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Antonelli A, Coppi M, Bonaiuto C, Giovacchini N, Vaggelli G, Farese A, Pollini S, Rossolini GM. Novel resistance ICEs carrying the blaFIM-1 metallo-β-lactamase gene from an ST235 Pseudomonas aeruginosa sublineage. Antimicrob Agents Chemother 2024; 68:e0120523. [PMID: 38206043 PMCID: PMC10848763 DOI: 10.1128/aac.01205-23] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 11/29/2023] [Indexed: 01/12/2024] Open
Abstract
FIM-1 is an acquired metallo-β-lactamase identified in a multidrug-resistant Pseudomonas aeruginosa (index strain FI-14/157) of clinical origin isolated in 2007 in Florence, Italy. Here we report on a second case of infection by FIM-1-positive P. aeruginosa (FI-17645), which occurred in 2020 in the same hospital. Both FIM-1-positive strains exhibited resistance to all anti-Pseudomonas antibiotics except colistin and cefiderocol. Comparative genomic characterization revealed that the two FIM-positive strains were closely related [core genome difference, 16 single nucleotide polymorphisms (SNPs)], suggesting a local circulation of similar strains. In the FI-14/157 index strain, the blaFIM-1 gene was associated with an ISCR19-like element that likely contributed to its capture downstream an integron platform inserted aboard a Tn21-like transposon, named Tn7703.1, which was associated with a large integrative and conjugative element (ICE) named ICE7705.1, integrated into an att site located within the 3'-end of tRNAGly CCC gene of the P. aeruginosa chromosome. In strain FI-17645, blaFIM-1 was associated with a closely related ICE, named ICE7705.2, integrated in the same chromosomal site. Similar ICE platforms, lacking the blaFIM-1-containing region, were detected in other ST235 P. aeruginosa strains from different geographic areas, suggesting a common ancestry and underscoring the role of these elements in the dissemination of resistance genes in P. aeruginosa. Sequence database mining revealed two draft P. aeruginosa genomes, one from Italy and one from the USA (both isolated in 2012), including a contig with blaFIM-1, suggesting that this resistance gene could have a broader distribution than originally anticipated.
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Affiliation(s)
- Alberto Antonelli
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
- Microbiology and Virology Unit, Florence Careggi University Hospital, Florence, Italy
| | - Marco Coppi
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
- Microbiology and Virology Unit, Florence Careggi University Hospital, Florence, Italy
| | - Chiara Bonaiuto
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
- Microbiology and Virology Unit, Florence Careggi University Hospital, Florence, Italy
| | - Nicla Giovacchini
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Guendalina Vaggelli
- Microbiology and Virology Unit, Florence Careggi University Hospital, Florence, Italy
| | - Alberto Farese
- Infectious and Tropical Diseases Unit, Florence Careggi University Hospital, Florence, Italy
| | - Simona Pollini
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
- Microbiology and Virology Unit, Florence Careggi University Hospital, Florence, Italy
| | - Gian Maria Rossolini
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
- Microbiology and Virology Unit, Florence Careggi University Hospital, Florence, Italy
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Giovacchini N, Antonelli A, Taddei E, Giani T, Rossolini GM. Evaluation of RESIST ACINETO immunochromatographic assay from positive blood cultures. J Antimicrob Chemother 2024; 79:469-471. [PMID: 38091586 DOI: 10.1093/jac/dkad380] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2024] Open
Affiliation(s)
- Nicla Giovacchini
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Alberto Antonelli
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
- Microbiology and Virology Unit, Careggi University Hospital, Florence, Italy
| | - Elia Taddei
- Microbiology and Virology Unit, Careggi University Hospital, Florence, Italy
| | - Tommaso Giani
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
- Microbiology and Virology Unit, Careggi University Hospital, Florence, Italy
| | - Gian Maria Rossolini
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
- Microbiology and Virology Unit, Careggi University Hospital, Florence, Italy
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Mazzoni A, Vanni A, Spinicci M, Capone M, Lamacchia G, Salvati L, Coppi M, Antonelli A, Carnasciali A, Farahvachi P, Giovacchini N, Aiezza N, Malentacchi F, Zammarchi L, Liotta F, Rossolini GM, Bartoloni A, Cosmi L, Maggi L, Annunziato F. SARS-CoV-2 Spike-Specific CD4+ T Cell Response Is Conserved Against Variants of Concern, Including Omicron. Front Immunol 2022; 13:801431. [PMID: 35154116 PMCID: PMC8826050 DOI: 10.3389/fimmu.2022.801431] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [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: 10/25/2021] [Accepted: 01/10/2022] [Indexed: 12/16/2022] Open
Abstract
Although accumulating data have investigated the effect of SARS-CoV-2 mutations on antibody neutralizing activity, less is known about T cell immunity. In this work, we found that the ancestral (Wuhan strain) Spike protein can efficaciously reactivate CD4+ T cell memory in subjects with previous Alpha variant infection. This finding has practical implications, as in many countries only one vaccine dose is currently administered to individuals with previous COVID-19, independently of which SARS-CoV-2 variant was responsible of the infection. We also found that only a minority of Spike-specific CD4+ T cells targets regions mutated in Alpha, Beta and Delta variants, both after natural infection and vaccination. Finally, we found that the vast majority of Spike-specific CD4+ T cell memory response induced by natural infection or mRNA vaccination is conserved also against Omicron variant. This is of importance, as this newly emerged strain is responsible for a sudden rise in COVID-19 cases worldwide due to its increased transmissibility and ability to evade antibody neutralization. Collectively, these observations suggest that most of the memory CD4+ T cell response is conserved against SARS-CoV-2 variants of concern, providing an efficacious line of defense that can protect from the development of severe forms of COVID-19.
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Affiliation(s)
- Alessio Mazzoni
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Anna Vanni
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Michele Spinicci
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy.,Infectious and Tropical Disease Unit, Careggi University Hospital, Florence, Italy
| | - Manuela Capone
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Giulia Lamacchia
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Lorenzo Salvati
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Marco Coppi
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Alberto Antonelli
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Alberto Carnasciali
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Parham Farahvachi
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Nicla Giovacchini
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Noemi Aiezza
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | | | - Lorenzo Zammarchi
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy.,Infectious and Tropical Disease Unit, Careggi University Hospital, Florence, Italy
| | - Francesco Liotta
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy.,Immunology and Cell Therapy Unit, Careggi University Hospital, Florence, Italy.,Flow Cytometry Diagnostic Center and Immunotherapy, Careggi University Hospital, Florence, Italy
| | - Gian Maria Rossolini
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy.,Microbiology and Virology Unit, Careggi University Hospital, Florence, Italy
| | - Alessandro Bartoloni
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy.,Infectious and Tropical Disease Unit, Careggi University Hospital, Florence, Italy
| | - Lorenzo Cosmi
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy.,Immunology and Cell Therapy Unit, Careggi University Hospital, Florence, Italy
| | - Laura Maggi
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Francesco Annunziato
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy.,Flow Cytometry Diagnostic Center and Immunotherapy, Careggi University Hospital, Florence, Italy
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Spinicci M, Mazzoni A, Borchi B, Graziani L, Mazzetti M, Bartalesi F, Botta A, Tilli M, Pieralli F, Coppi M, Giovacchini N, Colao MG, Saccardi R, Rossolini GM, Annunziato F, Bartoloni A. AIDS patient with severe T cell depletion achieved control but not clearance of SARS-CoV-2 infection. Eur J Immunol 2021; 52:352-355. [PMID: 34822185 PMCID: PMC9015404 DOI: 10.1002/eji.202149574] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [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: 08/12/2021] [Revised: 10/21/2021] [Accepted: 11/22/2021] [Indexed: 11/10/2022]
Abstract
A late presenter AIDS patient with severe T cell depletion presented non-severe COVID-19 symptoms, with prolonged viral shedding. Our case report supports the hypothesis that an effective T cell response may be dispensable for the control of COVID-19 progression to severe forms, while it may be necessary for SARS-CoV-2 clearance.
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Affiliation(s)
- Michele Spinicci
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy.,Infectious and Tropical Diseases Unit, Careggi University Hospital, Florence, Italy
| | - Alessio Mazzoni
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Beatrice Borchi
- Infectious and Tropical Diseases Unit, Careggi University Hospital, Florence, Italy
| | - Lucia Graziani
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Marcello Mazzetti
- Infectious and Tropical Diseases Unit, Careggi University Hospital, Florence, Italy
| | - Filippo Bartalesi
- Infectious and Tropical Diseases Unit, Careggi University Hospital, Florence, Italy
| | - Annarita Botta
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Marta Tilli
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Filippo Pieralli
- Intermediate Care Unit, Careggi University Hospital, Florence, Italy
| | - Marco Coppi
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Nicla Giovacchini
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Maria Grazia Colao
- Microbiology and Virology Unit, Careggi University Hospital, Florence, Italy
| | - Riccardo Saccardi
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy.,Department of Cellular Therapies and Transfusion Medicine, Careggi University Hospital, Florence, Italy
| | - Gian Maria Rossolini
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy.,Microbiology and Virology Unit, Careggi University Hospital, Florence, Italy
| | - Francesco Annunziato
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy.,Flow Cytometry Diagnostic Center and Immunotherapy (CDCI), Careggi University Hospital, Florence, Italy
| | - Alessandro Bartoloni
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy.,Infectious and Tropical Diseases Unit, Careggi University Hospital, Florence, Italy
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Giovacchini N, Coppi M, Aiezza N, Baccani I, Malentacchi F, Pollini S, Antonelli A, Rossolini GM. Rapid screening for SARS-CoV-2 VOC-Alpha (202012/01, B.1.1.7) using the Allplex™ SARS-CoV-2/FluA/FluB/RSV Assay. Int J Infect Dis 2021; 113:207-209. [PMID: 34628023 PMCID: PMC8496923 DOI: 10.1016/j.ijid.2021.10.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 09/01/2021] [Accepted: 10/02/2021] [Indexed: 11/26/2022] Open
Abstract
Background The emergence of SARS-CoV-2 variants of concern (VOCs) for increased transmissibility and being potentially capable of immune-escape mandates for epidemiological surveillance. Genomic alterations present in VOCs can affect the results of RT-qPCR assays for routine diagnostic purposes, leading to peculiar profiles that can be used for rapid screening of variants. This study reports a peculiar profile observed with the Allplex™ SARS-CoV-2/FluA/FluB/RSV assay and VOC-Alpha (202012/01, lineage B.1.1.7, also named VOC-UK), which was the first identified SARS-CoV-2 VOC. Methods Samples were analyzed by two RT-qPCR assays: the Allplex™ SARS-CoV-2/FluA/FluB/RSV assay (ASFR, Seegene Technologies Inc; Seoul, South Korea) and the TaqPath COVID-19 RT-PCR (Thermo Fisher Scientific, USA). Definition of the SARS-CoV-2 variant was carried out by Sanger sequencing of the relevant S-gene regions and, in some cases, by whole genome sequencing (WGS) using the ARTIC-nCoV workflow on a MiniION (Oxford Nanopore Technologies, Oxford, UK) or a Illumina MiSeq platform (San Diego, California, USA). Results Of the 173 SARS-CoV-2-positive specimens, all those of lineage B.1.1.7 (N=71) showed an average Cq difference between the N and S genes of +11±2 (range, +8/+15). None of the other specimens, including several different lineages (Wild-type for the analyzed regions, N=22; Gamma, N=63; Delta, N=9; B.1.258Δ, N=3; B.1.160, N=3; B.1.177.7, N=1; B.1.1.420, N=1), exhibited a similar difference in Cq values. Conclusions The peculiar pattern of delayed N gene positivity could constitute a convenient method for VOC-Alpha screening, simultaneous to viral detection, when using the Allplex™ SARS-CoV-2/FluA/FluB/RSV assay.
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Affiliation(s)
- Nicla Giovacchini
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Marco Coppi
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy; Microbiology and Virology Unit, Careggi University Hospital, Florence, Italy
| | - Noemi Aiezza
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Ilaria Baccani
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | | | - Simona Pollini
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy; Microbiology and Virology Unit, Careggi University Hospital, Florence, Italy
| | - Alberto Antonelli
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy; Microbiology and Virology Unit, Careggi University Hospital, Florence, Italy
| | - Gian Maria Rossolini
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy; Microbiology and Virology Unit, Careggi University Hospital, Florence, Italy.
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