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Brandolini M, Grumiro L, Farabegoli P, Dirani G, Zannoli S, Zaghi I, Guerra M, Taddei F, Gatti G, Marzucco A, Montanari MS, De Pascali AM, Semprini S, Cricca M, Sambri V. Evaluation of a rapid Loop Mediated Isothermal Amplification (LAMP) test for the laboratory diagnosis of sexually transmitted infections. PLoS One 2024; 19:e0298398. [PMID: 38512825 PMCID: PMC10956856 DOI: 10.1371/journal.pone.0298398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 01/25/2024] [Indexed: 03/23/2024] Open
Abstract
Sexually transmitted infections (STIs) have seen a considerable increase in the last years and given the health burden they may represent from both a personal and community perspective, they require surveillance and prevention programmes based on a timely and decentralized diagnosis. In this context, user-friendly rapid molecular tests may represent a good trade-off between diagnostic accuracy, accessibility and affordability. In this study we evaluated the diagnostic performance of a new real-time LAMP (Loop Mediated Isothermal Amplification) method for the rapid detection and differentiation of 7 major sexually transmissible pathogens by analysing real clinical samples (genital and extra-genital matrices) from individuals with suspected STIs. The assay showed good overall diagnostic performances in terms of sensitivity, specificity and concordance with a gold-standard PCR-based molecular method. This assay, not requiring specialised laboratory technicians or expensive instrumentation, but nonetheless capable of guaranteeing accurate results, is within the reach of outpatient settings, obstetrics, and gynaecology clinic, hence ensuring on-field access to early diagnosis.
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Affiliation(s)
- Martina Brandolini
- Unit of Microbiology, The Greater Romagna Area Hub Laboratory, Cesena, Italy
- Department Medical and Surgical Sciences (DIMEC)—Alma Mater Studiorum, University of Bologna, Bologna, Italy
| | - Laura Grumiro
- Unit of Microbiology, The Greater Romagna Area Hub Laboratory, Cesena, Italy
- Department Medical and Surgical Sciences (DIMEC)—Alma Mater Studiorum, University of Bologna, Bologna, Italy
| | - Patrizia Farabegoli
- Unit of Microbiology, The Greater Romagna Area Hub Laboratory, Cesena, Italy
| | - Giorgio Dirani
- Unit of Microbiology, The Greater Romagna Area Hub Laboratory, Cesena, Italy
| | - Silvia Zannoli
- Unit of Microbiology, The Greater Romagna Area Hub Laboratory, Cesena, Italy
| | - Irene Zaghi
- Unit of Microbiology, The Greater Romagna Area Hub Laboratory, Cesena, Italy
- Unit of Infectious Diseases, Santa Maria delle Croci Hospital, Ravenna, Italy
| | - Massimiliano Guerra
- Unit of Microbiology, The Greater Romagna Area Hub Laboratory, Cesena, Italy
| | - Francesca Taddei
- Unit of Microbiology, The Greater Romagna Area Hub Laboratory, Cesena, Italy
- Department Medical and Surgical Sciences (DIMEC)—Alma Mater Studiorum, University of Bologna, Bologna, Italy
| | - Giulia Gatti
- Unit of Microbiology, The Greater Romagna Area Hub Laboratory, Cesena, Italy
| | - Anna Marzucco
- Unit of Microbiology, The Greater Romagna Area Hub Laboratory, Cesena, Italy
| | | | - Alessandra Mistral De Pascali
- Unit of Microbiology, The Greater Romagna Area Hub Laboratory, Cesena, Italy
- Department Medical and Surgical Sciences (DIMEC)—Alma Mater Studiorum, University of Bologna, Bologna, Italy
| | - Simona Semprini
- Unit of Microbiology, The Greater Romagna Area Hub Laboratory, Cesena, Italy
| | - Monica Cricca
- Unit of Microbiology, The Greater Romagna Area Hub Laboratory, Cesena, Italy
- Department Medical and Surgical Sciences (DIMEC)—Alma Mater Studiorum, University of Bologna, Bologna, Italy
| | - Vittorio Sambri
- Unit of Microbiology, The Greater Romagna Area Hub Laboratory, Cesena, Italy
- Department Medical and Surgical Sciences (DIMEC)—Alma Mater Studiorum, University of Bologna, Bologna, Italy
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Marzucco A, Gatti G, Montanari MS, Fantini M, Colosimo C, Tamburini MV, Arfilli V, Morotti M, Schiavone P, Congestrì F, Manera M, Denicolò A, Brandolini M, Taddei F, Grumiro L, Zannoli S, Dirani G, De Pascali AM, Sambri V, Cricca M. Evaluation of Biofilm Production and Antifungal Susceptibility to Fluconazole in Clinical Isolates of Candida spp. in Both Planktonic and Biofilm Form. Microorganisms 2024; 12:153. [PMID: 38257980 PMCID: PMC10820201 DOI: 10.3390/microorganisms12010153] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Revised: 01/05/2024] [Accepted: 01/10/2024] [Indexed: 01/24/2024] Open
Abstract
Candida spp. are an important opportunistic pathogen that can represent a possible cause of severe infections, especially in immunocompromised individuals. The clinical impact of Candida spp. depends, in part, on the ability to form biofilms, communities of nestled cells into the extracellular matrix. In this study, we compared the biofilm formation ability of 83 strains of Candida spp. isolated from blood cultures and other materials, such as respiratory samples, urine, and exudate, and their sensitivity to fluconazole (FLZ). Strains were divided into tertiles to establish cut-offs to classify isolates as low, moderate, or high biofilm producers (<0.26, 0.266-0.839, >0.839) and biofilms with low, moderate, or high metabolic activity (<0.053, 0.053-0.183, >0.183). A non-linear relationship between biofilm production and metabolic activity was found in C. glabrata and C. tropicalis. In addition, the increase in minimum biofilm eradication concentrations (MBEC50) compared to the Minor Inhibitory Concentration (PMIC) of the planktonic form in Candida spp. confirms the role of biofilm in the induction of resistance to FLZ.
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Affiliation(s)
- Anna Marzucco
- Unit of Microbiology, The Great Romagna Hub Laboratory, 47522 Pievesestina, Italy; (M.S.M.); (M.V.T.); (V.A.); (M.M.); (P.S.); (F.C.); (M.M.); (A.D.); (F.T.); (L.G.); (S.Z.); (G.D.); (V.S.); (M.C.)
- Department of Medical and Surgical Sciences—DIMEC, Alma Mater Studiorum—University of Bologna, 40126 Bologna, Italy; (C.C.); (M.B.); (A.M.D.P.)
| | - Giulia Gatti
- DIN—Department of Industrial Engineering, Alma Mater Studiorum—University of Bologna, 40126 Bologna, Italy;
| | - Maria Sofia Montanari
- Unit of Microbiology, The Great Romagna Hub Laboratory, 47522 Pievesestina, Italy; (M.S.M.); (M.V.T.); (V.A.); (M.M.); (P.S.); (F.C.); (M.M.); (A.D.); (F.T.); (L.G.); (S.Z.); (G.D.); (V.S.); (M.C.)
| | - Michela Fantini
- Health Services Research, Evaluation and Policy Unit, AUSL Romagna, 42123 Rimini, Italy;
| | - Claudia Colosimo
- Department of Medical and Surgical Sciences—DIMEC, Alma Mater Studiorum—University of Bologna, 40126 Bologna, Italy; (C.C.); (M.B.); (A.M.D.P.)
| | - Maria Vittoria Tamburini
- Unit of Microbiology, The Great Romagna Hub Laboratory, 47522 Pievesestina, Italy; (M.S.M.); (M.V.T.); (V.A.); (M.M.); (P.S.); (F.C.); (M.M.); (A.D.); (F.T.); (L.G.); (S.Z.); (G.D.); (V.S.); (M.C.)
| | - Valentina Arfilli
- Unit of Microbiology, The Great Romagna Hub Laboratory, 47522 Pievesestina, Italy; (M.S.M.); (M.V.T.); (V.A.); (M.M.); (P.S.); (F.C.); (M.M.); (A.D.); (F.T.); (L.G.); (S.Z.); (G.D.); (V.S.); (M.C.)
| | - Manuela Morotti
- Unit of Microbiology, The Great Romagna Hub Laboratory, 47522 Pievesestina, Italy; (M.S.M.); (M.V.T.); (V.A.); (M.M.); (P.S.); (F.C.); (M.M.); (A.D.); (F.T.); (L.G.); (S.Z.); (G.D.); (V.S.); (M.C.)
| | - Pasqualina Schiavone
- Unit of Microbiology, The Great Romagna Hub Laboratory, 47522 Pievesestina, Italy; (M.S.M.); (M.V.T.); (V.A.); (M.M.); (P.S.); (F.C.); (M.M.); (A.D.); (F.T.); (L.G.); (S.Z.); (G.D.); (V.S.); (M.C.)
| | - Francesco Congestrì
- Unit of Microbiology, The Great Romagna Hub Laboratory, 47522 Pievesestina, Italy; (M.S.M.); (M.V.T.); (V.A.); (M.M.); (P.S.); (F.C.); (M.M.); (A.D.); (F.T.); (L.G.); (S.Z.); (G.D.); (V.S.); (M.C.)
| | - Martina Manera
- Unit of Microbiology, The Great Romagna Hub Laboratory, 47522 Pievesestina, Italy; (M.S.M.); (M.V.T.); (V.A.); (M.M.); (P.S.); (F.C.); (M.M.); (A.D.); (F.T.); (L.G.); (S.Z.); (G.D.); (V.S.); (M.C.)
| | - Agnese Denicolò
- Unit of Microbiology, The Great Romagna Hub Laboratory, 47522 Pievesestina, Italy; (M.S.M.); (M.V.T.); (V.A.); (M.M.); (P.S.); (F.C.); (M.M.); (A.D.); (F.T.); (L.G.); (S.Z.); (G.D.); (V.S.); (M.C.)
| | - Martina Brandolini
- Department of Medical and Surgical Sciences—DIMEC, Alma Mater Studiorum—University of Bologna, 40126 Bologna, Italy; (C.C.); (M.B.); (A.M.D.P.)
| | - Francesca Taddei
- Unit of Microbiology, The Great Romagna Hub Laboratory, 47522 Pievesestina, Italy; (M.S.M.); (M.V.T.); (V.A.); (M.M.); (P.S.); (F.C.); (M.M.); (A.D.); (F.T.); (L.G.); (S.Z.); (G.D.); (V.S.); (M.C.)
| | - Laura Grumiro
- Unit of Microbiology, The Great Romagna Hub Laboratory, 47522 Pievesestina, Italy; (M.S.M.); (M.V.T.); (V.A.); (M.M.); (P.S.); (F.C.); (M.M.); (A.D.); (F.T.); (L.G.); (S.Z.); (G.D.); (V.S.); (M.C.)
| | - Silvia Zannoli
- Unit of Microbiology, The Great Romagna Hub Laboratory, 47522 Pievesestina, Italy; (M.S.M.); (M.V.T.); (V.A.); (M.M.); (P.S.); (F.C.); (M.M.); (A.D.); (F.T.); (L.G.); (S.Z.); (G.D.); (V.S.); (M.C.)
| | - Giorgio Dirani
- Unit of Microbiology, The Great Romagna Hub Laboratory, 47522 Pievesestina, Italy; (M.S.M.); (M.V.T.); (V.A.); (M.M.); (P.S.); (F.C.); (M.M.); (A.D.); (F.T.); (L.G.); (S.Z.); (G.D.); (V.S.); (M.C.)
| | - Alessandra Mistral De Pascali
- Department of Medical and Surgical Sciences—DIMEC, Alma Mater Studiorum—University of Bologna, 40126 Bologna, Italy; (C.C.); (M.B.); (A.M.D.P.)
| | - Vittorio Sambri
- Unit of Microbiology, The Great Romagna Hub Laboratory, 47522 Pievesestina, Italy; (M.S.M.); (M.V.T.); (V.A.); (M.M.); (P.S.); (F.C.); (M.M.); (A.D.); (F.T.); (L.G.); (S.Z.); (G.D.); (V.S.); (M.C.)
- Department of Medical and Surgical Sciences—DIMEC, Alma Mater Studiorum—University of Bologna, 40126 Bologna, Italy; (C.C.); (M.B.); (A.M.D.P.)
| | - Monica Cricca
- Unit of Microbiology, The Great Romagna Hub Laboratory, 47522 Pievesestina, Italy; (M.S.M.); (M.V.T.); (V.A.); (M.M.); (P.S.); (F.C.); (M.M.); (A.D.); (F.T.); (L.G.); (S.Z.); (G.D.); (V.S.); (M.C.)
- Department of Medical and Surgical Sciences—DIMEC, Alma Mater Studiorum—University of Bologna, 40126 Bologna, Italy; (C.C.); (M.B.); (A.M.D.P.)
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Gatti G, Brandolini M, Mancini A, Taddei F, Zannoli S, Dirani G, Manera M, Arfilli V, Denicolò A, Marzucco A, Montanari MS, Zaghi I, Guerra M, Tennina R, Marino MM, Grumiro L, Cricca M, Sambri V. Genomic and Temporal Analysis of Deletions Correlated to qRT-PCR Dropout in N Gene in Alpha, Delta and Omicron Variants. Viruses 2023; 15:1630. [PMID: 37631974 PMCID: PMC10458892 DOI: 10.3390/v15081630] [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: 07/05/2023] [Revised: 07/21/2023] [Accepted: 07/24/2023] [Indexed: 08/27/2023] Open
Abstract
Since the first SARS-CoV-2 outbreak, mutations such as single nucleotide polymorphisms (SNPs) and insertion/deletions (INDELs) have changed and characterized the viral genome sequence, structure and protein folding leading to the onset of new variants. The presence of those alterations challenges not only the clinical field but also the diagnostic demand due to failures in gene detection or incompleteness of polymerase chain reaction (PCR) results. In particular, the analysis of understudied genes such as N and the investigation through whole-genome next generation sequencing (WG-NGS) of regions more prone to mutate can help in the identification of new or reacquired mutations, with the aim of designing robust and long-lasting primers. In 48 samples of SARS-CoV-2 (including Alpha, Delta and Omicron variants), a lack of N gene amplification was observed in the genomes analyzed through WG-NGS. Three gene regions were detected hosting the highest number of SNPs and INDELs. In several cases, the latter can interfere deeply with both the sensitivity of diagnostic methodologies and the final protein folding. The monitoring over time of the viral evolution and the reacquisition among different variants of the same mutations or different alterations within the same genomic positions can be relevant to avoid unnecessary consumption of resources.
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Affiliation(s)
- Giulia Gatti
- Department of Medical and Surgical Sciences (DIMEC)—Alma Mater Studiorum, University of Bologna, 40138 Bologna, Italy; (G.G.); (M.B.); (M.C.)
| | - Martina Brandolini
- Department of Medical and Surgical Sciences (DIMEC)—Alma Mater Studiorum, University of Bologna, 40138 Bologna, Italy; (G.G.); (M.B.); (M.C.)
| | - Andrea Mancini
- Unit of Microbiology, The Greater Romagna Area Hub Laboratory, 47522 Cesena, Italy; (A.M.); (F.T.); (S.Z.); (G.D.); (M.M.); (V.A.); (A.D.); (A.M.); (M.S.M.); (I.Z.); (M.G.); (L.G.)
| | - Francesca Taddei
- Unit of Microbiology, The Greater Romagna Area Hub Laboratory, 47522 Cesena, Italy; (A.M.); (F.T.); (S.Z.); (G.D.); (M.M.); (V.A.); (A.D.); (A.M.); (M.S.M.); (I.Z.); (M.G.); (L.G.)
| | - Silvia Zannoli
- Unit of Microbiology, The Greater Romagna Area Hub Laboratory, 47522 Cesena, Italy; (A.M.); (F.T.); (S.Z.); (G.D.); (M.M.); (V.A.); (A.D.); (A.M.); (M.S.M.); (I.Z.); (M.G.); (L.G.)
| | - Giorgio Dirani
- Unit of Microbiology, The Greater Romagna Area Hub Laboratory, 47522 Cesena, Italy; (A.M.); (F.T.); (S.Z.); (G.D.); (M.M.); (V.A.); (A.D.); (A.M.); (M.S.M.); (I.Z.); (M.G.); (L.G.)
| | - Martina Manera
- Unit of Microbiology, The Greater Romagna Area Hub Laboratory, 47522 Cesena, Italy; (A.M.); (F.T.); (S.Z.); (G.D.); (M.M.); (V.A.); (A.D.); (A.M.); (M.S.M.); (I.Z.); (M.G.); (L.G.)
| | - Valentina Arfilli
- Unit of Microbiology, The Greater Romagna Area Hub Laboratory, 47522 Cesena, Italy; (A.M.); (F.T.); (S.Z.); (G.D.); (M.M.); (V.A.); (A.D.); (A.M.); (M.S.M.); (I.Z.); (M.G.); (L.G.)
| | - Agnese Denicolò
- Unit of Microbiology, The Greater Romagna Area Hub Laboratory, 47522 Cesena, Italy; (A.M.); (F.T.); (S.Z.); (G.D.); (M.M.); (V.A.); (A.D.); (A.M.); (M.S.M.); (I.Z.); (M.G.); (L.G.)
| | - Anna Marzucco
- Unit of Microbiology, The Greater Romagna Area Hub Laboratory, 47522 Cesena, Italy; (A.M.); (F.T.); (S.Z.); (G.D.); (M.M.); (V.A.); (A.D.); (A.M.); (M.S.M.); (I.Z.); (M.G.); (L.G.)
| | - Maria Sofia Montanari
- Unit of Microbiology, The Greater Romagna Area Hub Laboratory, 47522 Cesena, Italy; (A.M.); (F.T.); (S.Z.); (G.D.); (M.M.); (V.A.); (A.D.); (A.M.); (M.S.M.); (I.Z.); (M.G.); (L.G.)
| | - Irene Zaghi
- Unit of Microbiology, The Greater Romagna Area Hub Laboratory, 47522 Cesena, Italy; (A.M.); (F.T.); (S.Z.); (G.D.); (M.M.); (V.A.); (A.D.); (A.M.); (M.S.M.); (I.Z.); (M.G.); (L.G.)
| | - Massimiliano Guerra
- Unit of Microbiology, The Greater Romagna Area Hub Laboratory, 47522 Cesena, Italy; (A.M.); (F.T.); (S.Z.); (G.D.); (M.M.); (V.A.); (A.D.); (A.M.); (M.S.M.); (I.Z.); (M.G.); (L.G.)
| | - Rita Tennina
- Unit of Laboratory Medicine—Local Health Authority 1 Complex Operative Unit, 67051 L’Aquila, Italy
| | - Maria Michela Marino
- Unit of Microbiology, The Greater Romagna Area Hub Laboratory, 47522 Cesena, Italy; (A.M.); (F.T.); (S.Z.); (G.D.); (M.M.); (V.A.); (A.D.); (A.M.); (M.S.M.); (I.Z.); (M.G.); (L.G.)
| | - Laura Grumiro
- Unit of Microbiology, The Greater Romagna Area Hub Laboratory, 47522 Cesena, Italy; (A.M.); (F.T.); (S.Z.); (G.D.); (M.M.); (V.A.); (A.D.); (A.M.); (M.S.M.); (I.Z.); (M.G.); (L.G.)
| | - Monica Cricca
- Department of Medical and Surgical Sciences (DIMEC)—Alma Mater Studiorum, University of Bologna, 40138 Bologna, Italy; (G.G.); (M.B.); (M.C.)
- Unit of Microbiology, The Greater Romagna Area Hub Laboratory, 47522 Cesena, Italy; (A.M.); (F.T.); (S.Z.); (G.D.); (M.M.); (V.A.); (A.D.); (A.M.); (M.S.M.); (I.Z.); (M.G.); (L.G.)
| | - Vittorio Sambri
- Department of Medical and Surgical Sciences (DIMEC)—Alma Mater Studiorum, University of Bologna, 40138 Bologna, Italy; (G.G.); (M.B.); (M.C.)
- Unit of Microbiology, The Greater Romagna Area Hub Laboratory, 47522 Cesena, Italy; (A.M.); (F.T.); (S.Z.); (G.D.); (M.M.); (V.A.); (A.D.); (A.M.); (M.S.M.); (I.Z.); (M.G.); (L.G.)
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