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Tchoupou Saha OLF, Dubourg G, Yacouba A, Tola R, Raoult D, Lagier JC. Description of nasopharyngeal bacterial pathogens associated with different SARS-CoV-2 variants. Microb Pathog 2024; 188:106561. [PMID: 38307371 DOI: 10.1016/j.micpath.2024.106561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 01/16/2024] [Accepted: 01/25/2024] [Indexed: 02/04/2024]
Abstract
The emergence of the coronavirus pandemic facilitated the acquisition of mutations in the SARS-CoV-2 genome, resulting in the appearance of new variants over the past three years. We previously identified several taxa associated with the clinical outcome of COVID-19 disease in a retrospective study involving 120 patients (infected patients and negative subjects). However, little is known about whether the different variants could influence variations in the composition of the nasopharyngeal microbiota. In this study, we used multiplex pathogen-specific PCR to analyse the presence of nasopharyngeal bacterial pathogens from 400 SARS-CoV-2 positive patients (equally distributed in the four SARS-CoV-2 variants studied: B.1.1.7 (Alpha), B.1 0.617.2 (Delta), B.1.160 (Marseille-4), and B.1.1.529 (omicron)). We then compared them to 400 patients who tested negative for all respiratory viruses tested in this study, including SARS-CoV-2. We first observed an enrichment of Staphylococcus aureus (P ≤ .05) and Corynebacterium propinquum (P ≤ .05) in COVID-19-positive patients, regardless of the variant, compared to negative subjects. We specifically highlighted a significantly higher frequency of S. aureus (P ≤ .0001), C. propinquum (P ≤ .0001), and Klebsiella pneumoniae (P ≤ .0001), in patients infected with the omicron variant, whereas that of Haemophilus influenzae was higher in patients infected with Marseille-4 (P ≤ .001) and Alpha (P ≤ .01) variants. Our results suggest that the nasopharyngeal bacterial pathogens have their own specificity according to the SARS-CoV-2 variant and independently of the season. Additional studies are needed to determine the role of these pathogens in the evolution of the clinical outcome of patients.
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Affiliation(s)
- Ornella La Fortune Tchoupou Saha
- Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), AP-HM, MEPHI, Marseille, France; IHU Méditerranée Infection, Marseille, France
| | - Grégory Dubourg
- Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), AP-HM, MEPHI, Marseille, France; IHU Méditerranée Infection, Marseille, France.
| | - Abdourahamane Yacouba
- Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), AP-HM, MEPHI, Marseille, France; IHU Méditerranée Infection, Marseille, France
| | | | - Didier Raoult
- Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), AP-HM, MEPHI, Marseille, France; IHU Méditerranée Infection, Marseille, France
| | - Jean-Christophe Lagier
- Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), AP-HM, MEPHI, Marseille, France; IHU Méditerranée Infection, Marseille, France.
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Yacouba A, Sissoko S, Saha OLFT, Haddad G, Dubourg G, Gouriet F, Alou MT, Alibar S, Million M, Lagier JC, Raoult D, Fenollar F, Fournier PE, Lo CI. Description of Acinetobacter ihumii sp. nov., Microbacterium ihumii sp. nov., and Gulosibacter massiliensis sp. nov., three new bacteria isolated from human blood. FEMS Microbiol Lett 2022; 369:6572836. [PMID: 35460225 PMCID: PMC9126734 DOI: 10.1093/femsle/fnac038] [Citation(s) in RCA: 2] [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: 02/11/2022] [Revised: 03/16/2022] [Accepted: 04/21/2022] [Indexed: 11/19/2022] Open
Abstract
Blood is precious tissue that is normally sterile. With the aim of diagnosing the cause
of bacteremia, three bacterial strains were isolated from three different individuals.
Strains Marseille-P7157T and Marseille-Q2854T are Gram-stain
positive, non-spore-forming rod-shaped bacteria, while strain Marseille-P8049T
is a Gram-stain negative, motile, non-spore-forming and rod-shaped bacterium. The major
fatty acids found (>30%) were hexadecanoic acid for strain Marseille-P8049T
and 12-methyl tetradecanoic acid for both strains Marseille-P7157T and
Marseille-Q2854T. The 16S rRNA gene sequence analysis shows that strains
Marseille-P8049 and Marseille-Q2854T have sequence similarity of 96.8%, 99.04%,
and 98.3% with Acinetobacter ursingii strain LUH3792 (NR_025392.1),
Gulosibacter faecalis strain B187 (NR_041812.1), and Schaalia
canis strain CCUG 41706 (NR_025366.1), respectively. In addition, strains
Marseille-Q2854T, Marseille-P8049T and Marseille-P7157T
shared with their closely related species cited above the following DDH values: 19.5%,
24.4%, and 20.2%, respectively. Based on these phenotypic and genomic findings, we
consider that strains Marseille-P8049T (= CSUR P8049 = CECT 30350),
Marseille-P2854T ( = CSUR Q2854 = CECT 30120) and Marseille-P7157T
( = CSUR P7157 = CECT 30048) are new bacterial species, for which the names
Acinetobacter ihumii sp. nov., Microbacterium ihumii
sp. nov., and Gulosibacter massiliensis sp. nov., are proposed.
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Affiliation(s)
- Abdourahamane Yacouba
- Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France.,IHU-Méditerranée Infection, Marseille, France.,Université Abdou Moumouni, Niamey, Niger
| | - Sibiri Sissoko
- Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | | | - Gabriel Haddad
- Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - Grégory Dubourg
- Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - Frédérique Gouriet
- Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - Maryam Tidjani Alou
- Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - Stéphane Alibar
- Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - Matthieu Million
- Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - Jean-Christophe Lagier
- Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - Didier Raoult
- Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France.,IHU-Méditerranée Infection, Marseille, France.,Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - Florence Fenollar
- IHU-Méditerranée Infection, Marseille, France.,Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - Pierre-Edouard Fournier
- IHU-Méditerranée Infection, Marseille, France.,Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - Cheikh Ibrahima Lo
- IHU-Méditerranée Infection, Marseille, France.,Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France
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