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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 October 2023) | Viewed by 18218

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Dr. Suresh Joshi

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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
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Special Issue Information

Dear Colleagues,

This Special Issue is the continuation of our previous special issue "Antimicrobial Testing (AMT)".

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

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Antimicrobial Testing (AMT) 3.0 in Microorganisms

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10 pages, 283 KiB

Open AccessArticle

Antimicrobial Resistance in Rapidly Growing Nontuberculous Mycobacteria among Domestic and Wild Animals Emphasizing the Zoonotic Potential

by Irena Reil, Silvio Špičić, Ljubo Barbić, Sanja Duvnjak, Gordan Kompes, Miroslav Benić, Dora Stojević, Željko Cvetnić, Jurica Arapović and Maja Zdelar-Tuk

Microorganisms 2023, 11(10), 2520; https://doi.org/10.3390/microorganisms11102520 - 09 Oct 2023

Viewed by 756

Abstract

Non-tuberculous mycobacteria (NTM) are opportunistic pathogens capable of causing infections in humans and animals. The aim of this study was to demonstrate the potential role of domestic and wild animals as a reservoir of multiple resistant, rapidly growing NTM strains representing a potential zoonotic threat to humans. A total of 87 animal isolates belonging to 11 rapidly growing species (visible colonies appear within three to seven days) were genotyped and tested for susceptibility to the 15 most commonly used antibiotics in the treatment of such infections in a human clinic. By determining the antimicrobial susceptibility, the most prevalent resistance was found to cephalosporins (>50%), followed by amoxicillin–clavulanate (31.0%), clarithromycin (23.0%), tobramycin (14.9%) and doxycycline (10.3%). Resistance to imipenem, ciprofloxacin, minocycline and linezolid was notably lower (<7.0%). All tested isolates were susceptible to amikacin and moxifloxacin. The most frequent resistance was proved in the most pathogenic species: M. fortuitum, M. neoaurum, M. vaccae and M. porcinum. Meanwhile, other species displayed a higher sensitivity rate. No significant resistance differences between domestic and wild animals were found. The established significant frequency of resistance highlights the significant zoonotic potential posed by circulating rapidly growing NTM strains, which could lead to challenges in the treatment of these infections. Full article

(This article belongs to the Special Issue Antimicrobial Testing (AMT) 2.0)

13 pages, 2081 KiB

Open AccessArticle

Antimicrobial Resistance Is Prevalent in E. coli and Other Enterobacterales Isolated from Public and Private Drinking Water Supplies in the Republic of Ireland

by Maureen Daly, James Powell, Nuala H. O’Connell, Liz Murphy and Colum P. Dunne

Microorganisms 2023, 11(5), 1224; https://doi.org/10.3390/microorganisms11051224 - 06 May 2023

Cited by 5 | Viewed by 2338

Abstract

High levels of bacterial antimicrobial resistance (AMR) have been reported in many environmental studies conducted in Ireland and elsewhere. The inappropriate use of antibiotics in both human and animal healthcare as well as concentrations of residual antibiotics being released into the environment from wastewaters are thought to be contributing factors. Few reports of AMR in drinking water-associated microbes are available for Ireland or internationally. We analysed 201 enterobacterales from group water schemes and public and private water supplies, only the latter having been surveyed in Ireland previously. The organisms were identified using conventional or molecular techniques. Antimicrobial susceptibility testing for a range of antibiotics was performed using the ARIS 2X interpreted in accordance with EUCAST guidelines. A total of 53 Escherichia coli isolates, 37 Serratia species, 32 Enterobacter species and enterobacterales from seven other genera were identified. A total of 55% of isolates were amoxicillin resistant, and 22% were amoxicillin-clavulanic acid resistant. A lower level of resistance (<10%) was observed to aztreonam, chloramphenicol, ciprofloxacin, gentamicin, ceftriaxone and trimethoprim-sulfamethoxazole. No resistance to amikacin, piperacillin/tazobactam, ertapenem or meropenem was detected. The level of AMR detected in this study was low but not insignificant and justifies ongoing surveillance of drinking water as a potential source of antimicrobial resistance. Full article

(This article belongs to the Special Issue Antimicrobial Testing (AMT) 2.0)

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17 pages, 1363 KiB

Open AccessArticle

Towards a Standardized Antimicrobial Susceptibility Testing Method for Mycoplasma hyorhinis

by Lisa Käbisch, Anne-Kathrin Schink, Doris Höltig, Joachim Spergser, Corinna Kehrenberg and Stefan Schwarz

Microorganisms 2023, 11(4), 994; https://doi.org/10.3390/microorganisms11040994 - 11 Apr 2023

Cited by 1 | Viewed by 1564

Abstract

Conducting antimicrobial susceptibility testing (AST) in a comparable manner requires the availability of a standardized method. Organizations, such as the Clinical and Laboratory Standards Institute (CLSI) or the European Committee on Antimicrobial Susceptibility Testing (EUCAST), provide standardized protocols for a range of fastidious bacteria but not for Mycoplasma hyorhinis. We developed a broth microdilution method for testing M. hyorhinis in a standardized and harmonized way using a modified Friis broth devoid of antimicrobial or otherwise bacterial growth-inhibiting agents. The type strain M. hyorhinis DSM 25591 was chosen to establish the methodology. The antimicrobial agents of interest were doxycycline, enrofloxacin, erythromycin, florfenicol, gentamicin, marbofloxacin, tetracycline, tiamulin, tilmicosin, tulathromycin, and tylosin, tested by using commercial Sensititre^TM microtiter plates. In addition, the suitability of the methodology was evaluated via variation of the individual ingredients of the modified Friis broth by either using different batches or choosing other distributors. Despite these alterations, the method provided reliable results. We obtained repeatable minimal inhibitory concentrations for all six tested field isolates and the M. hyorhinis type strain. With this newly proposed method, we aim to provide an improved AST method for diagnostic laboratories and monitoring purposes with better comparability between times and countries. In addition, this new method will allow for an improvement of targeted treatments using antimicrobial agents and thereby reduce the options for resistance development. Full article

(This article belongs to the Special Issue Antimicrobial Testing (AMT) 2.0)

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12 pages, 1818 KiB

Open AccessArticle

The Optimal Effective Concentration Combination (OPECC) as a Novel Method for Evaluating the Effects of Binary Application of Antibacterial Compounds

by Karl-Anton Hiller, Verena Wenzl, Eva-Maria Forster, Fabian Cieplik and Tim Maisch

Microorganisms 2023, 11(4), 830; https://doi.org/10.3390/microorganisms11040830 - 24 Mar 2023

Cited by 2 | Viewed by 1156

Abstract

Combination therapies appear to be beneficial for preventing bacterial resistance to antibacterial approaches. The aim of this study was to define and determine an optimal effective concentration combination (OPECC) for binary application of antibacterial compounds. The antiseptics chlorhexidine (CHX), benzalkonium chloride (BAC), and cetylpyridinium chloride (CPC), as well as the antibiotic ciprofloxacin (CIP), were tested against planktonic Escherichia coli in binary combinations by applying a checkerboard assay, and then evaluated according to the established synergism principles. Extending the checkerboard method, the optical density (OD) of the wells was measured photometrically. On the borderline between effective (OD = 0) and non-effective (OD > 0) eradication of the bacterial cultures, the OPECC was determined. Binary combinations of CPC or CHX with BAC were assessed as either synergistic or indifferent, respectively, while there was no OPECC to calculate. For all other binary combinations, an OPECC was derivable, and these were assessed as either synergistic or indifferent. In conclusion, the evaluation of the binary combination application of antibacterial compounds based on the checkerboard method was refined to such an extent that it was possible to determine at least one concentration pair that could be defined and considered as an OPECC, independently of the evaluation of the system according to the different synergy principles. In general, the method presented herein for determining an OPECC can be applied to any conceivable method or system aimed at the eradication of a pathogen. Full article

(This article belongs to the Special Issue Antimicrobial Testing (AMT) 2.0)

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12 pages, 2094 KiB

Open AccessArticle

Cherax quadricarinatus Resistant to Chequa iflavirus: A Pilot Study

by Geetika Nambiar, Leigh Owens and Jennifer Elliman

Microorganisms 2023, 11(3), 578; https://doi.org/10.3390/microorganisms11030578 - 24 Feb 2023

Viewed by 1148

Abstract

High mortalities of redclaw crayfish (Cherax quadricarinatus) were reported from northern Queensland farms, mainly attributed to two viruses, Chequa iflavirus and Athtab bunyavirus. From a research population of redclaw crayfish with these pre-existing viral infections, five individuals were found uninfected by Chequa iflavirus but infected with Athtab bunyavirus. A pilot study was designed to examine if progeny crayfish from this cohort were resistant to infections by Chequa iflavirus. Two experiments measured changes in viral load with RT-qPCR. Seven donors, four negative controls and six crayfish injected with a purified virus or saline were used. In Experiment 1, the purified viral inoculum was injected into the crayfish, and they were bled 14 days post-injection (dpi). In Experiment 2, haemolymph containing the viruses was injected into the same crayfish and they were bled at 24 hpi, 48 hpi, 7 dpi and 14 dpi. In Exp. 1, the crayfish cleared Chequa iflavirus infections within 14 dpi, while in Exp. 2, it was within 24 hpi. One mortality was observed, but that crayfish had cleared the virus before dying. The number of copies of Athtab bunyavirus and the weights of the crayfish did not differ significantly (p > 0.05) between the control and injected crayfish. Histology of crayfish all showed that the haemolymph vessels were clear of granulomas, suggesting no bacterial involvement. There was no melanisation in the gill tissue of control crayfish, but it was prominent in virus-injected crayfish. Neither group had haemocytic infiltration of the muscle fibres. Anti-viral immune mechanisms of RNA interference and Cherax quadricarinatus Down Syndrome Cell Adhesion Molecule (DSCAM) are hypothesised to be involved in viral clearance. We conclude that these crayfish were resistant to Chequa iflavirus infections and could be commercially exploited by aquaculturists as a nuclear breeding stock if numbers are increased over time. Full article

(This article belongs to the Special Issue Antimicrobial Testing (AMT) 2.0)

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19 pages, 7540 KiB

Open AccessArticle

Synthesis, Photophysical Characterization and Evaluation of Biological Properties of C7, a Novel Symmetric Tetra-Imidazolium-Bis-Heterocycle

by Hannah Kunstek, Melaine Wang, Hiba Hussein, Ines Dhouib, Bassem Khemakhem, Arnaud Risler, Stephanie Philippot, Celine Frochot, Philippe Arnoux, Bertrand Fournier, Mihayl Varbanov and Florence Dumarçay-Charbonnier

Microorganisms 2023, 11(2), 495; https://doi.org/10.3390/microorganisms11020495 - 16 Feb 2023

Cited by 1 | Viewed by 1647

Abstract

A novel symmetric tetra-imidazolium-bis-heterocycle, called C7, was designed and synthesized in a quick two-step pathway, with the objective to synthesize biologically active supramolecular assembly. The synthesized compound was then analyzed for its photophysical properties, for a potential application in theragnostic (fluorescence) or phototherapy (photodynamic therapy, with the production of reactive oxygen species, such as singlet oxygen ¹O₂). C7 was thus screened for its biological activity, in particular against important human pathogens of viral origin (respiratory viruses such as adenovirus type 2 and human coronavirus 229E) and of fungal and bacterial origin. The compound showed limited antiviral activity, combined with very good antiproliferative activity against breast cancer, and head and neck squamous cell carcinoma models. Interestingly, the selected compound showed excellent antibacterial activity against a large array of Gram-positive and Gram-negative clinically isolated pathogenic bacteria, with a possible inhibitory mechanism on the bacterial cell wall synthesis studied with electron microscopy and molecular docking tools. Collectively, the newly synthesized compound C7 could be considered as a potential lead for the development of new antibacterial treatment, endowed with basic photophysical properties, opening the door towards the future development of phototherapy approaches. Full article

(This article belongs to the Special Issue Antimicrobial Testing (AMT) 2.0)

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10 pages, 290 KiB

Open AccessArticle

Evaluation of a Shotgun Metagenomics Approach for Detection of ESBL- and/or Carbapenemase-Producing Enterobacterales in Culture Negative Patients Recovered from Acute Leukemia

by Pilar Lumbreras-Iglesias, Carlos Sabater, Ainhoa Fernández Moreno, Paula López de Ugarriza, Ana Fernández-Verdugo, Abelardo Margolles, María Rosario Rodicio, Teresa Bernal and Javier Fernández

Microorganisms 2023, 11(2), 402; https://doi.org/10.3390/microorganisms11020402 - 04 Feb 2023

Cited by 1 | Viewed by 1326

Abstract

Patients diagnosed with acute leukemia (AL) have a weakened immune system. Infections acquired by these patients are cause for concern and especially worrisome when Gram-negative multidrug-resistant (MDR) bacteria are involved, as they are difficult to treat, especially in the case of ESBL- and/or carbapenemase-producing Enterobacterales. Culture-based approaches have been relied on over the past decades as the method of choice for the early detection of gut colonization by MDR Gram-negative bacteria. However, various studies have indicated its limited sensitivity, underlining the need for new screening procedures in onco-hematological patients. Here, we evaluated a shotgun metagenomics approach to detect ESBL- and/or carbapenemase-producing Enterobacterales in the gut of 28 patients who had recovered from AL, which were previously colonized by these bacteria but cured at the time of sampling, as judged by culture-based methods. No ESBL or carbapenemase determinants were detected among the many resistance genes found by the metagenomics approach, supporting that patients were truly decolonized, with considerable consequences for their future clinical management. Due to the relatively low number of patients available for the present investigation, further studies should be conducted to support the utility and applicability of metagenomics for the routine screening of MDR bacteria in onco-hematological patients. Full article

(This article belongs to the Special Issue Antimicrobial Testing (AMT) 2.0)

12 pages, 2247 KiB

Open AccessArticle

3D Biofilm Models Containing Multiple Species for Antimicrobial Testing of Wound Dressings

by Kirsten Reddersen, Jörg Tittelbach and Cornelia Wiegand

Microorganisms 2022, 10(10), 2027; https://doi.org/10.3390/microorganisms10102027 - 13 Oct 2022

Viewed by 1814

Abstract

The treatment of chronic wounds presents a major challenge in medical care. In particular, the effective treatment of bacterial infections that occur in the form of biofilms is of crucial importance. To develop successful antibiofilm strategies for chronic wound treatment, biofilm models are needed that resemble the in vivo situation, are easy to handle, standardizable, and where results are readily transferable to the clinical situation. We established two 3D biofilm models to distinguish the effectiveness of wound dressings on important microorganisms present in chronic wounds. The first 3D biofilm model contains Staphylococcus aureus, Escherichia coli, and Acinetobacter baumannii, while the second is based on Pseudomonas aeruginosa. Bacteria are cultivated in a nutrient-rich agar/gelatin mix, into which air bubbles are incorporated. This results in a mature biofilm growing in clusters similar to its organization in chronic wounds. The models are convenient to use, have low variability and are easy to establish in the laboratory. Treatment with polihexanide and silver-containing wound dressings showed that the models are very well suited for antimicrobial testing and that they can detect differences in the efficacy of antimicrobial substances. Therefore, these models present valuable tools in the development of effective antibiofilm strategies in chronic wounds. Full article

(This article belongs to the Special Issue Antimicrobial Testing (AMT) 2.0)

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17 pages, 589 KiB

Open AccessReview

Anti-Infective and Toxicity Properties of Carbon Based Materials: Graphene and Functionalized Carbon Nanotubes

by Naghmeh Hadidi and Maryam Mohebbi

Microorganisms 2022, 10(12), 2439; https://doi.org/10.3390/microorganisms10122439 - 09 Dec 2022

Cited by 4 | Viewed by 1942

Abstract

Recently, antimicrobial activities of various carbon-based nanomaterials against specific pathogens have become one of the most significant research interests in this field. Carbon nanotubes (CNTs) are promising multidisciplinary nanostructures in biomedicine, drug delivery, genetic engineering, biosensors, and artificial implants. However, the biomedical administration of CNTs is dependent on their solubility, toxicity, and biocompatibility, as well as novel drug-delivery applications through optimization of the drug’s loading capacity, cellular absorption, and continuous release within the target cell. The usage of CNTs and Graphene materials as antimicrobial agents and nanocarriers for antibiotics delivery would possibly improve their bioavailability and facilitate better anti-infective therapy. However, it is worth mentioning that CNTs’ antimicrobial activity and toxicity are highly dependent on their preparation and synthesis method. Various types of research have confirmed that diameter, length, residual catalyst, metal content, surface coating, electronic structure, and dispersibility would affect CNTs’ toxicity toward bacteria and human cells. In this review article, a general study was performed on the antimicrobial properties of carbon-based nanomaterials, as well as their toxicity and applications in confronting different microorganisms. This study could be useful for researchers who are looking for new and effective drug delivery methods in the field of microbial resistance. Full article

(This article belongs to the Special Issue Antimicrobial Testing (AMT) 2.0)

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18 pages, 682 KiB

Open AccessReview

Overcoming Antibiotic Resistance with Novel Paradigms of Antibiotic Selection

by George Tetz and Victor Tetz

Microorganisms 2022, 10(12), 2383; https://doi.org/10.3390/microorganisms10122383 - 30 Nov 2022

Cited by 7 | Viewed by 2906

Abstract

Conventional antimicrobial susceptibility tests, including phenotypic and genotypic methods, are insufficiently accurate and frequently fail to identify effective antibiotics. These methods predominantly select therapies based on the antibiotic response of only the lead bacterial pathogen within pure bacterial culture. However, this neglects the fact that, in the majority of human infections, the lead bacterial pathogens are present as a part of multispecies communities that modulate the response of these lead pathogens to antibiotics and that multiple pathogens can contribute to the infection simultaneously. This discrepancy is a major cause of the failure of antimicrobial susceptibility tests to detect antibiotics that are effective in vivo. This review article provides a comprehensive overview of the factors that are missed by conventional antimicrobial susceptibility tests and it explains how accounting for these methods can aid the development of novel diagnostic approaches. Full article

(This article belongs to the Special Issue Antimicrobial Testing (AMT) 2.0)

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