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Advances in Antibiotic and Drug-Resistance Mechanisms

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A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Antimicrobial Agents and Resistance".

Deadline for manuscript submissions: closed (31 December 2023) | Viewed by 17554

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Dr. Thierry Naas

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Guest Editor

School of Medicine, University Paris Saclay, Hopital de Bicêtre, Service de Bactériologie, Bâtiment Broca, 3ème étage, 78 rue du Gal Leclerc, 94275 Le Kremlin-Bicêtre, France
Interests: genetics of antibiotic resistance; gram negatives; ß-lactamases; carbapenemases; diagnostics (biochemical, phenotypical, molecular) and diagnostics of antibiotics resistance genes; NGS; transcriptomics; microbiota
Special Issues, Collections and Topics in MDPI journals

Dr. Laura Dabos

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Centre for Plant Biotechnology and Genomics, Madrid, Spain
Interests: evolution of AMR

Special Issue Information

Dear Colleagues,

The discovery of antibiotics has revolutionized medicine by enabling efficient treatment of many life-threatening bacterial infections. Antimicrobial resistance (AMR) is today universally recognised as a global threat, because of the rapid emergence and dissemination of resistant bacteria and genes among humans, animals and the environment on a global scale and represents a heavy burden for healthcare systems all over the world. AMR-related mortality rates estimated currently worldwide are substantial and is an “ecosystem related” problem threatening the interplay of human-animal and environmental health (“One Health”). Resistant bacteria arising in one geographical area can spread via cross-reservoir transmission to other areas worldwide either by human-to human transmission, and /or exposure through the food chain and environmental contaminations. In Human, drivers of antibiotic resistance are complex and multi-sectorial, including food and companion animals, fish, vegetables, and the environmental resistance gene pool.

As the incidence of MDR bacterial infections for which few effective treatments are available increases, novel therapies are needed to curb with this serious problem. The recent commercialization of novel antibiotics resulted more or less rapidly in the emergence of bacterial isolates that either became during therapy, or were already resistant to these novel molecules. The aim of this special issue is to present state of the art data on last resort antibiotics, be they repurposed or novel antibiotics used in human therapy and their associated resistance mechanisms, with special emphasis on:

Their presence in the different compartments (human, animal, and environment).
One Health spectrum dynamics of transmission and the prevalence of community-acquired resistance in human, animals, and environment
Studies of the effects of antimicrobial agent exposure on the healthy human commensal microbiota and their negative consequences in terms of both colonization with antibiotic resistant bacteria but also bacterial population imbalance and dysfunctions in the susceptible bacterial microbiota
Structure-function analysis of AMR gene products
Companion diagnostic tools for safe use of novel therapies
Epidemiology
Genetic basis at the origin of their dispersion
The origin of the AMR genes
Novel antibiotics under development and in clinical use
Novel inhibitors of beta-lactamases/ combinations

Dr. Thierry Naas
Dr. Laura Dabos
Guest Editors

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Keywords

AMR
genetics
novel antibiotics
resistance
mechanisms
diagnostics
One Health
in vitro
in vivo
selection

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Published Papers (10 papers)

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Research

12 pages, 4096 KiB

Open AccessArticle

Analysis of Antibiotic Resistance Genes in Water Reservoirs and Related Wastewater from Animal Farms in Central China

by Yapei Rui and Gang Qiu

Microorganisms 2024, 12(2), 396; https://doi.org/10.3390/microorganisms12020396 - 16 Feb 2024

Viewed by 2007

Abstract

This study aimed to explore the phenotype and relationship of drug resistance genes in livestock and poultry farm wastewater and drinking water reservoirs to provide evidence for the transmission mechanisms of drug resistance genes, in order to reveal the spread of drug resistance genes in wastewater from intensive farms in Central China to urban reservoirs that serve as drinking water sources and provide preliminary data for the treatment of wastewater from animal farms to reduce the threat to human beings. DNA extraction and metagenomic sequencing were performed on eight groups of samples collected from four water reservoirs and four related wastewaters from animal farms in Central China. Metagenomic sequencing showed that the top 20 AROs with the highest abundance were vanT_gene, vanY_gene, adeF, qacG, Mtub_rpsL_STR, vanY_gene_, vanW_gene, Mtub_murA_FOF, vanY_gene, vanH_gene, FosG, rsmA, qacJ, RbpA, vanW_gene, aadA6, vanY_gene, sul4, sul1, and InuF. The resistance genes mentioned above belong to the following categories of drug resistance mechanisms: antibiotic target replacement, antibiotic target protection, antibiotic inactivation, and antibiotic efflux. The resistomes that match the top 20 genes are Streptococcus agalactiae and Streptococcus anginosus; Enterococcus faecalis; Enterococcus faecium; Actinomyces viscosus and Bacillus cereus. Enterococcus faecium; Clostridium tetani; Streptococcus agalactiae and Streptococcus anginosus; Streptococcus agalactiae and Streptococcus anginosus; Acinetobacter baumannii, Bifidobacterium bifidum, Bifidobacterium breve, Bifidobacterium longum, Corynebacterium jeikeium, Corynebacterium urealyticum, Mycobacterium kansasii, Mycobacterium tuberculosis, Schaalia odontolytica, and Trueperella pyogenes; Mycobacterium avium and Mycobacterium tuberculosis; Aeromonas caviae, Enterobacter hormaechei, Vibrio cholerae, Vibrio metoecus, Vibrio parahaemolyticus, and Vibrio vulnificus; Pseudomonas aeruginosa and Pseudomonas fluorescens; Staphylococcus aureus and Staphylococcus equorum; M. avium, Achromobacter xylosoxidans, and Acinetobacter baumannii; Sphingobium yanoikuyae, Acinetobacter indicus, Morganella morganii, Proteus mirabilis, Proteus vulgaris, Providencia rettgeri, and Providencia stuartii. Unreported drug resistance genes and drug-resistant bacteria in Central China were identified in 2023. In the transmission path of drug resistance genes, the transmission path from aquaculture wastewater to human drinking water sources cannot be ignored. For the sake of human health and ecological balance, the treatment of aquaculture wastewater needs to be further strengthened, and the effective blocking of drug resistance gene transmission needs to be considered. Full article

(This article belongs to the Special Issue Advances in Antibiotic and Drug-Resistance Mechanisms)

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9 pages, 1033 KiB

Open AccessArticle

A Novel Detection Procedure for Mutations in the 23S rRNA Gene of Macrolide-Resistant Mycoplasma pneumoniae with Two Non-Overlapping Probes Amplification Assay

by Liyong Liu, Caixin Xiang, Yiwei Zhang, Lihua He, Fanliang Meng, Jie Gong, Jie Liu and Fei Zhao

Microorganisms 2024, 12(1), 62; https://doi.org/10.3390/microorganisms12010062 - 28 Dec 2023

Cited by 1 | Viewed by 1486

Abstract

Mycoplasma pneumoniae is a significant cause of community-acquired pneumonia, which is often empirically treated with macrolides (MLs), but, presently, resistance to MLs has been a matter of close clinical concern. This assay is intended to contribute to resistance detection of M. pneumoniae in clinical practice. A novel real-time PCR assay with two non-overlapping probes on the same nucleic acid strand was designed in this study. It could effectively detect all mutation types of M. pneumoniae in 23S rRNA at loci 2063 and 2064. The results were determined by the following methods: ΔCT < 0.5 for MLs-sensitive M. pneumoniae; ΔCT > 2.0 for MLs-resistant M. pneumoniae; 10 copies as a limit of detection for all types. For detection of M. pneumoniae in 92 clinical specimens, the consistency between the results of this assay and the frequently used real-time PCR results was 95.65%. The consistency of MLs resistance results between PCR sequencing and this assay was 100% in all 43 specimens. The assay could not only cover a comprehensive range of targets and have high detection sensitivity but is also directly used for detection and MLs analysis of M. pneumoniae in specimens. Full article

(This article belongs to the Special Issue Advances in Antibiotic and Drug-Resistance Mechanisms)

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11 pages, 1861 KiB

Open AccessArticle

RETRACTED: Drug Resistance and Molecular Characteristics of Carbapenem-Resistant OXA-48-Producing Klebsiella pneumoniae Strains in Hainan, China

by Min Ye, Lei Liu, Bin Liu, Xiangdong Zhou and Qi Li

Microorganisms 2024, 12(1), 49; https://doi.org/10.3390/microorganisms12010049 - 27 Dec 2023

Cited by 1 | Viewed by 1301 | Retraction

Abstract

Background: The emergence and global spread of carbapenem-resistant hypervirulent Klebsiella pneumoniae (CR-hvKP) are of great concern to health services worldwide. These β-lactamases hydrolyze almost all β-lactams, are plasmid-encoded, and are easily transferable among bacterial species. They are mostly of the KPC types in CR-hvKp. OXA-48-producing hvKP strains have been rarely reported in the literature. Methods: OXA-48-producing hvKP strains were collected from clinical specimens at the First Affiliated Hospital of Hainan Medical University from January 2022 to March 2023. Hypervirulent strains were tested for virulence in a mouse lethality study and underwent whole genome sequencing to identify genomic features. Results: A total of 42 unique OXA-48-bearing K. pneumoniae strains were identified, including three CR-hvKP strains (KP2683-1, NCRE61, and KP2185), which were isolated from bacteremia, pulmonary abscess, and liver abscess separately. The three CR-hvKP strains belonged to two different clones of ST11 KL64 (KP2185 and NCRE61) and ST23 K1 (KP2683-1). The KP2683-1 strain had the highest virulence. Whole genome sequencing analysis indicated that NCRE61 and KP2185 acquired IncFIB-type plasmids with a set of virulence genes (iroBCDN, iucABCD, iutA, rmpA, and rmpA2), while KP2683-1 acquired an IncL-type bla_OXA-48-harboring plasmid. Consecutive cultures showed that the bla_OXA-48-harboring plasmids were highly stable in the three hvKP strains and could be transmitted to Escherichia coli J53 by conjugation. The drug susceptibility testing results show that Ceftazidime/avibactam is sensitive for OXA-48-producing hvKP. Conclusions: Our study highlighted the two evolutionary pathways of OXA-48-producing hvKP strains and confirmed their virulence through in vivo testing. Ceftazidime/avibactam may be a viable option for treating OXA-48-producing hvKP strains. Full article

(This article belongs to the Special Issue Advances in Antibiotic and Drug-Resistance Mechanisms)

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10 pages, 545 KiB

Open AccessArticle

Analysis of Phenotypic and Genotypic Susceptibility to Clarithromycin and Amikacin of Mycobacterium abscessus Complex Strains Isolated from Cystic Fibrosis Patients

by Juan Carlos Cao Yao, Jesús Navas Méndez and María Teresa Tórtola Fernández

Microorganisms 2023, 11(12), 2897; https://doi.org/10.3390/microorganisms11122897 - 30 Nov 2023

Cited by 2 | Viewed by 1251

Abstract

Mycobacterium abscessus complex infections are ever on the rise. To curb their increasing evolution, we performed an in-depth study of 43 clinical isolates of cystic fibrosis patients obtained from 2009 to 2020. We identified their subspecies, uncovered their genotypic resistance profiles, characterised their antibiotic-resistant genes, and assessed their phenotypic antibiotic susceptibilities. The phenotypic and genotypic methods showed total agreement in terms of resistance to clarithromycin and amikacin. Of the 43 clinical strains, 28 belonged to M. abscessus subsp. abscessus (65.1%), 13 to M. abscessus subsp. massiliense (30.2%), and 2 to M. abscessus subsp. bolletii (4.6%). The resistant rates for clarithromycin and amikacin, the two main drugs against M. abscessus complex pulmonary infections, were 64.2% and 14.2%, respectively. We found three strains of M. abscessus subsp. abscessus that showed heteroresistance in the rrl and rrs genes, and these strains also presented double-resistance since they were macrolide- and aminoglycoside-resistant. M. abscessus subsp. abscessus showed a high minimum inhibitory concentration (MIC) and a resistant percentage larger than or equal to 88% to cefoxitin, ciprofloxacin, moxifloxacin, doxycycline, imipenem, and trimethoprim-sulfamethoxazole. These results show a panorama of the high resistance of Mycobacterium abscessus complex to current drugs for cystic fibrosis patients. Thus, other treatment methods are urgently needed. Full article

(This article belongs to the Special Issue Advances in Antibiotic and Drug-Resistance Mechanisms)

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14 pages, 5196 KiB

Open AccessArticle

Metabolome and Transcriptome Combinatory Profiling Reveals Fluconazole Resistance Mechanisms of Trichosporon asahii and the Role of Farnesol in Fluconazole Tolerance

by Xiaoping Ma, Wanling Yang, Aining Yang, Dong Chen, Chengdong Wang, Shanshan Ling, Sanjie Cao, Zhicai Zuo, Ya Wang, Zhijun Zhong, Guangneng Peng, Ming He and Yu Gu

Microorganisms 2023, 11(11), 2798; https://doi.org/10.3390/microorganisms11112798 - 17 Nov 2023

Cited by 1 | Viewed by 1235

Abstract

Trichosporon asahii is a basidiomycete yeast that is pathogenic to humans and animals, and fluconazole-resistant strains have recently increased. Farnesol secreted by fungi is a factor that causes variations in fluconazole resistance; however, few studies have explored the underlying mechanisms. Therefore, this study aims to delineate the fluconazole resistance mechanisms of T. asahii and explore farnesol’s effects on these processes. A comparative metabolome–transcriptome analysis of untreated fluconazole-sensitive (YAN), fluconazole-resistant (PB) T. asahii strains, and 25 μM farnesol-treated strains (YAN-25 and PB-25, respectively) was performed. The membrane lipid-related genes and metabolites were upregulated in the PB vs. YAN and PB-25 vs. PB comparisons. Farnesol demonstrated strain-dependent mechanisms underlying fluconazole tolerance between the YAN and PB strains, and upregulated and downregulated efflux pumps in PB-25 and YAN-25 strains, respectively. Membrane lipid-related metabolites were highly correlated with transporter-coding genes. Fluconazole resistance in T. asahii was induced by membrane lipid bio-synthesis activation. Farnesol inhibited fluconazole resistance in the sensitive strain, but enhanced resistance in the resistant strain by upregulating efflux pump genes and membrane lipids. This study offers valuable insights into the mechanisms underlying fungal drug resistance and provides guidance for future research aimed at developing more potent antifungal drugs for clinical use. Full article

(This article belongs to the Special Issue Advances in Antibiotic and Drug-Resistance Mechanisms)

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14 pages, 1926 KiB

Open AccessArticle

Preliminary SAR of Novel Pleuromutilin–Polyamine Conjugates

by Kenneth Sue, Melissa M. Cadelis, Kerrin Hainsworth, Florent Rouvier, Marie-Lise Bourguet-Kondracki, Jean Michel Brunel and Brent R. Copp

Microorganisms 2023, 11(11), 2791; https://doi.org/10.3390/microorganisms11112791 - 17 Nov 2023

Cited by 1 | Viewed by 1324

Abstract

While pleuromutilin (1) and its clinically available derivatives (2–6) are highly effective against Gram-positive bacteria, they remain inactive against many pathogenic Gram-negative bacteria due to the efflux pump AcrAB-TolC. In an effort to broaden the spectrum of activity of pleuromutilin (1), we developed a series of novel pleuromutilin–polyamine conjugates (9a–f) which exhibited promising intrinsic antimicrobial properties, targeting both Gram-positive and Gram-negative bacteria, including Staphylococcus aureus, methicillin-resistant S. aureus (MRSA), and Escherichia coli, along with the fungal strain Cryptococcus neoformans, and were devoid of cytotoxic and hemolytic properties with the exception of one conjugate. Furthermore, this series displayed moderate to low antibiotic potentiation of legacy antibiotics doxycycline and erythromycin, with three conjugates enhancing the activity four-fold in combination with doxycycline. In comparison to pleuromutilin (1) and tiamulin (2), one of the conjugates exhibited an expanded spectrum of activity, including Gram-negative bacteria and fungi, making it a promising option for combating microbial infections. Full article

(This article belongs to the Special Issue Advances in Antibiotic and Drug-Resistance Mechanisms)

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16 pages, 4390 KiB

Open AccessArticle

Uncovering the Resistance Mechanisms in Extended-Drug-Resistant Pseudomonas aeruginosa Clinical Isolates: Insights from Gene Expression and Phenotypic Tests

by Răzvan Lucian Coșeriu, Anca Delia Mare, Felicia Toma, Camelia Vintilă, Cristina Nicoleta Ciurea, Radu Ovidiu Togănel, Anca Cighir, Anastasia Simion and Adrian Man

Microorganisms 2023, 11(9), 2211; https://doi.org/10.3390/microorganisms11092211 - 31 Aug 2023

Cited by 4 | Viewed by 1724

Abstract

(1) Background: The purpose of the study was to describe the activity of mex efflux pumps in Multidrug-Resistant (MDR) clinical isolates of Pseudomonas aeruginosa and to compare the carbapenem-resistance identification tests with PCR; (2) Methods: Sixty MDR P. aeruginosa were analyzed for detection of carbapenemase by disk diffusion inhibitory method, carbapenem inactivation method and Modified Hodge Test. Endpoint PCR was used to detect 7 carbapenemase genes (bla_KPC, bla_OXA48-like, bla_NDM, bla_GES-2, bla_SPM, bla_IMP, bla_VIM) and mcr-1 for colistin resistance. The expression of mexA, mexB, mexC, mexE and mexX genes corresponding to the four main efflux pumps was also evaluated; (3) Results: From the tested strains, 71.66% presented at least one carbapenemase gene, with bla_GES-2 as the most occurring gene (63.3%). Compared with the PCR, the accuracy of phenotypic tests did not exceed 25% for P. aeruginosa. The efflux pump genes were present in all strains except one. In 85% of the isolates, an overactivity of mexA, mexB and mostly mexC was detected. Previous treatment with ceftriaxone increased the activity of mexC by more than 160 times; (4) Conclusions: In our MDR P. aeruginosa clinical isolates, the carbapenem resistance is not accurately detected by phenotypic tests, due to the overexpression of mex efflux pumps and in a lesser amount, due to carbapenemase production. Full article

(This article belongs to the Special Issue Advances in Antibiotic and Drug-Resistance Mechanisms)

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26 pages, 8016 KiB

Open AccessArticle

Identification of Fungicide Combinations Targeting Plasmopara viticola and Botrytis cinerea Fungicide Resistance Using Machine Learning

by Junrui Zhang and Sandun D. Fernando

Microorganisms 2023, 11(5), 1341; https://doi.org/10.3390/microorganisms11051341 - 19 May 2023

Cited by 7 | Viewed by 2087

Abstract

Downy mildew (caused by Plasmopara viticola) and gray mold (caused by Botrytis cinerea) are fungal diseases that significantly impact grape production globally. Cytochrome b plays a significant role in the mitochondrial respiratory chain of the two fungi that cause these diseases and is a key target for quinone outside inhibitor (QoI)-based fungicide development. Since the mode of action (MOA) of QoI fungicides is restricted to a single active site, the risk of developing resistance to these fungicides is deemed high. Consequently, using a combination of fungicides is considered an effective way to reduce the development of QoI resistance. Currently, there is little information available to help in the selection of appropriate fungicides. This study used a combination of in silico simulations and quantitative structure–activity relationship (QSAR) machine learning algorithms to screen the most potent QoI-based fungicide combinations for wild-type (WT) and the G143A mutation of fungal cytochrome b. Based on in silico studies, mandestrobin emerged as the top binder for both WT Plasmopara viticola and WT Botrytis cinerea cytochrome b. Famoxadone appeared to be a versatile binder for G143A-mutated cytochrome b of both Plasmopara viticola and Botrytis cinerea. Thiram emerged as a reasonable, low-risk non-QoI fungicide that works on WT and G143A-mutated versions of both fungi. QSAR analysis revealed fenpropidin, fenoxanil, and ethaboxam non-QoIs to have a high affinity for G143A-mutated cytochrome b of Plasmopara viticola and Botrytis cinerea. Above-QoI and non-QoI fungicides can be considered for field studies in a fungicide management program against Plasmopara viticola- and Botrytis cinerea-based fungal infections. Full article

(This article belongs to the Special Issue Advances in Antibiotic and Drug-Resistance Mechanisms)

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12 pages, 301 KiB

Open AccessArticle

Prevalence of mecA and Panton-Valentine Leukocidin Genes in Staphylococcus aureus Clinical Isolates from Gaza Strip Hospitals

by Nabil Abdullah El Aila, Nahed Ali Al Laham and Thierry Naas

Microorganisms 2023, 11(5), 1155; https://doi.org/10.3390/microorganisms11051155 - 28 Apr 2023

Viewed by 1590

Abstract

Methicillin-resistant Staphylococcus aureus (MRSA) are spreading worldwide in hospital and community settings, thus posing a serious public health problem. Panton-Valentine Leukocidin (PVL), an important virulence factor of S. aureus, is a marker of community-acquired MRSA. Here we determined the prevalence of pvl genes among S. aureus isolates from different hospitals in the Gaza Strip, Palestine. A total of 285 S. aureus isolates were collected from five different hospitals in the Gaza Strip. All isolates were characterized for their susceptibility patterns to available antimicrobial agents and by using multiplex PCR for the detection of mecA and pvl genes. The overall prevalence of MRSA in Gaza hospitals was 70.2% (range: 76.3% to 65.5%) and that of pvl among S. aureus isolates was 29.8% (range: 32.9% to 26.2%). The pvl gene was equally prevalent among MRSA isolates (30.5%) and MSSA isolates (28.2%). The most effective antibiotics were rifampicin, vancomycin, and clindamycin, with susceptibility rates of 91.2%, 88.7%, and 84.6%, respectively. The highest percentage of strains were observed to be resistant to penicillin and amoxicillin with clavulanic acid—96.1% and 73.6%, respectively. Our results showed a high prevalence of MRSA and pvl-positive isolates in Gaza Strip hospitals, which likely reflects the situation in the community. It is mandatory to implement systematic surveillance of both hospital and community isolates, together with interventions (such as increased hand hygiene, use of hydroalcoholic solutions, and isolation of carriers) to limit their spread. Full article

(This article belongs to the Special Issue Advances in Antibiotic and Drug-Resistance Mechanisms)

17 pages, 1677 KiB

Open AccessArticle

Genomic Characterization of Multidrug-Resistant Extended Spectrum β-Lactamase-Producing Klebsiella pneumoniae from Clinical Samples of a Tertiary Hospital in South Kivu Province, Eastern Democratic Republic of Congo

by Leonid M. Irenge, Jérôme Ambroise, Bertrand Bearzatto, Jean-François Durant, Maxime Bonjean and Jean-Luc Gala

Microorganisms 2023, 11(2), 525; https://doi.org/10.3390/microorganisms11020525 - 18 Feb 2023

Cited by 1 | Viewed by 2311

Abstract

Multidrug-resistant (MDR) and extended spectrum β-lactamase (ESBL)-producing extra-intestinal K. pneumoniae are associated with increased morbidity and mortality. This study aimed to characterize the resistance and virulence profiles of extra-intestinal MDR ESBL-producing K. pneumoniae associated with infections at a tertiary hospital in South-Kivu province, DRC. Whole-genome sequencing (WGS) was carried out on 37 K. pneumoniae isolates displaying MDR and ESBL-producing phenotype. The assembled genomes were analysed for phylogeny, virulence factors and antimicrobial resistance genes (ARG) determinants. These isolates were compared to sub-Saharan counterparts. K. pneumoniae isolates displayed a high genetic variability with up to 16 sequence types (ST). AMR was widespread against β-lactamases (including third and fourth-generation cephalosporins, but not carbapenems), aminoglycosides, ciprofloxacin, tetracycline, erythromycin, nitrofurantoin, and cotrimoxazole. The bla_CTX-M-15 gene was the most common β-lactamase gene among K. pneumoniae isolates. No carbapenemase gene was found. ARG for aminoglycosides, quinolones, phenicols, tetracyclines, sulfonamides, nitrofurantoin were widely distributed among the isolates. Nine isolates had the colistin-resistant R256G substitution in the pmrB efflux pump gene without displaying reduced susceptibility to colistin. Despite carrying virulence genes, none had hypervirulence genes. Our results highlight the genetic diversity of MDR ESBL-producing K. pneumoniae isolates and underscore the importance of monitoring simultaneously the evolution of phenotypic and genotypic AMR in Bukavu and DRC, while calling for caution in administering colistin and carbapenem to patients. Full article

(This article belongs to the Special Issue Advances in Antibiotic and Drug-Resistance Mechanisms)

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