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Antibiotic Resistance: Appearance, Evolution, and Spread 2.0

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A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Microbiology".

Deadline for manuscript submissions: closed (10 April 2024) | Viewed by 16828

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Dr. Baltasar Mayo

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Departamento de Microbiología y Bioquímica, Instituto de Productos Lácteos de Asturias (IPLA), Consejo Superior de Investigaciones Científicas (CSIC), Paseo Río Linares s/n, 33300 Villaviciosa, Asturias, Spain
Interests: physiology and genetics of lactic acid bacteria and bifidobacteria (LAB&B); dairy starters; probiotics; molecular ecology of dairy products and human gastrointestinal tract; plasmids and vectors for LAB&B; antibiotic resistance in LAB&B
Special Issues, Collections and Topics in MDPI journals

Dr. Ana Belén Flórez

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Departamento de Microbiología y Bioquímica, Instituto de Productos Lácteos de Asturias (IPLA), Consejo Superior de Investigaciones Científicas (CSIC), Paseo Río Linares s/n, 33300 Villaviciosa, Asturias, Spain
Interests: food safety and quality; molecular ecology of dairy products; genome analysis and functional characterization of lactic acid bacteria (LAB); dairy starters; phenotypic and molecular analysis of antibiotic resistance in LAB
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The containment of the development and spread of antibiotic resistance is nowadays one of the major worldwide challenges for the maintenance of human health. If a continuous increase in antibiotic resistance occurs, public health services are expected to enter into the so-called postantibiotic era in a few decades, a situation similar to the one before the discovery of antibiotics. For years, most studies on antibiotic resistance have focused on clinical settings, while antibiotic resistance and transfer have been broadly seen everywhere in the environment. Therefore, studies on this topic have to be broadened to all environmental-, animal-, and human-associated ecosystems.

Understanding the molecular mechanisms involved in the promotion, evolution, distribution, and dissemination of antibiotic resistance in different niches is pivotal, as this might help to obtain scientific knowledge to fight against the appearance and/or spread of resistance. Therefore, we invite authors to submit articles to this Special Issue that will include new and updated principles on these matters from a multihierarchical viewpoint encompassing studies on ecology, molecular biology, and genetics of resistant populations, resistant bacteria, mobile genetic elements, and resistance transfer mechanisms. The integration of data from the application of multiomic approaches, such as genomics, transcriptomics, metagenomics, metatranscriptomics, etc, are of great relevance. However, pure clinical studies are not suitable for this issue, but clinical submissions with molecular experiments are welcomed.

Dr. Baltasar Mayo
Dr. Ana Belén Flórez
Guest Editors

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Keywords

antibiotic resistance
antimicrobial resistance
acquired resistance
cut-off values
resistant bacteria
resistome
resistance mechanisms
multidrug resistance
mobile genetic elements
horizontal gene transfer
resistance transfer
resistance dispersion modeling
omics approaches
biocide coresistance
resistance biological cost
resistance risk

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Published Papers (9 papers)

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Research

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20 pages, 3816 KiB

Open AccessArticle

From Proteome to Potential Drugs: Integration of Subtractive Proteomics and Ensemble Docking for Drug Repurposing against Pseudomonas aeruginosa RND Superfamily Proteins

by Gabriela Urra, Elizabeth Valdés-Muñoz, Reynier Suardiaz, Erix W. Hernández-Rodríguez, Jonathan M. Palma, Sofía E. Ríos-Rozas, Camila A. Flores-Morales, Melissa Alegría-Arcos, Osvaldo Yáñez, Luis Morales-Quintana, Vívian D’Afonseca and Daniel Bustos

Int. J. Mol. Sci. 2024, 25(15), 8027; https://doi.org/10.3390/ijms25158027 - 23 Jul 2024

Viewed by 1141

Abstract

Pseudomonas aeruginosa (P. aeruginosa) poses a significant threat as a nosocomial pathogen due to its robust resistance mechanisms and virulence factors. This study integrates subtractive proteomics and ensemble docking to identify and characterize essential proteins in P. aeruginosa, aiming to discover therapeutic targets and repurpose commercial existing drugs. Using subtractive proteomics, we refined the dataset to discard redundant proteins and minimize potential cross-interactions with human proteins and the microbiome proteins. We identified 12 key proteins, including a histidine kinase and members of the RND efflux pump family, known for their roles in antibiotic resistance, virulence, and antigenicity. Predictive modeling of the three-dimensional structures of these RND proteins and subsequent molecular ensemble-docking simulations led to the identification of MK-3207, R-428, and Suramin as promising inhibitor candidates. These compounds demonstrated high binding affinities and effective inhibition across multiple metrics. Further refinement using non-covalent interaction index methods provided deeper insights into the electronic effects in protein–ligand interactions, with Suramin exhibiting superior binding energies, suggesting its broad-spectrum inhibitory potential. Our findings confirm the critical role of RND efflux pumps in antibiotic resistance and suggest that MK-3207, R-428, and Suramin could be effectively repurposed to target these proteins. This approach highlights the potential of drug repurposing as a viable strategy to combat P. aeruginosa infections. Full article

(This article belongs to the Special Issue Antibiotic Resistance: Appearance, Evolution, and Spread 2.0)

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21 pages, 6955 KiB

Open AccessArticle

Integrative and Conjugative Elements and Prophage DNA as Carriers of Resistance Genes in Erysipelothrix rhusiopathiae Strains from Domestic Geese in Poland

by Marta Dec, Aldert Zomer, John Webster, Tomasz Nowak, Dagmara Stępień-Pyśniak and Renata Urban-Chmiel

Int. J. Mol. Sci. 2024, 25(9), 4638; https://doi.org/10.3390/ijms25094638 - 24 Apr 2024

Cited by 3 | Viewed by 1195

Abstract

Goose erysipelas is a serious problem in waterfowl breeding in Poland. However, knowledge of the characteristics of Erysipelothrix rhusiopathiae strains causing this disease is limited. In this study, the antimicrobial susceptibility and serotypes of four E. rhusiopathiae strains from domestic geese were determined, and their whole-genome sequences (WGSs) were analyzed to detect resistance genes, integrative and conjugative elements (ICEs), and prophage DNA. Sequence type and the presence of resistance genes and transposons were compared with 363 publicly available E. rhusiopathiae strains, as well as 13 strains of other Erysipelothrix species. Four strains tested represented serotypes 2 and 5 and the MLST groups ST 4, 32, 242, and 243. Their assembled circular genomes ranged from 1.8 to 1.9 kb with a GC content of 36–37%; a small plasmid was detected in strain 1023. Strains 1023 and 267 were multidrug-resistant. The resistance genes detected in the genome of strain 1023 were erm47, tetM, and lsaE-lnuB-ant(6)-Ia-spw cluster, while strain 267 contained the tetM and ermB genes. Mutations in the gyrA gene were detected in both strains. The tetM gene was embedded in a Tn916-like transposon, which in strain 1023, together with the other resistance genes, was located on a large integrative and conjugative-like element of 130 kb designated as ICEEr1023. A minor integrative element of 74 kb was identified in strain 1012 (ICEEr1012). This work contributes to knowledge about the characteristics of E. rhusiopathiae bacteria and, for the first time, reveals the occurrence of erm47 and ermB resistance genes in strains of this species. Phage infection appears to be responsible for the introduction of the ermB gene into the genome of strain 267, while ICEs most likely play a key role in the spread of the other resistance genes identified in E. rhusiopathiae. Full article

(This article belongs to the Special Issue Antibiotic Resistance: Appearance, Evolution, and Spread 2.0)

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14 pages, 2628 KiB

Open AccessArticle

The Inactivation of the Putative Two-Component System Sensor PA14_27940 Increases the Susceptibility to Several Antibiotics and Reduces the Motility of Pseudomonas aeruginosa

by Roberta Genova, Teresa Gil-Gil, Trinidad Cuesta, José Luis Martínez and Fernando Sanz-García

Int. J. Mol. Sci. 2023, 24(24), 17355; https://doi.org/10.3390/ijms242417355 - 11 Dec 2023

Cited by 2 | Viewed by 1408

Abstract

The identification of targets whose inactivation increases the activity of antibiotics helps to fight antibiotic resistance. Previous work showed that a transposon-insertion mutant in the gene PA14_27940 increases Pseudomonas aeruginosa susceptibility to aminoglycosides. Since polar effects may affect the phenotype, in the present work, we generated an in-frame PA14_27940 deletion mutant. A PA14_27940 deletion increased the susceptibility to aminoglycosides, tetracycline, tigecycline, erythromycin and fosfomycin. Excepting fosfomycin, the other antibiotics are inducers of the MexXY efflux pump. MexXY induction is required for P. aeruginosa resistance to these antibiotics, which is post-transcriptionally regulated by the anti-repressor ArmZ. Although mexXY is inducible by tobramycin in ΔPA14_27940, the induction level is lower than in the parental PA14 strain. Additionally, armZ is induced by tobramycin in PA14 and not in ΔPA14_27940, supporting that ΔPA14_27940 presents an ArmZ-mediated defect in mexXY induction. For its part, hypersusceptibility to fosfomycin may be due to a reduced expression of nagZ and agmK, which encode enzymes of the peptidoglycan recycling pathway. ΔPA14_27940 also presents defects in motility, an element with relevance in P. aeruginosa’s virulence. Overall, our results support that PA14_27940 is a good target for the search of adjuvants that will increase the activity of antibiotics and reduce the virulence of P. aeruginosa. Full article

(This article belongs to the Special Issue Antibiotic Resistance: Appearance, Evolution, and Spread 2.0)

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14 pages, 1475 KiB

Open AccessArticle

Mechanisms of Listeria monocytogenes Disinfection with Benzalkonium Chloride: From Molecular Dynamics to Kinetics of Time-Kill Curves

by Martín Pérez-Rodríguez, Marta López Cabo, Eva Balsa-Canto and Míriam R. García

Int. J. Mol. Sci. 2023, 24(15), 12132; https://doi.org/10.3390/ijms241512132 - 28 Jul 2023

Cited by 5 | Viewed by 1386

Abstract

Unravelling the mechanisms of action of disinfectants is essential to optimise dosing regimes and minimise the emergence of antimicrobial resistance. In this work, we examined the mechanisms of action of a commonly used disinfectant—benzalkonium chloride (BAC)—over a significant pathogen—L. monocytogenes—in the food industry. For that purpose, we used modelling at multiple scales, from the cell membrane to cell population inactivation. Molecular modelling revealed that the integration of the BAC into the membrane requires three phases: (1) the approaching of BAC to the cellular membrane, (2) the absorption of BAC to its surface, and (3) the integration of the compound into the lipid bilayer, where it remains at least for several nanoseconds, probably destabilising the membrane. We hypothesised that the equilibrium of adsorption, although fast, was limiting for sufficiently large BAC concentrations, and a kinetic model was derived to describe time–kill curves of a large population of cells. The model was tested and validated with time series data of free BAC decay and time–kill curves of L. monocytogenes at different inocula and BAC dose concentrations. The knowledge gained from the molecular simulation plus the proposed kinetic model offers the means to design novel disinfection processes rationally. Full article

(This article belongs to the Special Issue Antibiotic Resistance: Appearance, Evolution, and Spread 2.0)

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16 pages, 350 KiB

Open AccessArticle

Antibiotic Resistance/Susceptibility Profiles of Staphylococcus equorum Strains from Cheese, and Genome Analysis for Antibiotic Resistance Genes

by Lucía Vázquez, Mariela E. Srednik, Javier Rodríguez, Ana Belén Flórez and Baltasar Mayo

Int. J. Mol. Sci. 2023, 24(14), 11657; https://doi.org/10.3390/ijms241411657 - 19 Jul 2023

Cited by 3 | Viewed by 1350

Abstract

In food, bacteria carrying antibiotic resistance genes could play a prominent role in the spread of resistance. Staphylococcus equorum populations can become large in a number of fermented foods, yet the antibiotic resistance properties of this species have been little studied. In this work, the resistance/susceptibility (R/S) profile of S. equorum strains (n = 30) from cheese to 16 antibiotics was determined by broth microdilution. The minimum inhibitory concentration (MIC) for all antibiotics was low in most strains, although higher MICs compatible with acquired genes were also noted. Genome analysis of 13 strains showed the S. equorum resistome to be composed of intrinsic mechanisms, acquired mutations, and acquired genes. As such, a plasmidic cat gene providing resistance to chloramphenicol was found in one strain; this was able to provide resistance to Staphylococcus aureus after electroporation. An msr(A) polymorphic gene was identified in five strains. The Mrs(A) variants were associated with variable resistance to erythromycin. However, the genetic data did not always correlate with the phenotype. As such, all strains harbored a polymorphic fosB/fosD gene, although only one acquired copy was associated with strong resistance to fosfomycin. Similarly, a plasmid-associated blaR1-blaZI operon encoding a penicillinase system was identified in five ampicillin- and penicillin G-susceptible strains. Identified genes not associated with phenotypic resistance further included mph(C) in two strains and norA in all strains. The antibiotic R/S status and gene content of S. equorum strains intended to be employed in food systems should be carefully determined. Full article

(This article belongs to the Special Issue Antibiotic Resistance: Appearance, Evolution, and Spread 2.0)

23 pages, 3229 KiB

Open AccessArticle

Genomic Features of Antimicrobial Resistance in Staphylococcus pseudintermedius Isolated from Dogs with Pyoderma in Argentina and the United States: A Comparative Study

by Mariela E. Srednik, Claudia A. Perea, Gabriela I. Giacoboni, Jessica A. Hicks, Christine L. Foxx, Beth Harris and Linda K. Schlater

Int. J. Mol. Sci. 2023, 24(14), 11361; https://doi.org/10.3390/ijms241411361 - 12 Jul 2023

Cited by 7 | Viewed by 1729

Abstract

Staphylococcus pseudintermedius is the most common opportunistic pathogen in dogs and methicillin resistance (MRSP) has been identified as an emerging problem in canine pyoderma. Here, we evaluated the antimicrobial resistance (AMR) features and phylogeny of S. pseudintermedius isolated from canine pyoderma cases in Argentina (n = 29) and the United States (n = 29). 62% of isolates showed multi-drug resistance. The AMR genes found: mecA, blaZ, ermB, dfrG, catA, tetM, aac(6′)-aph(2″), in addition to tetK and lnuA (only found in U.S. isolates). Two point mutations were detected: grlA(S80I)-gyrA(S84L), and grlA(D84N)-gyrA(S84L) in one U.S. isolate. A mutation in rpoB (H481N) was found in two isolates from Argentina. SCCmec type III, SCCmec type V, ΨSCCmec₅₇₃₉₅ were identified in the Argentinian isolates; and SCCmec type III, SCCmec type IVg, SCCmec type V, and SCCmec type VII variant in the U.S. cohort. Sequence type (ST) ST71 belonging to a dominant clone was found in isolates from both countries, and ST45 only in Argentinian isolates. This is the first study to comparatively analyze the population structure of canine pyoderma-associated S. pseudintermedius isolates in Argentina and in the U.S. It is important to maintain surveillance on S. pseudintermedius populations to monitor AMR and gain further understanding of its evolution and dissemination. Full article

(This article belongs to the Special Issue Antibiotic Resistance: Appearance, Evolution, and Spread 2.0)

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11 pages, 749 KiB

Open AccessCommunication

The Molecular Epidemiology of Pneumococcal Strains Isolated from the Nasopharynx of Preschool Children 3 Years after the Introduction of the PCV Vaccination Program in Poland

by Karolina Kielbik, Ewelina Grywalska, Andrzej Glowniak, Grażyna Mielnik-Niedzielska and Izabela Korona-Glowniak

Int. J. Mol. Sci. 2023, 24(9), 7883; https://doi.org/10.3390/ijms24097883 - 26 Apr 2023

Viewed by 1582

Abstract

The genetic mechanisms of resistance, clonal composition, and the occurrence of pili were analyzed in 39 pneumococcal strains isolated from healthy children in the southeastern region of Poland. Strains with resistance to combinations of erythromycin, clindamycin, and tetracycline were found in clonal groups (CGs) related to Tennessee 23F-4 and Taiwan 19F-14 clones. Capsular switching possibly occurred in the Spain 9V-3 clone and its variants to serotypes 35B and 6A, as well as DLVs of Tennessee 23F-4 to serotype 23A. The double-locus variants of Colombia 23F-26 presented serotype 23B. The major transposons carrying the erythromycin and tetracycline resistance genes were Tn6002 (66.6%), followed by Tn916 (22.2%) and Tn2009 (11.1%). The macrolide efflux genetic assembly (MEGA) element was found in 41.7% of all erythromycin-resistant isolates. The majority of the isolates carrying the PI-1 gene belonged to the CGs related to the Spain 9V-3 clone expressing serotypes 35B and 6A, and the presence of both PI-1 and PI-2 was identified in CG4 consisting of the isolates related to the Taiwan 19F-14 clone expressing serotypes 19F and 19A. Importantly, in the nearest future, the piliated strains of serogroups 23B, 23A, and 35B may be of concern, being a possible origin of the emerging clones of piliated non-vaccine pneumococcal serotypes in Poland. This study reveals that nasopharyngeal carriage in children is an important reservoir for the selection and spreading of new drug-resistant pneumococcal clones in the community after the elimination of vaccine serotypes. Full article

(This article belongs to the Special Issue Antibiotic Resistance: Appearance, Evolution, and Spread 2.0)

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13 pages, 1239 KiB

Open AccessArticle

Antimicrobial Resistance and Genomic Characterization of Salmonella Infantis from Different Sources

by Angela Michela Immacolata Montone, Anna Cutarelli, Maria Francesca Peruzy, Immacolata La Tela, Roberta Brunetti, Maria Gerarda Pirofalo, Veronica Folliero, Anna Balestrieri, Nicoletta Murru and Federico Capuano

Int. J. Mol. Sci. 2023, 24(6), 5492; https://doi.org/10.3390/ijms24065492 - 13 Mar 2023

Cited by 6 | Viewed by 2562

Abstract

The epidemiology of Salmonella Infantis is complex in terms of its distribution and transmission. The continuous collection and analysis of updated data on the prevalence and antimicrobic resistance are essential. The present work aimed to investigate the antimicrobial resistance and the correlation among S. Infantis isolates from different sources through the multiple-locus variable-number of tandem repeat (VNTR) analysis (MLVA). A total of 562 Salmonella strains isolated from 2018 to 2020 from poultry, humans, swine, water buffalo, mussels, cattle, and wild boar were serotyped, and 185 S. Infantis strains (32.92%) were identified. S. Infantis was commonly isolated in poultry and, to a lesser extent, in other sources. The isolates were tested against 12 antimicrobials, and a high prevalence of resistant strains was recorded. S. Infantis showed high resistance against fluoroquinolones, ampicillin, and tetracycline, which are commonly used in human and veterinary medicine. From all S. Infantis isolates, five VNTR loci were amplified. The use of MLVA was not sufficient to understand the complexity of the epidemiological relationships between S. Infantis strains. In conclusion, an alternative methodology to investigate genetic similarities and differences among S. Infantis strains is needed. Full article

(This article belongs to the Special Issue Antibiotic Resistance: Appearance, Evolution, and Spread 2.0)

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Review

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17 pages, 1166 KiB

Open AccessReview

One Health Determinants of Escherichia coli Antimicrobial Resistance in Humans in the Community: An Umbrella Review

by Chloé C. H. Smit, Maarten Lambert, Kris Rogers, Steven P. Djordjevic, Antoine M. Van Oijen, Caitlin Keighley, Katja Taxis, Hamish Robertson and Lisa G. Pont

Int. J. Mol. Sci. 2023, 24(24), 17204; https://doi.org/10.3390/ijms242417204 - 6 Dec 2023

Cited by 1 | Viewed by 2984

Abstract

To date, the scientific literature on health variables for Escherichia coli antimicrobial resistance (AMR) has been investigated throughout several systematic reviews, often with a focus on only one aspect of the One Health variables: human, animal, or environment. The aim of this umbrella review is to conduct a systematic synthesis of existing evidence on Escherichia coli AMR in humans in the community from a One Health perspective. PubMed, EMBASE, and CINAHL were searched on “antibiotic resistance” and “systematic review” from inception until 25 March 2022 (PROSPERO: CRD42022316431). The methodological quality was assessed, and the importance of identified variables was tabulated across all included reviews. Twenty-three reviews were included in this study, covering 860 primary studies. All reviews were of (critically) low quality. Most reviews focused on humans (20), 3 on animals, and 1 on both human and environmental variables. Antibiotic use, urinary tract infections, diabetes, and international travel were identified as the most important human variables. Poultry farms and swimming in freshwater were identified as potential sources for AMR transmission from the animal and environmental perspectives. This umbrella review highlights a gap in high-quality literature investigating the time between variable exposure, AMR testing, and animal and environmental AMR variables. Full article

(This article belongs to the Special Issue Antibiotic Resistance: Appearance, Evolution, and Spread 2.0)

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