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Diagnostics
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Molecular Diagnostics of Antimicrobial Resistance
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Molecular Diagnostics of Antimicrobial Resistance

A special issue of Diagnostics (ISSN 2075-4418). This special issue belongs to the section "Diagnostic Microbiology and Infectious Disease".

Deadline for manuscript submissions: closed (31 August 2021) | Viewed by 19062

Special Issue Editors

Prof. Dr. Mariagrazia Perilli

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Guest Editor
Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, 67100 L’Aquila, Italy
Interests: molecular and epidemiological characterization of mechanisms of resistance to antibiotics in Gram-negatove pathogens; mobile genetic elements; beta-lactamases; beta-lactamase inhibitors; mechanisms of serine- and metallo-beta-lactamases
Special Issues, Collections and Topics in MDPI journals
Dr. Alessandra Piccirilli

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Guest Editor
Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, 67100 L’Aquila, Italy
Interests: enzymes; PCR; microbiology; cloning; biochemistry; electrophoresis; SDS-PAGE; protein expression; next generation sequencing; antibiotic resistance
Special Issues, Collections and Topics in MDPI journals
Dr. Maria del Mar Tavìo-Perez

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Guest Editor
Department of Clinical Sciences, University of Las Palmas De Gran Canaria, Gran Canaria, Spain

Special Issue Information

Dear Colleagues,

Antibiotic resistance is important for the national health system both in terms of economic impact and human sufferance. Epidemiological data are of primary importance to eventually identify new emerging resistance determinants in order to adapt antibiotic usage at the local level to limit therapeutic failures. Among Gram-negative and Gram-positive bacteria, Enterobacteriaceae, Pseudomonas aeruginosa, Acinetobacter baumannii, Enterococcus spp, Staphylococcus aureus, and Streptococcus pneumonia are the main emergent pathogens. In these species, resistance may affect all major classes of antimicrobial agents such as β-lactams, fluoroquinolones, aminoglycosides, glycopeptide, etc. Many of these organism harbor antibiotic resistant genes (ARGs), eventually inserted into genetic mobile platforms (plasmids, transposons, integrons) able to move between different DNA molecules and transfer the genetic determinants in different bacteria species. Surveillance of antimicrobial resistance is critical to providing early warning of emerging problems, monitoring changing patterns of resistance, and targeting and evaluating prevention and control measures. The following topics will be considered:

- Molecular epidemiology of multidrug-resistant Gram-negative and Gram-positive bacteria;

- Diagnostics of mobile genetic elements with innovative molecular approaches;

- Role of beta-lactamases in antibiotic resistance.

Prof. Dr. Mariagrazia Perilli
Dr. Alessandra Piccirilli
Dr. Maria del Mar Tavìo-Perez
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Diagnostics is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Published Papers (3 papers)

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Research

11 pages, 258 KiB  
Article
Resistome and Virulome of Multi-Drug Resistant E. coli ST131 Isolated from Residents of Long-Term Care Facilities in the Northern Italian Region
by Sabrina Cherubini, Mariagrazia Perilli, Anna Maria Azzini, Evelina Tacconelli, Laura Maccacaro, Alda Bazaj, Laura Naso, Gianfranco Amicosante, LTCF-Veneto Working Group, Giuliana Lo Cascio and Alessandra Piccirilli
Diagnostics 2022, 12(1), 213; https://0-doi-org.brum.beds.ac.uk/10.3390/diagnostics12010213 - 16 Jan 2022
Cited by 10 | Viewed by 1826
Abstract
Long-term care facilities (LTCFs) are important reservoirs of antimicrobial-resistant (AMR) bacteria which colonize patients transferred from the hospital, or they may emerge in the facility as a result of mutation or gene transfer. In the present study, we characterized, from a molecular point [...] Read more.
Long-term care facilities (LTCFs) are important reservoirs of antimicrobial-resistant (AMR) bacteria which colonize patients transferred from the hospital, or they may emerge in the facility as a result of mutation or gene transfer. In the present study, we characterized, from a molecular point of view, 43 E. coli strains collected from residents of LTCFs in Northern Italy. The most common lineage found was ST131, followed by sporadic presence of ST12, ST69, ST48, ST95, ST410 and ST1193. All strains were incubators of several virulence factors, with iss, sat, iha and senB being found in 84%, 72%, 63% and 51% of E. coli, respectively. Thirty of the ST131 analyzed were of the O25b:H4 serotype and H30 subclone. The ST131 isolates were found to be mainly associated with IncF plasmids, CTX-M-1, CTX-M-3, CTX-M-15, CTX-M-27 and gyrA/parC/parE mutations. Metallo-β-lactamases were not found in ST131, whereas KPC-3 carbapenemase was found only in two ST131 and one ST1193. In conclusion, we confirmed the spread of extended-spectrum β-lactamase genes in E. coli ST131 isolated from colonized residents living inside LTCFs. The ST131 represents an incubator of fluoroquinolones, aminoglycosides and other antibiotic resistance genes in addition to different virulence factors. Full article
(This article belongs to the Special Issue Molecular Diagnostics of Antimicrobial Resistance)
11 pages, 4448 KiB  
Communication
Genomic Characterization of VIM and MCR Co-Producers: The First Two Clinical Cases, in Italy
by Vittoria Mattioni Marchetti, Ibrahim Bitar, Mario Sarti, Elena Fogato, Erika Scaltriti, Chiara Bracchi, Jaroslav Hrabak, Stefano Pongolini and Roberta Migliavacca
Diagnostics 2021, 11(1), 79; https://0-doi-org.brum.beds.ac.uk/10.3390/diagnostics11010079 - 06 Jan 2021
Cited by 16 | Viewed by 2279
Abstract
Background: the co-production of carbapenemases and mcr-genes represents a worrisome event in the treatment of Enterobacteriaceae infections. The aim of the study was to characterize the genomic features of two clinical Enterobacter cloacae complex (ECC) isolates, co-producing VIM and MCR enzymes, in [...] Read more.
Background: the co-production of carbapenemases and mcr-genes represents a worrisome event in the treatment of Enterobacteriaceae infections. The aim of the study was to characterize the genomic features of two clinical Enterobacter cloacae complex (ECC) isolates, co-producing VIM and MCR enzymes, in Italy. Methods: species identification and antibiotic susceptibility profiling were performed using MALDI-TOF and broth microdilution methods, respectively. Transferability of the blaVIM- and mcr- type genes was verified through conjugation experiment. Extracted DNA was sequenced using long reads sequencing technology on the Sequel I platform (PacBio). Results: the first isolate showed clinical resistance against ertapenem yet was colistin susceptible (EUCAST 2020 breakpoints). The mcr-9.2 gene was harbored on a conjugative IncHI2 plasmid, while the blaVIM-1 determinant was harbored on a conjugative IncN plasmid. The second isolate, resistant to both carbapenems and colistin, harbored: mcr-9 gene and its two component regulatory genes for increased expression on the chromosome, mcr-4.3 on non-conjugative (yet co-transferable) ColE plasmid, and blaVIM-1 on a non-conjugative IncA plasmid. Conclusions: to our knowledge, this is the first report of co-production of VIM and MCR in ECC isolates in Italy. Full article
(This article belongs to the Special Issue Molecular Diagnostics of Antimicrobial Resistance)
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12 pages, 948 KiB  
Article
A Lateral Flow Immunoassay for the Rapid Identification of CTX-M-Producing Enterobacterales from Culture Plates and Positive Blood Cultures
by Sandrine Bernabeu, Kayaththiry Caroline Ratnam, Hervé Boutal, Camille Gonzalez, Anaïs Vogel, Karine Devilliers, Marc Plaisance, Saoussen Oueslati, Surbhi Malhotra-Kumar, Laurent Dortet, Nicolas Fortineau, Stéphanie Simon, Hervé Volland and Thierry Naas
Diagnostics 2020, 10(10), 764; https://0-doi-org.brum.beds.ac.uk/10.3390/diagnostics10100764 - 28 Sep 2020
Cited by 29 | Viewed by 14121
Abstract
We have developed a lateral flow immunoassay (LFIA), named NG-Test CTX-M MULTI (NG-Test), to detect group 1, 2, 8, 9, 25 CTX-M producers from agar plates and from positive blood cultures in less than 15 min. The NG-Test was validated retrospectively on 113 [...] Read more.
We have developed a lateral flow immunoassay (LFIA), named NG-Test CTX-M MULTI (NG-Test), to detect group 1, 2, 8, 9, 25 CTX-M producers from agar plates and from positive blood cultures in less than 15 min. The NG-Test was validated retrospectively on 113 well-characterized enterobacterial isolates, prospectively on 102 consecutively isolated ESBL-producers from the Bicêtre hospital and on 100 consecutive blood cultures positive with a gram-negative bacilli (GNB). The NG-Test was able to detect all CTX-M producers grown on the different agar plates used in clinical microbiology laboratories. No false positive nor negative results were observed. Among the 102 consecutive ESBL isolates, three hyper mucous isolates showed an incorrect migration leading to invalid results (no control band). Using an adapted protocol, the results could be validated. The NG-Test detected 99/102 ESBLs as being CTX-Ms. Three SHV producers were not detected. Among the 100 positive blood cultures with GNB tested 10/11 ESBL-producers were detected (8 CTX-M-15, 2 CTX-M-27). One SHV-2-producing-E. cloacae was missed. The NG-Test CTX-M MULTI showed 100% sensitivity and specificity with isolates cultured on agar plates and was able to detect 98% of the ESBL-producers identified in our clinical setting either from colonies or from positive blood cultures. Full article
(This article belongs to the Special Issue Molecular Diagnostics of Antimicrobial Resistance)
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