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Antibiotics
Special Issues
Rapid Diagnostics of the Antimicrobial Resistance
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Rapid Diagnostics of the Antimicrobial Resistance

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

Deadline for manuscript submissions: closed (31 December 2021) | Viewed by 30805

Special Issue Editors

Dr. Seok Hoon Jeong

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Guest Editor
Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
Interests: antimicrobial resistance surveillance; mechanism of antimicrobial resistance; rapid diagnosis of antimicrobial resistance
Dr. Eun-Jeong Yoon

E-Mail
Guest Editor
Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul 03722, Korea
Interests: acquired antimicrobial resistance; mobile genetic elements; antibacterial drugs; bacterial fitness; bacterial genetics

Special Issue Information

Dear Colleagues,

Antimicrobial resistance threatens greatly the public health by limiting the antimicrobial treatment useful for the patients with infectious diseases. Discovery of new antimicrobials is not as fast as the antimicrobial resistant bugs are evolving to be resistant to the existing drugs. Since misuse of antibiotics often accelarates the issue, rapid diagnostics of the antimicrobial resistance in the infection-causative pathogen, which can provide critical information for adequate definate therapy, has the top priority to fight against the enormous burden of infectious diseases by antimicrobial resistant pathogen.

The traditional method to diagnose antimicrobial resistance is based on bacteriological techniques. The development of molecular and biochemical methods, such as PCR and immunochromatography, helped in the rapid reporting of antimicrobial resistance. Recently, advanced diagnostic methods have been developed to guarantee not only accuracy and speed, but also cost.

In this Special Issue, we aim to highlight the recent developments in rapid diagnositcs for antimicrobial resistance, as well as up-to-date approaches on new diagnositcs systems.

We invite authors to submit manuscripts on the following topics:

  • Modified phenotypic methods (such as imaging) to detect antimicrobial resistance pathogens
  • New technical approaches to detect antimicrobial resistance pathogens
  • Novel approach for rapid diagnostic methods for antimicrobial resistance
  • Novel biomarkers to detect antimicrobial resistance pathogens
  • Evaluation of new diagnostic methods
  • Rapid point-of-care
  • Database to search for antimicrobial resistance determinants

Prof. Seok Hoon Jeong
Dr. Eun-Jeong Yoon
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. 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

  • Diagnosis
  • Antimicrobial resistance
  • Rapid diagnostics
  • Evaluation of novel diagnostic methods

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Published Papers (7 papers)

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Research

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7 pages, 244 KiB  
Communication
A Novel Method to Assess Antimicrobial Susceptibility in Commensal Oropharyngeal Neisseria—A Pilot Study
by Jolein Gyonne Elise Laumen, Saïd Abdellati, Christophe Van Dijck, Delphine Martiny, Irith De Baetselier, Sheeba Santhini Manoharan-Basil, Dorien Van den Bossche and Chris Kenyon
Antibiotics 2022, 11(1), 100; https://doi.org/10.3390/antibiotics11010100 - 13 Jan 2022
Cited by 4 | Viewed by 2014
Abstract
Commensal Neisseria provide a reservoir of resistance genes that can be transferred to the pathogens Neisseria gonorrhoeae and N. meningitidis in the human oropharynx. Surveillance programs are thus needed to monitor resistance in oropharyngeal commensal Neisseria, but currently the isolation and antimicrobial susceptibility [...] Read more.
Commensal Neisseria provide a reservoir of resistance genes that can be transferred to the pathogens Neisseria gonorrhoeae and N. meningitidis in the human oropharynx. Surveillance programs are thus needed to monitor resistance in oropharyngeal commensal Neisseria, but currently the isolation and antimicrobial susceptibility testing of these commensals is laborious, complex and expensive. In addition, the posterior oropharyngeal/tonsillar swab, which is commonly used to sample oropharyngeal Neisseria, is poorly tolerated by many individuals. We evaluated an alternative non-invasive method to isolate oropharyngeal commensal Neisseria and to detect decreased susceptibility to azithromycin using selective media (LBVT.SNR) with and without azithromycin (2 µg/mL). In this pilot study, we compared paired posterior oropharyngeal/tonsillar swabs and oral rinse-and-gargle samples from 10 participants and demonstrated that a similar Neisseria species diversity and number of colonies were isolated from both sample types. Moreover, the proportion of Neisseria colonies that had a decreased susceptibility to azithromycin was similar in the rinse samples compared to the swabs. This pilot study has produced encouraging data that a simple protocol of oral rinse-and-gargle and culture on plates selective for commensal Neisseria with and without a target antimicrobial can be used as a surveillance tool to monitor antimicrobial susceptibility in commensal oropharyngeal Neisseria. Larger studies are required to validate these findings. Full article
(This article belongs to the Special Issue Rapid Diagnostics of the Antimicrobial Resistance)
15 pages, 2242 KiB  
Article
Molecular Detection of Fluoroquinolone Resistance among Multidrug-, Extensively Drug-, and Pan-Drug-Resistant Campylobacter Species in Egypt
by Ahmed M. Ammar, Marwa I. Abd El-Hamid, Rania M. S. El-Malt, Doaa S. Azab, Sarah Albogami, Mohammad M. Al-Sanea, Wafaa E. Soliman, Mohammed M. Ghoneim and Mahmoud M. Bendary
Antibiotics 2021, 10(11), 1342; https://doi.org/10.3390/antibiotics10111342 - 3 Nov 2021
Cited by 34 | Viewed by 2857
Abstract
In recent times, resistant foodborne pathogens, especially of the Campylobacter species, have created several global crises. These crises have been compounded due to the evolution of multidrug-resistant (MDR) bacterial pathogens and the emergence of extensively drug-resistant (XDR) and pan-drug-resistant (PDR) strains. Therefore, this [...] Read more.
In recent times, resistant foodborne pathogens, especially of the Campylobacter species, have created several global crises. These crises have been compounded due to the evolution of multidrug-resistant (MDR) bacterial pathogens and the emergence of extensively drug-resistant (XDR) and pan-drug-resistant (PDR) strains. Therefore, this study aimed to investigate the development of resistance and the existence of both XDR and PDR among Campylobacter isolates. Moreover, we explored the use of the polymerase chain reaction–restriction fragment length polymorphism (PCR-RFLP) technique for the detection of fluoroquinolone (FQ)-resistant Campylobacter isolates. A total of 120 Campylobacter isolates were identified depending on both phenotypic and genotypic methods. Of note, cefoxitin and imipenem were the most effective drugs against the investigated Campylobacter isolates. Interestingly, the majority of our isolates (75%) were MDR. Unfortunately, both XDR and PDR isolates were detected in our study with prevalence rates of 20.8% and 4.2%, respectively. All FQ-resistant isolates with ciprofloxacin minimum inhibitory concentrations ≥4 µg/mL were confirmed by the genetic detection of gyrA chromosomal mutation via substitution of threonine at position 86 to isoleucine (Thr-86-to-Ile) using the PCR-RFLP technique. Herein, PCR-RFLP was a more practical and less expensive method used for the detection of FQ resistant isolates. In conclusion, we introduced a fast genetic method for the identification of FQ-resistant isolates to avoid treatment failure through the proper description of antimicrobials. Full article
(This article belongs to the Special Issue Rapid Diagnostics of the Antimicrobial Resistance)
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11 pages, 12108 KiB  
Article
Rapid and Accurate Detection of Escherichia coli and Klebsiella pneumoniae Strains Susceptible/Resistant to Cotrimoxazole through Evaluation of Cell Elongation
by Isidoro López, Fátima Otero, Rebeca Guillén, María del Carmen Fernández, Germán Bou, Jaime Gosálvez and José Luis Fernández
Antibiotics 2021, 10(6), 720; https://doi.org/10.3390/antibiotics10060720 - 15 Jun 2021
Cited by 2 | Viewed by 2101
Abstract
Trimethoprim-sulfamethoxazole is a well-known antibiotic that inhibits folic acid synthesis, a topic of renewed interest. Since resistant strains are increasingly more common, an early and accurate discrimination of susceptibility may assure confident therapy. Two morphological assays were performed in Escherichia coli (n [...] Read more.
Trimethoprim-sulfamethoxazole is a well-known antibiotic that inhibits folic acid synthesis, a topic of renewed interest. Since resistant strains are increasingly more common, an early and accurate discrimination of susceptibility may assure confident therapy. Two morphological assays were performed in Escherichia coli (n = 50; 27 non-susceptible) and Klebsiella pneumoniae (n = 52; 18 non-susceptible). First, the strains were incubated with the CLSI breakpoint of cotrimoxazole for 150 min, which induced cell lengthening in the susceptible strains. Second, the bacteria were incubated with mitomycin C (MMC) (0.5 mg/L) for 120 min to induce a SOS-linked cell enlargement higher than that obtained by cotrimoxazole alone. When cotrimoxazole was added 30 min before MMC, the inhibition of folic acid synthesis in the susceptible strain resulted in the suppression of MMC-induced extra elongation. In the non-susceptible strains, folic acid synthesis continued despite the antibiotic, so that the MMC-induced extra cell lengthening could not be impeded. Whereas the first assay resulted in five false negatives and four false positives of resistance, the results of the second assay matched those of the conventional antibiogram. This simple morphological procedure is performed in 2 h and 45 min and may allow a rapid selection of useful and relatively inexpensive therapy, thereby preserving the newer broad-spectrum antibiotics. Full article
(This article belongs to the Special Issue Rapid Diagnostics of the Antimicrobial Resistance)
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8 pages, 2884 KiB  
Article
Performance Evaluation of the Newly Developed In Vitro Rapid Diagnostic Test for Detecting OXA-48-Like, KPC-, NDM-, VIM- and IMP-Type Carbapenemases: The RESIST-5 O.K.N.V.I. Multiplex Lateral Flow Assay
by Junsung Hong, Dayoung Kang and Dokyun Kim
Antibiotics 2021, 10(4), 460; https://doi.org/10.3390/antibiotics10040460 - 19 Apr 2021
Cited by 8 | Viewed by 3393
Abstract
The objective of this study was to evaluate the performance of the RESIST-5 O.K.N.V.I. assay for identifying these five common domestic carbapenemases among a large number of clinical isolates in South Korea. A total of 268 non-duplicated clinical isolates of gram-negative bacilli were [...] Read more.
The objective of this study was to evaluate the performance of the RESIST-5 O.K.N.V.I. assay for identifying these five common domestic carbapenemases among a large number of clinical isolates in South Korea. A total of 268 non-duplicated clinical isolates of gram-negative bacilli were included in this study as follows: 258 carbapenemase-producing (CP) strains (OXA-48-like, KPC, NDM, VIM, IMP, GES, OXA-23 and two or more carbapenemase producers) and 10 non-CP carbapenem-resistant Enterobacterales (non-CP CREs). Overall sensitivity and specificity were 98.4% and 100%, respectively. In addition, all non-targeted carbapenemase producers including GES and OXA-23 producers and non-CP CREs were correctly identified as negative results. There were only four discrepant cases in which three VIM carbapenemase producers and one NDM carbapenemase producer were not detected. The RESIST-5 O.K.N.V.I. assay as an in vitro diagnostic test for detecting five common carbapenemases provided rapid and accurate results in a short time, indicating that this method could provide an innovative solution for early detection, resulting in appropriate antimicrobial treatment in the clinical field. Full article
(This article belongs to the Special Issue Rapid Diagnostics of the Antimicrobial Resistance)
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Review

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25 pages, 3276 KiB  
Review
Diagnosis of Bloodstream Infections: An Evolution of Technologies towards Accurate and Rapid Identification and Antibiotic Susceptibility Testing
by Kristel C. Tjandra, Nikhil Ram-Mohan, Ryuichiro Abe, Marjan M. Hashemi, Jyong-Huei Lee, Siew Mei Chin, Manuel A. Roshardt, Joseph C. Liao, Pak Kin Wong and Samuel Yang
Antibiotics 2022, 11(4), 511; https://doi.org/10.3390/antibiotics11040511 - 12 Apr 2022
Cited by 26 | Viewed by 8188
Abstract
Bloodstream infections (BSI) are a leading cause of death worldwide. The lack of timely and reliable diagnostic practices is an ongoing issue for managing BSI. The current gold standard blood culture practice for pathogen identification and antibiotic susceptibility testing is time-consuming. Delayed diagnosis [...] Read more.
Bloodstream infections (BSI) are a leading cause of death worldwide. The lack of timely and reliable diagnostic practices is an ongoing issue for managing BSI. The current gold standard blood culture practice for pathogen identification and antibiotic susceptibility testing is time-consuming. Delayed diagnosis warrants the use of empirical antibiotics, which could lead to poor patient outcomes, and risks the development of antibiotic resistance. Hence, novel techniques that could offer accurate and timely diagnosis and susceptibility testing are urgently needed. This review focuses on BSI and highlights both the progress and shortcomings of its current diagnosis. We surveyed clinical workflows that employ recently approved technologies and showed that, while offering improved sensitivity and selectivity, these techniques are still unable to deliver a timely result. We then discuss a number of emerging technologies that have the potential to shorten the overall turnaround time of BSI diagnosis through direct testing from whole blood—while maintaining, if not improving—the current assay’s sensitivity and pathogen coverage. We concluded by providing our assessment of potential future directions for accelerating BSI pathogen identification and the antibiotic susceptibility test. While engineering solutions have enabled faster assay turnaround, further progress is still needed to supplant blood culture practice and guide appropriate antibiotic administration for BSI patients. Full article
(This article belongs to the Special Issue Rapid Diagnostics of the Antimicrobial Resistance)
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14 pages, 1144 KiB  
Review
MALDI-TOF Mass Spectrometry Technology as a Tool for the Rapid Diagnosis of Antimicrobial Resistance in Bacteria
by Eun-Jeong Yoon and Seok Hoon Jeong
Antibiotics 2021, 10(8), 982; https://doi.org/10.3390/antibiotics10080982 - 14 Aug 2021
Cited by 37 | Viewed by 7816
Abstract
Species identification by using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is a routine diagnostic process for infectious diseases in current clinical settings. The rapid, low-cost, and simple to conduct methodology is expanding its application in clinical microbiology laboratories to diagnose the [...] Read more.
Species identification by using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is a routine diagnostic process for infectious diseases in current clinical settings. The rapid, low-cost, and simple to conduct methodology is expanding its application in clinical microbiology laboratories to diagnose the antimicrobial resistance (AMR) in microorganisms. Primarily, antimicrobial susceptibility testing is able to be carried out either by comparing the area under curve of MALDI spectra of bacteria grown in media with antimicrobial drugs or by identifying the shift peaks of bacteria grown in media including 13C isotope with antimicrobial drugs. Secondly, the antimicrobial resistance is able to be determined through identifying (i) the antimicrobial-resistant clonal groups based on the fingerprints of the clone, (ii) the shift peak of the modified antimicrobial drug, which is inactivated by the resistance determinant, (iii) the shift peak of the modified antimicrobial target, (iv) the peak specific for the antimicrobial determinant, and (v) the biomarkers that are coproduced proteins with AMR determinants. This review aims to present the current usage of the MALDI-TOF MS technique for diagnosing antimicrobial resistance in bacteria, varied approaches for AMR diagnostics using the methodology, and the future applications of the methods for the accurate and rapid identification of AMR in infection-causing bacterial pathogens. Full article
(This article belongs to the Special Issue Rapid Diagnostics of the Antimicrobial Resistance)
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Other

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6 pages, 861 KiB  
Brief Report
RapidResa Polymyxin Acinetobacter NP® Test for Rapid Detection of Polymyxin Resistance in Acinetobacter baumannii
by Maxime Bouvier, Mustafa Sadek, Stefano Pomponio, Fernando D’Emidio, Laurent Poirel and Patrice Nordmann
Antibiotics 2021, 10(5), 558; https://doi.org/10.3390/antibiotics10050558 - 11 May 2021
Cited by 1 | Viewed by 3001
Abstract
A homemade and culture-based test, relying on the visual detection of the reduction of the resazurin reagent (a cell viability indicator), has been developed for the rapid detection of polymyxin resistance in Acinetobacter baumannii. Here, we evaluated the industrial version of this [...] Read more.
A homemade and culture-based test, relying on the visual detection of the reduction of the resazurin reagent (a cell viability indicator), has been developed for the rapid detection of polymyxin resistance in Acinetobacter baumannii. Here, we evaluated the industrial version of this test, the RapidResa Polymyxin Acinetobacter NP® test (Liofilchem, Italy). A well-characterized panel of 68 clinical A. baumannii strains (36 polymyxin-susceptible, 26 polymyxin-resistant A. baumannii, and 6 colistin-heteroresistant isolates) of worldwide origin was tested. All the colistin-susceptible A. baumannii isolates gave negative results according to the RapidResa Polymyxin Acinetobacter NP® test, except for a single isolate that gave a false-positive result. Out of the 26 colistin-resistant A. baumannii strains, 25 were correctly identified as colistin resistant using the RapidResa Polymyxin Acinetobacter NP® test. Only a single colistin-resistant A. baumannii strain gave a false-negative result. Additionally, the six colistin-heteroresistant isolates tested gave positive results. Altogether, the sensitivity and the specificity of the test were found to be 96% and 97%, respectively. The turn-around-time of this easy-to-perform test was 3-4h, which showed excellent reliability for identification of polymyxin resistance in A. baumannii. The RapidResa Polymyxin Acinetobacter NP® test allows a rapid differentiation between polymyxin-susceptible and -resistant A. baumannii isolates, which may contribute to optimization of the use of polymyxins for treating infections due to multidrug-resistant A. baumannii. Full article
(This article belongs to the Special Issue Rapid Diagnostics of the Antimicrobial Resistance)
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