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Antibiotics
Special Issues
Antimicrobial Resistance and Virulence – 3rd Volume
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Antimicrobial Resistance and Virulence – 3rd Volume

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

Deadline for manuscript submissions: closed (31 March 2023) | Viewed by 35107

Special Issue Editors

Dr. Manuela Oliveira

E-Mail Website1 Website2
Guest Editor
Centre for Interdisciplinary Research in Animal Health (CIISA), Faculty of Veterinary Medicine, Universidade de Lisboa, Lisbon, Portugal
Interests: antimicrobial resistance; bacterial virulence; biofilms; genomics; infections pathogenesis; food safety
Special Issues, Collections and Topics in MDPI journals
Dr. Elisabete Silva

E-Mail Website1 Website2
Guest Editor
CIISA – Centre for Interdisciplinary Research in Animal Health, Faculty of Veterinary Medicine of Lisbon, Lisboa, Portugal
Interests: animal reproduction; bacterial infections; host–bacterial interactions; molecular biology; genomics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The use of antibiotics for the treatment of infectious diseases began in the 1940s with penicillin. In spite of their unquestionable contribution to the decline of morbidity and mortality rates in both human and veterinary medicine, antibiotics administration prompted the emergence and dissemination of multiresistant bacterial strains. This phenomenon represents a major concern for Public and Animal Health worldwide and has instigated the development of a new generation of antibiotics. However, these new molecules soon became ineffective due to the capability of bacteria to evolve, in particular through mutations or horizontal gene transfer.

Global dissemination of resistant bacteria, in particular to last-resource antibiotics, has been referred to as the next pandemic. In 2017, the World Health Organization (WHO) has published a list of antimicrobial-resistant "priority pathogens" for which new therapeutic solutions are urgent, which include a group of microorganisms with high level resistance to multiple drugs, named ESKAPE pathogens, comprising of vancomycin resistant Enterococcus faecium (VRE), methicillin and vancomycin resistant Staphylococcus aureus (MRSA and VRSA), extended spectrum β-lactamase (ESBL) or carbapenem resistant Klebsiella pneumoniae, carbapenem resistant Acinetobacter baumannii, carbapenem resistant Pseudomonas aeruginosa and extended spectrum β-lactamase (ESBL) or carbapenem resistant Enterobacter spp.

These bacteria also have the ability to produce several virulence factors, which have a major influence on infectious disease outcome. In fact, some virulence factors, such as biofilm-producing ability and others, contribute to an increased resistance ability. Surveillance of important resistant and virulent clones is of major relevance for the establishment of control measures to be applied to the prevention of infections promoted by these strains in both human and veterinary medicine, and is also relevant to address the role of natural environments in the circulation of these strains.

This Special Issue constitutes a Third Volume focusing on Antimicrobial Resistance and Virulence, and aims to publish manuscripts that further clarify on the impact of bacterial antimicrobial resistance and virulence in the three areas of the One Health triad, i.e., animal, human, and environmental health.

Dr. Manuela Oliveira
Dr. Elisabete Silva
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

  • antimicrobial resistance
  • bacterial virulence
  • biofilms
  • epidemiology
  • genomics
  • infections pathogenesis
  • One Health

Published Papers (15 papers)

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Research

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8 pages, 971 KiB  
Communication
A New Integrative and Mobilizable Element Is a Major Contributor to Tetracycline Resistance in Streptococcus dysgalactiae subsp. equisimilis
by Guillem López de Egea, Aida González-Díaz, Gérard Guédon, Julie Lao, Dàmaris Berbel, Antonio Casabella, José María Marimón, Emilia Cercenado, Lucía Fernández-Delgado, Hélène Chiapello, Thomas Lacroix, María Ángeles Domínguez, Nathalie Leblond-Bourget and Carmen Ardanuy
Antibiotics 2023, 12(3), 579; https://doi.org/10.3390/antibiotics12030579 - 15 Mar 2023
Viewed by 1412
Abstract
Tetracycline resistance in streptococci is mainly due to ribosomal protection mediated by the tet(M) gene that is usually located in the integrative and conjugative elements (ICEs) of the Tn916-family. In this study, we analyzed the genes involved in tetracycline resistance [...] Read more.
Tetracycline resistance in streptococci is mainly due to ribosomal protection mediated by the tet(M) gene that is usually located in the integrative and conjugative elements (ICEs) of the Tn916-family. In this study, we analyzed the genes involved in tetracycline resistance and the associated mobile genetic elements (MGEs) in Streptococcus dysgalactiae subsp. equisimilis (SDSE) causing invasive disease. SDSE resistant to tetracycline collected from 2012 to 2019 in a single hospital and from 2018 in three other hospitals were analyzed by whole genome sequencing. Out of a total of 84 SDSE isolates, 24 (28.5%) were resistant to tetracycline due to the presence of tet(M) (n = 22), tet(W) (n = 1), or tet(L) plus tet(W) (n = 1). The tet(M) genes were found in the ICEs of the Tn916-family (n = 10) and in a new integrative and mobilizable element (IME; n = 12). Phylogenetic analysis showed a higher genetic diversity among the strains carrying Tn916 than those having the new IME, which were closely related, and all belonged to CC15. In conclusion, tetracycline resistance in SDSE is mostly due to the tet(M) gene associated with ICEs belonging to the Tn916-family and a new IME. This new IME is a major cause of tetracycline resistance in invasive Streptococcus dysgalactiae subsp. equisimilis in our settings. Full article
(This article belongs to the Special Issue Antimicrobial Resistance and Virulence – 3rd Volume)
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12 pages, 1227 KiB  
Article
In Vivo Effect of a Nisin–Biogel on the Antimicrobial and Virulence Signatures of Canine Oral Enterococci
by Eva Cunha, Ana Filipa Ferreira, Sara Valente, Alice Matos, Luís Miguel Carreira, Marta Videira, Lélia Chambel, Luís Tavares and Manuela Oliveira
Antibiotics 2023, 12(3), 468; https://doi.org/10.3390/antibiotics12030468 - 25 Feb 2023
Cited by 2 | Viewed by 1303
Abstract
Periodontal disease is a relevant oral disease in dogs and nisin–biogel has been previously proposed to be used in its control. Enterococci, as inhabitants of the oral cavity with a high genetic versatility, are a reliable bacterial model for antimicrobial studies. Our [...] Read more.
Periodontal disease is a relevant oral disease in dogs and nisin–biogel has been previously proposed to be used in its control. Enterococci, as inhabitants of the oral cavity with a high genetic versatility, are a reliable bacterial model for antimicrobial studies. Our goal was to evaluate the in vivo influence of the long-term dental application of the nisin–biogel on the virulence and antimicrobial signatures of canine oral enterococci. Twenty dogs were randomly allocated to one of two groups (treatment group—TG with nisin–biogel dental application, or control group—CG without treatment) and submitted to dental plaque sampling at day 0 and after 90 days (T90). Samples were processed for Enterococcus spp. isolation, quantification, identification, molecular typing and antimicrobial and virulence characterization. From a total of 140 enterococci, molecular typing allowed us to obtain 70 representative isolates, mostly identified as E. faecalis and E. faecium. No significant differences (p > 0.05) were observed in the virulence index of the isolates obtained from samples collected from the TG and CG at T90. At T90, a statistically significant difference (p = 0.0008) was observed in the antimicrobial resistance index between the isolates from the TC and CG. Oral enterococci were revealed to be reservoirs of high resistant and virulent phenotypes. Full article
(This article belongs to the Special Issue Antimicrobial Resistance and Virulence – 3rd Volume)
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14 pages, 1224 KiB  
Article
Bats Are Carriers of Antimicrobial-Resistant Staphylococcaceae in Their Skin
by Natália Carrillo Gaeta, João Eduardo Cavalcante Brito, Juliana Maria Nunes Batista, Beatriz Gagete Veríssimo de Mello, Ricardo Augusto Dias and Marcos B. Heinemann
Antibiotics 2023, 12(2), 331; https://doi.org/10.3390/antibiotics12020331 - 04 Feb 2023
Cited by 1 | Viewed by 1860
Abstract
Bats have emerged as potential carriers of zoonotic viruses and bacteria, including antimicrobial-resistant bacteria. Staphylococcaceae has been isolated from their gut and nasopharynx, but there is little information about Staphylococcaceae on bat skin. Therefore, this study aimed to decipher the Staphylococci species in [...] Read more.
Bats have emerged as potential carriers of zoonotic viruses and bacteria, including antimicrobial-resistant bacteria. Staphylococcaceae has been isolated from their gut and nasopharynx, but there is little information about Staphylococcaceae on bat skin. Therefore, this study aimed to decipher the Staphylococci species in bat skin and their antimicrobial susceptibility profile. One hundred and forty-seven skin swabs were collected from bats during the spring and summer of 2021 and 2022. Bats were captured in different areas of the Metropolitan Region of São Paulo, Brazil, according to the degree of anthropization: Area 1 (Forested), Area 2 (Rural), Area 3 (Residential-A), Area 4 (Slum-– up to two floors), Area 5 (Residential-B—condo buildings), and Area 6 (Industrial). Swabs were kept in peptone water broth at 37 °C for 12 h when bacterial growth was streaked in Mannitol salt agar and incubated at 37 °C for 24 h. The disc-diffusion test evaluated antimicrobial susceptibility. Staphylococcaceae were isolated from 42.8% of bats, mostly from young, from the rural area, and during summer. M. sciuri was the most frequent species; S. aureus was also isolated. About 95% of isolates were resistant to at least one drug, and most strains were penicillin resistant. Eight isolates were methicillin resistant, and the mecA gene was detected in one isolate (S. haemolyticus). Antimicrobial resistance is a One Health issue that is not evaluated enough in bats. The results indicate that bats are carriers of clinically meaningful S. aureus and antimicrobial-resistant bacteria. Finally, the results suggest that we should intensify action plans to control the spread of resistant bacteria. Full article
(This article belongs to the Special Issue Antimicrobial Resistance and Virulence – 3rd Volume)
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14 pages, 3025 KiB  
Article
Plant-Derived Xanthones against Clostridial Enteric Infections
by Ying Liu, Jianfei Zhu, Shaoqi Qu, Jianzhong Shen and Kui Zhu
Antibiotics 2023, 12(2), 232; https://doi.org/10.3390/antibiotics12020232 - 21 Jan 2023
Cited by 1 | Viewed by 1636
Abstract
Intestinal bacterial infections are a major threat to human and animal health. In this study, we found plant-derived antibacterial xanthones, particularly α-mangostin (AMG) from the mangosteen peel, exhibiting extraordinary activities against Clostridium perfringens. Structure–activity relationship analysis showed that prenylation modulated the [...] Read more.
Intestinal bacterial infections are a major threat to human and animal health. In this study, we found plant-derived antibacterial xanthones, particularly α-mangostin (AMG) from the mangosteen peel, exhibiting extraordinary activities against Clostridium perfringens. Structure–activity relationship analysis showed that prenylation modulated the activity of xanthones. The efficacy of AMG (4, 8, 20 mg/kg body weight) was also demonstrated in the broiler chicken necrotic enteritis model infected with Clostridium perfringens. In the models (n = 6 per group), feed supplementation of AMG maintained the homeostasis of the gut microbiome by reducing the colonization of clostridia and promoting the integrity of intestinal barriers via the upregulation of mucin expression. These results suggest that plant-derived xanthones may be a potential alternative to antibiotics for treating clostridial enteric infections in the clinic. Full article
(This article belongs to the Special Issue Antimicrobial Resistance and Virulence – 3rd Volume)
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18 pages, 791 KiB  
Article
Antimicrobial Resistance, Virulence Factors, and Genotypes of Enterococcus faecalis and Enterococcus faecium Clinical Isolates in Northern Japan: Identification of optrA in ST480 E. faecalis
by Meiji Soe Aung, Noriko Urushibara, Mitsuyo Kawaguchiya, Nobuhide Ohashi, Mina Hirose, Kenji Kudo, Naoyuki Tsukamoto, Masahiko Ito and Nobumichi Kobayashi
Antibiotics 2023, 12(1), 108; https://doi.org/10.3390/antibiotics12010108 - 06 Jan 2023
Cited by 8 | Viewed by 3400
Abstract
Enterococcus faecalis and E. faecium are the major pathogens causing community- and healthcare-associated infections, with an ability to acquire resistance to multiple antimicrobials. The present study was conducted to determine the prevalence of virulence factors, drug resistance and its genetic determinants, and clonal [...] Read more.
Enterococcus faecalis and E. faecium are the major pathogens causing community- and healthcare-associated infections, with an ability to acquire resistance to multiple antimicrobials. The present study was conducted to determine the prevalence of virulence factors, drug resistance and its genetic determinants, and clonal lineages of E. faecalis and E. faecium clinical isolates in northern Japan. A total of 480 (426 E. faecalis and 54 E. faecium) isolates collected over a four-month period were analyzed. Three virulence factors promoting bacterial colonization (asa1, efaA, and ace) were more prevalent among E. faecalis (46–59%) than E. faecium, while a similar prevalence of enterococcal surface protein gene (esp) was found in these species. Between E. faecalis and E. faecium, an evident difference was noted for resistance to erythromycin, gentamicin, and levofloxacin and its responsible resistance determinants. Oxazolidinone resistance gene optrA and phenicol exporter gene fexA were identified in an isolate of E. faecalis belonging to ST480 and revealed to be located on a cluster similar to those of isolates reported in other Asian countries. The E. faecalis isolates analyzed were differentiated into 12 STs, among which ST179 and ST16 of clonal complex (CC) 16 were the major lineage. Nearly all the E. faecium isolates were assigned into CC17, which consisted of 10 different sequence types (STs), including a dominant ST17 containing multidrug resistant isolates and ST78 with isolates harboring the hyaluronidase gene (hyl). The present study revealed the genetic profiles of E. faecalis and E. faecium clinical isolates, with the first identification of optrA in ST480 E. faecalis in Japan. Full article
(This article belongs to the Special Issue Antimicrobial Resistance and Virulence – 3rd Volume)
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16 pages, 1376 KiB  
Article
Virulence Potential of Biofilm-Producing Staphylococcus pseudintermedius, Staphylococcus aureus and Staphylococcus coagulans Causing Skin Infections in Companion Animals
by Mariana Andrade, Ketlyn Oliveira, Catarina Morais, Patrícia Abrantes, Constança Pomba, Adriana E. Rosato, Isabel Couto and Sofia Santos Costa
Antibiotics 2022, 11(10), 1339; https://doi.org/10.3390/antibiotics11101339 - 30 Sep 2022
Cited by 7 | Viewed by 2076
Abstract
Coagulase-positive staphylococci (CoPS) account for most bacteria-related pyoderma in companion animals. Emergence of methicillin-resistant strains of Staphylococcus pseudintermedius (MRSP), Staphylococcus aureus (MRSA) or Staphylococcus coagulans (MRSC), often with multidrug-resistant (MDR) phenotypes, is a public health concern. The study collection comprised 237 staphylococci ( [...] Read more.
Coagulase-positive staphylococci (CoPS) account for most bacteria-related pyoderma in companion animals. Emergence of methicillin-resistant strains of Staphylococcus pseudintermedius (MRSP), Staphylococcus aureus (MRSA) or Staphylococcus coagulans (MRSC), often with multidrug-resistant (MDR) phenotypes, is a public health concern. The study collection comprised 237 staphylococci (S. pseudintermedius (n = 155), S. aureus (n = 55) and S. coagulans (n = 27)) collected from companion animals, previously characterized regarding resistance patterns and clonal lineages. Biofilm production was detected for 51.0% (79/155), 94.6% (52/55) and 88.9% (24/27) of the S. pseudintermedius, S. aureus and S. coagulans, respectively, and was a frequent trait of the predominant S. pseudintermedius and S. aureus clonal lineages. The production of biofilm varied with NaCl supplementation of the growth media. All S. pseudintermedius and S. aureus strains carried icaADB. Kaplan–Meier survival analysis of Galleria mellonella infected with different CoPS revealed a higher virulence potential of S. aureus when compared with other CoPS. Our study highlights a high frequency of biofilm production by prevalent antimicrobial-resistant clonal lineages of CoPS associated with animal pyoderma, potentially related with a higher virulence potential and persistent or recurrent infections. Full article
(This article belongs to the Special Issue Antimicrobial Resistance and Virulence – 3rd Volume)
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20 pages, 5231 KiB  
Article
Phage-Related Ribosomal Proteases (Prps): Discovery, Bioinformatics, and Structural Analysis
by Julia A. Hotinger, Allison Hannah Gallagher and Aaron E. May
Antibiotics 2022, 11(8), 1109; https://doi.org/10.3390/antibiotics11081109 - 16 Aug 2022
Viewed by 1886
Abstract
Many new antimicrobials are analogs of existing drugs, sharing the same targets and mechanisms of action. New antibiotic targets are critically needed to combat the growing threat of antimicrobial-resistant bacteria. Phage-related ribosomal proteases (Prps) are a recently structurally characterized antibiotic target found in [...] Read more.
Many new antimicrobials are analogs of existing drugs, sharing the same targets and mechanisms of action. New antibiotic targets are critically needed to combat the growing threat of antimicrobial-resistant bacteria. Phage-related ribosomal proteases (Prps) are a recently structurally characterized antibiotic target found in pathogens such as Staphylococcus aureus, Clostridioides difficile, and Streptococcus pneumoniae. These bacteria encode an N-terminal extension on their ribosomal protein L27 that is not present in other bacteria. The cleavage of this N-terminal extension from L27 by Prp is necessary to create a functional ribosome. Thus, Prp inhibition may serve as an alternative to direct binding and inhibition of the ribosome. This bioinformatic and structural analysis covers the discovery, function, and structural characteristics of known Prps. This information will be helpful in future endeavors to design selective therapeutics targeting the Prps of important pathogens. Full article
(This article belongs to the Special Issue Antimicrobial Resistance and Virulence – 3rd Volume)
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18 pages, 2128 KiB  
Article
Thymol as an Adjuvant to Restore Antibiotic Efficacy and Reduce Antimicrobial Resistance and Virulence Gene Expression in Enterotoxigenic Escherichia coli Strains
by Andrea Bonetti, Benedetta Tugnoli, Andrea Piva and Ester Grilli
Antibiotics 2022, 11(8), 1073; https://doi.org/10.3390/antibiotics11081073 - 08 Aug 2022
Cited by 5 | Viewed by 2154
Abstract
The continuous spread of antimicrobial resistance is endangering the efficient control of enterotoxigenic Escherichia coli (ETEC), which is mainly responsible for post-weaning diarrhea onset in piglets. Thymol, the key constituent of thyme essential oil, is already used in animal nutrition for its antimicrobial [...] Read more.
The continuous spread of antimicrobial resistance is endangering the efficient control of enterotoxigenic Escherichia coli (ETEC), which is mainly responsible for post-weaning diarrhea onset in piglets. Thymol, the key constituent of thyme essential oil, is already used in animal nutrition for its antimicrobial action. The aim of this study was to investigate the potential adjuvant effect of thymol to re-establish antibiotic efficacy against highly resistant ETEC field strains. Secondly, we evaluated the modulation of virulence and antibiotic resistance genes. Thymol showed the capacity to control ETEC growth and, when combined with ineffective antibiotics, it increased their antimicrobial power. In particular, it showed significant effects when blended with colistin and tetracycline, suggesting that the adjuvant effects rely on the presence of complementary mechanisms of action between molecules, or the absence of resistance mechanisms that inactivate antibiotics and target sites. Furthermore, our findings demonstrate that, when added to antibiotics, thymol can help to further downregulate several virulence and antibiotic resistance genes, offering new insights on the potential mechanisms of action. Therefore, in a one-health approach, our study supports the beneficial effects of combining thymol with antibiotics to restore their efficacy, together with the possibility of targeting gene expression as a pioneering approach to manage ETEC pathogenicity. Full article
(This article belongs to the Special Issue Antimicrobial Resistance and Virulence – 3rd Volume)
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11 pages, 554 KiB  
Article
Antioxidant and Antimicrobial Properties of Helichrysum italicum (Roth) G. Don Hydrosol
by Katja Bezek, Katja Kramberger and Darja Barlič-Maganja
Antibiotics 2022, 11(8), 1017; https://doi.org/10.3390/antibiotics11081017 - 28 Jul 2022
Cited by 6 | Viewed by 1866
Abstract
(1) Background: According to the emergence and spread of antibiotic resistance, there is an urge for new promising substances. The purpose of the study was to test the antioxidant, cytotoxic and antimicrobial properties of the Helichrysum italicum (Roth) G. Don essential oil (EO) [...] Read more.
(1) Background: According to the emergence and spread of antibiotic resistance, there is an urge for new promising substances. The purpose of the study was to test the antioxidant, cytotoxic and antimicrobial properties of the Helichrysum italicum (Roth) G. Don essential oil (EO) and hydrosol. (2) Methods: The antioxidant potential was determined using the DPPH (2,2-diphenyl-1-picrylhydrazyl) method. The cytotoxicity for human skin and intestinal cells was tested using primary and immortalized cell line models. The minimum inhibitory concentration (MIC) of hydrosol was then determined for six bacterial strains covering four commonly reported food pathogens. Further on, the hydrosol at a concentration of 1/8 MIC was used to test the antiadhesive effect by the crystal violet (CV) staining method. (3) Results: the EO showed a 100-times higher antioxidant and 180- to 25.000-times higher cytotoxic activity, when compared to hydrosol. Nevertheless, all bacterial strains, with the exception of Staphylococcus aureus, were sensitive to hydrosol in the range of 12.5% (V/V) for Campylobacter jejuni, to MIC values of 100% (V/V) for Escherichia coli and Pseudomonas aeruginosa. The antiadhesive potential of hydrosol was also shown. (4) Conclusions: Even though hydrosols are a by-product of the EO distillation process, they possess valuable biological activities. Full article
(This article belongs to the Special Issue Antimicrobial Resistance and Virulence – 3rd Volume)
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16 pages, 2278 KiB  
Article
Nisin Mutant Prevention Concentration and the Role of Subinhibitory Concentrations on Resistance Development by Diabetic Foot Staphylococci
by Margarida Costa, Cláudia Meirinhos, Eva Cunha, Diana Gomes, Marcelo Pereira, Ricardo Dias, Luís Tavares and Manuela Oliveira
Antibiotics 2022, 11(7), 972; https://doi.org/10.3390/antibiotics11070972 - 19 Jul 2022
Viewed by 1737
Abstract
The most prevalent microorganism in diabetic foot infections (DFI) is Staphylococcus aureus, an important multidrug-resistant pathogen. The antimicrobial peptide nisin is a promising compound for DFI treatment, being effective against S. aureus. However, to avoid the selection of resistant mutants, correct [...] Read more.
The most prevalent microorganism in diabetic foot infections (DFI) is Staphylococcus aureus, an important multidrug-resistant pathogen. The antimicrobial peptide nisin is a promising compound for DFI treatment, being effective against S. aureus. However, to avoid the selection of resistant mutants, correct drug therapeutic doses must be established, being also important to understand if nisin subinhibitory concentrations (subMIC) can potentiate resistant genes transfer between clinical isolates or mutations in genes associated with nisin resistance. The mutant selection window (MSW) of nisin was determined for 23 DFI S. aureus isolates; a protocol aiming to prompt vanA horizontal transfer between enterococci to clinical S. aureus was performed; and nisin subMIC effect on resistance evolution was assessed through whole-genome sequencing (WGS) applied to isolates subjected to a MEGA-plate assay. MSW ranged from 5–360 μg/mL for two isolates, from 5–540 μg/mL for three isolates, and from 5–720 μg/mL for one isolate. In the presence of nisin subMIC values, no transconjugants were obtained, indicating that nisin does not seem to promote vanA transfer. Finally, WGS analysis showed that incubation in the presence of nisin subMIC did not promote the occurrence of significant mutations in genes related to nisin resistance, supporting nisin application to DFI treatment. Full article
(This article belongs to the Special Issue Antimicrobial Resistance and Virulence – 3rd Volume)
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8 pages, 388 KiB  
Communication
Genomic Characterization of Clinical Acinetobacter baumannii Isolates Obtained from COVID-19 Patients in Russia
by Andrey Shelenkov, Yulia Mikhaylova, Lyudmila Petrova, Irina Gaidukova, Mikhail Zamyatin and Vasiliy Akimkin
Antibiotics 2022, 11(3), 346; https://doi.org/10.3390/antibiotics11030346 - 06 Mar 2022
Cited by 2 | Viewed by 2328
Abstract
The coronavirus disease 2019 (COVID-19) pandemic has already affected all realms of public healthcare and, in particular, has led to increasing use of various antibiotics to treat possible bacterial coinfections even in cases for which such infections were not confirmed clinically. This could [...] Read more.
The coronavirus disease 2019 (COVID-19) pandemic has already affected all realms of public healthcare and, in particular, has led to increasing use of various antibiotics to treat possible bacterial coinfections even in cases for which such infections were not confirmed clinically. This could lead to an increase in the fraction and severity of multidrug-resistant bacterial isolates in healthcare facilities, especially in intensive care units (ICU). However, detailed epidemiological investigations, possibly including whole genome sequencing (WGS), are required to confirm the increase in antibiotic resistance and changes, if any, in the population and clonal structures of bacterial pathogens. In this study, we performed a comprehensive genomic and phenotypic characterization of selected multidrug-resistant A. baumannii isolates obtained from the patients of a dedicated COVID-19 ICU in Moscow, Russia. Hybrid short- and long-read sequencing allowed us to obtain complete profiles of genomic antimicrobial resistance and virulence determinants, as well as to reveal the plasmid structure. We demonstrated the genomic similarity in terms of cgMLST profiles of the isolates studied with a clone previously identified in the same facility. We believe that the data provided will contribute to better understanding the changes imposed by the COVID-19 pandemic on the population structure and the antimicrobial resistance of bacterial pathogens in healthcare facilities. Full article
(This article belongs to the Special Issue Antimicrobial Resistance and Virulence – 3rd Volume)
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Review

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18 pages, 721 KiB  
Review
Soil Component: A Potential Factor Affecting the Occurrence and Spread of Antibiotic Resistance Genes
by Hongyu Shi, Xinyi Hu, Wenxuan Li, Jin Zhang, Baolan Hu and Liping Lou
Antibiotics 2023, 12(2), 333; https://doi.org/10.3390/antibiotics12020333 - 04 Feb 2023
Cited by 6 | Viewed by 2935
Abstract
In recent years, antibiotic resistance genes (ARGs) and antibiotic-resistant bacteria (ARB) in soil have become research hotspots in the fields of public health and environmental ecosystems, but the effects of soil types and soil components on the occurrence and spread of ARGs still [...] Read more.
In recent years, antibiotic resistance genes (ARGs) and antibiotic-resistant bacteria (ARB) in soil have become research hotspots in the fields of public health and environmental ecosystems, but the effects of soil types and soil components on the occurrence and spread of ARGs still lack systematic sorting and in-depth research. Firstly, investigational information about ARB and ARGs contamination of soil was described. Then, existing laboratory studies about the influence of the soil component on ARGs were summarized in the following aspects: the influence of soil types on the occurrence of ARGs during natural or human activities and the control of exogenously added soil components on ARGs from the macro perspectives, the effects of soil components on the HGT of ARGs in a pure bacterial system from the micro perspectives. Following that, the similarities in pathways by which soil components affect HGT were identified, and the potential mechanisms were discussed from the perspectives of intracellular responses, plasmid activity, quorum sensing, etc. In the future, related research on multi-component systems, multi-omics methods, and microbial communities should be carried out in order to further our understanding of the occurrence and spread of ARGs in soil. Full article
(This article belongs to the Special Issue Antimicrobial Resistance and Virulence – 3rd Volume)
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15 pages, 1347 KiB  
Review
Newly Discovered Mechanisms of Antibiotic Self-Resistance with Multiple Enzymes Acting at Different Locations and Stages
by Xiaorong Chen, Hai-Xue Pan and Gong-Li Tang
Antibiotics 2023, 12(1), 35; https://doi.org/10.3390/antibiotics12010035 - 26 Dec 2022
Cited by 2 | Viewed by 2513
Abstract
Self-resistance determinants are essential for the biosynthesis of bioactive natural products and are closely related to drug resistance in clinical settings. The study of self-resistance mechanisms has long moved forward on the discovery of new resistance genes and the characterization of enzymatic reactions [...] Read more.
Self-resistance determinants are essential for the biosynthesis of bioactive natural products and are closely related to drug resistance in clinical settings. The study of self-resistance mechanisms has long moved forward on the discovery of new resistance genes and the characterization of enzymatic reactions catalyzed by these proteins. However, as more examples of self-resistance have been reported, it has been revealed that the enzymatic reactions contribute to self-protection are not confined to the cellular location where the final toxic compounds are present. In this review, we summarize representative examples of self-resistance mechanisms for bioactive natural products functional at different cell locations to explore the models of resistance strategies involved. Moreover, we also highlight those resistance determinants that are widespread in nature and describe the applications of self-resistance genes in natural product mining to interrogate the landscape of self-resistance genes in drug resistance-related new drug discovery. Full article
(This article belongs to the Special Issue Antimicrobial Resistance and Virulence – 3rd Volume)
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23 pages, 932 KiB  
Review
Enterococcus Virulence and Resistant Traits Associated with Its Permanence in the Hospital Environment
by Catarina Geraldes, Luís Tavares, Solange Gil and Manuela Oliveira
Antibiotics 2022, 11(7), 857; https://doi.org/10.3390/antibiotics11070857 - 26 Jun 2022
Cited by 14 | Viewed by 3674
Abstract
Enterococcus are opportunistic pathogens that have been gaining importance in the clinical setting, especially in terms of hospital-acquired infections. This problem has mainly been associated with the fact that these bacteria are able to present intrinsic and extrinsic resistance to different classes of [...] Read more.
Enterococcus are opportunistic pathogens that have been gaining importance in the clinical setting, especially in terms of hospital-acquired infections. This problem has mainly been associated with the fact that these bacteria are able to present intrinsic and extrinsic resistance to different classes of antibiotics, with a great deal of importance being attributed to vancomycin-resistant enterococci. However, other aspects, such as the expression of different virulence factors including biofilm-forming ability, and its capacity of trading genetic information, makes this bacterial genus more capable of surviving harsh environmental conditions. All these characteristics, associated with some reports of decreased susceptibility to some biocides, all described in this literary review, allow enterococci to present a longer survival ability in the hospital environment, consequently giving them more opportunities to disseminate in these settings and be responsible for difficult-to-treat infections. Full article
(This article belongs to the Special Issue Antimicrobial Resistance and Virulence – 3rd Volume)
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18 pages, 1351 KiB  
Systematic Review
Antibiotic Resistance in Campylobacter: A Systematic Review of South American Isolates
by Ana Beatriz Portes, Pedro Panzenhagen, Anamaria Mota Pereira dos Santos and Carlos Adam Conte Junior
Antibiotics 2023, 12(3), 548; https://doi.org/10.3390/antibiotics12030548 - 09 Mar 2023
Cited by 14 | Viewed by 2903
Abstract
In recent years, Campylobacter has become increasingly resistant to antibiotics, especially those first-choice drugs used to treat campylobacteriosis. Studies in South America have reported cases of antibiotic-resistant Campylobacter in several countries, mainly in Brazil. To understand the current frequency of antibiotic-resistant Campylobacter in [...] Read more.
In recent years, Campylobacter has become increasingly resistant to antibiotics, especially those first-choice drugs used to treat campylobacteriosis. Studies in South America have reported cases of antibiotic-resistant Campylobacter in several countries, mainly in Brazil. To understand the current frequency of antibiotic-resistant Campylobacter in humans, farm animals, and food of animal origin in South America, we systematically searched for different studies that have reported Campylobacter resistance. The most commonly reported species were C. jejuni and C. coli. Resistance to ciprofloxacin was found to be ubiquitous in the isolates. Nalidixic acid and tetracycline showed a significantly expressed resistance. Erythromycin, the antibiotic of first choice for the treatment of campylobacteriosis, showed a low rate of resistance in isolates but was detected in almost all countries. The main sources of antibiotic-resistant Campylobacter isolates were food of animal origin and farm animals. The results demonstrate that resistant Campylobacter isolates are disseminated from multiple sources linked to animal production in South America. The level of resistance that was identified may compromise the treatment of campylobacteriosis in human and animal populations. In this way, we are here showing all South American communities the need for the constant surveillance of Campylobacter resistance and the need for the strategic use of antibiotics in animal production. These actions are likely to decrease future difficulties in the treatment of human campylobacteriosis. Full article
(This article belongs to the Special Issue Antimicrobial Resistance and Virulence – 3rd Volume)
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