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Pathogens
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Detection and Characterization of Drug-Resistant Organisms
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Detection and Characterization of Drug-Resistant Organisms

A special issue of Pathogens (ISSN 2076-0817).

Deadline for manuscript submissions: closed (30 October 2022) | Viewed by 53612

Special Issue Editors

Dr. Andaleeb Sajid

E-Mail Website
Guest Editor
Section of Infectious Diseases, Yale School of Medicine, Yale university, New Haven 06519, Connecticut USA
Interests: vaccine and drug development; pharmacology; drug resistance; host–pathogen interactions; biochemistry; molecular biology; microbiology
Special Issues, Collections and Topics in MDPI journals
Dr. Gunjan Arora

E-Mail Website
Guest Editor
Section of Infectious Diseases, Yale School of Medicine, Yale university, New Haven 06519, CT, USA
Interests: malaria vaccine; innate immunology
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

In this era, several nations are facing the scourge of more than one pathogen. This situation has raised significant awareness, and more efforts are being given to find the treatment of infectious diseases, primarily caused by bacteria, parasites, and viruses. Several drugs and derivatives are being discovered that have a range of effects against pathogens. Despite reasonable success in disease prognosis and in resolving the issue, development of resistant forms of these pathogens has been a setback. There are multiple levels of resistance, namely: multi-drug resistant (MDR), extremely drug resistant (XDR), and, in some cases, totally drug resistant (TDR) strains of the pathogens have also evolved. These include bacterial diseases, such as tuberculosis, pneumonia, and gonorrhea; viral diseases, such as HIV; and parasitic diseases, such as Lyme disease and malaria. Besides resistance, pathogens also exhibit persistence or tolerance to the drugs, without actually mutating. This Special Issue, entitled “Detection and Characterization of Antibiotic Resistant Organisms”, focuses on the concepts of resistance, persistence, and tolerance in human pathogens and their detection, characterization, and treatment. This Special Issue emphasizes the escalating problem of drug-resistance in pathogens, and supplements the existing literature on several diseases.

In this Issue, the discussion is open to a range of topics, including the following:

  • Manuscripts can be focused on the reasons behind the development of drug-resistance: (a) variations at a pathogen level, including mutations, molecular alterations, gene expression, post-translational modifications, evolution, dormancy, and persistence; (b) host level variations, such as level of infection, immune response, microbiome, compliance, and side-effects; and (c) drug designing, substrates of efflux-pumps, pharmacokinetics, activation, chemical properties, drug-targets, etc.
  • Detection of drug resistant organisms: the detection of drug resistant strains of the pathogens has been a major obstacle for all diseases. The diagnosis of a disease and its treatment with appropriate drugs can only be achieved once the pathogen’s sensitivity level has been defined. With this background, we will discuss the small-scale and high-throughput screening of the patient samples, which will help in detection.
  • Unfortunately, a large number of infections now exhibit resistance to one or more drugs, and need to be treated after careful diagnosis. The extent of the problem can be understood from the emergence of infections that are untreatable with the currently available regimen. In view of this, there will be discussions on the characterization of drug resistant organisms and strategies to combat and resolve the drug resistance. This can extend from the prevention to the treatment of infections.
  • Other topics that are not mentioned here but are still relevant to the broad topic of this Special Issue are also welcome.

Dr. Andaleeb Sajid
Dr. Gunjan Arora
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. Pathogens 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

  • antibiotics
  • drugs
  • resistance
  • bacterial pathogens
  • viruses
  • vector-borne diseases
  • persistence
  • drug targets
  • genetic mutations
  • MDR
  • XDR
  • high-throughput screening

Published Papers (16 papers)

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20 pages, 994 KiB  
Article
Serotypes, Antibiotic Susceptibility, Genotypic Virulence Profiles and SpaA Variants of Erysipelothrix rhusiopathiae Strains Isolated from Pigs in Poland
by Marta Dec, Dominik Łagowski, Tomasz Nowak, Dorota Pietras-Ożga and Klaudia Herman
Pathogens 2023, 12(3), 409; https://0-doi-org.brum.beds.ac.uk/10.3390/pathogens12030409 - 03 Mar 2023
Cited by 3 | Viewed by 1879
Abstract
The aim of the study was phenotypic and genotypic characterization of Erysipelothrix rhusiopathiae strains isolated from diseased pigs in Poland and comparison of the SpaA (Surface protective antigen A) sequence of wild-type strains with the sequence of the R32E11 vaccine strain. The antibiotic [...] Read more.
The aim of the study was phenotypic and genotypic characterization of Erysipelothrix rhusiopathiae strains isolated from diseased pigs in Poland and comparison of the SpaA (Surface protective antigen A) sequence of wild-type strains with the sequence of the R32E11 vaccine strain. The antibiotic susceptibility of the isolates was assessed using the broth microdilution method. Resistance genes, virulence genes, and serotype determinants were detected using PCR. The gyrA and spaA amplicons were sequenced to determine nonsynonymous mutations. The E. rhusiopathiae isolates (n = 14) represented serotypes 1b (42.8%), 2 (21.4%), 5 (14.3%), 6 (7.1%), 8 (7.1%), and N (7.1%). All strains were susceptible to β-lactams, macrolides and florfenicol. One isolate showed resistance to lincosamides and tiamulin, and most strains were resistant to tetracycline and enrofloxacin. High MIC values of gentamicin, kanamycin, neomycin, trimethoprim, trimethoprim/sulfadiazine, and rifampicin were recorded for all isolates. Phenotypic resistance was correlated with the presence of the tetM, int-Tn, lasE, and lnuB genes. Resistance to enrofloxacin was due to a mutation in the gyrA gene. All strains contained the spaA gene and several other genes putatively involved in pathogenesis (nanH.1, nanH.2, intl, sub, hlyA, fbpA, ERH_1356, cpsA, algI, rspA and rspB) Seven variants of the SpaA protein were found in the tested strains, and a relationship between the structure of SpaA and the serotype was noted. E. rhusiopathiae strains occurring in pigs in Poland are diverse in terms of serotype and SpaA variant and differ antigenically from the R32E11 vaccine strain. Beta-lactam antibiotics, macrolides, or phenicols should be the first choice for treatment of swine erysipelas in Poland. However, due to the small number of tested strains, this conclusion should be approached with caution. Full article
(This article belongs to the Special Issue Detection and Characterization of Drug-Resistant Organisms)
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9 pages, 273 KiB  
Article
Cefiderocol against Multi-Drug and Extensively Drug-Resistant Escherichia coli: An In Vitro Study in Poland
by Patrycja Zalas-Więcek, Katarzyna Płachta and Eugenia Gospodarek-Komkowska
Pathogens 2022, 11(12), 1508; https://0-doi-org.brum.beds.ac.uk/10.3390/pathogens11121508 - 09 Dec 2022
Cited by 2 | Viewed by 1380
Abstract
Cefiderocol (CFDC) is a novel, broad-spectrum siderophore cephalosporin with potential activity against multi-drug (MDR) and extensively drug-resistant (XDR) Enterobacterales, including carbapenem-resistant strains. We assessed the in vitro susceptibility to CFDC of MDR, and XDR E. coli isolates derived from clinical samples of hospitalized [...] Read more.
Cefiderocol (CFDC) is a novel, broad-spectrum siderophore cephalosporin with potential activity against multi-drug (MDR) and extensively drug-resistant (XDR) Enterobacterales, including carbapenem-resistant strains. We assessed the in vitro susceptibility to CFDC of MDR, and XDR E. coli isolates derived from clinical samples of hospitalized patients. Disk diffusion (DD) and MIC (minimum inhibitory concentration) test strip (MTS) methods were used. The results were interpreted based on EUCAST (version 12.0 2022) recommendations. Among all E. coli isolates, 98 (94.2%) and 99 (95.2%) were susceptible to CFDC when the DD and MTS methods were used, respectively (MIC range: <0.016–4 µg/mL, MIC50: 0.19 µg/mL, MIC90: 0.75 µg/mL). With the DD and MTS methods, all (MIC range: 0.016–2 µg/mL, MIC50: 0.19 µg/mL, MIC90: 0.75 µg/mL) but three (96.6%) ESBL-positive isolates were susceptible to CFDC. Out of all the metallo-beta-lactamase-positive E. coli isolates (MIC range: 0.016–4 µg/mL, MIC50: 0.5 µg/mL, MIC90: 1.5 µg/mL), 16.7% were resistant to CFDC with the DD method, while 11.1% were resistant to CFDC when the MTS method was used. CFDC is a novel therapeutic option against MDR and XDR E. coli isolates and is promising in the treatment of carbapenem-resistant E. coli strains, also for those carrying Verona integron-encoded metallo-beta-lactamases, when new beta-lactam-beta-lactamase inhibitors cannot be used. Full article
(This article belongs to the Special Issue Detection and Characterization of Drug-Resistant Organisms)
17 pages, 1009 KiB  
Article
Bacterial Communities and Antibiotic Resistance of Potential Pathogens Involved in Food Safety and Public Health in Fish and Water of Lake Karla, Thessaly, Greece
by Dimitrios A. Anagnostopoulos, Foteini F. Parlapani, Stamatia Natoudi, Faidra Syropoulou, Maria Kyritsi, Ioannis Vergos, Christos Hadjichristodoulou, Ifigenia Kagalou and Ioannis S. Boziaris
Pathogens 2022, 11(12), 1473; https://0-doi-org.brum.beds.ac.uk/10.3390/pathogens11121473 - 05 Dec 2022
Cited by 4 | Viewed by 1787
Abstract
Bacterial communities, microbial populations, and antibiotic resistance of potential pathogens in the water and fish (Cyprinus carpio, flesh and gut) from different areas (A1, A2 and A3—A1 was linked with river water, A2 with cattle activity, and A3 with waters of [...] Read more.
Bacterial communities, microbial populations, and antibiotic resistance of potential pathogens in the water and fish (Cyprinus carpio, flesh and gut) from different areas (A1, A2 and A3—A1 was linked with river water, A2 with cattle activity, and A3 with waters of a spring after heavy rains) of Lake Karla (Thessaly, Central Greece) were investigated. The isolated bacteria were identified using Matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) and were tested for resistance in 21 antibiotics. The microbiota composition of fish flesh was also studied using 16S amplicon-based sequencing Serratia fonticola and several species of Aeromonas (e.g., Aeromonas salmonicida, Aeromonas bestiarium, Aeromonas veronii, etc.) exhibited the highest abundances in all studied samples, while the microbiota profile between the three studied areas was similar, according to the culture-dependent analysis. Of them, S. fonticola was found to be resistant in the majority of the antibiotics for the water and fish (gut and flesh), mainly of the areas A1 and A2. Regarding 16S metabarcoding, the presence of Serratia and Aeromonas at genus level was confirmed, but they found at very lower abundances than those reported using the culture-dependent analysis. Finally, the TVC and the rest of the studied microbiological parameters were found at acceptable levels (4 log cfu/mL or cfu/g and 2–4 log cfu/mL or cfu/g, extremely low levels of E. coli/coliforms) in both water and fish flesh. Based on our findings, the water of Lake Karla would be used for activities such as irrigation, recreation and fishing, however, the development and implementation of a quality management tool for Lake Karla, to ensure environmental hygiene and prevention of zoonosis during the whole year, is imperative. Full article
(This article belongs to the Special Issue Detection and Characterization of Drug-Resistant Organisms)
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22 pages, 2791 KiB  
Article
Assessment of the Susceptibility of Clinical Gram-Negative and Gram-Positive Bacterial Strains to Fosfomycin and Significance of This Antibiotic in Infection Treatment
by Beata Kowalska-Krochmal, Beata Mączyńska, Danuta Rurańska-Smutnicka, Anna Secewicz, Grzegorz Krochmal, Małgorzata Bartelak, Aleksandra Górzyńska, Klaudyna Laufer, Krystyna Woronowicz, Joanna Łubniewska, Jolanta Łappo, Magdalena Czwartos and Ruth Dudek-Wicher
Pathogens 2022, 11(12), 1441; https://0-doi-org.brum.beds.ac.uk/10.3390/pathogens11121441 - 30 Nov 2022
Cited by 5 | Viewed by 2650
Abstract
Multidrug resistance of bacteria has prompted intensive development work on new medicines, but also the search for effective options among the oldest antibiotics. Although intravenous fosfomycin (IVFOS) seems to be an interesting proposal, the recommended agar dilution method for susceptibility determination poses a [...] Read more.
Multidrug resistance of bacteria has prompted intensive development work on new medicines, but also the search for effective options among the oldest antibiotics. Although intravenous fosfomycin (IVFOS) seems to be an interesting proposal, the recommended agar dilution method for susceptibility determination poses a major problem in routine diagnostic testing. As a consequence, there is a lack of comprehensive data on the frequency of isolation of susceptible or resistant strains. This fact triggered the disposition of EUCAST concerning the revision of IVFOS breakpoints (BPs), including withdrawal of BPs for Enterobacterales (excluding E. coli) and coagulase-negative staphylococci. Therefore, the aim of this study was to assess the activity of fosfomycin against numerous clinical strains using recommended methods. Materials and methods: A total of 997 bacterial strains were tested from the following genera: Enterobacterales, Pseudomonas spp., Staphylococcus spp., Acinetobacter spp., and Enterococcus spp., for which there are currently no BPs. The strains were isolated from various clinical materials from patients hospitalized in five hospitals. During the investigation, the recommended agar dilution method was used. Susceptibility to other antibiotics and resistance mechanisms were determined using an automatic method (Phoenix) the disk diffusion method, and E-tests. MIC values of fosfomycin were estimated for all strains and for susceptible and multidrug-resistant (MDR) strains individually. Results: Except for Acinetobacter and Enterococcus, 83% of the strains were susceptible to IVFOS, including the largest percentage of S. aureus and E. coli. Klebsiella spp. turned out to be the least susceptible strains (66%). The highest proportion of susceptibility to fosfomycin was found among strains that were sensitive to other antibiotics (80.9%), and the lowest was found among Gram-negative carbapenemase-producing bacteria (55.6%) and ESBL+ bacteria (61.6%). The MIC evaluation revealed the lowest MIC50 and MIC90 values for S. aureus (0.5 mg/L and 1 mg/L, respectively) and E. coli (4 mg/L and 32 mg/L, respectively). The highest values of MIC50 were found for Acinetobacter spp. (256 mg/L), while the highest values of MIC90 were found for Acinetobacter spp. and Klebsiella spp. (256 mg/L and 512 mg/L, respectively). Conclusions: IVFOS appears to be suitable for the treatment of many infections, including the empirical treatment of polymicrobial infections and those caused by MDR strains, since the sensitivity of the studied strains to this antibiotic in different groups ranged from 66% to as much as 99%. Sensitivity to fosfomycin was also demonstrated by 60% of carbapenem-resistant strains; therefore, IVFOS is one of the few therapeutic options that can be effective against the most resistant Gram-negative rods. In light of the general consultation posted by EUCAST, obtaining data such as IVFOS MIC value distributions may be vital for the decision of implementing fosfomycin into breakpoint tables. Full article
(This article belongs to the Special Issue Detection and Characterization of Drug-Resistant Organisms)
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12 pages, 261 KiB  
Article
The Accelerate Pheno™ System—A New Tool in Microbiological Diagnostics of Bloodstream Infections: A Pilot Study from Poland
by Patrycja Zalas-Więcek, Tomasz Bogiel and Eugenia Gospodarek-Komkowska
Pathogens 2022, 11(12), 1415; https://0-doi-org.brum.beds.ac.uk/10.3390/pathogens11121415 - 24 Nov 2022
Cited by 1 | Viewed by 1614
Abstract
The aim of this study was to evaluate the usefulness of the Accelerate Pheno™ system (APS) (Accelerate Diagnostics, Denver, CO, USA) for rapid laboratory diagnosis of bloodstream infections. The study included 45 positive blood samples obtained from patients hospitalized in University Hospital No. [...] Read more.
The aim of this study was to evaluate the usefulness of the Accelerate Pheno™ system (APS) (Accelerate Diagnostics, Denver, CO, USA) for rapid laboratory diagnosis of bloodstream infections. The study included 45 positive blood samples obtained from patients hospitalized in University Hospital No. 1 in Bydgoszcz, Poland. In 40 (88.9%) blood samples, the APS was capable of identification of at least one microorganism at the genus or species level and in 38 (84.4%) of them additionally assessed antimicrobial susceptibility. The time of identification and the time to result of antimicrobial susceptibility ranged from 1:32 to 1:42 and 5:02 to 5:36 h, respectively. Six positive blood samples revealed a poly-microbial culture. In these cases, only one out of two or three microorganisms was detected by the APS, and the system assessed antimicrobial susceptibility only for them. For 78.6% positive blood samples, agreement on identification compared to mass spectrometry was found. For all but one sample, a 96–100% compliance of the resistance category was achieved when comparing the antimicrobial susceptibility testing results to conventional methods. Using the APS, the total time to report was reduced from 13:34 to even 63:47 h compared to the standard microbiological laboratory workflow. The APS is a very useful system, especially for the rapid assessment of antimicrobial susceptibility of bacteria directly from positive blood samples, offering the greatest potential for microbiology laboratories operating around the clock. Full article
(This article belongs to the Special Issue Detection and Characterization of Drug-Resistant Organisms)
9 pages, 1069 KiB  
Article
Antimicrobial Resistance and Virulence Factors of Proteus mirabilis Isolated from Dog with Chronic Otitis Externa
by Jun Kwon, Myoung-Hwan Yang, Hyoung-Joon Ko, Sang-Guen Kim, Chul Park and Se-Chang Park
Pathogens 2022, 11(10), 1215; https://0-doi-org.brum.beds.ac.uk/10.3390/pathogens11101215 - 21 Oct 2022
Cited by 7 | Viewed by 2552
Abstract
Otitis externa is among the most prevalent diseases in dogs. If the underlying cause is not addressed, bacterial reinfection becomes frequent, necessitating antibiotic administration for an extended period of time. Prolonged treatment promotes the emergence of antibiotic-resistant bacteria and increases the risk of [...] Read more.
Otitis externa is among the most prevalent diseases in dogs. If the underlying cause is not addressed, bacterial reinfection becomes frequent, necessitating antibiotic administration for an extended period of time. Prolonged treatment promotes the emergence of antibiotic-resistant bacteria and increases the risk of their transmission from animals to humans. This study aimed to analyze the antibiotic resistance pattern of the emerging pathogen Proteus mirabilis to identify bacterial virulence and antibiotic selection. Samples were collected from randomly encountered dogs with chronic otitis externa. Thirty-two strains of P. mirabilis were isolated and identified, using MALDI-TOF. The Kirby-Bauer disk diffusion method was used to assess the antibiotic susceptibility of P. mirabilis to 11 antibiotics. The isolates (n = 32) were most resistant to cefazolin (75%), trimethoprim–sulfamethoxazole (72%), chloramphenicol (72%), amoxicillin–clavulanate (63%), ampicillin (59%), cefepime (56%), ciprofloxacin (53%), aztreonam (50%), ceftazidime avibactam (50%), gentamicin (22%), and amikacin (16%). Moreover, 75% of isolates were found to be multidrug-resistant bacteria. P. mirabilis was found to have a high resistance-pattern ratio. Although the exact cause is unknown, continuous antibiotic use is thought to be a major factor. We concluded that antibiotic use must be prudent and selective to prevent antibiotic resistance. Full article
(This article belongs to the Special Issue Detection and Characterization of Drug-Resistant Organisms)
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11 pages, 1235 KiB  
Article
Antibiotic Resistance and Plasmid Profile Analysis of Salmonella Enteritidis Isolated in Siberia and the Far East of Russia between 1990 and 2017
by Alexey V. Rakov and Natalya A. Kuznetsova
Pathogens 2021, 10(10), 1240; https://0-doi-org.brum.beds.ac.uk/10.3390/pathogens10101240 - 25 Sep 2021
Cited by 1 | Viewed by 2073
Abstract
Salmonella is one of the major causes of foodborne disease outbreaks globally. Specifically, Salmonella enterica subsp. enterica serovar Enteritidis (S. Enteritidis) is one of the major causes of zoonotic Salmonella infection in humans worldwide. In this study, we present data on antimicrobial [...] Read more.
Salmonella is one of the major causes of foodborne disease outbreaks globally. Specifically, Salmonella enterica subsp. enterica serovar Enteritidis (S. Enteritidis) is one of the major causes of zoonotic Salmonella infection in humans worldwide. In this study, we present data on antimicrobial resistance (AMR) and plasmid profiles of S. Enteritidis strains isolated from patients, food, and the environment in Siberia and the Far East of Russia obtained during Salmonella monitoring between 1990 and 2017. A total of 345 S. Enteritidis isolates were tested by the disk diffusion method with a set of 15 antibiotics using EUCAST breakpoints v. 10 and by plasmid profile analysis using the alkaline lysis method. The results have shown a substantial decrease in susceptibility to aminoglycosides and quinolones during the study period. No significant differences were found in the susceptibility of strains between regions as well as in the its correlation with different plasmid types of the pathogen. Several S. Enteritidis strains were found to be resistant to ampicillin, kanamycin, tetracycline, chloramphenicol, and cephalosporins. All tested S. Enteritidis strains were susceptible only to imipenem. In this study, we observed a relatively low level of AMR in S. Enteritidis strains isolated in Siberia and the Far East of Russia. Nevertheless, it is important to continue the molecular genetic monitoring and AMR surveillance of S. Enteritidis to track further increases in AMR using conventional phenotypic susceptibility testing and by introducing whole-genome sequencing to identify AMR mechanisms. Full article
(This article belongs to the Special Issue Detection and Characterization of Drug-Resistant Organisms)
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14 pages, 644 KiB  
Article
Antibiotic Resistance and Virulence Profiles of Escherichia coli Strains Isolated from Wild Birds in Poland
by Anna Nowaczek, Marta Dec, Dagmara Stępień-Pyśniak, Renata Urban-Chmiel, Agnieszka Marek and Paweł Różański
Pathogens 2021, 10(8), 1059; https://0-doi-org.brum.beds.ac.uk/10.3390/pathogens10081059 - 20 Aug 2021
Cited by 12 | Viewed by 2717
Abstract
Wild animals are increasingly reported as carriers of antibiotic-resistant and pathogenic bacteria including Enterobacteriaceae. However, the role of free-living birds as reservoirs for potentially dangerous microbes is not yet thoroughly understood. In our work, we examined Escherichia coli strains from wild birds [...] Read more.
Wild animals are increasingly reported as carriers of antibiotic-resistant and pathogenic bacteria including Enterobacteriaceae. However, the role of free-living birds as reservoirs for potentially dangerous microbes is not yet thoroughly understood. In our work, we examined Escherichia coli strains from wild birds in Poland in relation to their antimicrobial agents susceptibility, virulence and phylogenetic affiliation. Identification of E. coli was performed using MALDI-TOF mass spectrometry. The antibiotic susceptibility of the isolates was determined by the broth microdilution method, and resistance and virulence genes were detected by PCR. E. coli bacteria were isolated from 32 of 34 samples. The strains were most often classified into phylogenetic groups B1 (50%) and A (25%). Resistance to tetracycline (50%), ciprofloxacin (46.8%), gentamicin (34.3%) and ampicillin (28.1%) was most frequently reported, and as many as 31.2% of E. coli isolates exhibited a multidrug resistance phenotype. Among resistance genes, sul2 (31.2% of isolates) and blaTEM (28.1%) were identified most frequently, while irp-2 (31.2%) and ompT (28.1%) were the most common virulence-associated genes. Five strains were included in the APEC group. The study indicates that wild birds can be carriers of potentially dangerous E. coli strains and vectors for the spread of resistant bacteria and resistance determinants in the environment. Full article
(This article belongs to the Special Issue Detection and Characterization of Drug-Resistant Organisms)
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7 pages, 247 KiB  
Article
Detection and Characterization of Clinical Bordetella trematum Isolates from Chronic Wounds
by Christian Buechler, Claudio Neidhöfer, Thorsten Hornung, Marcel Neuenhoff and Marijo Parčina
Pathogens 2021, 10(8), 966; https://0-doi-org.brum.beds.ac.uk/10.3390/pathogens10080966 - 30 Jul 2021
Cited by 5 | Viewed by 2959
Abstract
Bordetella trematum is a relatively newly discovered and potentially frequently overlooked Bordetella species, mostly isolated from chronic wounds and predominantly in those of the lower extremities. Its susceptibility profile and clinical significance is still debated, given the limited amount of available data. We [...] Read more.
Bordetella trematum is a relatively newly discovered and potentially frequently overlooked Bordetella species, mostly isolated from chronic wounds and predominantly in those of the lower extremities. Its susceptibility profile and clinical significance is still debated, given the limited amount of available data. We contribute providing a molecular and phenotypical analysis of three unique clinical B. trematum isolates detected between August 2019 and January 2020 to aid the matter. Cryo-conserved isolates were subcultured and re-identified using various routine means of identification. Bacterial genomes were fully Illumina-sequenced and phenotypical susceptibility was determined by broth microdilution and gradient-strip tests. All isolates displayed increased susceptibility to piperacillin–tazobactam (<2/4 mg/L), imipenem (<1 mg/L), and meropenem (<0.047 mg/L), whereas they displayed decreased susceptibility to all tested cephalosporins and fluoroquinolones (according to PK-PD, EUCAST 10.0 2020). One isolate carried a beta-lactamase (EC 3.5.2.6) and a sulfonamide resistance gene (sul2) and cells displayed resistance to ampicillin, ampicillin/sulbactam, and trimethoprim/sulfamethoxazole. All isolates carried genes conferring decreased susceptibility to aminoglycosides (aadA), fosfomycin (fosA) and fluoroquinolones (gyrB EC 5.99.1.3). Awareness that B. trematum can be resistant to trimethoprim/sulfamethoxazole is warranted. Full article
(This article belongs to the Special Issue Detection and Characterization of Drug-Resistant Organisms)
18 pages, 5957 KiB  
Article
In Vitro Susceptibility of Multi-Drug Resistant Klebsiellapneumoniae Strains Causing Nosocomial Infections to Fosfomycin. A Comparison of Determination Methods
by Beata Mączyńska, Justyna Paleczny, Monika Oleksy-Wawrzyniak, Irena Choroszy-Król and Marzenna Bartoszewicz
Pathogens 2021, 10(5), 512; https://0-doi-org.brum.beds.ac.uk/10.3390/pathogens10050512 - 23 Apr 2021
Cited by 11 | Viewed by 2686
Abstract
Introduction: Over the past few decades, Klebsiella pneumoniae strains increased their pathogenicity and antibiotic resistance, thereby becoming a major therapeutic challenge. One of the few available therapeutic options seems to be intravenous fosfomycin. Unfortunately, the determination of sensitivity to fosfomycin performed in hospital [...] Read more.
Introduction: Over the past few decades, Klebsiella pneumoniae strains increased their pathogenicity and antibiotic resistance, thereby becoming a major therapeutic challenge. One of the few available therapeutic options seems to be intravenous fosfomycin. Unfortunately, the determination of sensitivity to fosfomycin performed in hospital laboratories can pose a significant problem. Therefore, the aim of the present research was to evaluate the activity of fosfomycin against clinical, multidrug-resistant Klebsiella pneumoniae strains isolated from nosocomial infections between 2011 and 2020, as well as to evaluate the methods routinely used in hospital laboratories to assess bacterial susceptibility to this antibiotic. Materials and Methods: 43 multidrug-resistant Klebsiella strains isolates from various infections were tested. All the strains had ESBL enzymes, and 20 also showed the presence of carbapenemases. Susceptibility was determined using the diffusion method (E-test) and the automated system (Phoenix), which were compared with the reference method (agar dilution). Results: For the reference method and for the E-test, the percentage of strains sensitive to fosfomycin was 65%. For the Phoenix system, the percentage of susceptible strains was slightly higher and stood at 72%. The percentage of fosfomycin-resistant strains in the Klebsiella carbapenemase-producing group was higher (45% for the reference method and E-test and 40% for the Phoenix method) than in carbapenemase-negative strains (25%, 25%, and 20%, respectively). Full (100%) susceptibility categorical agreement was achieved for the E-test and the reference method. Agreement between the automated Phoenix system and the reference method reached 86%. Conclusions: Fosfomycin appears to be the antibiotic with a potential for use in the treatment of infections with multidrug-resistant Klebsiella strains. Susceptibility to this drug is exhibited by some strains, which are resistant to colistin and carbapenems. The E-test, unlike the Phoenix method, can be an alternative to the reference method in the routine determination of fosfomycin susceptibility, as it shows agreement in terms of sensitivity categories and only slight differences in MIC values. The Phoenix system, in comparison to the reference method, shows large discrepancies in the MIC values and in the susceptibility category. Full article
(This article belongs to the Special Issue Detection and Characterization of Drug-Resistant Organisms)
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11 pages, 514 KiB  
Article
Evidence of Antimicrobial Resistance and Presence of Pathogenicity Genes in Yersinia enterocolitica Isolate from Wild Boars
by Paola Modesto, Chiara Grazia De Ciucis, Walter Vencia, Maria Concetta Pugliano, Walter Mignone, Enrica Berio, Chiara Masotti, Carlo Ercolini, Laura Serracca, Tiziana Andreoli, Monica Dellepiane, Daniela Adriano, Simona Zoppi, Daniela Meloni and Elisabetta Razzuoli
Pathogens 2021, 10(4), 398; https://0-doi-org.brum.beds.ac.uk/10.3390/pathogens10040398 - 27 Mar 2021
Cited by 10 | Viewed by 2096
Abstract
Yersinia enterocolitica (Ye) is a very important zoonosis andwild boars play a pivotal role in its transmission. In the last decade, the wild boar population has undergone a strong increase that haspushed them towards urbanized areas, facilitating the human–wildlife interface and [...] Read more.
Yersinia enterocolitica (Ye) is a very important zoonosis andwild boars play a pivotal role in its transmission. In the last decade, the wild boar population has undergone a strong increase that haspushed them towards urbanized areas, facilitating the human–wildlife interface and the spread of infectious diseases from wildlife to domestic animals and humans. Therefore, it is important to know the serotype, antimicrobial resistance and presence of pathogenicity genes of Yersinia enterocolitica (Ye) isolated in species. From 2013 to 2018, we analyzed the liver of 4890 wild boars hunted in Liguria region; we isolated and serotyped 126 Ye positive samples. A decisive role in the pathogenicity is given by the presence of virulence genes; in Ye isolated we found ystB (~70%), ymoA (45.2%), ail (43.6%) and ystA (~20%). Moreover, we evaluated the susceptibility at various antimicrobic agents (Ampicillin, Chloramphenicol, Enrofloxacin, Gentamicin, Kanamycin, Trimethoprim–Sulfamethoxazole, Sulfisoxazole, Ceftiofur and Tetracycline). The antibiotic resistance was analyzed, and we found a time-dependent increase. It is important to shed light on the role of the wild boars as a reserve of potentially dangerous diseases for humans, and also on the antibiotic resistance that represents a public health problem. Full article
(This article belongs to the Special Issue Detection and Characterization of Drug-Resistant Organisms)
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21 pages, 1713 KiB  
Article
Development of a Multiplex Real-Time PCR Assay for Predicting Macrolide and Tetracycline Resistance Associated with Bacterial Pathogens of Bovine Respiratory Disease
by Enakshy Dutta, John Dustin Loy, Caitlyn A. Deal, Emily L. Wynn, Michael L. Clawson, Jennifer Clarke and Bing Wang
Pathogens 2021, 10(1), 64; https://0-doi-org.brum.beds.ac.uk/10.3390/pathogens10010064 - 13 Jan 2021
Cited by 10 | Viewed by 2987
Abstract
Antimicrobial resistance (AMR) in bovine respiratory disease (BRD) is an emerging concern that may threaten both animal and public health. Rapid and accurate detection of AMR is essential for prudent drug therapy selection during BRD outbreaks. This study aimed to develop a multiplex [...] Read more.
Antimicrobial resistance (AMR) in bovine respiratory disease (BRD) is an emerging concern that may threaten both animal and public health. Rapid and accurate detection of AMR is essential for prudent drug therapy selection during BRD outbreaks. This study aimed to develop a multiplex quantitative real-time polymerase chain reaction assay (qPCR) to provide culture-independent information regarding the phenotypic AMR status of BRD cases and an alternative to the gold-standard, culture-dependent test. Bovine clinical samples (297 lung and 111 nasal) collected in Nebraska were subjected to qPCR quantification of macrolide (MAC) and tetracycline (TET) resistance genes and gold-standard determinations of AMR of BRD pathogens. Receiver operating characteristic curve analysis was used to classify AMR based on the qPCR results. For lung tissues, the qPCR method showed good agreement with the gold-standard test for both MACs and TETs, with a sensitivity of 67–81% and a specificity higher than 80%. For nasal swabs, qPCR results passed validation criteria only for TET resistance detection, with a sensitivity of 88%, a specificity of 80% and moderate agreement. The culture-independent assay developed here provides the potential for more rapid AMR characterization of BRD cases directly from clinical samples at equivalent accuracy and higher time efficiency compared with the gold-standard, culture-based test. Full article
(This article belongs to the Special Issue Detection and Characterization of Drug-Resistant Organisms)
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15 pages, 1363 KiB  
Article
Molecular Typing of Neisseria gonorrhoeae Clinical Isolates in Russia, 2018–2019: A Link Between penA Alleles and NG-MAST Types
by Ilya Kandinov, Ekaterina Dementieva, Dmitry Kravtsov, Alexander Chestkov, Alexey Kubanov, Victoria Solomka, Dmitry Deryabin, Dmitry Gryadunov and Boris Shaskolskiy
Pathogens 2020, 9(11), 941; https://0-doi-org.brum.beds.ac.uk/10.3390/pathogens9110941 - 12 Nov 2020
Cited by 7 | Viewed by 2418
Abstract
This work aimed to study penA gene polymorphisms in clinical isolates of Neisseria gonorrhoeae collected in Russia in 2018–2019 and the contribution of the penA allele type to susceptibility to β-lactam antibiotics. A total of 182 isolates were analyzed. penA allele types were [...] Read more.
This work aimed to study penA gene polymorphisms in clinical isolates of Neisseria gonorrhoeae collected in Russia in 2018–2019 and the contribution of the penA allele type to susceptibility to β-lactam antibiotics. A total of 182 isolates were analyzed. penA allele types were determined by sequencing, and the minimum inhibitory concentrations (MICs) of benzylpenicillin and ceftriaxone were measured. The influence of genetic factors on MICs was evaluated by regression analysis. All isolates were susceptible to ceftriaxone, and 40.1% of isolates were susceptible to penicillin. Eleven penA allele types were identified. The mosaic type XXXIV penA allele and the Gly120Lys substitution in PorB made the greatest contributions to increasing the ceftriaxone MIC; the presence of the blaTEM plasmid, Gly120Asp, Ala121Gly/Asn substitutions in PorB, and the adenine deletion in the promoter region of the mtrR gene caused an increase in the penicillin MIC. Among 61 NG-MAST types identified, the most frequent were types 228, 807, 9486, 1993, and 6226. A link between penA alleles and Neisseria gonorrhoeae multi-antigen sequence typing (NG-MAST) types was established. Resistance to two groups of β-lactam antibiotics was associated with non-identical changes in penA alleles. To prevent the emergence of ceftriaxone resistance in Russia, NG-MAST genotyping must be supplemented with penA allele analysis. Full article
(This article belongs to the Special Issue Detection and Characterization of Drug-Resistant Organisms)
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12 pages, 1470 KiB  
Article
Identification of Essential Oils Including Garlic Oil and Black Pepper Oil with High Activity against Babesia duncani
by Yumin Zhang, Chunxiang Bai, Wanliang Shi, Hector Alvarez-Manzo and Ying Zhang
Pathogens 2020, 9(6), 466; https://0-doi-org.brum.beds.ac.uk/10.3390/pathogens9060466 - 12 Jun 2020
Cited by 8 | Viewed by 6156
Abstract
Some evidence indicated that human babesiosis caused by Babesia duncani has spread widely in North America. However, current therapeutic regimens (atovaquone + azithromycin) for human babesiosis are suboptimal with frequent recrudescence and side effects, and furthermore, there is no specific treatment for human [...] Read more.
Some evidence indicated that human babesiosis caused by Babesia duncani has spread widely in North America. However, current therapeutic regimens (atovaquone + azithromycin) for human babesiosis are suboptimal with frequent recrudescence and side effects, and furthermore, there is no specific treatment for human babesiosis caused by B. duncani. Here, we screened 97 essential oils and identified 10 essential oils (garlic, black pepper, tarragon, palo santo, coconut, pine, meditation, cajeput, moringa, and stress relief) at a low concentration (0.001%; v/v) that showed good inhibitory activity against B. duncani in the hamster red blood cell culture model. Among them, garlic oil and black pepper oil performed best, as well as their potential active ingredients diallyl disulfide (DADS) and β-caryophyllene (BCP), respectively. Interestingly, further subculture study indicated that B. duncani could relapse after treatment with current therapeutic drugs atovaquone or azithromycin even at high concentrations. In contrast, the combination of garlic oil or DADS and azithromycin showed eradication of B. duncani at low concentrations without regrowth. These results are encouraging and suggest that the garlic-derived sulfur compound DADS and β-caryophyllene (BCP) may be promising drug candidates for evaluation of their ability to cure persistent B. duncani infections in the future. Full article
(This article belongs to the Special Issue Detection and Characterization of Drug-Resistant Organisms)
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Review

Jump to: Research

14 pages, 2642 KiB  
Review
Stringent Response in Mycobacteria: From Biology to Therapeutic Potential
by Kuldeepkumar Ramnaresh Gupta, Gunjan Arora, Abid Mattoo and Andaleeb Sajid
Pathogens 2021, 10(11), 1417; https://0-doi-org.brum.beds.ac.uk/10.3390/pathogens10111417 - 01 Nov 2021
Cited by 10 | Viewed by 3046
Abstract
Mycobacterium tuberculosis is a human pathogen that can thrive inside the host immune cells for several years and cause tuberculosis. This is due to the propensity of M. tuberculosis to synthesize a sturdy cell wall, shift metabolism and growth, secrete virulence factors to [...] Read more.
Mycobacterium tuberculosis is a human pathogen that can thrive inside the host immune cells for several years and cause tuberculosis. This is due to the propensity of M. tuberculosis to synthesize a sturdy cell wall, shift metabolism and growth, secrete virulence factors to manipulate host immunity, and exhibit stringent response. These attributes help M. tuberculosis to manage the host response, and successfully establish and maintain an infection even under nutrient-deprived stress conditions for years. In this review, we will discuss the importance of mycobacterial stringent response under different stress conditions. The stringent response is mediated through small signaling molecules called alarmones “(pp)pGpp”. The synthesis and degradation of these alarmones in mycobacteria are mediated by Rel protein, which is both (p)ppGpp synthetase and hydrolase. Rel is important for all central dogma processes—DNA replication, transcription, and translation—in addition to regulating virulence, drug resistance, and biofilm formation. Rel also plays an important role in the latent infection of M. tuberculosis. Here, we have discussed the literature on alarmones and Rel proteins in mycobacteria and highlight that (p)ppGpp-analogs and Rel inhibitors could be designed and used as antimycobacterial compounds against M. tuberculosis and non-tuberculous mycobacterial infections. Full article
(This article belongs to the Special Issue Detection and Characterization of Drug-Resistant Organisms)
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21 pages, 2104 KiB  
Review
Artificial Intelligence in Surveillance, Diagnosis, Drug Discovery and Vaccine Development against COVID-19
by Gunjan Arora, Jayadev Joshi, Rahul Shubhra Mandal, Nitisha Shrivastava, Richa Virmani and Tavpritesh Sethi
Pathogens 2021, 10(8), 1048; https://0-doi-org.brum.beds.ac.uk/10.3390/pathogens10081048 - 18 Aug 2021
Cited by 39 | Viewed by 12957
Abstract
As of August 6th, 2021, the World Health Organization has notified 200.8 million laboratory-confirmed infections and 4.26 million deaths from COVID-19, making it the worst pandemic since the 1918 flu. The main challenges in mitigating COVID-19 are effective vaccination, treatment, and agile containment [...] Read more.
As of August 6th, 2021, the World Health Organization has notified 200.8 million laboratory-confirmed infections and 4.26 million deaths from COVID-19, making it the worst pandemic since the 1918 flu. The main challenges in mitigating COVID-19 are effective vaccination, treatment, and agile containment strategies. In this review, we focus on the potential of Artificial Intelligence (AI) in COVID-19 surveillance, diagnosis, outcome prediction, drug discovery and vaccine development. With the help of big data, AI tries to mimic the cognitive capabilities of a human brain, such as problem-solving and learning abilities. Machine Learning (ML), a subset of AI, holds special promise for solving problems based on experiences gained from the curated data. Advances in AI methods have created an unprecedented opportunity for building agile surveillance systems using the deluge of real-time data generated within a short span of time. During the COVID-19 pandemic, many reports have discussed the utility of AI approaches in prioritization, delivery, surveillance, and supply chain of drugs, vaccines, and non-pharmaceutical interventions. This review will discuss the clinical utility of AI-based models and will also discuss limitations and challenges faced by AI systems, such as model generalizability, explainability, and trust as pillars for real-life deployment in healthcare. Full article
(This article belongs to the Special Issue Detection and Characterization of Drug-Resistant Organisms)
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