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Ono T, Taniguchi I, Nakamura K, Nagano DS, Nishida R, Gotoh Y, Ogura Y, Sato MP, Iguchi A, Murase K, Yoshimura D, Itoh T, Shima A, Dubois D, Oswald E, Shiose A, Gotoh N, Hayashi T. Global population structure of the Serratia marcescens complex and identification of hospital-adapted lineages in the complex. Microb Genom 2022; 8:000793. [PMID: 35315751 PMCID: PMC9176281 DOI: 10.1099/mgen.0.000793] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Serratia marcescens is an important nosocomial pathogen causing various opportunistic infections, such as urinary tract infections, bacteremia and sometimes even hospital outbreaks. The recent emergence and spread of multidrug-resistant (MDR) strains further pose serious threats to global public health. This bacterium is also ubiquitously found in natural environments, but the genomic differences between clinical and environmental isolates are not clear, including those between S. marcescens and its close relatives. In this study, we performed a large-scale genome analysis of S. marcescens and closely related species (referred to as the 'S. marcescens complex'), including more than 200 clinical and environmental strains newly sequenced here. Our analysis revealed their phylogenetic relationships and complex global population structure, comprising 14 clades, which were defined based on whole-genome average nucleotide identity. Clades 10, 11, 12 and 13 corresponded to S. nematodiphila, S. marcescens sensu stricto, S. ureilytica and S. surfactantfaciens, respectively. Several clades exhibited distinct genome sizes and GC contents and a negative correlation of these genomic parameters was observed in each clade, which was associated with the acquisition of mobile genetic elements (MGEs), but different types of MGEs, plasmids or prophages (and other integrative elements), were found to contribute to the generation of these genomic variations. Importantly, clades 1 and 2 mostly comprised clinical or hospital environment isolates and accumulated a wide range of antimicrobial resistance genes, including various extended-spectrum β-lactamase and carbapenemase genes, and fluoroquinolone target site mutations, leading to a high proportion of MDR strains. This finding suggests that clades 1 and 2 represent hospital-adapted lineages in the S. marcescens complex although their potential virulence is currently unknown. These data provide an important genomic basis for reconsidering the classification of this group of bacteria and reveal novel insights into their evolution, biology and differential importance in clinical settings.
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Affiliation(s)
- Tomoyuki Ono
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Higashi-ku, Fukuoka, 812-8582, Japan
- Department of Cardiovascular Surgery, Graduate School of Medical Sciences, Kyushu University, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Itsuki Taniguchi
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Keiji Nakamura
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Debora Satie Nagano
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Ruriko Nishida
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Yasuhiro Gotoh
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Yoshitoshi Ogura
- Division of Microbiology, Department of Infectious Medicine, Kurume University School of Medicine, Asahi-machi, Kurume, Fukuoka, 830-0011, Japan
| | - Mitsuhiko P. Sato
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Higashi-ku, Fukuoka, 812-8582, Japan
- Present address: Department of Frontier Research and Development, Kazusa DNA Research Institute, Kisarazu, Chiba, 292-0818, Japan
| | - Atsushi Iguchi
- Faculty of Agriculture, University of Miyazaki, Miyazaki, Miyazaki, 889-8192, Japan
| | - Kazunori Murase
- Department of Microbiology, Graduate School of Medicine, Kyoto University, Sakyou-ku, Kyoto, 6060-8501, Japan
| | - Dai Yoshimura
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Meguro-ku, Tokyo, 152-8550, Japan
| | - Takehiko Itoh
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Meguro-ku, Tokyo, 152-8550, Japan
| | - Ayaka Shima
- IRSD, INSERM, ENVT, INRAE, Université de Toulouse, UPS, Toulouse, France
- Present address: Anicon Insurance, Inc., 8-17-1 Nishi-shinjuku, Shinjuku, Tokyo, 160-0023, Japan
| | - Damien Dubois
- IRSD, INSERM, ENVT, INRAE, Université de Toulouse, UPS, Toulouse, France
- CHU Toulouse, Hôpital Purpan, Service de Bactériologie-Hygiène, Toulouse, France
| | - Eric Oswald
- IRSD, INSERM, ENVT, INRAE, Université de Toulouse, UPS, Toulouse, France
- CHU Toulouse, Hôpital Purpan, Service de Bactériologie-Hygiène, Toulouse, France
| | - Akira Shiose
- Department of Cardiovascular Surgery, Graduate School of Medical Sciences, Kyushu University, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Naomasa Gotoh
- Kyoto Pharmaceutical University, Yamashiro, Kyoto, 607-8414, Japan
| | - Tetsuya Hayashi
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Higashi-ku, Fukuoka, 812-8582, Japan
- *Correspondence: Tetsuya Hayashi,
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Sánchez-Juanes F, Teixeira-Martín V, González-Buitrago JM, Velázquez E, Flores-Félix JD. Identification of Species and Subspecies of Lactic Acid Bacteria Present in Spanish Cheeses Type "Torta" by MALDI-TOF MS and pheS gene Analyses. Microorganisms 2020; 8:microorganisms8020301. [PMID: 32098253 PMCID: PMC7074959 DOI: 10.3390/microorganisms8020301] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 02/13/2020] [Accepted: 02/18/2020] [Indexed: 01/02/2023] Open
Abstract
Several artisanal cheeses are elaborated in European countries, being commonly curdled with rennets of animal origin. However, in some Spanish regions some cheeses of type “Torta” are elaborated using Cynara cardunculus L. rennets. Two of these cheeses, “Torta del Casar” and “Torta de Trujillo”, are elaborated in Cáceres province with ewe’s raw milk and matured over at least 60 days without starters. In this work, we identified the lactic acid bacteria present in these cheeses using MALDI-TOF MS and pheS gene analyses, which showed they belong to the species Lactobacillus curvatus, Lactobacillus diolivorans, Lactobacillus paracasei, Lactobacillus plantarum, Lactobacillus rhamnosus, Lactococcus lactis and Leuconostoc mesenteroides. The pheS gene analysis also allowed the identification of the subspecies La. plantarum subsp. plantarum, La. paracasei subsp. paracasei and Le. mesenteroides subsp. jonggajibkimchii. Low similarity values were found in this gene for some currently accepted subspecies of Lc. lactis and for the two subspecies of La. plantarum, and values near to 100% for the subspecies of Le. mesenteroides and La. paracasei. These results, which were confirmed by the calculated ANIb and dDDH values of their whole genomes, showed the need to revise the taxonomic status of these species and their subspecies.
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Affiliation(s)
- Fernando Sánchez-Juanes
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Complejo Asistencial Universitario de Salamanca, Universidad de Salamanca, CSIC, 37007 Salamanca, Spain; (F.S.-J.); (J.M.G.-B.)
- Departamento de Bioquímica y Biología Molecular, Universidad de Salamanca, 37007 Salamanca, Spain
| | - Vanessa Teixeira-Martín
- Departamento de Microbiología y Genética and Instituto Hispanoluso de Investigaciones Agrarias (CIALE), Universidad de Salamanca, Edificio Departamental de Biología, Lab 209. Av. Doctores de la Reina S/N, 37007 Salamanca, Spain;
| | - José Manuel González-Buitrago
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Complejo Asistencial Universitario de Salamanca, Universidad de Salamanca, CSIC, 37007 Salamanca, Spain; (F.S.-J.); (J.M.G.-B.)
- Departamento de Bioquímica y Biología Molecular, Universidad de Salamanca, 37007 Salamanca, Spain
| | - Encarna Velázquez
- Departamento de Microbiología y Genética and Instituto Hispanoluso de Investigaciones Agrarias (CIALE), Universidad de Salamanca, Edificio Departamental de Biología, Lab 209. Av. Doctores de la Reina S/N, 37007 Salamanca, Spain;
- Unidad Asociada Grupo de Interacción Planta-Microorganismo (Universidad de Salamanca-IRNASA-CSIC), 37007 Salamanca, Spain
- Correspondence: (E.V.); (J.D.F.-F.); Tel.: +34-923-294532 (E.V. & J.D.F.-F.)
| | - José David Flores-Félix
- Departamento de Microbiología y Genética and Instituto Hispanoluso de Investigaciones Agrarias (CIALE), Universidad de Salamanca, Edificio Departamental de Biología, Lab 209. Av. Doctores de la Reina S/N, 37007 Salamanca, Spain;
- Correspondence: (E.V.); (J.D.F.-F.); Tel.: +34-923-294532 (E.V. & J.D.F.-F.)
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