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Microorganisms
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Antimicrobial Testing (AMT)
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Antimicrobial Testing (AMT)

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Antimicrobial Agents and Resistance".

Deadline for manuscript submissions: closed (31 May 2022) | Viewed by 20578

Special Issue Editor

Dr. Suresh Joshi

E-Mail Website
Guest Editor
1. Center for Surgical Infection and Biofilm, College of Medicine, Drexel University, Philadelphia, PA 19104, USA
2. Drexel School of Biomedical Engineering, Science & Health Systems, Drexel University, Philadelphia, PA 19104, USA
Interests: antimicrobial agent; resistance; bacterial pathogenesis; biofilm; host-pathogen interaction; infection control; translational medicine
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Antimicrobial susceptibility testing (AST) can be dated as early as 1924, when Dr. Fleming introduced the ditch plate technique for evaluation of antimicrobial qualities of antiseptic solutions. Since then, scientists have continued to work on advancements and evaluations of AST. Antimicrobial testing (AMT) is the world’s most widely used category of techniques, used daily by thousands of healthcare centers globally, to determine the potential effectiveness of specific antimicrobial agents on microorganisms, notably, the disk diffusion (Kirby–Bauer) method and broth dilution technique. Based on the AMT finding, it is predicted which antimicrobial will inhibit the growth of a microorganism causing a specific infection, and which antimicrobial therapy will be successful. There are lots of variations in susceptibility and resistance patterns globally, largely dependent on the regional practices of antimicrobial therapy, which not only amaze clinicians, microbiologists, and laboratory medicine scientists but challenge epidemiologists, public health personnel, and the pharmaceutical industry. As rapid diagnostic testing is pivotal in initiating specific antimicrobial therapy (and to avert development of resistance), recently, biomedical engineers and scientists have developed alternative, novel, rapid AST techniques, such as microfluidic-based optical, spectroscopy, electrochemical, piezoelectric plate sensor AST, next-generation sequencing, and many more. Additionally, automation in testing is continuously explored to save time and cost associated with in vitro testing and diagnostics.

In this Special Issue of Microorganisms, we invite original contributions (that are unpublished and not under consideration elsewhere) of research and reviews focusing on novel findings on and interpretations and significance of all different AST methods, novel strategies to determine antimicrobial resistance, unusual AST patterns of common or rare pathogens, comparison of AMT methods, in vitro synergism, antimicrobial mechanism-based studies involving AST (both phenotypic and genotypic methods), antimicrobial testing and efficacy in biofilms, novel qualitative and quantitative antimicrobial testing of natural products, synthetic molecules, and antimicrobial nanoparticles.

Prof. Dr. Suresh Joshi
Guest Editor

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. Microorganisms 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 2700 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

  • antibiogram
  • antibiotic susceptibility test
  • antimicrobial testing
  • bacterial resistance
  • biofilm-embedded bacteria
  • antifungal test
  • genotypic AMT
  • multidrug resistance
  • antimicrobial nanoparticle

Published Papers (8 papers)

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Research

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13 pages, 1345 KiB  
Article
Resistome Analysis of Campylobacter jejuni Strains Isolated from Human Stool and Primary Sterile Samples in Croatia
by Silvija Šoprek, Sanja Duvnjak, Gordan Kompes, Luka Jurinović and Arjana Tambić Andrašević
Microorganisms 2022, 10(7), 1410; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms10071410 - 13 Jul 2022
Cited by 2 | Viewed by 1482
Abstract
Campylobacteriosis represents a global health challenge due to continuously increasing trends of antimicrobial resistance in Campylobacter jejuni. C. jejuni can sometimes cause life-threatening and severe systematic infections (bacteremia, meningitis, and other extraintestinal infections) with very few antibiotics left as treatment options. Bearing [...] Read more.
Campylobacteriosis represents a global health challenge due to continuously increasing trends of antimicrobial resistance in Campylobacter jejuni. C. jejuni can sometimes cause life-threatening and severe systematic infections (bacteremia, meningitis, and other extraintestinal infections) with very few antibiotics left as treatment options. Bearing in mind that C. jejuni is the predominant species in humans, in this paper, we present a study of the C. jejuni differences in antimicrobial resistance and genotype distribution between strains isolated from stool and primary sterile sites. We compared the genomic data obtained through whole genome sequencing (WGS) and phenotypic susceptibility data of C. jejuni strains. Once antimicrobial susceptibility testing of C. jejuni strains was carried out by the broth microdilution method for six of interest, results were compared to the identified genotypic determinants derived from WGS. The high rate of resistance to fluoroquinolones presented in this study is in accordance with national surveillance data. The proportion of strains with acquired resistance was 71% for ciprofloxacin and 20% for tetracycline. When invasive isolates were analysed separately, 40% exhibited MIC values of ciprofloxacin higher than the ECOFFs, suggesting a lower flouroquinolone resistance rate in invasive isolates. All isolates demonstrated wilde-type phenotype for chloramphenicol, erythromycin, gentamicin, and ertapenem. A special focus and review in this study was performed on a group of C.jejuni strains found in primary sterile samples. Apart from demonstrating a lower resistance rate, these isolates seem genetically more uniform, showing epidemiologically more homogenous patterns, which cluster to several clonal complexes, with CC49 being the most represented clonal complex. Full article
(This article belongs to the Special Issue Antimicrobial Testing (AMT))
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8 pages, 253 KiB  
Article
In Vitro Synergism of Penicillin and Ceftriaxone against Enterococcus faecalis
by Lara Thieme, Simon Briggs, Eamon Duffy, Oliwia Makarewicz and Mathias W. Pletz
Microorganisms 2021, 9(10), 2150; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9102150 - 14 Oct 2021
Cited by 3 | Viewed by 2766
Abstract
Enterococcus faecalis infective endocarditis is commonly treated with intravenous ampicillin/ceftriaxone combination therapy. Ampicillin, however, is unsuitable for outpatient parenteral antibiotic therapy (OPAT) regimens due to its instability in 24 h continuous infusors, and has been successfully replaced by benzylpenicillin used together with ceftriaxone [...] Read more.
Enterococcus faecalis infective endocarditis is commonly treated with intravenous ampicillin/ceftriaxone combination therapy. Ampicillin, however, is unsuitable for outpatient parenteral antibiotic therapy (OPAT) regimens due to its instability in 24 h continuous infusors, and has been successfully replaced by benzylpenicillin used together with ceftriaxone in a few small case series. Since in vitro synergy data of penicillin/ceftriaxone against E. faecalis are still lacking, checkerboard assays were performed for 28 clinical E. faecalis isolates and one laboratory standard strain. Synergistic effects (both lowest and median FICI) were observed for penicillin/ceftriaxone in 15/29 isolates, while ampicillin/ceftriaxone exhibited synergism in 22/29 isolates. For isolates with ceftriaxone MICs ≤ 256 mg/L, the addition of free ceftriaxone trough concentrations to penicillin or ampicillin resulted in comparable synergistic effects for both combinations. In contrast, for isolates with ceftriaxone MICs ≥ 512 mg/L free ceftriaxone trough concentrations were only sufficient to exhibit synergistic effects in combination with ampicillin, but not penicillin. This study suggests that benzylpenicillin/ceftriaxone would be expected to be suitable for the OPAT treatment of enterococcal endocarditis for E. faecalis isolates with ceftriaxone MICs ≤ 256 mg/L. However, combination therapy would be expected to provide no advantage over benzylpenicillin monotherapy for isolates with ceftriaxone MICs ≥ 512 mg/L. Further investigation is required to analyse the relationship between ceftriaxone susceptibility and penicillin/ceftriaxone synergy, especially for isolates with ceftriaxone MICs of 64 to 512 mg/L. Full article
(This article belongs to the Special Issue Antimicrobial Testing (AMT))
7 pages, 225 KiB  
Communication
Provisional Use of CLSI-Approved Quality Control Strains for Antimicrobial Susceptibility Testing of Mycoplasma (‘Mesomycoplasma’) hyorhinis
by Lisa Käbisch, Anne-Kathrin Schink, Corinna Kehrenberg and Stefan Schwarz
Microorganisms 2021, 9(9), 1829; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9091829 - 28 Aug 2021
Cited by 4 | Viewed by 2068
Abstract
Antimicrobial susceptibility testing (AST) should be conducted in a standardized manner prior to the start of an antimicrobial treatment. For fastidious bacteria, such as porcine Mycoplasma (‘Mesomycoplasma’) spp., specifically M. hyorhinis, neither guidelines or standards for the performance of AST, [...] Read more.
Antimicrobial susceptibility testing (AST) should be conducted in a standardized manner prior to the start of an antimicrobial treatment. For fastidious bacteria, such as porcine Mycoplasma (‘Mesomycoplasma’) spp., specifically M. hyorhinis, neither guidelines or standards for the performance of AST, nor quality control strains for the validation of AST results are approved by organizations like the Clinical and Laboratory Standards Institute (CLSI) or the European Committee on Antimicrobial Susceptibility Testing (EUCAST). The CLSI- and EUCAST-approved quality control strains Enterococcus faecalis ATCC 29212 and Staphylococcus aureus ATCC 29213 were chosen to validate AST by broth microdilution using modified Friis broth, developed as growth medium for porcine Mycoplasma (‘Mesomycoplasma’) spp. The antimicrobial agents doxycycline, enrofloxacin, erythromycin, florfenicol, gentamicin, marbofloxacin, tetracycline, tiamulin, tilmicosin, tulathromycin, and tylosin were examined using customized SensititreTM microtiter plates. Minimal inhibitory concentrations, determined after 24, 48, and 72 h, were mostly within the CLSI-approved quality control ranges for defined antimicrobial agents. We propose the use of the combination of E. faecalis ATCC 29212 and S. aureus ATCC 29213 as surrogate quality control strains for the validation of future AST results obtained for M. hyorhinis by broth microdilution using modified Friis broth. Full article
(This article belongs to the Special Issue Antimicrobial Testing (AMT))
17 pages, 3833 KiB  
Article
Reporter-Phage-Based Detection and Antibiotic Susceptibility Testing of Yersinia pestis for a Rapid Plague Outbreak Response
by Sarit Moses, Moshe Aftalion, Emanuelle Mamroud, Shahar Rotem and Ida Steinberger-Levy
Microorganisms 2021, 9(6), 1278; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9061278 - 11 Jun 2021
Cited by 5 | Viewed by 2311
Abstract
Pneumonic plague is a lethal infectious disease caused by Yersinia pestis, a Tier-1 biothreat agent. Antibiotic treatment can save infected patients; however, therapy should begin within 24 h of symptom onset. As some Y. pestis strains showed an antibiotic resistance phenotype, an [...] Read more.
Pneumonic plague is a lethal infectious disease caused by Yersinia pestis, a Tier-1 biothreat agent. Antibiotic treatment can save infected patients; however, therapy should begin within 24 h of symptom onset. As some Y. pestis strains showed an antibiotic resistance phenotype, an antibiotic susceptibility test (AST) must be performed. Performing the Clinical and Laboratory Standards Institute (CLSI)-recommended standard process, which includes bacterial isolation, enumeration and microdilution testing, lasts several days. Thus, rapid AST must be developed. As previously published, the Y. pestis-specific reporter phage ϕA1122::luxAB can serve for rapid identification and AST (ID-AST). Herein, we demonstrate the ability to use ϕA1122::luxAB to determine minimal inhibitory concentration (MIC) values and antibiotic susceptibility categories for various Y. pestis therapeutic antibiotics. We confirmed the assay by testing several nonvirulent Y. pestis isolates with reduced susceptibility to doxycycline or ciprofloxacin. Moreover, the assay can be performed directly on positive human blood cultures. Furthermore, as Y. pestis may naturally or deliberately be spread in the environment, we demonstrate the compatibility of this direct method for this scenario. This direct phage-based ID-AST shortens the time needed for standard AST to less than a day, enabling rapid and correct treatment, which may also prevent the spread of the disease. Full article
(This article belongs to the Special Issue Antimicrobial Testing (AMT))
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15 pages, 253 KiB  
Article
Evaluation of the European Committee on Antimicrobial Susceptibility Testing Guidelines for Rapid Antimicrobial Susceptibility Testing of Bacillus anthracis-, Yersinia pestis- and Francisella tularensis-Positive Blood Cultures
by Ohad Shifman, Tamar Aminov, Moshe Aftalion, David Gur, Hila Cohen, Elad Bar-David, Ofer Cohen, Emanuelle Mamroud, Haim Levy, Ronit Aloni-Grinstein, Ida Steinberger-Levy and Shahar Rotem
Microorganisms 2021, 9(5), 1055; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9051055 - 13 May 2021
Cited by 7 | Viewed by 2608
Abstract
Rapid determination of bacterial antibiotic susceptibility is important for proper treatment of infections. The European Committee on Antimicrobial Susceptibility Testing (EUCAST) has recently published guidelines for rapid antimicrobial susceptibility testing (RAST) performed directly from positive blood culture vials. These guidelines, however, were only [...] Read more.
Rapid determination of bacterial antibiotic susceptibility is important for proper treatment of infections. The European Committee on Antimicrobial Susceptibility Testing (EUCAST) has recently published guidelines for rapid antimicrobial susceptibility testing (RAST) performed directly from positive blood culture vials. These guidelines, however, were only published for a limited number of common pathogenic bacteria. In this study, we evaluated the applicability of these guidelines to three Tier 1 bioterror agents (Bacillus anthracis, Yersinia pestis and Francisella tularensis) that require prompt antibiotic treatment to mitigate morbidity and mortality. We used spiked-in human blood incubated in a BACTEC™ FX40 system to determine the proper conditions for RAST using disc-diffusion and Etest assays. We found that reliable disc-diffusion inhibition diameters and Etest MIC values could be obtained in remarkably short times. Compared to the EUCAST-recommended disc-diffusion assays that will require adjusted clinical breakpoint tables, Etest-based RAST was advantageous, as the obtained MIC values were similar to the standard MIC values, enabling the use of established category breakpoint tables. Our results demonstrate the promising applicability of the EUCAST RAST for B. anthracis-, Y. pestis- or F. tularensis-positive blood cultures, which can lead to shorter diagnostics and prompt antibiotic treatment of these dangerous pathogens. Full article
(This article belongs to the Special Issue Antimicrobial Testing (AMT))
18 pages, 32976 KiB  
Article
Combining Visible Light and Non-Focused Ultrasound Significantly Reduces Propionibacterium acnes Biofilm While Having Limited Effect on Host Cells
by Mark E. Schafer and Tessie McNeely
Microorganisms 2021, 9(5), 929; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9050929 - 26 Apr 2021
Cited by 2 | Viewed by 2183
Abstract
Bacterial biofilms are highly resistant to antibiotics and have been implicated in the etiology of 60%–80% of chronic microbial infections. We tested a novel combination of low intensity ultrasound and blue light against biofilm and planktonic bacteria. A laboratory prototype was built which [...] Read more.
Bacterial biofilms are highly resistant to antibiotics and have been implicated in the etiology of 60%–80% of chronic microbial infections. We tested a novel combination of low intensity ultrasound and blue light against biofilm and planktonic bacteria. A laboratory prototype was built which produced both energies uniformly and coincidently from a single treatment head, impinging upon a 4.45 cm2 target. To demonstrate proof of concept, Propionibacterium acnes biofilms were cultured on Millicell hanging inserts in 6-well plates. Hanging inserts with biofilms were treated in a custom exposure chamber designed to minimize unwanted ultrasound reflections. Coincident delivery of both energies demonstrated synergy over either alone, killing both stationary planktonic and biofilm cultures of P. acnes. Reduction in biofilm bacteria was dose dependent on exposure time (i.e., energy delivered). P. acnes biofilms were significantly reduced by dual energy treatment (p < 0.0001), with a >1 log10 reduction after a 5 min (9 J/cm2) and >3 log10 reduction after a 30 min (54 J/cm2) treatment (p < 0.05). Mammalian cells were found to be unaffected by the treatment. Both the light and the ultrasound energies are at levels previously cleared by the FDA. Therefore, this combination treatment could be used as a safe, efficacious method to treat biofilm related syndromes. Full article
(This article belongs to the Special Issue Antimicrobial Testing (AMT))
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Review

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18 pages, 343 KiB  
Review
An Association of Pathogens and Biofilms with Alzheimer’s Disease
by Sandhya T. Chakravarthi and Suresh G. Joshi
Microorganisms 2022, 10(1), 56; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms10010056 - 28 Dec 2021
Cited by 5 | Viewed by 2826
Abstract
As one of the leading causes of dementia, Alzheimer’s disease (AD) is a condition in which individuals experience progressive cognitive decline. Although it is known that beta-amyloid (Aβ) deposits and neurofibrillary tangles (NFT) of tau fibrils are hallmark characteristics of AD, the exact [...] Read more.
As one of the leading causes of dementia, Alzheimer’s disease (AD) is a condition in which individuals experience progressive cognitive decline. Although it is known that beta-amyloid (Aβ) deposits and neurofibrillary tangles (NFT) of tau fibrils are hallmark characteristics of AD, the exact causes of these pathologies are still mostly unknown. Evidence that infectious diseases may cause AD pathology has been accumulating for decades. The association between microbial pathogens and AD is widely studied, and there are noticeable correlations between some bacterial species and AD pathologies, especially spirochetes and some of the oral microbes. Borrelia burgdorferi has been seen to correlate with Aβ plaques and NFTs in infected cells. Because of the evidence of spirochetes in AD patients, Treponema pallidum and other oral treponemes are speculated to be a potential cause of AD. T. pallidum has been seen to form aggregates in the brain when the disease disseminates to the brain that closely resemble the Aβ plaques of AD patients. This review examines the evidence as to whether pathogens could be the cause of AD and its pathology. It offers novel speculations that treponemes may be able to induce or correlate with Alzheimer’s disease. Full article
(This article belongs to the Special Issue Antimicrobial Testing (AMT))
17 pages, 592 KiB  
Review
Beating the Bio-Terror Threat with Rapid Antimicrobial Susceptibility Testing
by Shahar Rotem, Ida Steinberger-Levy, Ofir Israeli, Eran Zahavy and Ronit Aloni-Grinstein
Microorganisms 2021, 9(7), 1535; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9071535 - 19 Jul 2021
Cited by 2 | Viewed by 2719
Abstract
A bioterror event using an infectious bacterium may lead to catastrophic outcomes involving morbidity and mortality as well as social and psychological stress. Moreover, a bioterror event using an antibiotic resistance engineered bacterial agent may raise additional concerns. Thus, preparedness is essential to [...] Read more.
A bioterror event using an infectious bacterium may lead to catastrophic outcomes involving morbidity and mortality as well as social and psychological stress. Moreover, a bioterror event using an antibiotic resistance engineered bacterial agent may raise additional concerns. Thus, preparedness is essential to preclude and control the dissemination of the bacterial agent as well as to appropriately and promptly treat potentially exposed individuals or patients. Rates of morbidity, death, and social anxiety can be drastically reduced if the rapid delivery of antimicrobial agents for post-exposure prophylaxis and treatment is initiated as soon as possible. Availability of rapid antibiotic susceptibility tests that may provide key recommendations to targeted antibiotic treatment is mandatory, yet, such tests are only at the development stage. In this review, we describe the recently published rapid antibiotic susceptibility tests implemented on bioterror bacterial agents and discuss their assimilation in clinical and environmental samples. Full article
(This article belongs to the Special Issue Antimicrobial Testing (AMT))
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