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Diagnostics
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Diagnostics of Antimicrobial Resistance (AMR): From Phenotypic to Molecular
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Diagnostics of Antimicrobial Resistance (AMR): From Phenotypic to Molecular

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 (30 June 2022) | Viewed by 15720

Special Issue Editors

Dr. Thierry Naas

E-Mail Website
Guest Editor
School of Medicine, University Paris Saclay, Hopital de Bicêtre, Service de Bactériologie, Bâtiment Broca, 3ème étage, 78 rue du Gal Leclerc, 94275 Le Kremlin-Bicêtre, France
Interests: genetics of antibiotic resistance; Gram negatives; ß-lactamases; carbapenemases; diagnostics (biochemical, phenotypical, molecular) and diagnostics of antibiotics resistance genes; NGS; transcriptomics; microbiota
Special Issues, Collections and Topics in MDPI journals
Dr. Herve Volland

E-Mail Website
Guest Editor
Département Médicaments et Technologies pour la Santé, Université Paris Saclay, CEA, INRAE, SPI, 91191 Gif-sur-Yvette, France
Interests: immunoassay; monoclonal antibodies; ELISA; antibody production; antibody conjugation; monoclonal; antibody purification
Dr. Saoussen Oueslati

E-Mail Website
Guest Editor
School of Medicine, University Paris Saclay, Hopital de Bicêtre, Service de Bactériologie, Bâtiment Broca, 3ème étage, 78 rue du Gal Leclerc, 94275 Le Kremlin-Bicêtre, France
Interests: AMR; enterobacterales; gram negative; kinetics; beta-lactamase; diagnostics; genetics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Multidrug resistant bacteria are increasingly isolated and responsible for hospital outbreaks, associated with significant morbidity and mortality. Accordingly, their global dissemination poses a serious threat to public health. The rapid detection of these bacteria is crucial to help physicians quickly implementing appropriate infection control measures, to adapt antibiotic treatment rapidly and to optimize care strategies and outcomes.

Resistance is emerging in many clinically-relevant bacteria of Gram-negatives (Enterobacterales, Pseudomonas sp. and Acinetobacter sp. with ESBLs, Carbapenemases or RNA methylases,…) of Gram-positives (Staphylococci, Enterococci, …) and in Mycobacteria. Early detection requires rapid, easy and efficient diagnostic tools that can be adapted to many resource settings, including Low and Middle ones.

Screening protocols are mainly based on cultures of nasal and/or rectal swab specimens on selective screening media, followed by confirmation tests such as phenotypic, biochemical, lateral flow immunoassays, Mass spectrometryl (such as MALDI-TOF) tests. Culture of nasal/rectal swab specimens followed by confirmation testing are long, and often not compatible with rapid implementation of reinforced hygiene measures. Molecular based techniques such as PCR, and whole genome sequencing remain the gold standard for the precise identification of resistance genes. Molecular methods are now available for detecting resistance genes from bacterial cultures but also directly from clinical specimens in less than an hour. However, due to their high costs, they are often used on a risk based assessment of the patient’s history (recent travel, hospitalization, treatment, etc..).

This special issue is dedicated to recent developments and clinical validation of classical but also innovative tools for qualitatively/quantitatively detecting resistance traits on cultured bacteria or directly in clinical samples, with special emphasis on the positioning of these tests in the routine setting and on the clinical usefulness of these tests.

Dr. Thierry Naas
Dr. Herve Volland
Dr. Saoussen Oueslati
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.

Keywords

  • antimicrobial resistance
  • detection
  • diagnostics
  • phenotypic
  • Molecular

Published Papers (5 papers)

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Research

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9 pages, 742 KiB  
Communication
Molecular Characterization by Whole-Genome Sequencing of Clinical and Environmental Serratia marcescens Strains Isolated during an Outbreak in a Neonatal Intensive Care Unit (NICU)
by Alessandra Piccirilli, Sabrina Cherubini, Fabrizia Brisdelli, Paolo Fazii, Andrea Stanziale, Susanna Di Valerio, Valentina Chiavaroli, Luigi Principe and Mariagrazia Perilli
Diagnostics 2022, 12(9), 2180; https://0-doi-org.brum.beds.ac.uk/10.3390/diagnostics12092180 - 09 Sep 2022
Cited by 11 | Viewed by 1443
Abstract
The whole-genome sequencing (WGS) of eighteen S. marcescens clinical strains isolated from 18 newborns hospitalized in the Neonatal Intensive Care Unit (NICU) at Pescara Public Hospital, Italy, was compared with that of S. marcescens isolated from cradles surfaces in the same ward. The [...] Read more.
The whole-genome sequencing (WGS) of eighteen S. marcescens clinical strains isolated from 18 newborns hospitalized in the Neonatal Intensive Care Unit (NICU) at Pescara Public Hospital, Italy, was compared with that of S. marcescens isolated from cradles surfaces in the same ward. The identical antibiotic resistance genes (ARGs) and virulence factors were found in both clinical and environmental S. marcescens strains. The aac(6′)-Ic, tetA(41), blaSRT-3, adeFGH, rsmA, and PBP3 (D350N) genes were identified in all strains. The SRT-3 enzyme, which exhibited 10 amino acid substitutions with respect to SST-1, the constitutive AmpC β-lactamase in S. marcescens, was partially purified and tested against some β-lactams. It showed a good activity against cefazolin. Both clinical and environmental S. marcescens strains exhibited susceptibility to all antibiotics tested, with the exception of amoxicillin/clavulanate. Full article
(This article belongs to the Special Issue Diagnostics of Antimicrobial Resistance (AMR): From Phenotypic to Molecular)
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7 pages, 1141 KiB  
Article
Real-Time PCR Assay for Rapid and Simultaneous Detection of vanA and vanB Genes in Clinical Strains
by Hanane Zerrouki, Sid-Ahmed Rebiahi, Linda Hadjadj, Jean-Marc Rolain and Seydina M. Diene
Diagnostics 2021, 11(11), 2081; https://0-doi-org.brum.beds.ac.uk/10.3390/diagnostics11112081 - 10 Nov 2021
Cited by 1 | Viewed by 1905
Abstract
Here, we develop a robust and sensitive real-time PCR assay which allows the simultaneous detection of vanA and vanB genes using common primers. The system was designed using the Primer3 online software. The specificity of primers and probes was first checked by in [...] Read more.
Here, we develop a robust and sensitive real-time PCR assay which allows the simultaneous detection of vanA and vanB genes using common primers. The system was designed using the Primer3 online software. The specificity of primers and probes was first checked by in silico PCR and by BlastN analysis. The genomic DNA of 255 bacterial isolates, including Enterococcus spp., Gram-negative, and Gram-positive strains, as well as a collection of 50 stool and 50 rectal swab samples, were tested to evaluate the specificity of the new real-time PCR (RT-PCR) system. The results of the designed RT-PCR were 100% specific and 100% positive on tested vancomycin resistant isolates harboring either the vanA or vanB gene. RT-PCR assays were negative for all other bacterial species tested including vancomycin-sensitive Enterococci and Enterococcus strains harboring vanC genes. The limit of detection of vanA and vanB genes by RT-PCR assay was 47 CFU/mL and 32 CFU/mL, respectively. The rapid and accurate detection of vancomycin-resistant Enterococci is the cornerstone for minimizing the risk of nosocomial transmissions and outbreaks. We believe that this assay will strengthen routine diagnostics and surveillance programs. Full article
(This article belongs to the Special Issue Diagnostics of Antimicrobial Resistance (AMR): From Phenotypic to Molecular)
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10 pages, 1778 KiB  
Article
Rapid Detection of VanA/B-Producing Vancomycin-Resistant Enterococci Using Lateral Flow Immunoassay
by Saoussen Oueslati, Camille Gonzalez, Hervé Volland, Vincent Cattoir, Sandrine Bernabeu, Delphine Girlich, Duncan Dulac, Marc Plaisance, Laure Boutigny, Laurent Dortet, Stéphanie Simon and Thierry Naas
Diagnostics 2021, 11(10), 1805; https://0-doi-org.brum.beds.ac.uk/10.3390/diagnostics11101805 - 29 Sep 2021
Cited by 5 | Viewed by 2450
Abstract
Vancomycin-resistant enterococci (VREs) have become one of the most important nosocomial pathogens worldwide, associated with increased treatment costs, prolonged hospital stays and high mortality. Rapid detection is crucial to reduce their spread and prevent infections and outbreaks. The lateral flow immunoassay NG-Test VanB [...] Read more.
Vancomycin-resistant enterococci (VREs) have become one of the most important nosocomial pathogens worldwide, associated with increased treatment costs, prolonged hospital stays and high mortality. Rapid detection is crucial to reduce their spread and prevent infections and outbreaks. The lateral flow immunoassay NG-Test VanB (NG Biotech) was evaluated for the rapid detection of VanB-producing vancomycin-resistant enterococci (VanB-VREs) using 104 well-characterized enterococcal isolates. The sensitivity and specificity were both 100% when bacterial cells were grown in the presence of vancomycin used as a VanB inducer. The NG-Test VanB is an efficient, rapid and easy to implement assay in clinical microbiology laboratories for the confirmation of VanB-VREs from colonies. Together with the NG-Test VanA, they could replace the already existing tests available for the confirmation of acquired vancomycin resistance in enterococci, especially from selective media or from antibiograms, with 100% sensitivity and specificity. Rapid detection in less than 15 min will result in more efficient management of carriers and infected patients. In addition, these tests may be used for positive blood cultures, given a 3.5 h sub-culturing step on Chocolate agar PolyViteX in the presence of a 5-µg vancomycin disk, which is routinely performed in many clinical microbiology laboratories for every positive blood culture for subsequent MALDI-TOF identification of the growing bacteria. Full article
(This article belongs to the Special Issue Diagnostics of Antimicrobial Resistance (AMR): From Phenotypic to Molecular)
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14 pages, 1067 KiB  
Article
Occurrence of NDM-1 and VIM-2 Co-Producing Escherichia coli and OprD Alteration in Pseudomonas aeruginosa Isolated from Hospital Environment Samples in Northwestern Tunisia
by Raouaa Maaroufi, Olfa Dziri, Linda Hadjadj, Seydina M. Diene, Jean-Marc Rolain and Chedly Chouchani
Diagnostics 2021, 11(9), 1617; https://0-doi-org.brum.beds.ac.uk/10.3390/diagnostics11091617 - 04 Sep 2021
Cited by 2 | Viewed by 1957
Abstract
Hospital environments constitute the main reservoir of multidrug-resistant bacteria. In this study we aimed to investigate the presence of Gram-negative bacteria in one Northwestern Tunisian hospital environment, and characterize the genes involved in bacterial resistance. A total of 152 environmental isolates were collected [...] Read more.
Hospital environments constitute the main reservoir of multidrug-resistant bacteria. In this study we aimed to investigate the presence of Gram-negative bacteria in one Northwestern Tunisian hospital environment, and characterize the genes involved in bacterial resistance. A total of 152 environmental isolates were collected from various surfaces and isolated using MacConkey medium supplemented with cefotaxime or imipenem, with 81 fermenter bacteria (27 Escherichia coli, and 54 Enterobacter spp., including 46 Enterobacter cloacae), and 71 non-fermenting bacteria (69 Pseudomonas spp., including 54 Pseudomonas aeruginosa, and 2 Stenotrophomonas maltophilia) being identified by the MALDI-TOF-MS method. Antibiotic susceptibility testing was performed by disk diffusion method and E-Test was used to determine MICs for imipenem. Several genes implicated in beta-lactams resistance were characterized by PCR and sequencing. Carbapenem resistance was detected among 12 isolates; nine E. coli (blaNDM-1 (n = 8); blaNDM-1 + blaVIM-2 (n = 1)) and three P. aeruginosa were carbapenem-resistant by loss of OprD porin. The whole-genome sequencing of P. aeruginosa 97H was determined using Illumina MiSeq sequencer, typed ST285, and harbored blaOXA-494. Other genes were also detected, notably blaTEM (n = 23), blaCTX-M-1 (n = 10) and blaCTX-M-9 (n = 6). These new epidemiological data imposed new surveillance strategies and strict hygiene rules to decrease the spread of multidrug-resistant bacteria in this area. Full article
(This article belongs to the Special Issue Diagnostics of Antimicrobial Resistance (AMR): From Phenotypic to Molecular)
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Review

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33 pages, 1228 KiB  
Review
Recent Developments in Phenotypic and Molecular Diagnostic Methods for Antimicrobial Resistance Detection in Staphylococcus aureus: A Narrative Review
by Andrea Sanchini
Diagnostics 2022, 12(1), 208; https://0-doi-org.brum.beds.ac.uk/10.3390/diagnostics12010208 - 15 Jan 2022
Cited by 16 | Viewed by 5608
Abstract
Staphylococcus aureus is an opportunistic pathogen responsible for a wide range of infections in humans, such as skin and soft tissue infections, pneumonia, food poisoning or sepsis. Historically, S. aureus was able to rapidly adapt to anti-staphylococcal antibiotics and become resistant to several [...] Read more.
Staphylococcus aureus is an opportunistic pathogen responsible for a wide range of infections in humans, such as skin and soft tissue infections, pneumonia, food poisoning or sepsis. Historically, S. aureus was able to rapidly adapt to anti-staphylococcal antibiotics and become resistant to several classes of antibiotics. Today, methicillin-resistant S. aureus (MRSA) is a multidrug-resistant pathogen and is one of the most common bacteria responsible for hospital-acquired infections and outbreaks, in community settings as well. The rapid and accurate diagnosis of antimicrobial resistance in S. aureus is crucial to the early initiation of directed antibiotic therapy and to improve clinical outcomes for patients. In this narrative review, I provide an overview of recent phenotypic and molecular diagnostic methods for antimicrobial resistance detection in S. aureus, with a particular focus on MRSA detection. I consider methods for resistance detection in both clinical samples and isolated S. aureus cultures, along with a brief discussion of the advantages and the challenges of implementing such methods in routine diagnostics. Full article
(This article belongs to the Special Issue Diagnostics of Antimicrobial Resistance (AMR): From Phenotypic to Molecular)
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