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A special issue of Antibiotics (ISSN 2079-6382).

Deadline for manuscript submissions: 30 April 2025 | Viewed by 15328

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Dr. Gabriele Bianco

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Microbiology and Virology Unit, Turin University, 10124 Turin, Italy
Interests: clinical microbiology; rapid diagnostic; antibiotic resistance; MALDI-TOF MS; lateral flow immunoassay; Real Time PCR; DNA sequencing; β-lactamases; antimicrobial susceptibility testing; synergy testing; time kill assay; new β-lactam/β-lactamase
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Dear Colleagues,

Microbiological diagnostics plays a key role in the determination of the appropriate treatment for infectious diseases. Recent technological advances have enabled accurate microbiological diagnoses with shorter turnaround times. In addition, several antimicrobial molecules have been introduced to the market for the treatment of infections due to multidrug-resistant bacteria.

Therefore, for this Special Issue, we invite authors to contribute original research and review papers describing the application of innovative diagnostic techniques for the detection or identification of bacterial agents and the application of rapid or conventional methods for the determination of in vitro antimicrobial susceptibility.

Dr. Gabriele Bianco
Guest Editor

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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. Antibiotics is an international peer-reviewed open access monthly 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 2900 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

identification methods
rapid diagnostics
MALDI-TOF MS
molecular testing
rapid antimicrobial susceptibility testing
antimicrobial susceptibility
synergy testing
β-lactam/β-lactamase inhibitor
fosfomycin
colistin

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Published Papers (7 papers)

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Research

14 pages, 1510 KiB

Open AccessArticle

First Detection of High-Level Aminoglycoside-Resistant Klebsiella pneumoniae and Enterobacter cloacae Isolates Due to 16S rRNA Methyltransferases with and Without bla_NDM in Uruguay

by Romina Papa-Ezdra, Nicolás F. Cordeiro, Federica Ferreira, Virginia García-Fulgueiras, Lucía Araújo, María Inés Mota, Matilde Outeda, Verónica Seija, Rafael Vignoli and Inés Bado

Antibiotics 2024, 13(11), 1029; https://doi.org/10.3390/antibiotics13111029 - 31 Oct 2024

Viewed by 1173

Abstract

Background: The increase in antimicrobial resistance includes emerging mechanisms such as 16S ribosomal RNA methylases, which confer high-level resistance to aminoglycosides. In this regard, the most predominant genes observed worldwide are rmtB and armA, but their presence in Uruguay is unknown. Objectives: We describe the genomic characterization of isolates carrying rmtB and rmtC, together with bla_NDM-5 and bla_NDM-1, respectively, and rmtD in our country. Methology: Five isolates from patients admitted to three hospitals were studied. Identification and antibiotic susceptibility testing were performed using the Vitek2 System. Whole Genome Sequencing was conducted, and hybrid assembly was performed with Unicycler. In silico analysis using the Center for Genomic Epidemiology’s tools was undertaken to predict antibiotic resistance determinants, plasmid incompatibility groups, and sequence types. Results: We report three K. pneumoniae ST307 isolates with an IncR plasmid carrying bla_NDM-5/bla_CTX-M-15/bla_TEM-1B/rmtB/dfrA14/dfrA12/sul1/qacEΔ1/ermB/mphA, one K. pneumoniae ST258 harboring an IncC plasmid containing rmtC/bla_NDM-1/bla_CMY-6/aac(6′)-Ib/sul1, and one E. cloacae ST88 isolate with an IncFIB/II plasmid hosting rmtD, within a novel Tn21-like transposon named Tn7825, alongside bla_OXA-101/sul1/tet(G)/floR, and a new variant of bla_TEM assigned as bla_TEM-258. One of the strains, named UH_B2, also carried an IncM1 plasmid encoding qnrE1/bla_TEM-1/bla_CTX-M-8 associated with ISEcp1. Conclusions: This is the first description of plasmids harboring 16S rRNA methyltransferases in Uruguay. The association and dissemination of diverse antibiotic-resistant genes underpin the health threat they represent, highlighting the lack of available antibiotics effective against multidrug-resistant microorganisms. Full article

(This article belongs to the Special Issue Bacterial Detection, Identification, and Antimicrobial Susceptibility Testing)

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17 pages, 2143 KiB

Open AccessArticle

Rapid Minimum Inhibitory Concentration (MIC) Analysis Using Lyophilized Reagent Beads in a Novel Multiphase, Single-Vessel Assay

by Tejas Suresh Khire, Wei Gao, Brian Bales, Kuangwen Hsieh, Greg Grossmann, Dong Jin M. Park, Christine O’Keefe, Arnyah Brown-Countess, Sara Peterson, Fan-En Chen, Ralf Lenigk, Alex Trick, Tza-Huei Wang and Christopher Puleo

Antibiotics 2023, 12(11), 1641; https://doi.org/10.3390/antibiotics12111641 - 19 Nov 2023

Cited by 1 | Viewed by 3388

Abstract

Antimicrobial resistance (AMR) is a global threat fueled by incorrect (and overuse) of antibiotic drugs, giving rise to the evolution of multi- and extreme drug-resistant bacterial strains. The longer time to antibiotic administration (TTA) associated with the gold standard bacterial culture method has been responsible for the empirical usage of antibiotics and is a key factor in the rise of AMR. While polymerase chain reaction (PCR) and other nucleic acid amplification methods are rapidly replacing traditional culture methods, their scope has been restricted mainly to detect genotypic determinants of resistance and provide little to no information on phenotypic susceptibility to antibiotics. The work presented here aims to provide phenotypic antimicrobial susceptibility testing (AST) information by pairing short growth periods (~3–4 h) with downstream PCR assays to ultimately predict minimum inhibitory concentration (MIC) values of antibiotic treatment. To further simplify the dual workflows of the AST and PCR assays, these reactions are carried out in a single-vessel format (PCR tube) using novel lyophilized reagent beads (LRBs), which store dried PCR reagents along with primers and enzymes, and antibiotic drugs separately. The two reactions are separated in space and time using a melting paraffin wax seal, thus eliminating the need to transfer reagents across different consumables and minimizing user interactions. Finally, these two-step single-vessel reactions are multiplexed by using a microfluidic manifold that allows simultaneous testing of an unknown bacterial sample against different antibiotics at varying concentrations. The LRBs used in the microfluidic system showed no interference with the bacterial growth and PCR assays and provided an innovative platform for rapid point-of-care diagnostics (POC-Dx). Full article

(This article belongs to the Special Issue Bacterial Detection, Identification, and Antimicrobial Susceptibility Testing)

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12 pages, 573 KiB

Open AccessArticle

Polyclonal Multidrug ESBL-Producing Klebsiella pneumoniae and Emergence of Susceptible Hypervirulent Klebsiella pneumoniae ST23 Isolates in Mozambique

by José João Sumbana, Antonella Santona, Nader Abdelmalek, Maura Fiamma, Massimo Deligios, Alice Manjate, Jahit Sacarlal, Salvatore Rubino and Bianca Paglietti

Antibiotics 2023, 12(9), 1439; https://doi.org/10.3390/antibiotics12091439 - 12 Sep 2023

Cited by 2 | Viewed by 1609

Abstract

Globally, antibiotic-resistant Klebsiella spp. cause healthcare-associated infections with high mortality rates, and the rise of hypervirulent Klebsiella pneumoniae (hvKp) poses a significant threat to human health linked to community-acquired infections and increasing non-susceptibility. We investigated the phenotypic and genetic features of 36 Klebsiella isolates recovered from invasive infections at Hospital Central of Maputo in Mozambique during one year. The majority of the isolates displayed multidrug resistance (MDR) (29/36) to cephalosporins, gentamicin, ciprofloxacin, and trimethoprim–sulfamethoxazole but retained susceptibility to amikacin, carbapenems, and colistin. Most isolates were ESBLs-producing (28/36), predominantly carrying the bla_CTX-M-15 and other beta-lactamase genes (bla_SHV, bla_TEM-1, and bla_OXA-1). Among the 16 genomes sequenced, multiple resistance genes from different antibiotic classes were identified, with bla_CTX-M-15, mostly in the ISEcp1-bla_CTX-M-15-orf477 genetic environment, co-existing with bla_TEM-1 and aac(3)-IIa in five isolates. Our results highlight the presence of polyclonal MDR ESBL-producing K. pneumoniae from eight sequence types (ST), mostly harbouring distinct yersiniabactin within the conjugative integrative element (ICE). Further, we identified susceptible hvKp ST23, O1-K1-type isolates carrying yersiniabactin (ybt1/ICEKp10), colibactin, salmochelin, aerobactin, and hypermucoid locus (rmpADC), associated with severe infections in humans. These findings are worrying and underline the importance of implementing surveillance strategies to avoid the risk of the emergence of the most threatening MDR hvKp. Full article

(This article belongs to the Special Issue Bacterial Detection, Identification, and Antimicrobial Susceptibility Testing)

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12 pages, 1587 KiB

Open AccessArticle

QUIRMIA—A Phenotype-Based Algorithm for the Inference of Quinolone Resistance Mechanisms in Escherichia coli

by Frank Imkamp, Elias Bodendoerfer and Stefano Mancini

Antibiotics 2023, 12(7), 1119; https://doi.org/10.3390/antibiotics12071119 - 28 Jun 2023

Cited by 4 | Viewed by 1540

Abstract

Objectives: Quinolone resistance in Escherichia coli occurs mainly as a result of mutations in the quinolone-resistance-determining regions of gyrA and parC, which encode the drugs’ primary targets. Mutational alterations affecting drug permeability or efflux as well as plasmid-based resistance mechanisms can also contribute to resistance, albeit to a lesser extent. Simplifying and generalizing complex evolutionary trajectories, low-level resistance towards fluoroquinolones arises from a single mutation in gyrA, while clinical high-level resistance is associated with two mutations in gyrA plus one mutation in parC. Both low- and high-level resistance can be detected phenotypically using nalidixic acid and fluoroquinolones such as ciprofloxacin, respectively. The aim of this study was to develop a decision tree based on disc diffusion data and to define epidemiological cut-offs to infer resistance mechanisms and to predict clinical resistance in E. coli. This diagnostic algorithm should provide a coherent genotype/phenotype classification, which separates the wildtype from any non-wildtype and further differentiates within the non-wildtype. Methods: Phenotypic susceptibility of 553 clinical E. coli isolates towards nalidixic acid, ciprofloxacin, norfloxacin and levofloxacin was determined by disc diffusion, and the genomes were sequenced. Based on epidemiological cut-offs, we developed a QUInolone Resistance Mechanisms Inference Algorithm (QUIRMIA) to infer the underlying resistance mechanisms responsible for the corresponding phenotypes, resulting in the categorization as “susceptible” (wildtype), “low-level resistance” (non-wildtype) and “high-level resistance” (non-wildtype). The congruence of phenotypes and whole genome sequencing (WGS)-derived genotypes was then assigned using QUIRMIA- and EUCAST-based AST interpretation. Results: QUIRMIA-based inference of resistance mechanisms and sequencing data were highly congruent (542/553, 98%). In contrast, EUCAST-based classification with its binary classification into “susceptible” and “resistant” isolates failed to recognize and properly categorize low-level resistant isolates. Conclusions: QUIRMIA provides a coherent genotype/phenotype categorization and may be integrated in the EUCAST expert rule set, thereby enabling reliable detection of low-level resistant isolates, which may help to better predict outcome and to prevent the emergence of clinical resistance. Full article

(This article belongs to the Special Issue Bacterial Detection, Identification, and Antimicrobial Susceptibility Testing)

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11 pages, 736 KiB

Open AccessArticle

Influence of Multiplex PCR in the Management of Antibiotic Treatment in Patients with Bacteremia

by Alina-Ioana Andrei, Daniela Tălăpan, Alexandru Rafila and Gabriel Adrian Popescu

Antibiotics 2023, 12(6), 1038; https://doi.org/10.3390/antibiotics12061038 - 10 Jun 2023

Viewed by 1792

Abstract

The multiplex PCR assay can be a helpful diagnostic tool for patients with bacteremia. Herein, we assessed the impact of a Blood Culture Identification Panel (BCID) on both the diagnosis and treatment of patients with bacteremia. We performed a retrospective study using laboratory and clinical data to evaluate the impact of syndromic testing using a multiplex PCR testing system (BioFire^® FilmArray) for the management of patients with bloodstream infections. BCID detected the pathogen in 102 (87.9%) samples out of the 116 positive blood cultures tested. The average time from the blood culture collection to the communication of the molecular test result was 23.93 h (range: 10.67–69.27 h). The main pathogen detected was Klebsiella pneumoniae (17.6%). The antimicrobial therapy was changed in accordance with the BCID results in 28 (40.6%) out of the 69 cases, wherein the treatment could have been theoretically adjusted. This allowed the adjustment of the therapy to be performed 1305.1 h faster than it would have been possible if conventional diagnostic methods had been used; this was the case for only 35.1% of the time gained if treatment was adjusted for all patients with positive BCID. Thus, although molecular tests can make a difference in the management of bloodstream infections, there is room for improvement in the clinical application of BCID results. Full article

(This article belongs to the Special Issue Bacterial Detection, Identification, and Antimicrobial Susceptibility Testing)

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12 pages, 295 KiB

Open AccessArticle

In Vitro Activities of Ceftobiprole, Dalbavancin, Tedizolid and Comparators against Clinical Isolates of Methicillin-Resistant Staphylococcus aureus Associated with Skin and Soft Tissue Infections

by Sofia Maraki, Viktoria Eirini Mavromanolaki, Dimitra Stafylaki, Evangelia Iliaki-Giannakoudaki and George Hamilos

Antibiotics 2023, 12(5), 900; https://doi.org/10.3390/antibiotics12050900 - 12 May 2023

Cited by 3 | Viewed by 1839

Abstract

Skin and soft tissue infections (SSTIs) are associated with significant morbidity and healthcare costs, especially when caused by methicillin-resistant Staphylococcus aureus (MRSA). Vancomycin is a preferred antimicrobial therapy for the management of complicated SSTIs (cSSTIs) caused by MRSA, with linezolid and daptomycin regarded as alternative therapeutic options. Due to the increased rates of antimicrobial resistance in MRSA, several new antibiotics with activity against MRSA have been recently introduced in clinical practice, including ceftobiprole, dalbavancin, and tedizolid. We evaluated the in vitro activities of the aforementioned antibiotics against 124 clinical isolates of MRSA obtained from consecutive patients with SSTIs during the study period (2020–2022). Minimum inhibitory concentrations (MICs) for vancomycin, daptomycin, ceftobiprole, dalbavancin, linezolid and tedizolid were evaluated by the MIC Test Strip using Liofilchem strips. We found that when compared to the in vitro activity of vancomycin (MIC₉₀ = 2 μg/mL), dalbavancin possessed the lowest MIC₉₀ (MIC₉₀ = 0.094 μg/mL), followed by tedizolid (MIC₉₀ = 0.38 μg/mL), linezolid, ceftobiprole, and daptomycin (MIC₉₀ = 1 μg/mL). Dalbavancin demonstrated significantly lower MIC₅₀ and MIC₉₀ values compared to vancomycin (0.064 vs. 1 and 0.094 vs. 2, respectively). Tedizolid exhibited an almost threefold greater level of in vitro activity than linezolid, and also had superior in vitro activity compared to ceftobiprole, daptomycin and vancomycin. Multidrug-resistant (MDR) phenotypes were detected among 71.8% of the isolates. In conclusion, ceftobiprole, dalbavancin and tedizolid exhibited potent activity against MRSA and are promising antimicrobials in the management of SSTIs caused by MRSA. Full article

(This article belongs to the Special Issue Bacterial Detection, Identification, and Antimicrobial Susceptibility Testing)

9 pages, 250 KiB

Open AccessArticle

Disc Diffusion and ComASP^® Cefiderocol Microdilution Panel to Overcome the Challenge of Cefiderocol Susceptibility Testing in Clinical Laboratory Routine

by Gabriele Bianco, Matteo Boattini, Sara Comini, Giuliana Banche, Rossana Cavallo and Cristina Costa

Antibiotics 2023, 12(3), 604; https://doi.org/10.3390/antibiotics12030604 - 17 Mar 2023

Cited by 14 | Viewed by 2738

Abstract

Cefiderocol susceptibility testing represents a major challenge for clinical microbiology. Although disc diffusion showed robustness to test cefiderocol susceptibility, large areas of technical uncertainty (ATU) are reported by current EUCAST breakpoints. Herein, we evaluated the in vitro activity of cefiderocol on a collection of 286 difficult-to-treat Gram-negative isolates using disc diffusion and ComASP^® cefiderocol microdilution panel. Broth microdilution (BMD) in iron-depleted Mueller–Hinton broth was used as reference method. Following the EUCAST guidelines, disc diffusion allowed to determine cefiderocol susceptibility (susceptible or resistant) in 78.6%, 88.1%, 85.4% and 100% of Enterobacterales, P. aeruginosa, A. baumannii and S. maltophilia isolates tested, respectively. ComASP^® cefiderocol panel showed 94% and 84% of overall categorical agreement and essential agreement. Only one very major error and two major errors were observed, for MIC values nearly close to the resistance breakpoint (2 mg/L). Overall, 20.5% of the carbapenemase-producing Enterobacterales that achieved ATU results by the disc diffusion method tested resistant by both ComASP^® panel and reference BMD. Conversely, all VIM-producing P. aeruginosa showed MIC values in the susceptible range (≤2 mg/L). Lastly, only six out of seven (85.7%) A. baumannii isolates showing inhibition zones <17 mm tested resistant by both ComASP^® panel and the reference BMD suggesting that inhibition zone <17 mm are not unequivocally suggestive of resistance. Our results, although obtained on a limited number of isolates, suggest that the combination of disc diffusion with a ComASP^® cefiderocol microdilution panel could be a viable solution to overcome the challenge of cefiderocol susceptibility testing in routine microbiology laboratories. Full article

(This article belongs to the Special Issue Bacterial Detection, Identification, and Antimicrobial Susceptibility Testing)

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