151
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Atzori A, Malloci G, Cardamone F, Bosin A, Vargiu AV, Ruggerone P. Molecular Interactions of Carbapenem Antibiotics with the Multidrug Efflux Transporter AcrB of Escherichia coli. Int J Mol Sci 2020; 21:E860. [PMID: 32013182 PMCID: PMC7037162 DOI: 10.3390/ijms21030860] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 01/26/2020] [Indexed: 12/22/2022] Open
Abstract
The drug/proton antiporter AcrB, engine of the major efflux pump AcrAB(Z)-TolC of Escherichia coli and other bacteria, is characterized by its impressive ability to transport chemically diverse compounds, conferring a multi-drug resistance (MDR) phenotype. Although hundreds of small molecules are known to be AcrB substrates, only a few co-crystal structures are available to date. Computational methods have been therefore intensively employed to provide structural and dynamical fingerprints related to transport and inhibition of AcrB. In this work, we performed a systematic computational investigation to study the interaction between representative carbapenem antibiotics and AcrB. We focused on the interaction of carbapenems with the so-called distal pocket, a region known for its importance in binding inhibitors and substrates of AcrB. Our findings reveal how the different physico-chemical nature of these antibiotics is reflected on their binding preference for AcrB. The molecular-level information provided here could help design new antibiotics less susceptible to the efflux mechanism.
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Affiliation(s)
| | - Giuliano Malloci
- Department of Physics, University of Cagliari, 09042 Monserrato (CA), Italy; (A.A.); (F.C.); (A.B.); (P.R.)
| | | | | | - Attilio Vittorio Vargiu
- Department of Physics, University of Cagliari, 09042 Monserrato (CA), Italy; (A.A.); (F.C.); (A.B.); (P.R.)
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152
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Pseudomonas aeruginosa Toxin ExoU as a Therapeutic Target in the Treatment of Bacterial Infections. Microorganisms 2019; 7:microorganisms7120707. [PMID: 31888268 PMCID: PMC6955817 DOI: 10.3390/microorganisms7120707] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 12/10/2019] [Accepted: 12/14/2019] [Indexed: 12/20/2022] Open
Abstract
The opportunistic pathogen Pseudomonas aeruginosa employs the type III secretion system (T3SS) and four effector proteins, ExoS, ExoT, ExoU, and ExoY, to disrupt cellular physiology and subvert the host’s innate immune response. Of the effector proteins delivered by the T3SS, ExoU is the most toxic. In P. aeruginosa infections, where the ExoU gene is expressed, disease severity is increased with poorer prognoses. This is considered to be due to the rapid and irreversible damage exerted by the phospholipase activity of ExoU, which cannot be halted before conventional antibiotics can successfully eliminate the pathogen. This review will discuss what is currently known about ExoU and explore its potential as a therapeutic target, highlighting some of the small molecule ExoU inhibitors that have been discovered from screening approaches.
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153
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Beggs GA, Brennan RG, Arshad M. MarR family proteins are important regulators of clinically relevant antibiotic resistance. Protein Sci 2019; 29:647-653. [PMID: 31682303 DOI: 10.1002/pro.3769] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 10/28/2019] [Accepted: 10/29/2019] [Indexed: 12/14/2022]
Abstract
There has been a rapid spread of multidrug-resistant (MDR) bacteria across the world. MDR efflux transporters are an important mechanism of antibiotic resistance in many pathogens among both Gram positive and Gram negative bacteria. These pumps can recognize a variety of chemically and structurally different compounds, including innate and clinically administered antibiotics. Intriguingly, these efflux pumps are often regulated by transcription factors that themselves bind a diverse set of substrates thereby allowing them to regulate the expression of their cognate MDR efflux pumps. One significant family of such transcription factors is the Multiple antibiotic resistance Repressor (MarR) family. Members of this family are well conserved across different bacterial species and in some cases are known to regulate vital bacterial functions. This review focusses on the role of MarR family transcriptional factors in antibiotic resistance within a select group of clinically relevant pathogens.
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Affiliation(s)
- Grace A Beggs
- Department of Biochemistry, Duke University, Durham, North Carolina
| | | | - Mehreen Arshad
- Department of Pediatrics, Ann and Robert H. Lurie Children's Hospital, Northwestern University, Chicago, Illinois
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154
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Ulusoy BH, Chirkena K. Two perspectives of Listeria monocytogenes hazards in dairy products: the prevalence and the antibiotic resistance. FOOD QUALITY AND SAFETY 2019. [DOI: 10.1093/fqsafe/fyz035] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Abstract
Listeria monocytogenes is among the most food-borne pathogens. It has the ability to grow over a range of temperature, including refrigeration temperature. Foods kept in refrigerator more than the prescribed period of time create an opportunity for the occurrence of Listeria monocytogenes. As this review shows, the prevalence of L. monocytogenes has more likely evident in pasteurized milk than other dairy products, such as raw milk. Inadequate temperature and faults in technology during pasteurization can be the disposing factors for the presence of the organism in dairy products. The organism, on the other hand, has been found to be resistant to those commonly known antibiotics that have human and veterinary importance, namely, ampicillin, Tetracycline, and chloramphenicol, streptomycin, erytromycin, penicillin G., and others. Resistance ability of the organism can be mediated by different natural and acquired resistance mechanisms, such as self-transferrable plasmids, mobilizable plasmids, and conjugative transposons. The emergence and spread of antibiotic resistance of L. monocytogenes has serious public health and economic impacts at large. This paper has reviewed the prevalence and the antibiotic resistance of L. monocytogenes isolates of dairy products and the strategic mechanisms of the organism develop resistance against the antibiotics.
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Affiliation(s)
- Beyza H Ulusoy
- Faculty of Veterinary Medicine, Department of Food Hygiene and Technology, Near East University, Nicosia, Cyprus
| | - Kefyalew Chirkena
- Faculty of Veterinary Medicine, Department of Food Hygiene and Technology, Near East University, Nicosia, Cyprus
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155
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Plant-derived secondary metabolites as the main source of efflux pump inhibitors and methods for identification. J Pharm Anal 2019; 10:277-290. [PMID: 32923005 PMCID: PMC7474127 DOI: 10.1016/j.jpha.2019.11.002] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 10/05/2019] [Accepted: 11/04/2019] [Indexed: 12/25/2022] Open
Abstract
The upsurge of multiple drug resistance (MDR) bacteria substantially diminishes the effectiveness of antibiotic arsenal and therefore intensifies the rate of therapeutic failure. The major factor in MDR is efflux pump-mediated resistance. A unique pump can make bacteria withstand a wide range of structurally diverse compounds. Therefore, their inhibition is a promising route to eliminate resistance phenomenon in bacteria. Phytochemicals are excellent alternatives as resistance-modifying agents. They can directly kill bacteria or interact with the crucial events of pathogenicity, thereby decreasing the ability of bacteria to develop resistance. Numerous botanicals display noteworthy efflux pumps inhibitory activities. Edible plants are of growing interest. Likewise, some plant families would be excellent sources of efflux pump inhibitors (EPIs) including Apocynaceae, Berberidaceae, Convolvulaceae, Cucurbitaceae, Fabaceae, Lamiaceae, and Zingiberaceae. Easily applicable methods for screening plant-derived EPIs include checkerboard synergy test, berberine uptake assay and ethidium bromide test. In silico high-throughput virtual detection can be evaluated as a criterion of excluding compounds with efflux substrate-like characteristics, thereby improving the selection process and extending the identification of EPIs. To ascertain the efflux activity inhibition, real-time PCR and quantitative mass spectrometry can be applied. This review emphasizes on efflux pumps and their roles in transmitting bacterial resistance and an update plant-derived EPIs and strategies for identification. Active efflux as the main resistance strategy in bacteria. Phytochemicals as promising alternatives against efflux pumps-mediated MDR. Herbals-based efflux pump inhibitors screening, the methods.
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156
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Antimicrobial Resistance in Bacteria: Mechanisms, Evolution, and Persistence. J Mol Evol 2019; 88:26-40. [PMID: 31659373 DOI: 10.1007/s00239-019-09914-3] [Citation(s) in RCA: 284] [Impact Index Per Article: 56.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 10/02/2019] [Indexed: 01/29/2023]
Abstract
In recent years, we have seen antimicrobial resistance rapidly emerge at a global scale and spread from one country to the other faster than previously thought. Superbugs and multidrug-resistant bacteria are endemic in many parts of the world. There is no question that the widespread use, overuse, and misuse of antimicrobials during the last 80 years have been associated with the explosion of antimicrobial resistance. On the other hand, the molecular pathways behind the emergence of antimicrobial resistance in bacteria were present since ancient times. Some of these mechanisms are the ancestors of current resistance determinants. Evidently, there are plenty of putative resistance genes in the environment, however, we cannot yet predict which ones would be able to be expressed as phenotypes in pathogenic bacteria and cause clinical disease. In addition, in the presence of inhibitory and sub-inhibitory concentrations of antibiotics in natural habitats, one could assume that novel resistance mechanisms will arise against antimicrobial compounds. This review presents an overview of antimicrobial resistance mechanisms, and describes how these have evolved and how they continue to emerge. As antimicrobial strategies able to bypass the development of resistance are urgently needed, a better understanding of the critical factors that contribute to the persistence and spread of antimicrobial resistance may yield innovative perspectives on the design of such new therapeutic targets.
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157
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Alav I, Sutton JM, Rahman KM. Role of bacterial efflux pumps in biofilm formation. J Antimicrob Chemother 2019; 73:2003-2020. [PMID: 29506149 DOI: 10.1093/jac/dky042] [Citation(s) in RCA: 258] [Impact Index Per Article: 51.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Efflux pumps are widely implicated in antibiotic resistance because they can extrude the majority of clinically relevant antibiotics from within cells to the extracellular environment. However, there is increasing evidence from many studies to suggest that the pumps also play a role in biofilm formation. These studies have involved investigating the effects of efflux pump gene mutagenesis and efflux pump inhibitors on biofilm formation, and measuring the levels of efflux pump gene expression in biofilms. In particular, several key pathogenic species associated with increasing multidrug resistance, such as Acinetobacter baumannii, Escherichia coli, Pseudomonas aeruginosa and Staphylococcus aureus, have been investigated, whilst other studies have focused on Salmonella enterica serovar Typhimurium as a model organism and problematic pathogen. Studies have shown that efflux pumps, including AcrAB-TolC of E. coli, MexAB-OprM of P. aeruginosa, AdeFGH of A. baumannii and AcrD of S. enterica, play important roles in biofilm formation. The substrates for such pumps, and whether changes in their efflux activity affect biofilm formation directly or indirectly, remain to be determined. By understanding the roles that efflux pumps play in biofilm formation, novel therapeutic strategies can be developed to inhibit their function, to help disrupt biofilms and improve the treatment of infections. This review will discuss and evaluate the evidence for the roles of efflux pumps in biofilm formation and the potential approaches to overcome the increasing problem of biofilm-based infections.
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Affiliation(s)
- Ilyas Alav
- School of Cancer and Pharmaceutical Science, King's College London, London, UK
| | - J Mark Sutton
- Public Health England, National Infection Service, Porton Down, Salisbury, UK
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158
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Novel Inducers of the Expression of Multidrug Efflux Pumps That Trigger Pseudomonas aeruginosa Transient Antibiotic Resistance. Antimicrob Agents Chemother 2019; 63:AAC.01095-19. [PMID: 31501142 DOI: 10.1128/aac.01095-19] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 09/03/2019] [Indexed: 01/13/2023] Open
Abstract
The study of the acquisition of antibiotic resistance (AR) has mainly focused on inherited processes, namely, mutations and acquisition of AR genes. However, inducible, noninheritable AR has received less attention, and most information in this field derives from the study of antibiotics as inducers of their associated resistance mechanisms. Less is known about nonantibiotic compounds or situations that can induce AR during infection. Multidrug resistance efflux pumps are a category of AR determinants characterized by the tight regulation of their expression. Their contribution to acquired AR relies in their overexpression. Here, we analyzed potential inducers of the expression of the chromosomally encoded Pseudomonas aeruginosa clinically relevant efflux pumps, MexCD-OprJ and MexAB-OprM. For this purpose, we developed a set of luxCDABE-based P. aeruginosa biosensor strains, which allows the high-throughput analysis of compounds able to modify the expression of these efflux pumps. Using these strains, we analyzed a set of 240 compounds present in Biolog phenotype microarrays. Several inducers of the expression of the genes that encode these efflux pumps were found. The study focused in dequalinium chloride, procaine, and atropine, compounds that can be found in clinical settings. Using real-time PCR, we confirmed that these compounds indeed induce the expression of the mexCD-oprJ operon. In addition, P. aeruginosa presents lower susceptibility to ciprofloxacin (a MexCD-OprJ substrate) when dequalinium chloride, procaine, or atropine are present. This study emphasizes the need to study compounds that can trigger transient AR during antibiotic treatment, a phenotype difficult to discover using classical susceptibility tests.
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159
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Zhan Z, Hu L, Jiang X, Zeng L, Feng J, Wu W, Chen W, Yang H, Yang W, Gao B, Yin Z, Zhou D. Plasmid and chromosomal integration of four novel blaIMP-carrying transposons from Pseudomonas aeruginosa, Klebsiella pneumoniae and an Enterobacter sp. J Antimicrob Chemother 2019; 73:3005-3015. [PMID: 30351436 DOI: 10.1093/jac/dky288] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2018] [Accepted: 06/25/2018] [Indexed: 12/11/2022] Open
Abstract
Objectives To provide detailed genetic characterization of four novel blaIMP-carrying transposons from Pseudomonas aeruginosa, Klebsiella pneumoniae and an Enterobacter sp. Methods P. aeruginosa 60512, K. pneumoniae 447, P. aeruginosa 12939 and Enterobacter sp. A1137 were subjected to genome sequencing. The complete nucleotide sequences of two plasmids (p60512-IMP from the 60512 isolate and p447-IMP from the 447 isolate) and two chromosomes (the 12939 and A1137 isolates) were determined, then a genomic comparison of p60512-IMP, p447-IMP and four novel blaIMP-carrying transposons (Tn6394, Tn6375, Tn6411 and Tn6397) with related sequences was performed. Transferability of the blaIMP gene and bacterial antimicrobial susceptibility were tested. Results Tn6394 and Tn6375 were located in p60512-IMP and p447-IMP, respectively, while Tn6411 and Tn6397 were integrated into the 12939 and A1137 chromosomes, respectively. Tn6394 was an ISPa17-based transposition unit that harboured the integron In992 (carrying blaIMP-1). In73 (carrying blaIMP-8), In73 and In992, together with the ISEcp1:IS1R-blaCTX-M-14-IS903D unit, the macAB-tolC region and the truncated aacC2-tmrB region, respectively, were integrated into the prototype transposons Tn1722, Tn1696 and Tn7, respectively, generating the Tn3-family unit transposons, Tn6375 and Tn6378, and the Tn7-family unit transposon Tn6411, respectively. Tn6397 was a large integrative and conjugative element carrying Tn6378. Conclusions Complex events of transposition and homologous recombination have occurred during the original formation and further plasmid and chromosomal integration of these four transposons, promoting accumulation and spread of antimicrobial resistance genes.
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Affiliation(s)
- Zhe Zhan
- Anhui Medical University, Hefei, China.,State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Lingfei Hu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Xiaoyuan Jiang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Lijun Zeng
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Jiao Feng
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Weili Wu
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Weijun Chen
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Huiying Yang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Wenhui Yang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Bo Gao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Zhe Yin
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Dongsheng Zhou
- Anhui Medical University, Hefei, China.,State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
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160
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Cooper R, Kirketerp-Møller K. Non-antibiotic antimicrobial interventions and antimicrobial stewardship in wound care. J Wound Care 2019; 27:355-377. [PMID: 29883284 DOI: 10.12968/jowc.2018.27.6.355] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Control of wound infection today relies largely on antibiotics, but the continual emergence of antibiotic-resistant microorganisms threatens a return to the pre-antibiotic era when physicians used antiseptics to prevent and manage infection. Some of those antiseptics are still used today, and others have become available. A diverse variety of non-antibiotic antimicrobial interventions are found on modern formularies. Unlike the mode of action of antibiotics, which affect specific cellular target sites of pathogens, many non-antibiotic antimicrobials affect multiple cellular target sites in a non-specific way. Although this reduces the likelihood of selecting for resistant strains of microorganisms, some have emerged and cross-resistance between antibiotics and antiseptics has been detected. With the prospect of a post-antibiotic era looming, ways to maintain and extend our antimicrobial armamentarium must be found. In this narrative review, current and emerging non-antibiotic antimicrobial strategies will be considered and the need for antimicrobial stewardship in wound care will be explained.
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Affiliation(s)
- Rose Cooper
- Professor of Microbiology, Department of Biomedical Science, Cardiff School of Health Sciences, Cardiff Metropolitan University, Western Avenue, Cardiff, UK
| | - Klaus Kirketerp-Møller
- Orthopaedic Surgeon, Copenhagen Wound Healing Center, Department of Dermatology and Wounds, Bispebjerg University Hospital, Bispebjerg Bakke 23, DK-2400 Copenhagen NV
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161
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Wu B, Yang X, Yan M. Synthesis and Structure-Activity Relationship Study of Antimicrobial Auranofin against ESKAPE Pathogens. J Med Chem 2019; 62:7751-7768. [PMID: 31386365 PMCID: PMC7941214 DOI: 10.1021/acs.jmedchem.9b00550] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Auranofin, an FDA-approved arthritis drug, has recently been repurposed as a potential antimicrobial agent; it performed well against many Gram-positive bacteria, including multidrug resistant strains. It is, however, inactive toward Gram-negative bacteria, for which we are in dire need of new therapies. In this work, 40 auranofin analogues were synthesized by varying the structures of the thiol and phosphine ligands, and their activities were tested against ESKAPE pathogens. The study identified compounds that exhibited bacterial inhibition (MIC) and killing (MBC) activities up to 65 folds higher than that of auranofin, making them effective against Gram-negative pathogens. Both thiol and the phosphine structures influence the activities of the analogues. The trimethylphosphine and triethylphosphine ligands gave the highest activities against Gram-negative and Gram-positive bacteria, respectively. Our SAR study revealed that the thiol ligand is also very important, the structure of which can modulate the activities of the AuI complexes for both Gram-negative and Gram-positive bacteria. Moreover, these analogues had mammalian cell toxicities either similar to or lower than that of auranofin.
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Affiliation(s)
- Bin Wu
- Department of Chemistry, The University of Massachusetts, Lowell, Massachusetts 01854, United States
| | - Xiaojian Yang
- Department of Chemistry, The University of Massachusetts, Lowell, Massachusetts 01854, United States
| | - Mingdi Yan
- Department of Chemistry, The University of Massachusetts, Lowell, Massachusetts 01854, United States
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162
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Nascimento RJ, Frasão BS, Dias TS, Nascimento ER, Tavares LS, Almeida VL, Aquino MHC. Detection of efflux pump CmeABC in enrofloxacin resistant Campylobacter spp. strains isolated from broiler chickens (Gallus gallus domesticus) in the state of Rio de Janeiro, Brazil. PESQUISA VETERINÁRIA BRASILEIRA 2019. [DOI: 10.1590/1678-5150-pvb-6004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
ABSTRACT: Fowls are the main reservoirs of the highly important food-originating pathogen called Campylobacter spp. and broilers’ meat and byproducts are the main vehicles of this microorganism. Increasing of Campylobacter spp. resistant strains to fluorquinolones, an antimicrobial class often employed in poultry farming and in human medicine has become a great concern to poultry breeders. In fact, several studies evaluated increasing bacterial resistance against these antimicrobial agents. The role of CmeABC efflux system has been underscored among the resistance mechanisms in Campylobacter spp. to fluorquinolones. This study investigated the occurrence of CmeABC efflux pump in 81 and 78 enrofloxacin resistant strains of Campylobacter jejuni and C. coli respectively, isolated from broilers collected from six abattoirs situated at São José do Vale do Rio Preto/RJ poultry center and from two commercial abattoirs situated at Metropolitan Region of Rio de Janeiro, from 2013 to 2016. The resistance to enrofloxacin was assessed by agar dilution to determine minimum inhibitory concentration (MIC). The CmeABC efflux system was investigated through the detection of genes genes cmeA, cmeB and cmeC by PCR. The activity of CmeABC efflux pump was investigated in 20 strains by using the efflux pump inhibitor Phenylalanine-Arginine β-Naphthylamide (PAβN). The three genes cmeA, cmeB and cmeC were detected in 94.3% of the strains (C. jejuni = 80 and C. coli = 70), whereas the system was absent or incomplete in 5.7% of strains (C. jejuni = 1 and C. coli = 8). MIC varied between 0.5μg/ml and 64μg/ml, and 88.7% of strains were enrofloxacin resistant and 11.3% featuring intermediate resistance. The inhibition of the efflux pump by PAβN reduced the MIC to enrofloxacin up to eight times in fifteen strains (75%). These results indicate that this system is frequent and active in Campylobacter spp. Resistant strains in the presence of enrofloxacin.
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163
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Longo LGA, de Sousa VS, Kraychete GB, Justo-da-Silva LH, Rocha JA, Superti SV, Bonelli RR, Martins IS, Moreira BM. Colistin resistance emerges in pandrug-resistant Klebsiella pneumoniae epidemic clones in Rio de Janeiro, Brazil. Int J Antimicrob Agents 2019; 54:579-586. [PMID: 31479740 DOI: 10.1016/j.ijantimicag.2019.08.017] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 08/09/2019] [Accepted: 08/24/2019] [Indexed: 12/12/2022]
Abstract
Klebsiella pneumoniae is an important human pathogen, able to accumulate and disseminate a variety of antimicrobial resistance genes. Resistance to colistin, one of the last therapeutic options for multi-drug-resistant bacteria, has been reported increasingly. Colistin-resistant K. pneumoniae (ColRKp) emerged in two hospitals in Rio de Janeiro state, Brazil in 2016. The aim of this study was to investigate if these ColRKp isolates were clonally related when compared between hospitals, to identify the molecular mechanisms of colistin resistance, and to describe other antimicrobial resistance genes carried by isolates. Twenty-three isolates were successively recovered, and the whole-genome sequence was analysed for 10, each of a different pulsed-field gel electrophoresis (PFGE) type. Although some PFGE clusters were found, none of them included isolates from both hospitals. Half of the isolates were assigned to CC258, three to ST152 and two to ST15. One isolate was pandrug resistant, one was extensively drug resistant, and the others were multi-drug resistant. Colistin resistance was related to mutations in mgrB, pmrB, phoQ and crrB. Eleven new mutations were found in these genes, including two nucleotide deletions in mgrB. All isolates were carbapenem resistant, and seven were associated with carbapenemase carriage (blaKPC-2 in six isolates and blaOXA-370 in one isolate). All isolates had a blaCTX-M, and two had a 16S ribosomal RNA methyltransferase encoding gene (armA and rmtB). ColRKp were composed of epidemic clones, but cross-dissemination between hospitals was not detected. Colistin resistance emerged with several novel mutations amid highly resistant strains, further restricting the number of drugs available and leading to pandrug resistance.
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Affiliation(s)
- Luís G A Longo
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Viviane S de Sousa
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Gabriela B Kraychete
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Lívia H Justo-da-Silva
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Jaqueline A Rocha
- Hospital Universitário Antônio Pedro, Faculdade de Medicina, Universidade Federal Fluminense, Niterói, Brazil
| | | | - Raquel R Bonelli
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Ianick S Martins
- Departamento de Medicina Clínica, Faculdade de Medicina, Universidade Federal Fluminense, Niterói, Brazil
| | - Beatriz M Moreira
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.
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164
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Dwivedi GR, Maurya A, Yadav DK, Khan F, Gupta MK, Gupta P, Darokar MP, Srivastava SK. Comparative Drug Resistance Reversal Potential of Natural Glycosides: Potential of Synergy Niaziridin & Niazirin. Curr Top Med Chem 2019; 19:847-860. [DOI: 10.2174/1568026619666190412120008] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 03/10/2019] [Accepted: 03/14/2019] [Indexed: 11/22/2022]
Abstract
Background:
Due to the limited availability of antibiotics, Gram-negative bacteria (GNB) acquire
different levels of drug resistance. It raised an urgent need to identify such agents, which can reverse the phenomenon
of drug resistance.
Objective:
To understand the mechanism of drug resistance reversal of glycosides; niaziridin and niazirin isolated
from the pods of Moringa oleifera and ouabain (control) against the clinical isolates of multidrug-resistant
Escherichia coli.
Methods:
The MICs were determined following the CLSI guidelines for broth micro-dilution. In-vitro combination
studies were performed by broth checkerboard method followed by Time-Kill studies, the efflux pump
inhibition assay, ATPase inhibitory activity, mutation prevention concentration and in-silico studies.
Results:
The results showed that both glycosides did not possess antibacterial activity of their own, but in combination,
they reduced the MIC of tetracycline up to 16 folds. Both were found to inhibit efflux pumps, but
niaziridin was the best. In real time expression pattern analysis, niaziridin was also found responsible for the
down expression of the two important efflux pump acrB & yojI genes alone as well as in combination.
Niaziridin was also able to over express the porin forming genes (ompA & ompX). These glycosides decreased
the mutation prevention concentration of tetracycline.
Conclusion:
This is the first ever report on glycosides, niazirin and niaziridin acting as drug resistance reversal
agent through efflux pump inhibition and modulation of expression pattern drug resistant genes. This study
may be helpful in preparing an effective antibacterial combination against the drug-resistant GNB from a
widely growing Moringa oleifera.
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Affiliation(s)
- Gaurav R. Dwivedi
- Molecular Bioprospection Department, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow-226015, India
| | - Anupam Maurya
- Medicinal Chemistry Department, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow-226015, India
| | - Dharmendra K. Yadav
- Metabolic & Structural Biology, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow-226015, India
| | - Feroz Khan
- Metabolic & Structural Biology, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow-226015, India
| | - Mahendra K. Gupta
- Department of Microbiology, King George Medical University, Lucknow, India
| | - Prashant Gupta
- Department of Microbiology, King George Medical University, Lucknow, India
| | - Mahendra P. Darokar
- Molecular Bioprospection Department, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow-226015, India
| | - Santosh K. Srivastava
- Medicinal Chemistry Department, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow-226015, India
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165
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Singh K, Dwivedi GR, Sanket AS, Pati S. Therapeutic Potential of Endophytic Compounds: A Special Reference to Drug Transporter Inhibitors. Curr Top Med Chem 2019; 19:754-783. [DOI: 10.2174/1568026619666190412095105] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 03/08/2019] [Accepted: 03/09/2019] [Indexed: 12/11/2022]
Abstract
From the discovery to the golden age of antibiotics (miracle), millions of lives have been saved. The era of negligence towards chemotherapeutic agents gave birth to drug resistance. Among all the regulators of drug resistance, drug transporters are considered to be the key regulators for multidrug resistance. These transporters are prevalent from prokaryotes to eukaryotes. Endophytes are one of the unexplored wealths of nature. Endophytes are a model mutualistic partner of plants. They are the reservoir of novel therapeutics. The present review deals with endophytes as novel drug resistance reversal agents by inhibiting the drug transporters across the genera. This review also focuses on drug transporters, and mutualistic chemical diversity, exploring drug transporter modulating potential of endophytes.
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Affiliation(s)
- Khusbu Singh
- Microbiology Department, ICMR-Regional Medical Research Centre, Bhubaneswar, India
| | - Gaurav Raj Dwivedi
- Microbiology Department, ICMR-Regional Medical Research Centre, Bhubaneswar, India
| | - A. Swaroop Sanket
- Microbiology Department, ICMR-Regional Medical Research Centre, Bhubaneswar, India
| | - Sanghamitra Pati
- Microbiology Department, ICMR-Regional Medical Research Centre, Bhubaneswar, India
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166
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Singh H, Das S, Yadav J, Srivastava VK, Jyoti A, Kaushik S. In search of novel protein drug targets for treatment of Enterococcus faecalis infections. Chem Biol Drug Des 2019; 94:1721-1739. [PMID: 31260188 DOI: 10.1111/cbdd.13582] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 06/08/2019] [Accepted: 06/17/2019] [Indexed: 12/27/2022]
Abstract
Enterococcus faecalis (Ef) is one of the major pathogens involved in hospital-acquired infections. It can cause nosocomial bacteremia, surgical wound infection, and urinary tract infection. It is important to mention here that Ef is developing resistance against many commonly occurring antibiotics. The occurrence of multidrug resistance (MDR) and extensive-drug resistance (XDR) is now posing a major challenge to the medical community. In this regard, to combat the infections caused by Ef, we have to look for an alternative. Rational structure-based drug design exploits the three-dimensional structure of the target protein, which can be unraveled by various techniques such as X-ray crystallography or nuclear magnetic resonance (NMR) spectroscopy. In this review, we have discussed the complete picture of Ef infections, the possible treatment available at present, and the alternative treatment options to be explored. This study will help in better understanding of novel biological targets against Ef and the compounds, which are likely to bind with these targets. Using these detailed structural informations, rational structure-based drug design is achievable and tight inhibitors against Ef can be prepared.
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Affiliation(s)
- Harpreet Singh
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur, India
| | - Satyajeet Das
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur, India
| | - Jyoti Yadav
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur, India
| | | | - Anupam Jyoti
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur, India
| | - Sanket Kaushik
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur, India
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167
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Paul D, Chakraborty R, Mandal SM. Biocides and health-care agents are more than just antibiotics: Inducing cross to co-resistance in microbes. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2019; 174:601-610. [PMID: 30875553 DOI: 10.1016/j.ecoenv.2019.02.083] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2018] [Revised: 02/13/2019] [Accepted: 02/25/2019] [Indexed: 06/09/2023]
Abstract
Health-care chemicals are used worldwide as important components of different industries as consumer products, food industry, animal husbandry and agribusiness. There are innumerable reports on the effect of these chemicals (biocides) impacting the development of cross to co-resistance in pathogenic bacteria. However, reports are limited on the concurrent use of agricides (pesticides, herbicides, fungicides and insecticides) which influence the microbial activities in soils and contribute to the increase in incidences of co-resistance. Undoubtedly, indiscriminate use of biocides and agricides has contaminated both water and soil environments. This review describes the onset of cross and co-resistance to biocides and antibiotics which is increasingly being exhibited by specific bacteria under a persistent selective pressure. It also re-examines the significance of mobile genetic platforms and horizontal gene transfer from one to another bacterial species, for understanding the kinetics and efficiency of genetic exchange in stressed environments leading to natural selection of tolerant strains over susceptible ones. The investigation is much warranted, particularly with respect to agricides that commonly occur in recalcitrant states in soil and water ecosystem, livestock, etc and is transmitted either directly or via the food-chain to human beings, facilitating the switch from cross to co-resistance.
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Affiliation(s)
- Debarati Paul
- Amity Institute of Biotechnology, Amity University, Noida 201313, India
| | - Ranadhir Chakraborty
- OMICS Laboratory, Department of Biotechnology, University of North Bengal, Siliguri 734013, WB, India
| | - Santi M Mandal
- Central Research Facility, Indian Institute of Technology Kharagpur, Kharagpur 721302, WB, India.
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168
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Shi X, Chen M, Yu Z, Bell JM, Wang H, Forrester I, Villarreal H, Jakana J, Du D, Luisi BF, Ludtke SJ, Wang Z. In situ structure and assembly of the multidrug efflux pump AcrAB-TolC. Nat Commun 2019; 10:2635. [PMID: 31201302 PMCID: PMC6570770 DOI: 10.1038/s41467-019-10512-6] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 05/08/2019] [Indexed: 11/09/2022] Open
Abstract
Multidrug efflux pumps actively expel a wide range of toxic substrates from the cell and play a major role in intrinsic and acquired drug resistance. In Gram-negative bacteria, these pumps form tripartite assemblies that span the cell envelope. However, the in situ structure and assembly mechanism of multidrug efflux pumps remain unknown. Here we report the in situ structure of the Escherichia coli AcrAB-TolC multidrug efflux pump obtained by electron cryo-tomography and subtomogram averaging. The fully assembled efflux pump is observed in a closed state under conditions of antibiotic challenge and in an open state in the presence of AcrB inhibitor. We also observe intermediate AcrAB complexes without TolC and discover that AcrA contacts the peptidoglycan layer of the periplasm. Our data point to a sequential assembly process in living bacteria, beginning with formation of the AcrAB subcomplex and suggest domains to target with efflux pump inhibitors.
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Affiliation(s)
- Xiaodong Shi
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
- Jiangsu Province Key Laboratory of Anesthesiology and Jiangsu Province Key Laboratory of Anesthesia and Analgesia Application, Xuzhou Medical University, Xuzhou, Jiangsu, 221004, China
| | - Muyuan Chen
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Zhili Yu
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - James M Bell
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
- Graduate Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Hans Wang
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Isaac Forrester
- CryoEM Core at Baylor College of Medicine, Houston, TX, 77030, USA
| | | | - Joanita Jakana
- CryoEM Core at Baylor College of Medicine, Houston, TX, 77030, USA
| | - Dijun Du
- Department of Biochemistry, University of Cambridge, Cambridge, CB21GA, UK
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Ben F Luisi
- Department of Biochemistry, University of Cambridge, Cambridge, CB21GA, UK
| | - Steven J Ludtke
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Zhao Wang
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA.
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, 77030, USA.
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169
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Douafer H, Andrieu V, Phanstiel O, Brunel JM. Antibiotic Adjuvants: Make Antibiotics Great Again! J Med Chem 2019; 62:8665-8681. [PMID: 31063379 DOI: 10.1021/acs.jmedchem.8b01781] [Citation(s) in RCA: 160] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Multiple approaches have been developed to combat bacterial resistance. However, the combination of antibiotic resistance mechanisms by bacteria and the limited number of effective antibiotics available decreases the effective interventions for the treatment of current bacterial infections. This review covers the many ways that bacteria resist antibiotics including antibiotic target modification, the use of efflux pumps, and antibiotic inactivation. As a pertinent example, the use of beta lactamase inhibitors in combination with β-lactam containing antibiotics is discussed in detail. The solution to emerging antibiotic resistance may involve combination therapies of existing antibiotics and potentiating adjuvants, which re-empower the antibiotic agent to become efficacious against the resistant strain of interest. We report herein that a reasoned adjuvant design permits one to perform polypharmacy on bacteria by not only providing greater internal access to the codosed antibiotics but also by de-energizing the efflux pumps used by the bacteria to escape antibiotic action.
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Affiliation(s)
- Hana Douafer
- Aix Marseille University , INSERM, SSA, MCT , 13385 Marseille , France
| | - Véronique Andrieu
- Aix Marseille University , IRD, APHM, MEPHI, IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie , 13385 Marseille , France
| | - Otto Phanstiel
- 12722 Research Parkway, College of Medicine , University of Central Florida , Orlando , Florida 32826 , United States
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170
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Lehtinen S, Blanquart F, Lipsitch M, Fraser C. On the evolutionary ecology of multidrug resistance in bacteria. PLoS Pathog 2019; 15:e1007763. [PMID: 31083687 PMCID: PMC6532944 DOI: 10.1371/journal.ppat.1007763] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 05/23/2019] [Accepted: 04/15/2019] [Indexed: 11/23/2022] Open
Abstract
Resistance against different antibiotics appears on the same bacterial strains more often than expected by chance, leading to high frequencies of multidrug resistance. There are multiple explanations for this observation, but these tend to be specific to subsets of antibiotics and/or bacterial species, whereas the trend is pervasive. Here, we consider the question in terms of strain ecology: explaining why resistance to different antibiotics is often seen on the same strain requires an understanding of the competition between strains with different resistance profiles. This work builds on models originally proposed to explain another aspect of strain competition: the stable coexistence of antibiotic sensitivity and resistance observed in a number of bacterial species. We first identify a partial structural similarity in these models: either strain or host population structure stratifies the pathogen population into evolutionarily independent sub-populations and introduces variation in the fitness effect of resistance between these sub-populations, thus creating niches for sensitivity and resistance. We then generalise this unified underlying model to multidrug resistance and show that models with this structure predict high levels of association between resistance to different drugs and high multidrug resistance frequencies. We test predictions from this model in six bacterial datasets and find them to be qualitatively consistent with observed trends. The higher than expected frequencies of multidrug resistance are often interpreted as evidence that these strains are out-competing strains with lower resistance multiplicity. Our work provides an alternative explanation that is compatible with long-term stability in resistance frequencies.
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Affiliation(s)
- Sonja Lehtinen
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - François Blanquart
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, PSL Research University, Paris, France
- IAME, UMR 1137, INSERM, Université Paris Diderot, Paris, France
| | - Marc Lipsitch
- Center for Communicable Disease Dynamics, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, United States of America
- Departments of Epidemiology and Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Christophe Fraser
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
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171
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Venter H. Reversing resistance to counter antimicrobial resistance in the World Health Organisation's critical priority of most dangerous pathogens. Biosci Rep 2019; 39:BSR20180474. [PMID: 30910848 PMCID: PMC6465202 DOI: 10.1042/bsr20180474] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 03/18/2019] [Accepted: 03/22/2019] [Indexed: 02/07/2023] Open
Abstract
The speed at which bacteria develop antimicrobial resistance far outpace drug discovery and development efforts resulting in untreatable infections. The World Health Organisation recently released a list of pathogens in urgent need for the development of new antimicrobials. The organisms that are listed as the most critical priority are all Gram-negative bacteria resistant to the carbapenem class of antibiotics. Carbapenem resistance in these organisms is typified by intrinsic resistance due to the expression of antibiotic efflux pumps and the permeability barrier presented by the outer membrane, as well as by acquired resistance due to the acquisition of enzymes able to degrade β-lactam antibiotics. In this perspective article we argue the case for reversing resistance by targeting these resistance mechanisms - to increase our arsenal of available antibiotics and drastically reduce antibiotic discovery times - as the most effective way to combat antimicrobial resistance in these high priority pathogens.
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Affiliation(s)
- Henrietta Venter
- School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, Australia
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172
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Abstract
Staphylococcus aureus is capable of becoming resistant to all classes of antibiotics clinically available and resistance can develop through de novo mutations in chromosomal genes or through acquisition of horizontally transferred resistance determinants. This review covers the most important antibiotics available for treatment of S. aureus infections and a special emphasis is dedicated to the current knowledge of the wide variety of resistance mechanisms that S. aureus employ to withstand antibiotics. Since resistance development has been inevitable for all currently available antibiotics, new therapies are continuously under development. Besides development of new small molecules affecting cell viability, alternative approaches including anti-virulence and bacteriophage therapeutics are being investigated and may become important tools to combat staphylococcal infections in the future.
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173
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Lamut A, Peterlin Mašič L, Kikelj D, Tomašič T. Efflux pump inhibitors of clinically relevant multidrug resistant bacteria. Med Res Rev 2019; 39:2460-2504. [PMID: 31004360 DOI: 10.1002/med.21591] [Citation(s) in RCA: 113] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 03/31/2019] [Accepted: 04/02/2019] [Indexed: 12/29/2022]
Abstract
Bacterial infections are an increasingly serious issue worldwide. The inability of existing therapies to treat multidrug-resistant pathogens has been recognized as an important challenge of the 21st century. Efflux pumps are important in both intrinsic and acquired bacterial resistance and identification of small molecule efflux pump inhibitors (EPIs), capable of restoring the effectiveness of available antibiotics, is an active research field. In the last two decades, much effort has been made to identify novel EPIs. However, none of them has so far been approved for therapeutic use. In this article, we explore different structural families of currently known EPIs for multidrug resistance efflux systems in the most extensively studied pathogens (NorA in Staphylococcus aureus, AcrAB-TolC in Escherichia coli, and MexAB-OprM in Pseudomonas aeruginosa). Both synthetic and natural compounds are described, with structure-activity relationship studies and optimization processes presented systematically for each family individually. In vitro activities against selected test strains are presented in a unifying manner for all the EPIs described, together with the most important toxicity, pharmacokinetic and in vivo efficacy data. A critical evaluation of lead-likeness characteristics and the potential for clinical development of the most promising inhibitors of the three efflux systems is described. This overview of EPIs is a good starting point for the identification of novel effective antibacterial drugs.
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Affiliation(s)
- Andraž Lamut
- Chair of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
| | - Lucija Peterlin Mašič
- Chair of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
| | - Danijel Kikelj
- Chair of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
| | - Tihomir Tomašič
- Chair of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
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174
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Aminoglycoside Revival: Review of a Historically Important Class of Antimicrobials Undergoing Rejuvenation. EcoSal Plus 2019; 8. [PMID: 30447062 DOI: 10.1128/ecosalplus.esp-0002-2018] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Aminoglycosides are cidal inhibitors of bacterial protein synthesis that have been utilized for the treatment of serious bacterial infections for almost 80 years. There have been approximately 15 members of this class approved worldwide for the treatment of a variety of infections, many serious and life threatening. While aminoglycoside use declined due to the introduction of other antibiotic classes such as cephalosporins, fluoroquinolones, and carbapenems, there has been a resurgence of interest in the class as multidrug-resistant pathogens have spread globally. Furthermore, aminoglycosides are recommended as part of combination therapy for empiric treatment of certain difficult-to-treat infections. The development of semisynthetic aminoglycosides designed to overcome common aminoglycoside resistance mechanisms, and the shift to once-daily dosing, has spurred renewed interest in the class. Plazomicin is the first new aminoglycoside to be approved by the FDA in nearly 40 years, marking the successful start of a new campaign to rejuvenate the class.
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175
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Monserrat-Martinez A, Gambin Y, Sierecki E. Thinking Outside the Bug: Molecular Targets and Strategies to Overcome Antibiotic Resistance. Int J Mol Sci 2019; 20:E1255. [PMID: 30871132 PMCID: PMC6470534 DOI: 10.3390/ijms20061255] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 03/04/2019] [Accepted: 03/04/2019] [Indexed: 12/25/2022] Open
Abstract
Since their discovery in the early 20th century, antibiotics have been used as the primary weapon against bacterial infections. Due to their prophylactic effect, they are also used as part of the cocktail of drugs given to treat complex diseases such as cancer or during surgery, in order to prevent infection. This has resulted in a decrease of mortality from infectious diseases and an increase in life expectancy in the last 100 years. However, as a consequence of administering antibiotics broadly to the population and sometimes misusing them, antibiotic-resistant bacteria have appeared. The emergence of resistant strains is a global health threat to humanity. Highly-resistant bacteria like Staphylococcus aureus (methicillin-resistant) or Enterococcus faecium (vancomycin-resistant) have led to complications in intensive care units, increasing medical costs and putting patient lives at risk. The appearance of these resistant strains together with the difficulty in finding new antimicrobials has alarmed the scientific community. Most of the strategies currently employed to develop new antibiotics point towards novel approaches for drug design based on prodrugs or rational design of new molecules. However, targeting crucial bacterial processes by these means will keep creating evolutionary pressure towards drug resistance. In this review, we discuss antibiotic resistance and new options for antibiotic discovery, focusing in particular on new alternatives aiming to disarm the bacteria or empower the host to avoid disease onset.
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Affiliation(s)
- Ana Monserrat-Martinez
- European Molecular Biology Laboratory Australia (EMBL Australia) Node in Single Molecule Science, Sydney, NSW 2031, Australia.
- School of Medical Sciences, The University of New South Wales, Sydney, NSW 2031, Australia.
| | - Yann Gambin
- European Molecular Biology Laboratory Australia (EMBL Australia) Node in Single Molecule Science, Sydney, NSW 2031, Australia.
- School of Medical Sciences, The University of New South Wales, Sydney, NSW 2031, Australia.
| | - Emma Sierecki
- European Molecular Biology Laboratory Australia (EMBL Australia) Node in Single Molecule Science, Sydney, NSW 2031, Australia.
- School of Medical Sciences, The University of New South Wales, Sydney, NSW 2031, Australia.
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176
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Chavhan Y, Karve S, Dey S. Adapting in larger numbers can increase the vulnerability of Escherichia coli populations to environmental changes. Evolution 2019; 73:836-846. [PMID: 30793291 DOI: 10.1111/evo.13700] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 02/14/2019] [Indexed: 12/28/2022]
Abstract
Larger populations generally adapt faster to their existing environment. However, it is unknown if the population size experienced during evolution influences the ability to face sudden environmental changes. To investigate this issue, we subjected replicate Escherichia coli populations of different sizes to experimental evolution in an environment containing a cocktail of three antibiotics. In this environment, the ability to actively efflux molecules outside the cell is expected to be a major fitness-affecting trait. We found that all the populations eventually reached similar fitness in the antibiotic cocktail despite adapting at different speeds, with the larger populations adapting faster. Surprisingly, although efflux activity (EA) enhanced in the smaller populations, it decayed in the larger ones. The evolution of EA was largely shaped by pleiotropic responses to selection and not by drift. This demonstrates that quantitative differences in population size can lead to qualitative differences (decay/enhancement) in the fate of a character during adaptation to identical environments. Furthermore, the larger populations showed inferior fitness upon sudden exposure to several alternative stressful environments. These observations provide a novel link between population size and vulnerability to environmental changes. Counterintuitively, adapting in larger numbers can render bacterial populations more vulnerable to abrupt environmental changes.
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Affiliation(s)
- Yashraj Chavhan
- Indian Institute of Science Education and Research (IISER) Pune, Pune, Maharashtra, 411008, India
| | - Shraddha Karve
- Indian Institute of Science Education and Research (IISER) Pune, Pune, Maharashtra, 411008, India.,Current Address: Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, 8057, Switzerland
| | - Sutirth Dey
- Indian Institute of Science Education and Research (IISER) Pune, Pune, Maharashtra, 411008, India
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177
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Serra C, Bouharkat B, Tir Touil-Meddah A, Guénin S, Mullié C. MexXY Multidrug Efflux System Is More Frequently Overexpressed in Ciprofloxacin Resistant French Clinical Isolates Compared to Hospital Environment Ones. Front Microbiol 2019; 10:366. [PMID: 30863391 PMCID: PMC6399115 DOI: 10.3389/fmicb.2019.00366] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 02/12/2019] [Indexed: 12/23/2022] Open
Abstract
Modulation of the membrane permeability through a decrease in porin-mediated antibiotic entry and/or an increase in antibiotic efflux is one of the resistance mechanisms to antibiotics evolved by Gram-negative bacteria. To assess whether the outer membrane porin OprD and Resistance-Nodulation-Division (RND) efflux pumps were similarly expressed in 33 ciprofloxacin-resistant clinical strains of Pseudomonas aeruginosa and in 30 non-clinical strains originating from the hospital environment (mainly waterborne Pseudomonas aeruginosa), the expression of oprD, mexB, mexF, and mexY genes was investigated. Overall, the expression of oprD was not detected by RT-qPCR in 14 (22%) strains and underexpressed in 35 (56%) more. No significant difference in oprD expression was detected between clinical and non-clinical strains. As for efflux pumps, 23 (70%) of the clinical strains overexpressed at least one of the tested RND genes. Overexpression of mexB, mexF and mexY was detected in 27, 12, and 45% of the clinical strains, respectively. In the 30 non-clinical strains, no overexpression could be found for mexB, mexF, or mexY. On the contrary, a global underexpression of the tested efflux pump genes was recorded. In both clinical and environmental strains, a positive correlation was found between the expressions of oprD and mexB. Similarly, the expressions of oprD and mexF were positively correlated. This result contrasts with the inverse correlation between both MexAB-OprM/MexEF-OprN and OprD previously described in carbapenem-resistant P. aeruginosa strains. The only positive correlation between phenotypic ciprofloxacin minimum inhibitory concentrations (MICs) and the expression of efflux pump gene was witnessed with mexY (analysis on pooled results for clinical and environmental strains). However, in clinical strains, no statistically significant link could be found between the degree of reduction in ciprofloxacin MICs witnessed with Phenylalanine-Arginine β-naphthylamide (PAβN) and the expression of any of the 3 RND genes tested.
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Affiliation(s)
- Cristiano Serra
- Laboratoire des Agents Infectieux, Resistance et Chimiothérapie - EA 4294, UFR de Pharmacie, Université de Picardie Jules Verne, Amiens, France
| | - Bakhta Bouharkat
- Laboratoire de Bioconversion, Génie Microbiologique et Sécurité Sanitaire N°145, Faculté des Sciences de la Nature et de la Vie, Université Mustapha Stambouli, Mascara, Algeria
| | - Aicha Tir Touil-Meddah
- Laboratoire de Bioconversion, Génie Microbiologique et Sécurité Sanitaire N°145, Faculté des Sciences de la Nature et de la Vie, Université Mustapha Stambouli, Mascara, Algeria
| | - Stéphanie Guénin
- Centre de Ressources Régionales en Biologie Moléculaire, UFR des Sciences, Université de Picardie Jules Verne, Amiens, France
| | - Catherine Mullié
- Laboratoire des Agents Infectieux, Resistance et Chimiothérapie - EA 4294, UFR de Pharmacie, Université de Picardie Jules Verne, Amiens, France.,Laboratoire d'Hygiène Hospitalière, Centre Hospitalier Universitaire Amiens-Picardie, Amiens, France
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178
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He H, Zhou P, Shimabuku KK, Fang X, Li S, Lee Y, Dodd MC. Degradation and Deactivation of Bacterial Antibiotic Resistance Genes during Exposure to Free Chlorine, Monochloramine, Chlorine Dioxide, Ozone, Ultraviolet Light, and Hydroxyl Radical. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2019; 53:2013-2026. [PMID: 30712343 DOI: 10.1021/acs.est.8b04393] [Citation(s) in RCA: 90] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
This work investigated degradation (measured by qPCR) and biological deactivation (measured by culture-based natural transformation) of extra- and intracellular antibiotic resistance genes (eARGs and iARGs) by free available chlorine (FAC), NH2Cl, O3, ClO2, and UV light (254 nm), and of eARGs by •OH, using a chromosomal ARG ( blt) of multidrug-resistant Bacillus subtilis 1A189. Rate constants for degradation of four 266-1017 bp amplicons adjacent to or encompassing the acfA mutation enabling blt overexpression increased in proportion to #AT+GC bps/amplicon, or in proportion to #5'-GG-3' or 5'-TT-3' doublets/amplicon, with respective values ranging from 0.59 to 2.3 (×1011 M-1 s-1) for •OH, 1.8-6.9 (×104 M-1 s-1) for O3, 3.9-9.2 (×103 M-1 s-1) for FAC, 0.35-1.2(×101 M-1 s-1) for ClO2, and 2.0-8.8 (×10-2 cm2/mJ) for UV at pH 7, and from 1.7-4.4 M-1 s-1 for NH2Cl at pH 8. For FAC, NH2Cl, O3, ClO2, and UV, ARG deactivation paralleled degradation of amplicons approximating a ∼800-1000 bp acfA-flanking sequence required for natural transformation in B. subtilis, whereas deactivation outpaced degradation for •OH. At practical disinfectant exposures, eARGs and iARGs were ≥90% degraded/deactivated by FAC, O3, and UV, but recalcitrant to NH2Cl and ClO2. iARG degradation/ deactivation always lagged cell inactivation. These findings provide a quantitative framework for evaluating ARG fate during disinfection/oxidation, and support using qPCR as a proxy for tracking ARG deactivation under carefully selected circumstances.
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Affiliation(s)
- Huan He
- Department of Civil and Environmental Engineering , University of Washington (UW) , Seattle , Washington 98195-2700 , United States
| | - Peiran Zhou
- Department of Civil and Environmental Engineering , University of Washington (UW) , Seattle , Washington 98195-2700 , United States
| | - Kyle K Shimabuku
- Department of Civil and Environmental Engineering , University of Washington (UW) , Seattle , Washington 98195-2700 , United States
| | - Xuzhi Fang
- Department of Civil and Environmental Engineering , University of Washington (UW) , Seattle , Washington 98195-2700 , United States
| | - Shu Li
- Department of Civil and Environmental Engineering , University of Washington (UW) , Seattle , Washington 98195-2700 , United States
| | - Yunho Lee
- School of Earth Sciences and Environmental Engineering , Gwangju Institute of Science and Technology (GIST) , Gwangju 61005 , Republic of Korea
| | - Michael C Dodd
- Department of Civil and Environmental Engineering , University of Washington (UW) , Seattle , Washington 98195-2700 , United States
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179
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Robinson JA. Folded Synthetic Peptides and Other Molecules Targeting Outer Membrane Protein Complexes in Gram-Negative Bacteria. Front Chem 2019; 7:45. [PMID: 30788339 PMCID: PMC6372539 DOI: 10.3389/fchem.2019.00045] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 01/17/2019] [Indexed: 02/06/2023] Open
Abstract
Conformationally constrained peptidomimetics have been developed to mimic interfacial epitopes and target a wide selection of protein-protein interactions. ß-Hairpin mimetics based on constrained macrocyclic peptides have provided access to excellent structural mimics of ß-hairpin epitopes and found applications as interaction inhibitors in many areas of biology and medicinal chemistry. Recently, ß-hairpin peptidomimetics and naturally occurring ß-hairpin-shaped peptides have also been discovered with potent antimicrobial activity and novel mechanisms of action, targeting essential outer membrane protein (OMP) complexes in Gram-negative bacteria. This includes the Lpt complex, required for transporting LPS to the cell surface during OM biogenesis and the BAM complex that folds OMPs and inserts them into the OM bilayer. The Lpt complex is a macromolecular superstructure comprising seven different proteins (LptA-LptG) that spans the entire bacterial cell envelope, whereas the BAM complex is a folding machine comprising a ß-barrel OMP (BamA) and four different lipoproteins (BamB-BamE). Folded synthetic and natural ß-hairpin-shaped peptides appear well-suited for interacting with proteins within the Lpt and BAM complexes that are rich in ß-structure. Recent progress in identifying antibiotics targeting these complexes are reviewed here. Already a clinical candidate has been developed (murepavadin) that targets LptD, with potent antimicrobial activity specifically against pseudmonads. The ability of folded synthetic ß-hairpin epitope mimetics to interact with ß-barrel and ß-jellyroll domains in the Lpt and Bam complexes represent new avenues for antibiotic discovery, which may lead to the development of much needed new antimicrobials to combat the rise of drug-resistant pathogenic Gram-negative bacteria.
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Affiliation(s)
- John A Robinson
- Department of Chemistry, University of Zurich, Zurich, Switzerland
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180
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Matzneller P, Kussmann M, Eberl S, Maier-Salamon A, Jäger W, Bauer M, Langer O, Zeitlinger M, Poeppl W. Pharmacokinetics of the P-gp Inhibitor Tariquidar in Rats After Intravenous, Oral, and Intraperitoneal Administration. Eur J Drug Metab Pharmacokinet 2019; 43:599-606. [PMID: 29616423 PMCID: PMC6133083 DOI: 10.1007/s13318-018-0474-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Background and objective P-glycoprotein (P-gp), a transmembrane transporter expressed at the blood–brain barrier, restricts the distribution of diverse central nervous system-targeted drugs from blood into brain, reducing their therapeutic efficacy. The third-generation P-gp inhibitor tariquidar (XR9576) was shown to enhance brain distribution of P-gp substrate drugs in humans. Oral bioavailability of tariquidar was found to be low in humans requiring the compound to be administered intravenously, which hinders a broader clinical use. The objective of the present study was to investigate the plasma pharmacokinetics of tariquidar in rats after single intravenous, oral, and intraperitoneal administration. Methods Two different tariquidar formulations (A and B) were used, both at a dosage of 15 mg/kg, respectively. Formulation A was a solution and formulation B was a microemulsion which was previously shown to improve the oral bioavailability of the structurally related P-gp inhibitor elacridar in mice. Results In contrast to human data, the present study found a high bioavailability of tariquidar in rats after oral dosing. Oral bioavailability was significantly higher (p = 0.032) for formulation B (86.3%) than for formulation A (71.6%). After intraperitoneal dosing bioavailability was 91.4% for formulation A and 99.6% for formulation B. Conclusion The present findings extend the available information on tariquidar and provide a basis for future studies involving oral administration of this compound.
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Affiliation(s)
- Peter Matzneller
- Department of Clinical Pharmacology, Medical University of Vienna, Währinger Gürtel 18-20, 1090, Vienna, Austria
| | - Manuel Kussmann
- Department of Internal Medicine I, Clinical Division of Infectious Diseases and Tropical Medicine, Medical University Vienna, Vienna, Austria
| | - Sabine Eberl
- Department of Clinical Pharmacology, Medical University of Vienna, Währinger Gürtel 18-20, 1090, Vienna, Austria
| | | | - Walter Jäger
- Department of Clinical Pharmacy and Diagnostics, University of Vienna, Vienna, Austria
| | - Martin Bauer
- Department of Clinical Pharmacology, Medical University of Vienna, Währinger Gürtel 18-20, 1090, Vienna, Austria
| | - Oliver Langer
- Department of Clinical Pharmacology, Medical University of Vienna, Währinger Gürtel 18-20, 1090, Vienna, Austria. .,Biomedical Systems, Center for Health and Bioresources, AIT Austrian Institute of Technology GmbH, Seibersdorf, Austria. .,Division of Nuclear Medicine, Department of Biomedical Imaging and Image-guided Therapy, Medical University of Vienna, Vienna, Austria.
| | - Markus Zeitlinger
- Department of Clinical Pharmacology, Medical University of Vienna, Währinger Gürtel 18-20, 1090, Vienna, Austria
| | - Wolfgang Poeppl
- Department of Internal Medicine I, Clinical Division of Infectious Diseases and Tropical Medicine, Medical University Vienna, Vienna, Austria.,Department of Dermatology and Tropical Medicine, Military Medical Cluster East, Austrian Armed Forces, Vienna, Austria
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181
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Sun Y, Hu X, Guo D, Shi C, Zhang C, Peng X, Yang H, Xia X. Disinfectant Resistance Profiles and Biofilm Formation Capacity of Escherichia coli Isolated from Retail Chicken. Microb Drug Resist 2019; 25:703-711. [PMID: 30614760 DOI: 10.1089/mdr.2018.0175] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Disinfectant resistance and biofilm formation capacity are two important characteristics that contribute to the persistence of microorganisms in food processing environments and contamination of food products. This study investigated the susceptibility of 510 Escherichia coli isolates against 5 disinfectants and the prevalence of 10 disinfectant-resistant genes in these isolates. The biofilm formation capacity of 194 isolates was determined, and the correlation between disinfectant resistance and biofilm formation was analyzed. The minimal inhibitory concentrations (MICs) of cetyltrimethylammonium bromide (CTAB), benzalkonium chloride (BC), cetylpyridinium chloride, and chlorhexidine (CHX) against isolates were 32-512, 16-256, 32-256, and 2-32 mg/L, respectively. The MICs of triclosan against 88.43% of isolates were 8-1,024 mg/L, while the MICs for the rest of isolates exceed 2,048 mg/L. The presence of ydgE, ydgF, and qacF genes was significantly correlated with the CHX resistance of E. coli isolates, while the presence of qacF and qacEΔ1 genes was significantly correlated with CTAB and BC resistance, respectively. The biofilm formation capacity (adjusted optical density value) was positively correlated with BC resistance (r = 0.201, p < 0.01) and showed no correlation with other disinfectants. The presence of sugE(p) was positively correlated with biofilm formation, while four genes were negatively correlated with biofilm formation. This study provides useful data on disinfectant resistance and biofilm formation capacity of E. coli contaminating poultry products, which could be helpful in guiding proper disinfectant usage and establishing effective biofilm eradication strategy in food industry.
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Affiliation(s)
- Yi Sun
- 1 Department of Food Safety and Nutrition, College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi, China
| | - Xueyan Hu
- 1 Department of Food Safety and Nutrition, College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi, China
| | - Du Guo
- 1 Department of Food Safety and Nutrition, College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi, China
| | - Chao Shi
- 1 Department of Food Safety and Nutrition, College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi, China
| | - Chunling Zhang
- 1 Department of Food Safety and Nutrition, College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi, China
| | - Xiaoli Peng
- 1 Department of Food Safety and Nutrition, College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi, China
| | - Hua Yang
- 2 Institute of Quality and Standard for Agro-Products, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Xiaodong Xia
- 1 Department of Food Safety and Nutrition, College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi, China.,3 Department of Microbial Food Safety, Sino-US Joint Research Center for Food Safety, Northwest A&F University, Yangling, Shaanxi, China.,4 Technical Center, Jiangsu Ecolovo Food Group Co., Ltd., Suqian, Jiangsu, China
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182
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Abstract
Members of the highly heterogeneous family Pasteurellaceae cause a wide variety of diseases in humans and animals. Antimicrobial agents are the most powerful tools to control such infections. However, the acquisition of resistance genes, as well as the development of resistance-mediating mutations, significantly reduces the efficacy of the antimicrobial agents. This article gives a brief description of the role of selected members of the family Pasteurellaceae in animal infections and of the most recent data on the susceptibility status of such members. Moreover, a review of the current knowledge of the genetic basis of resistance to antimicrobial agents is included, with particular reference to resistance to tetracyclines, β-lactam antibiotics, aminoglycosides/aminocyclitols, folate pathway inhibitors, macrolides, lincosamides, phenicols, and quinolones. This article focusses on the genera of veterinary importance for which sufficient data on antimicrobial susceptibility and the detection of resistance genes are currently available (Pasteurella, Mannheimia, Actinobacillus, Haemophilus, and Histophilus). Additionally, the role of plasmids, transposons, and integrative and conjugative elements in the spread of the resistance genes within and beyond the aforementioned genera is highlighted to provide insight into horizontal dissemination, coselection, and persistence of antimicrobial resistance genes. The article discusses the acquisition of diverse resistance genes by the selected Pasteurellaceae members from other Gram-negative or maybe even Gram-positive bacteria. Although the susceptibility status of these members still looks rather favorable, monitoring of their antimicrobial susceptibility is required for early detection of changes in the susceptibility status and the newly acquired/developed resistance mechanisms.
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183
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Updates on the pathogenicity status of Pseudomonas aeruginosa. Drug Discov Today 2019; 24:350-359. [DOI: 10.1016/j.drudis.2018.07.003] [Citation(s) in RCA: 128] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 07/03/2018] [Accepted: 07/16/2018] [Indexed: 01/06/2023]
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184
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Rehman A, Patrick WM, Lamont IL. Mechanisms of ciprofloxacin resistance in Pseudomonas aeruginosa: new approaches to an old problem. J Med Microbiol 2019; 68:1-10. [DOI: 10.1099/jmm.0.000873] [Citation(s) in RCA: 85] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Affiliation(s)
- Attika Rehman
- 1Department of Biochemistry, University of Otago, New Zealand
| | - Wayne M. Patrick
- 1Department of Biochemistry, University of Otago, New Zealand
- 2School of Biological Sciences, Victoria University of Wellington, New Zealand
| | - Iain L. Lamont
- 1Department of Biochemistry, University of Otago, New Zealand
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185
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Shriram V, Khare T, Bhagwat R, Shukla R, Kumar V. Inhibiting Bacterial Drug Efflux Pumps via Phyto-Therapeutics to Combat Threatening Antimicrobial Resistance. Front Microbiol 2018; 9:2990. [PMID: 30619113 PMCID: PMC6295477 DOI: 10.3389/fmicb.2018.02990] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 11/19/2018] [Indexed: 12/04/2022] Open
Abstract
Antibiotics, once considered the lifeline for treating bacterial infections, are under threat due to the emergence of threatening antimicrobial resistance (AMR). These drug-resistant microbes (or superbugs) are non-responsive to most of the commonly used antibiotics leaving us with few treatment options and escalating mortality-rates and treatment costs. The problem is further aggravated by the drying-pipeline of new and potent antibiotics effective particularly against the drug-resistant strains. Multidrug efflux pumps (EPs) are established as principal determinants of AMR, extruding multiple antibiotics out of the cell, mostly in non-specific manner and have therefore emerged as potent drug-targets for combating AMR. Plants being the reservoir of bioactive compounds can serve as a source of potent EP inhibitors (EPIs). The phyto-therapeutics with noteworthy drug-resistance-reversal or re-sensitizing activities may prove significant for reviving the otherwise fading antibiotics arsenal and making this combination-therapy effective. Contemporary attempts to potentiate the antibiotics with plant extracts and pure phytomolecules have gained momentum though with relatively less success against Gram-negative bacteria. Plant-based EPIs hold promise as potent drug-leads to combat the EPI-mediated AMR. This review presents an account of major bacterial multidrug EPs, their roles in imparting AMR, effective strategies for inhibiting drug EPs with phytomolecules, and current account of research on developing novel and potent plant-based EPIs for reversing their AMR characteristics. Recent developments including emergence of in silico tools, major success stories, challenges and future prospects are also discussed.
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Affiliation(s)
- Varsha Shriram
- Department of Botany, Prof. Ramkrishna More College, Savitribai Phule Pune University, Pune, India
| | - Tushar Khare
- Department of Biotechnology, Modern College of Arts, Science and Commerce (Savitribai Phule Pune University), Pune, India
| | - Rohit Bhagwat
- Department of Environmental Science, Savitribai Phule Pune University, Pune, India
| | - Ravi Shukla
- Centre for Advanced Materials and Industrial Chemistry, School of Science, RMIT University, Melbourne, VIC, Australia
| | - Vinay Kumar
- Department of Biotechnology, Modern College of Arts, Science and Commerce (Savitribai Phule Pune University), Pune, India.,Department of Environmental Science, Savitribai Phule Pune University, Pune, India
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186
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Influence of the T to S mutation at the STMK motif on antibiotic resistance of penicillin binding protein 1A: A comprehensive computational study. J Mol Graph Model 2018; 87:185-191. [PMID: 30553158 DOI: 10.1016/j.jmgm.2018.12.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Revised: 11/13/2018] [Accepted: 12/04/2018] [Indexed: 11/21/2022]
Abstract
The emergence of antibiotic resistance has attracted the attention of scientists and scientific circles over the decades. β-Lactam antibiotics resistance is a worldwide therapeutic challenge in bacterial infections, mediated through several mechanisms of which mutations in Penicillin Binding Proteins (PBPs) are an important issue, making critical therapeutic problems in the human population. Accordingly, investigating the dynamic structures of mutant variants could result in a profound understanding of such a specific resistance. Therefore, this work investigated structural properties sampled by all-atom molecular dynamics (MD) simulations, umbrella sampling, and binding free energy calculations for both a wild-type and a cefotaxime-resistant T to S mutant of PBP1A. The T to S mutation significantly reduces the binding affinity of cefotaxime (a frequently clinically-administrated β-lactam antibiotic) as the PBP1A inhibitor. In the conventional MD simulations presented here, more fluctuations of the mutant's active site cleft margins were detected. The cleft of the mutant protein also opened remarkably more than the wild-type's cleft and displayed more flexibility. Thus, our findings have shown that flexibility of cleft margins of the active site in the mutant PBP1A immediately results in the catalytic cleft opening. In addition, binding free energy calculation suggests that reducing hydrophobic contacts and increasing the polar contribution in the binding energy may play an important role in cefotaxime resistance.
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187
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Isidro J, Menezes J, Serrano M, Borges V, Paixão P, Mimoso M, Martins F, Toscano C, Santos A, Henriques AO, Oleastro M. Genomic Study of a Clostridium difficile Multidrug Resistant Outbreak-Related Clone Reveals Novel Determinants of Resistance. Front Microbiol 2018; 9:2994. [PMID: 30574133 PMCID: PMC6291485 DOI: 10.3389/fmicb.2018.02994] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 11/20/2018] [Indexed: 12/15/2022] Open
Abstract
Background:Clostridium difficile infection (CDI) is prevalent in healthcare settings. The emergence of hypervirulent and antibiotic resistant strains has led to an increase in CDI incidence and frequent outbreaks. While the main virulence factors are the TcdA and TcdB toxins, antibiotic resistance is thought to play a key role in the infection by and dissemination of C. difficile. Methods: A CDI outbreak involving 12 patients was detected in a tertiary care hospital, in Lisbon, which extended from January to July, with a peak in February, in 2016. The C. difficile isolates, obtained from anaerobic culture of stool samples, were subjected to antimicrobial susceptibility testing with Etest®strips against 11 antibiotics, determination of toxin genes profile, PCR-ribotyping, multilocus variable-number tandem-repeat analysis (MLVA) and whole genome sequencing (WGS). Results: Of the 12 CDI cases detected, 11 isolates from 11 patients were characterized. All isolates were tcdA-/tcdB+ and belonged to ribotype 017, and showed high level resistance to clindamycin, erythromycin, gentamicin, imipenem, moxifloxacin, rifampicin and tetracycline. The isolates belonged to four genetically related MLVA types, with six isolates forming a clonal cluster. Three outbreak isolates, each from a different MLVA type, were selected for WGS. Bioinformatics analysis showed the presence of several antibiotic resistance determinants, including the Thr82Ile substitution in gyrA, conferring moxifloxacin resistance, the substitutions His502Asn and Arg505Lys in rpoB for rifampicin resistance, the tetM gene, associated with tetracycline resistance, and two genes encoding putative aminoglycoside-modifying enzymes, aadE and aac(6′)-aph(2″). Furthermore, a not previously described 61.3 kb putative mobile element was identified, presenting a mosaic structure and containing the genes ermG, mefA/msrD and vat, associated with macrolide, lincosamide and streptogramins resistance. A substitution found in a class B penicillin-binding protein, Cys721Ser, is thought to contribute to imipenem resistance. Conclusion: We describe an epidemic, tcdA-/tcdB+, multidrug resistant clone of C. difficile from ribotype 017 associated with a hospital outbreak, providing further evidence that the lack of TcdA does not impair the infectious potential of these strains. We identified several determinants of antimicrobial resistance, including new ones located in mobile elements, highlighting the importance of horizontal gene transfer in the pathogenicity and epidemiological success of C. difficile.
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Affiliation(s)
- Joana Isidro
- Departamento de Doenças Infecciosas, Instituto Nacional de Saúde Doutor Ricardo Jorge, Lisbon, Portugal.,Departamento de Genética Humana, Unidade de Tecnologia e Inovação, Instituto Nacional de Saúde Doutor Ricardo Jorge, Lisbon, Portugal
| | - Juliana Menezes
- Departamento de Doenças Infecciosas, Instituto Nacional de Saúde Doutor Ricardo Jorge, Lisbon, Portugal
| | - Mónica Serrano
- Instituto de Tecnologia Química e Biológica António Xavier, Oeiras, Portugal
| | - Vítor Borges
- Departamento de Doenças Infecciosas, Instituto Nacional de Saúde Doutor Ricardo Jorge, Lisbon, Portugal
| | - Pedro Paixão
- Centro Hospitalar Lisboa Ocidental, Lisbon, Portugal
| | | | | | | | - Andrea Santos
- Departamento de Doenças Infecciosas, Instituto Nacional de Saúde Doutor Ricardo Jorge, Lisbon, Portugal
| | - Adriano O Henriques
- Instituto de Tecnologia Química e Biológica António Xavier, Oeiras, Portugal
| | - Mónica Oleastro
- Departamento de Doenças Infecciosas, Instituto Nacional de Saúde Doutor Ricardo Jorge, Lisbon, Portugal
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188
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Peterson E, Kaur P. Antibiotic Resistance Mechanisms in Bacteria: Relationships Between Resistance Determinants of Antibiotic Producers, Environmental Bacteria, and Clinical Pathogens. Front Microbiol 2018; 9:2928. [PMID: 30555448 PMCID: PMC6283892 DOI: 10.3389/fmicb.2018.02928] [Citation(s) in RCA: 439] [Impact Index Per Article: 73.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 11/14/2018] [Indexed: 11/13/2022] Open
Abstract
Emergence of antibiotic resistant pathogenic bacteria poses a serious public health challenge worldwide. However, antibiotic resistance genes are not confined to the clinic; instead they are widely prevalent in different bacterial populations in the environment. Therefore, to understand development of antibiotic resistance in pathogens, we need to consider important reservoirs of resistance genes, which may include determinants that confer self-resistance in antibiotic producing soil bacteria and genes encoding intrinsic resistance mechanisms present in all or most non-producer environmental bacteria. While the presence of resistance determinants in soil and environmental bacteria does not pose a threat to human health, their mobilization to new hosts and their expression under different contexts, for example their transfer to plasmids and integrons in pathogenic bacteria, can translate into a problem of huge proportions, as discussed in this review. Selective pressure brought about by human activities further results in enrichment of such determinants in bacterial populations. Thus, there is an urgent need to understand distribution of resistance determinants in bacterial populations, elucidate resistance mechanisms, and determine environmental factors that promote their dissemination. This comprehensive review describes the major known self-resistance mechanisms found in producer soil bacteria of the genus Streptomyces and explores the relationships between resistance determinants found in producer soil bacteria, non-producer environmental bacteria, and clinical isolates. Specific examples highlighting potential pathways by which pathogenic clinical isolates might acquire these resistance determinants from soil and environmental bacteria are also discussed. Overall, this article provides a conceptual framework for understanding the complexity of the problem of emergence of antibiotic resistance in the clinic. Availability of such knowledge will allow researchers to build models for dissemination of resistance genes and for developing interventions to prevent recruitment of additional or novel genes into pathogens.
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Affiliation(s)
- Elizabeth Peterson
- Department of Biology, Georgia State University, Atlanta, GA, United States
| | - Parjit Kaur
- Department of Biology, Georgia State University, Atlanta, GA, United States
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189
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Pal R, Hameed S, Fatima Z. Altered drug efflux under iron deprivation unveils abrogated MmpL3 driven mycolic acid transport and fluidity in mycobacteria. Biometals 2018; 32:49-63. [PMID: 30430296 DOI: 10.1007/s10534-018-0157-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2018] [Accepted: 11/12/2018] [Indexed: 11/30/2022]
Abstract
Tuberculosis (TB) caused by Mycobacterium tuberculosis (MTB) is a global threat to human health hence better understanding of the MTB pathogenesis for improved therapeutics requires immediate attention. Emergence of drug-resistant strains has stimulated an urgent need for adopting new strategies that could be implemented to control TB. One of the contributing mechanisms by which MTB evades drug doses is overexpression of drug efflux pumps. Thus blocking or modulating the functionality of efflux pumps represents an attractive approach to combat drug resistance. Iron is a critical micronutrient required for MTB survival and not freely available inside the host. In this study, we demonstrated that iron deprivation impairs drug efflux pump activity and confers synergism for anti-TB drugs in presence of efflux pump inhibitors against MTB. Mechanistic insights revealed that iron deprivation inhibit resistance nodulation division superfamily transporter activity. This was evident from enhanced Nile red accumulation and reduced expression of MmpL3, a transmembrane promising target involved in mycolic acid transport across membrane. Furthermore, iron deprivation led to abrogated MA transport particularly of class methoxy-MA which was confirmed by TLC and mass spectrometry based lipidome analysis. Additionally, iron deprivation leads to enhanced membrane fluidity in MTB. Together, MmpL3 being a promiscuous anti-TB target, metal chelation strategy could be adopted to boost the effectiveness of current anti-TB drug regimes to combat drug resistance TB.
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Affiliation(s)
- Rahul Pal
- Amity Institute of Biotechnology, Amity University Haryana, Gurugram, Manesar, 122413, India
| | - Saif Hameed
- Amity Institute of Biotechnology, Amity University Haryana, Gurugram, Manesar, 122413, India.
| | - Zeeshan Fatima
- Amity Institute of Biotechnology, Amity University Haryana, Gurugram, Manesar, 122413, India.
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190
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Santos RS, Figueiredo C, Azevedo NF, Braeckmans K, De Smedt SC. Nanomaterials and molecular transporters to overcome the bacterial envelope barrier: Towards advanced delivery of antibiotics. Adv Drug Deliv Rev 2018; 136-137:28-48. [PMID: 29248479 DOI: 10.1016/j.addr.2017.12.010] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Revised: 12/10/2017] [Accepted: 12/12/2017] [Indexed: 01/13/2023]
Abstract
With the dramatic consequences of bacterial resistance to antibiotics, nanomaterials and molecular transporters have started to be investigated as alternative antibacterials or anti-infective carrier systems to improve the internalization of bactericidal drugs. However, the capability of nanomaterials/molecular transporters to overcome the bacterial cell envelope is poorly understood. It is critical to consider the sophisticated architecture of bacterial envelopes and reflect how nanomaterials/molecular transporters can interact with these envelopes, being the major aim of this review. The first part of this manuscript overviews the permeability of bacterial envelopes and how it limits the internalization of common antibiotic and novel oligonucleotide drugs. Subsequently we critically discuss the mechanisms that allow nanomaterials/molecular transporters to overcome the bacterial envelopes, focusing on the most promising ones to this end - siderophores, cyclodextrins, metal nanoparticles, antimicrobial/cell-penetrating peptides and fusogenic liposomes. This review may stimulate drug delivery and microbiology scientists in designing effective nanomaterials/molecular transporters against bacterial infections.
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191
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Lim MY, Cho Y, Rho M. Diverse Distribution of Resistomes in the Human and Environmental Microbiomes. Curr Genomics 2018; 19:701-711. [PMID: 30532649 PMCID: PMC6225452 DOI: 10.2174/1389202919666180911130845] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 04/14/2018] [Accepted: 09/03/2018] [Indexed: 11/22/2022] Open
Abstract
The routine therapeutic use of antibiotics has caused resistance genes to be disseminated across microbial populations. In particular, bacterial strains having antibiotic resistance genes are frequently observed in the human microbiome. Moreover, multidrug-resistant pathogens are now widely spread, threatening public health. Such genes are transferred and spread among bacteria even in different environments. Advances in high throughput sequencing technology and computational algorithms have accelerated investigation into antibiotic resistance genes of bacteria. Such studies have revealed that the antibiotic resistance genes are located close to the mobility-associated genes, which promotes their dissemination. An increasing level of information on genomic sequences of resistome should expedite research on drug-resistance in our body and environment, thereby contributing to the development of public health policy. In this review, the high prevalence of antibiotic resistance genes and their exchange in the human and environmental microbiome is discussed with respect to the genomic contents. The relationships among diverse resistomes, related bacterial species, and the antibiotics are reviewed. In addition, recent advances in bioinformatics approaches to investigate such relationships are discussed.
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Affiliation(s)
- Mi Young Lim
- 1Research Group of Healthcare, Korea Food Research Institute, Jeollabuk-do 55365, South Korea; 2Department of Computer Science and Engineering, Hanyang University, Seoul133-791, South Korea; 3Department of Biomedical Informatics, Hanyang University, Seoul133-791, South Korea
| | - Youna Cho
- 1Research Group of Healthcare, Korea Food Research Institute, Jeollabuk-do 55365, South Korea; 2Department of Computer Science and Engineering, Hanyang University, Seoul133-791, South Korea; 3Department of Biomedical Informatics, Hanyang University, Seoul133-791, South Korea
| | - Mina Rho
- 1Research Group of Healthcare, Korea Food Research Institute, Jeollabuk-do 55365, South Korea; 2Department of Computer Science and Engineering, Hanyang University, Seoul133-791, South Korea; 3Department of Biomedical Informatics, Hanyang University, Seoul133-791, South Korea
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192
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Rapid diversification of Pseudomonas aeruginosa in cystic fibrosis lung-like conditions. Proc Natl Acad Sci U S A 2018; 115:10714-10719. [PMID: 30275334 DOI: 10.1073/pnas.1721270115] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Chronic infection of the cystic fibrosis (CF) airway by the opportunistic pathogen Pseudomonas aeruginosa is the leading cause of morbidity and mortality for adult CF patients. Prolonged infections are accompanied by adaptation of P. aeruginosa to the unique conditions of the CF lung environment, as well as marked diversification of the pathogen into phenotypically and genetically distinct strains that can coexist for years within a patient. Little is known, however, about the causes of this diversification and its impact on patient health. Here, we show experimentally that, consistent with ecological theory of diversification, the nutritional conditions of the CF airway can cause rapid and extensive diversification of P. aeruginosa Mucin, the substance responsible for the increased viscosity associated with the thick mucus layer in the CF airway, had little impact on within-population diversification but did promote divergence among populations. Furthermore, in vitro evolution recapitulated traits thought to be hallmarks of chronic infection, including reduced motility and increased biofilm formation, and the range of phenotypes observed in a collection of clinical isolates. Our results suggest that nutritional complexity and reduced dispersal can drive evolutionary diversification of P. aeruginosa independent of other features of the CF lung such as an active immune system or the presence of competing microbial species. We suggest that diversification, by generating extensive phenotypic and genetic variation on which selection can act, may be a key first step in the development of chronic infections.
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193
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Subedi D, Vijay AK, Kohli GS, Rice SA, Willcox M. Association between possession of ExoU and antibiotic resistance in Pseudomonas aeruginosa. PLoS One 2018; 13:e0204936. [PMID: 30265709 PMCID: PMC6161911 DOI: 10.1371/journal.pone.0204936] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 09/17/2018] [Indexed: 12/22/2022] Open
Abstract
Virulent strains of Pseudomonas aeruginosa are often associated with an acquired cytotoxic protein, exoenzyme U (ExoU) that rapidly destroys the cell membranes of host cells by its phospholipase activity. Strains possessing the exoU gene are predominant in eye infections and are more resistant to antibiotics. Thus, it is essential to understand treatment options for these strains. Here, we have investigated the resistance profiles and genes associated with resistance for fluoroquinolone and beta-lactams. A total of 22 strains of P. aeruginosa from anterior eye infections, microbial keratitis (MK), and the lungs of cystic fibrosis (CF) patients were used. Based on whole genome sequencing, the prevalence of the exoU gene was 61.5% in MK isolates whereas none of the CF isolates possessed this gene. Overall, higher antibiotic resistance was observed in the isolates possessing exoU. Of the exoU strains, all except one were resistant to fluoroquinolones, 100% were resistant to beta-lactams. 75% had mutations in quinolone resistance determining regions (T81I gyrA and/or S87L parC) which correlated with fluoroquinolone resistance. In addition, exoU strains had mutations at K76Q, A110T, and V126E in ampC, Q155I and V356I in ampR and E114A, G283E, and M288R in mexR genes that are associated with higher beta-lactamase and efflux pump activities. In contrast, such mutations were not observed in the strains lacking exoU. The expression of the ampC gene increased by up to nine-fold in all eight exoU strains and the ampR was upregulated in seven exoU strains compared to PAO1. The expression of mexR gene was 1.4 to 3.6 fold lower in 75% of exoU strains. This study highlights the association between virulence traits and antibiotic resistance in pathogenic P. aeruginosa.
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Affiliation(s)
- Dinesh Subedi
- School of Optometry and Vision Science, University of New South Wales, Sydney, Australia
- * E-mail:
| | - Ajay Kumar Vijay
- School of Optometry and Vision Science, University of New South Wales, Sydney, Australia
| | - Gurjeet Singh Kohli
- The Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore
| | - Scott A. Rice
- The Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore
- The School of Biological Sciences, Nanyang Technological University, Singapore
- The ithree institute, The University of Technology Sydney, Sydney NSW Australia
| | - Mark Willcox
- School of Optometry and Vision Science, University of New South Wales, Sydney, Australia
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194
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Franklin MW, Nepomnyachiy S, Feehan R, Ben-Tal N, Kolodny R, Slusky JSG. Efflux Pumps Represent Possible Evolutionary Convergence onto the β-Barrel Fold. Structure 2018; 26:1266-1274.e2. [PMID: 30057025 PMCID: PMC6125174 DOI: 10.1016/j.str.2018.06.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Revised: 05/17/2018] [Accepted: 06/20/2018] [Indexed: 11/22/2022]
Abstract
There are around 100 varieties of outer membrane proteins in each Gram-negative bacteria. All of these proteins have the same fold-an up-down β-barrel. It has been suggested that all membrane β-barrels excluding lysins are homologous. Here we suggest that β-barrels of efflux pumps have converged on this fold as well. By grouping structurally solved outer membrane β-barrels (OMBBs) by sequence we find that the membrane environment may have led to convergent evolution of the barrel fold. Specifically, the lack of sequence linkage to other barrels coupled with distinctive structural differences, such as differences in strand tilt and barrel radius, suggest that the outer membrane factor of efflux pumps evolutionarily converged on the barrel. Rather than being related to other OMBBs, sequence and structural similarity in the periplasmic region of the outer membrane factor of efflux pumps suggests an evolutionary link to the periplasmic subunit of the same pump complex.
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Affiliation(s)
| | - Sergey Nepomnyachiy
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Tel Aviv 69978, Israel; Department of Computer Science, University of Haifa, Mount Carmel, Haifa 3498838, Israel
| | - Ryan Feehan
- Center for Computational Biology, University of Kansas, Lawrence, KS 66045, USA
| | - Nir Ben-Tal
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Tel Aviv 69978, Israel
| | - Rachel Kolodny
- Department of Computer Science, University of Haifa, Mount Carmel, Haifa 3498838, Israel
| | - Joanna S G Slusky
- Center for Computational Biology, University of Kansas, Lawrence, KS 66045, USA; Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66045, USA.
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195
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Travers T, Wang KJ, López CA, Gnanakaran S. Sequence- and structure-based computational analyses of Gram-negative tripartite efflux pumps in the context of bacterial membranes. Res Microbiol 2018; 169:414-424. [DOI: 10.1016/j.resmic.2018.01.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Revised: 12/28/2017] [Accepted: 01/21/2018] [Indexed: 01/12/2023]
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196
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Fluoroquinolone-resistant Achromobacter xylosoxidans clinical isolates from Serbia: high prevalence of the aac-(6')-Ib-cr gene among resistant isolates. Folia Microbiol (Praha) 2018; 64:153-159. [PMID: 30105450 DOI: 10.1007/s12223-018-0639-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2018] [Accepted: 08/07/2018] [Indexed: 10/28/2022]
Abstract
The aim of this study was to evaluate the contribution of plasmid-mediated genes and efflux to fluoroquinolone resistance in collection of Achromobacter spp. gathered during a 3-year period. Susceptibility to ciprofloxacin and levofloxacin was tested by disk diffusion and microdilution tests for a collection of 98 Achromobacter spp. clinical isolates. Identification of fluoroquinolone-resistant isolates was performed by sequencing and phylogenetic analyses of the nrdA gene. Genetic relatedness among resistant isolates was determined by pulsed-field gel electrophoresis (PFGE) analysis. The influence of an H+ conductor cyanide m-chlorophenyl hydrazone (CCCP) and a resistance-nodulation-division-type efflux pump inhibitor phenylalanine-arginine beta-naphthylamide (PAβN) on minimal inhibitory concentration (MIC) value was evaluated by broth microdilution. The presence of the plasmid-mediated qnrA, qnrB, qnrC, qnrS, and aac-(6')-Ib-cr genes was investigated by PCR and sequencing. Achromobacter spp. isolates that were resistant or intermediately resistant to fluoroquinolones in disk diffusion tests (44/98) were subjected to microdilution. As a result, 20/98 isolates were confirmed to be resistant to ciprofloxacin while 10/98 was resistant to levofloxacin. CCCP decreased twofold MIC value for ciprofloxacin in six isolates and more than 16 times in one isolate, while MIC value for levofloxacin was decreased in all isolates (twofold to more than eightfold). Fluoroquinolone-resistant isolates were identified as A. xylosoxidans with the nrdA gene sequencing. PFGE revealed that resistant isolates belonged to seven different genotypes. Ten isolates belonging to four genotypes were positive for the aac-(6')-Ib-cr gene. Although resistance to fluoroquinolones was not widespread among analyzed isolates, detected contribution of efflux pumps and the presence of the aac-(6')-Ib-cr gene present a platform for emergence of more resistant strains.
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197
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Durão P, Balbontín R, Gordo I. Evolutionary Mechanisms Shaping the Maintenance of Antibiotic Resistance. Trends Microbiol 2018; 26:677-691. [DOI: 10.1016/j.tim.2018.01.005] [Citation(s) in RCA: 130] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 01/05/2018] [Accepted: 01/24/2018] [Indexed: 01/10/2023]
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198
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Johnson WL, Ramachandran A, Torres NJ, Nicholson AC, Whitney AM, Bell M, Villarma A, Humrighouse BW, Sheth M, Dowd SE, McQuiston JR, Gustafson JE. The draft genomes of Elizabethkingia anophelis of equine origin are genetically similar to three isolates from human clinical specimens. PLoS One 2018; 13:e0200731. [PMID: 30024943 PMCID: PMC6053191 DOI: 10.1371/journal.pone.0200731] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Accepted: 05/28/2018] [Indexed: 12/20/2022] Open
Abstract
We report the isolation and characterization of two Elizabethkingia anophelis strains (OSUVM-1 and OSUVM-2) isolated from sources associated with horses in Oklahoma. Both strains appeared susceptible to fluoroquinolones and demonstrated high MICs to all cell wall active antimicrobials including vancomycin, along with aminoglycosides, fusidic acid, chloramphenicol, and tetracycline. Typical of the Elizabethkingia, both draft genomes contained multiple copies of β-lactamase genes as well as genes predicted to function in antimicrobial efflux. Phylogenetic analysis of the draft genomes revealed that OSUVM-1 and OSUVM-2 differ by only 6 SNPs and are in a clade with 3 strains of Elizabethkingia anophelis that were responsible for human infections. These findings therefore raise the possibility that Elizabethkingia might have the potential to move between humans and animals in a manner similar to known zoonotic pathogens.
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Affiliation(s)
- William L. Johnson
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, Oklahoma, United States of America
| | - Akhilesh Ramachandran
- Oklahoma Animal Disease Diagnostic Laboratory, Center for Veterinary Health Sciences, Oklahoma State University, Stillwater, Oklahoma, United States of America
- * E-mail: (AR); (JEG)
| | - Nathanial J. Torres
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, Oklahoma, United States of America
| | - Ainsley C. Nicholson
- Special Bacteriology Reference Laboratory, Bacterial Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Anne M. Whitney
- Special Bacteriology Reference Laboratory, Bacterial Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Melissa Bell
- Special Bacteriology Reference Laboratory, Bacterial Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Aaron Villarma
- Special Bacteriology Reference Laboratory, Bacterial Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Ben W. Humrighouse
- Special Bacteriology Reference Laboratory, Bacterial Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Mili Sheth
- Division of Scientific Resources, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Scot E. Dowd
- Molecular Research DNA Laboratory, Shallowater, Texas, United States of America
| | - John R. McQuiston
- Special Bacteriology Reference Laboratory, Bacterial Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - John E. Gustafson
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, Oklahoma, United States of America
- * E-mail: (AR); (JEG)
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199
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Bellio P, Luzi C, Mancini A, Cracchiolo S, Passacantando M, Di Pietro L, Perilli M, Amicosante G, Santucci S, Celenza G. Cerium oxide nanoparticles as potential antibiotic adjuvant. Effects of CeO 2 nanoparticles on bacterial outer membrane permeability. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2018; 1860:2428-2435. [PMID: 30026034 DOI: 10.1016/j.bbamem.2018.07.002] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 06/29/2018] [Accepted: 07/09/2018] [Indexed: 01/07/2023]
Abstract
BACKGROUND Therapeutic options against Multi Drug Resistant (MDR) pathogens are limited and the overall strategy would be the development of adjuvants able to enhance the activity of therapeutically available antibiotics. Non-specific outer membrane permeabilizer, like metal-oxide nanoparticles, can be used to increase the activity of antibiotics in drug-resistant pathogens. The study aims to investigate the effect of cerium oxide nanoparticles (CeO2 NPs) on bacterial outer membrane permeability and their application in increasing the antibacterial activity of antibiotics against MDR pathogens. METHODS The ability of CeO2 NPs to permeabilize Gram-negative bacterial outer membrane was investigated by calcein-loaded liposomes. The extent of the damage was evaluated using lipid vesicles loaded with FITC-dextran probes. The effect on bacterial outer membrane was evaluated by measuring the coefficient of permeability at increasing concentrations of CeO2 NPs. The interaction between CeO2 NPs and beta-lactams was evaluated by chequerboard assay against a Klebsiella pneumoniae clinical isolate expressing high levels of resistance against those antibiotics. RESULTS Calcein leakage increases as NPs concentrations increase while no leakage was observed in FITC-dextran loaded liposomes. In Escherichia coli the outer membrane permeability coefficient increases in presence of CeO2 NPs. The antibacterial activity of beta-lactam antibiotics against K. pneumoniae was enhanced when combined with NPs. CONCLUSIONS CeO2 NPs increases the effectiveness of antimicrobials which activity is compromised by drug resistance mechanisms. The synergistic effect is the result of the interaction of NPs with the bacterial outer membrane. The low toxicity of CeO2 NPs makes them attractive as antibiotic adjuvants against MDR pathogens.
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Affiliation(s)
- Pierangelo Bellio
- Department of Biotechnological and Applied Clinical Sciences, University of l'Aquila, via Vetoio, 67100 L'Aquila, Italy.
| | - Carla Luzi
- Department of Biotechnological and Applied Clinical Sciences, University of l'Aquila, via Vetoio, 67100 L'Aquila, Italy
| | - Alisia Mancini
- Department of Biotechnological and Applied Clinical Sciences, University of l'Aquila, via Vetoio, 67100 L'Aquila, Italy
| | - Salvatore Cracchiolo
- Department of Biotechnological and Applied Clinical Sciences, University of l'Aquila, via Vetoio, 67100 L'Aquila, Italy
| | - Maurizio Passacantando
- Department of Physical and Chemical Sciences, University of L'Aquila, via Vetoio, 67100 L'Aquila, Italy
| | - Letizia Di Pietro
- Department of Biotechnological and Applied Clinical Sciences, University of l'Aquila, via Vetoio, 67100 L'Aquila, Italy
| | - Mariagrazia Perilli
- Department of Biotechnological and Applied Clinical Sciences, University of l'Aquila, via Vetoio, 67100 L'Aquila, Italy
| | - Gianfranco Amicosante
- Department of Biotechnological and Applied Clinical Sciences, University of l'Aquila, via Vetoio, 67100 L'Aquila, Italy
| | - Sandro Santucci
- Department of Physical and Chemical Sciences, University of L'Aquila, via Vetoio, 67100 L'Aquila, Italy
| | - Giuseppe Celenza
- Department of Biotechnological and Applied Clinical Sciences, University of l'Aquila, via Vetoio, 67100 L'Aquila, Italy
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200
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He Q, Hou Q, Wang Y, Li J, Li W, Kwok LY, Sun Z, Zhang H, Zhong Z. Comparative genomic analysis of Enterococcus faecalis: insights into their environmental adaptations. BMC Genomics 2018; 19:527. [PMID: 29996769 PMCID: PMC6042284 DOI: 10.1186/s12864-018-4887-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Accepted: 06/19/2018] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Enterococcus faecalis is widely studied as a common gut commensal and a nosocomial pathogen. In fact, Enterococcus faecalis is ubiquitous in nature, and it has been isolated from various niches, including the gastrointestinal tract, faeces, blood, urine, water, and fermented foods (such as dairy products). In order to elucidate the role of habitat in shaping the genome of Enterococcus faecalis, we performed a comparative genomic analysis of 78 strains of various origins. RESULTS Although no correlation was found between the strain isolation habitat and the phylogeny of Enterococcus faecalis from our whole genome-based phylogenetic analysis, our results revealed some environment-associated features in the analysed Enterococcus faecalis genomes. Significant differences were found in the genome size and the number of predicted open reading frames (ORFs) between strains originated from different environments. In general, strains from water sources had the smallest genome size and the least number of predicted ORFs. We also identified 293 environment-specific genes, some of which might link to the adaptive strategies for survival in particular environments. In addition, the number of antibiotic resistance genes was significantly different between strains isolated from dairy products, water, and blood. Strains isolated from blood had the largest number of antibiotic resistance genes. CONCLUSION These findings improve our understanding of the role of habitat in shaping the genomes of Enterococcus faecalis.
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Affiliation(s)
- Qiuwen He
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education P.R. C, Inner Mongolia Agricultural University, Huhhot, 010018, People's Republic of China.,Key Laboratory of Dairy Products Processing, Ministry of Agriculture P.R.C, Inner Mongolia Agricultural University, Huhhot, 010018, People's Republic of China
| | - Qiangchuan Hou
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education P.R. C, Inner Mongolia Agricultural University, Huhhot, 010018, People's Republic of China.,Key Laboratory of Dairy Products Processing, Ministry of Agriculture P.R.C, Inner Mongolia Agricultural University, Huhhot, 010018, People's Republic of China
| | - Yanjie Wang
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education P.R. C, Inner Mongolia Agricultural University, Huhhot, 010018, People's Republic of China.,Key Laboratory of Dairy Products Processing, Ministry of Agriculture P.R.C, Inner Mongolia Agricultural University, Huhhot, 010018, People's Republic of China
| | - Jing Li
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education P.R. C, Inner Mongolia Agricultural University, Huhhot, 010018, People's Republic of China.,Key Laboratory of Dairy Products Processing, Ministry of Agriculture P.R.C, Inner Mongolia Agricultural University, Huhhot, 010018, People's Republic of China
| | - Weicheng Li
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education P.R. C, Inner Mongolia Agricultural University, Huhhot, 010018, People's Republic of China.,Key Laboratory of Dairy Products Processing, Ministry of Agriculture P.R.C, Inner Mongolia Agricultural University, Huhhot, 010018, People's Republic of China
| | - Lai-Yu Kwok
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education P.R. C, Inner Mongolia Agricultural University, Huhhot, 010018, People's Republic of China.,Key Laboratory of Dairy Products Processing, Ministry of Agriculture P.R.C, Inner Mongolia Agricultural University, Huhhot, 010018, People's Republic of China
| | - Zhihong Sun
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education P.R. C, Inner Mongolia Agricultural University, Huhhot, 010018, People's Republic of China.,Key Laboratory of Dairy Products Processing, Ministry of Agriculture P.R.C, Inner Mongolia Agricultural University, Huhhot, 010018, People's Republic of China
| | - Heping Zhang
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education P.R. C, Inner Mongolia Agricultural University, Huhhot, 010018, People's Republic of China.,Key Laboratory of Dairy Products Processing, Ministry of Agriculture P.R.C, Inner Mongolia Agricultural University, Huhhot, 010018, People's Republic of China
| | - Zhi Zhong
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education P.R. C, Inner Mongolia Agricultural University, Huhhot, 010018, People's Republic of China. .,Key Laboratory of Dairy Products Processing, Ministry of Agriculture P.R.C, Inner Mongolia Agricultural University, Huhhot, 010018, People's Republic of China.
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