimicrobial class used in Streptococcus spp. infections; however, no phenotypical resistance was observed. In addition, we predicted the presence of 33 virulence factors in the analyzed genomes. High phylogenetic similarity was observed between clinical and reference strains, yet no clonality was suggested. We also proposed dnaN, gki, pros, and xpt as housekeeping candidates to be used in S. didelphis sequence typing. This is the first whole-genome characterization of S. didelphis, whose data provide important insights into its pathogenicity.
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Affiliation(s)
- Gabriela Merker Breyer
- Laboratório de Bacteriologia Veterinária, Departamento de Patologia Veterinária, Universidade Federal do Rio Grande do Sul, 9090 Bento Gonçalves Avenue, 91540-000 - Porto Alegre/RS, Brazil
- Programa de Pós-Graduação em Ciências Veterinárias, Universidade Federal do Rio Grande do Sul, 9090 Bento Gonçalves Avenue, 91540-000 - Porto Alegre/RS, Brazil
| | - Maria Eduarda Rocha Jacques da Silva
- Laboratório de Bacteriologia Veterinária, Departamento de Patologia Veterinária, Universidade Federal do Rio Grande do Sul, 9090 Bento Gonçalves Avenue, 91540-000 - Porto Alegre/RS, Brazil
- Programa de Pós-Graduação em Ciências Veterinárias, Universidade Federal do Rio Grande do Sul, 9090 Bento Gonçalves Avenue, 91540-000 - Porto Alegre/RS, Brazil
| | - Mônica Slaviero
- Programa de Pós-Graduação em Ciências Veterinárias, Universidade Federal do Rio Grande do Sul, 9090 Bento Gonçalves Avenue, 91540-000 - Porto Alegre/RS, Brazil
- Laboratório de Patologia Veterinária, Departamento de Patologia Veterinária, Universidade Federal do Rio Grande do Sul, 9090 Bento Gonçalves Avenue, 91540-000 - Porto Alegre/RS, Brazil
| | - Bruno Albuquerque de Almeida
- Programa de Pós-Graduação em Ciências Veterinárias, Universidade Federal do Rio Grande do Sul, 9090 Bento Gonçalves Avenue, 91540-000 - Porto Alegre/RS, Brazil
- Laboratório de Patologia Veterinária, Departamento de Patologia Veterinária, Universidade Federal do Rio Grande do Sul, 9090 Bento Gonçalves Avenue, 91540-000 - Porto Alegre/RS, Brazil
| | - Emanoelly Machado Sousa da Silva
- Programa de Pós-Graduação em Ciências Veterinárias, Universidade Federal do Rio Grande do Sul, 9090 Bento Gonçalves Avenue, 91540-000 - Porto Alegre/RS, Brazil
- Laboratório de Patologia Veterinária, Departamento de Patologia Veterinária, Universidade Federal do Rio Grande do Sul, 9090 Bento Gonçalves Avenue, 91540-000 - Porto Alegre/RS, Brazil
| | - Victória Regina de Queiroz Schmidt
- Preservas-Núcleo de Conservação e Reabilitação de Animais Silvestres, Hospital de Clínicas Veterinárias, Universidade Federal do Rio Grande do Sul, 9090 Bento Gonçalves Avenue, 91540-000 - Porto Alegre/RS, Brazil
| | - Marcelo Alievi
- Programa de Pós-Graduação em Ciências Veterinárias, Universidade Federal do Rio Grande do Sul, 9090 Bento Gonçalves Avenue, 91540-000 - Porto Alegre/RS, Brazil
- Preservas-Núcleo de Conservação e Reabilitação de Animais Silvestres, Hospital de Clínicas Veterinárias, Universidade Federal do Rio Grande do Sul, 9090 Bento Gonçalves Avenue, 91540-000 - Porto Alegre/RS, Brazil
| | - Grazieli Maboni
- Department of Pathobiology, University of Guelph, 50 Stone Road East, NIG 2W1 - Guelph/ON, Canada
| | - Saulo Petinatti Pavarini
- Programa de Pós-Graduação em Ciências Veterinárias, Universidade Federal do Rio Grande do Sul, 9090 Bento Gonçalves Avenue, 91540-000 - Porto Alegre/RS, Brazil
- Laboratório de Patologia Veterinária, Departamento de Patologia Veterinária, Universidade Federal do Rio Grande do Sul, 9090 Bento Gonçalves Avenue, 91540-000 - Porto Alegre/RS, Brazil
| | - Franciele Maboni Siqueira
- Laboratório de Bacteriologia Veterinária, Departamento de Patologia Veterinária, Universidade Federal do Rio Grande do Sul, 9090 Bento Gonçalves Avenue, 91540-000 - Porto Alegre/RS, Brazil
- Programa de Pós-Graduação em Ciências Veterinárias, Universidade Federal do Rio Grande do Sul, 9090 Bento Gonçalves Avenue, 91540-000 - Porto Alegre/RS, Brazil
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Update on Novel Taxa and Revised Taxonomic Status of Bacteria Isolated from Nondomestic Animals Described in 2018 to 2021. J Clin Microbiol 2023; 61:e0142522. [PMID: 36533958 PMCID: PMC9945507 DOI: 10.1128/jcm.01425-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Revisions and new additions to bacterial taxonomy can have a significant widespread impact on clinical practice, infectious disease epidemiology, veterinary microbiology laboratory operations, and wildlife conservation efforts. The expansion of genome sequencing technologies has revolutionized our knowledge of the microbiota of humans, animals, and insects. Here, we address novel taxonomy and nomenclature revisions of veterinary significance that impact bacteria isolated from nondomestic wildlife, with emphasis being placed on bacteria that are associated with disease in their hosts or were isolated from host animal species that are culturally significant, are a target of conservation efforts, or serve as reservoirs for human pathogens.
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Streptococcus bouchesdurhonensis sp. nov. isolated from a bronchoalveolar lavage of a patient with pneumonia. Arch Microbiol 2022; 205:3. [PMID: 36436132 DOI: 10.1007/s00203-022-03348-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 11/17/2022] [Accepted: 11/19/2022] [Indexed: 11/28/2022]
Abstract
Strain Marseille-Q6994 was isolated from a 72-year-old patient with pneumonia from Bouches-du-Rhône department, in France. Cells were Gram positive, non-motile, catalase and oxidase-negative cocci. The major fatty acids were hexadecanoic (47.4%) and tetradecanoic acids (28.3%). 16S rRNA gene sequence comparison suggested that strain Marseille-Q6994 was affiliated to the Streptococcus genus. GroEL phylogenetic analysis separated strain Marseille-Q6994 in a distinct branch from the closely related Streptococcus-type strains with standing in nomenclature. Whole genome sequencing-based methods (OrthoAverage Nucleotide Identity, digital DNA-DNA hybridization and pangenome analysis) supported the classification of the strain into a novel species. Therefore, based on the phenotypic, genomic, and phylogenetic analyses, we propose the name Streptococcus bouchesdurhonensis sp. nov for which strain Marseille-Q6994T (CSUR Marseille-Q6994 = DSMZ 113892) is the type strain.
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Volokhov DV, Zagorodnyaya TA, Shen Z, Blom J, Furtak VA, Eisenberg T, Fan P, Jeong KC, Gao Y, Zhang S, Amselle M. Streptococcus vicugnae sp. nov., isolated from faeces of alpacas ( Vicugna pacos) and cattle ( Bos taurus), Streptococcus zalophi sp. nov., and Streptococcus pacificus sp. nov., isolated from respiratory tract of California sea lions ( Zalophus californianus). Int J Syst Evol Microbiol 2021; 71. [PMID: 33999792 DOI: 10.1099/ijsem.0.004826] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Four novel independent strains of Streptococcus spp. were isolated from faeces of alpaca (SL1232T), cattle (KCJ4950), and from respiratory tract of wild California sea lions (CSL7508T, CSL7591T). The strains were indole-, oxidase- and catalase-negative, non-spore-forming, non-motile Gram-positive cocci in short and long chains, facultative anaerobes. The 16S rRNA gene of SL1232T and KCJ4950 shared 99.40-99.60% nucleotide similarity to strains of S. equinus, S. lutetiensis, S. infantarius, and the 16S rRNA gene of CSL7508T and CSL7591T demonstrated 98.72 and 98.92% similarity, respectively, to S. marimammalium. All other known Streptococcus species had the 16S rRNA gene sequence similarities of ≤95%. The genomes were sequenced for the novel strains. Average nucleotide identity (ANI) analysis for strains SL1232T and KCJ4950, showed the highest similarity to S. equinus, S. lutetiensis, and S. infantarius with 85.21, 87.17, 88.47, 85.54, 87.47 and 88.89%, respectively, and strains CSL7508T and CSL7591T to S. marimammalium with 87.16 and 83.97%, respectively. Results of ANI were confirmed by pairwise digital DNA-DNA hybridization and phylogeny, which also revealed that the strains belong to three novel species of the genus Streptococcus. Phenotypical features of the novel species were in congruence with closely related members of the genus Streptococcus and gave negative reactions with the tested Lancefield serological groups (A-D, F and G). MALDI-TOF mass spectrometry supported identification of the species. Based on these data, we propose three novel species of the genus Streptococcus, for which the name Streptococcus vicugnae sp. nov. is proposed with the type strain SL1232T (=NCTC 14341T=DSM 110741T=CCUG 74371T), Streptococcus zalophi sp. nov. is proposed with the type strain CSL7508T (=NCTC 14410T=DSM 110742T=CCUG 74374T) and Streptococcus pacificus sp. nov. is proposed with the type strain CSL7591T (=NCTC 14455T=DSM 111148T=CCUG 74655T). The genome G+C content is 36.89, 34.85, and 35.34 % and draft genome sizes are 1906993, 1581094 and 1656080 bp for strains SL1232T, CSL7508T, and CSL7591T, respectively.
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Affiliation(s)
- Dmitriy V Volokhov
- Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD 20993, USA
| | - Tatiana A Zagorodnyaya
- Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD 20993, USA
| | - Zhenyu Shen
- Department of Veterinary Pathobiology, Veterinary Medical Diagnostic Laboratory, College of Veterinary Medicine, University of Missouri, 901 East Campus Loop, Columbia, MO 65211, USA
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus-Liebig-University Giessen, Heinrich Buff Ring 58, 35392, Giessen, Germany
| | - Vyacheslav A Furtak
- Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD 20993, USA
| | - Tobias Eisenberg
- Institute of Hygiene and Infectious Diseases of Animals, Justus-Liebig-University Giessen, Frankfurter Strasse 89-91, 35392 Giessen, Germany.,Hessian State Laboratory (LHL), Department of Veterinary Medicine, Schubertstrasse 60, 35392, Giessen, Germany
| | - Peixin Fan
- Department of Animal Sciences, Emerging Pathogens Institute, University of Florida, 2055 Mowry Road, Gainesville, FL 32611, USA
| | - Kwangcheol Casey Jeong
- Department of Animal Sciences, Emerging Pathogens Institute, University of Florida, 2055 Mowry Road, Gainesville, FL 32611, USA
| | - Yamei Gao
- Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD 20993, USA
| | - Shuping Zhang
- Department of Veterinary Pathobiology, Veterinary Medical Diagnostic Laboratory, College of Veterinary Medicine, University of Missouri, 901 East Campus Loop, Columbia, MO 65211, USA
| | - Megan Amselle
- American Type Culture Collection (ATCC), 10801 University Blvd., Manassas, VA 20110, USA
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