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Do DT, Yang MR, Vo TNS, Le NQK, Wu YW. Unitig-centered pan-genome machine learning approach for predicting antibiotic resistance and discovering novel resistance genes in bacterial strains. Comput Struct Biotechnol J 2024; 23:1864-1876. [PMID: 38707536 PMCID: PMC11067008 DOI: 10.1016/j.csbj.2024.04.035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 04/13/2024] [Accepted: 04/13/2024] [Indexed: 05/07/2024] Open
Abstract
In current genomic research, the widely used methods for predicting antimicrobial resistance (AMR) often rely on prior knowledge of known AMR genes or reference genomes. However, these methods have limitations, potentially resulting in imprecise predictions owing to incomplete coverage of AMR mechanisms and genetic variations. To overcome these limitations, we propose a pan-genome-based machine learning approach to advance our understanding of AMR gene repertoires and uncover possible feature sets for precise AMR classification. By building compacted de Brujin graphs (cDBGs) from thousands of genomes and collecting the presence/absence patterns of unique sequences (unitigs) for Pseudomonas aeruginosa, we determined that using machine learning models on unitig-centered pan-genomes showed significant promise for accurately predicting the antibiotic resistance or susceptibility of microbial strains. Applying a feature-selection-based machine learning algorithm led to satisfactory predictive performance for the training dataset (with an area under the receiver operating characteristic curve (AUC) of > 0.929) and an independent validation dataset (AUC, approximately 0.77). Furthermore, the selected unitigs revealed previously unidentified resistance genes, allowing for the expansion of the resistance gene repertoire to those that have not previously been described in the literature on antibiotic resistance. These results demonstrate that our proposed unitig-based pan-genome feature set was effective in constructing machine learning predictors that could accurately identify AMR pathogens. Gene sets extracted using this approach may offer valuable insights into expanding known AMR genes and forming new hypotheses to uncover the underlying mechanisms of bacterial AMR.
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Affiliation(s)
- Duyen Thi Do
- Graduate Institute of Biomedical Informatics, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
| | - Ming-Ren Yang
- Graduate Institute of Biomedical Informatics, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
- Department of Electrical Engineering, National Taiwan University of Science and Technology, Taipei, Taiwan
| | - Tran Nam Son Vo
- Department of Business Administration, College of Management, Lunghwa University of Science and Technology, Taoyuan City, Taiwan
| | - Nguyen Quoc Khanh Le
- Professional Master Program in Artificial Intelligence in Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Yu-Wei Wu
- Graduate Institute of Biomedical Informatics, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
- Clinical Big Data Research Center, Taipei Medical University Hospital, Taipei, Taiwan
- TMU Research Center for Digestive Medicine, Taipei Medical University, Taipei, Taiwan
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Lin X, Xu G, Li Y, Yu Y. Chemical fertilizers promote dissemination of ARGs in maize rhizosphere: An overlooked risk revealed after 37-year traditional agriculture practice. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 941:173737. [PMID: 38844214 DOI: 10.1016/j.scitotenv.2024.173737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 06/01/2024] [Accepted: 06/01/2024] [Indexed: 06/10/2024]
Abstract
Bacterial communities in soil and rhizosphere maintain a large collection of antibiotic resistance genes (ARGs). However, few of these ARGs and antibiotic resistant bacteria (ARB) are well-characterized under traditional farming practices. Here we compared the ARG profiles of maize rhizosphere and their bulk soils using metagenomic analysis to identify the ARG dissemination and explored the potential impact of chemical fertilization on ARB. Results showed a relatively lower abundance but higher diversity of ARGs under fertilization than straw-return. Moreover, the abundance and diversity of MGEs were significantly promoted by chemical fertilizer inputs in the rhizosphere compared to bulk soil. Machine learning and bipartite networks identified three bacterial genera (Pseudomonas, Bacillus and Streptomyces) as biomarkers for ARG accumulation. Thus we cultured 509 isolates belonging to these three genera from the rhizosphere and tested their antimicrobial susceptibility, and found that multi-resistance was frequently observed among Pseudomonas isolates. Assembly-based tracking explained that ARGs and four class I integrons (LR134330, LS998783, CP065848, LT883143) were co-occurred among contigs from Pseudomonas sp. Chemical fertilizers may shape the resistomes of maize rhizosphere, highlighting that rhizosphere carried multidrug-resistant Pseudomonas isolates, which may pose a risk to animal and human health. This study adds knowledge of long-term chemical fertilization on ARG dissemination in farmland systems and provides information for decision-making in agricultural production and monitoring.
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Affiliation(s)
- Xiaolong Lin
- Key Laboratory of Wetland Ecology and Environment, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China; School of Agriculture, Sun Yat-sen University, Guangzhou 510275, China
| | - Guanghui Xu
- Key Laboratory of Wetland Ecology and Environment, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
| | - Yanjun Li
- Key Laboratory of Wetland Ecology and Environment, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
| | - Yong Yu
- Key Laboratory of Wetland Ecology and Environment, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China.
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Hsiao CY, Lee YC, Shyu DJH, Su CP, Lin MY, Guo NY, Chiang CL, Chen YY. Molecular Characterization of High and Low Virulent Escherichia coli Clinical Strains Isolated from Patients with Urinary Tract Infections with or without Bacteremia in Southern Taiwan. Infect Drug Resist 2024; 17:2389-2399. [PMID: 38903152 PMCID: PMC11186960 DOI: 10.2147/idr.s458925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Accepted: 06/04/2024] [Indexed: 06/22/2024] Open
Abstract
Objective The most common extraintestinal pathogen and infection site is uropathogenic Escherichia coli (UPEC), which causes urinary tract infections (UTIs). UPEC is also a common pathogen in bloodstream infections; in severe cases, it can lead to death. Although host and bacterial virulence factors have been demonstrated to be associated with UTI pathogenesis, the role of the related contributing factors in UTI and urinary source bacteremia is not yet fully understood. This study aimed to compare and analyze the factors contributing to urinary bacteremia in patients with UTI. Methods A total of 171 E. coli strains collected from patients with UTI and urinary source bacteremia at Chiayi Christian Hospital were used. Phylogenetic groups and virulence factors were determined using PCR. Drug resistance patterns were determined using the disk diffusion assay. Results Previous studies have demonstrated that fimbriae and papGII may be associated with first-step infections and severe UTIs, respectively. As expected, highly virulent E. coli strains (belonging to the phylogenetic B2 and D groups) were dominant in the bacteremic UTI (90%) and UTI (86.27%) groups. However, our results showed that the UTI group had a significantly higher prevalence of sfa/focDE (belonging to the S and FIC fimbriae) than the bacteremic UTI group (29.4% vs 12.5%; p=0.008). In the bacteremic group, we found that sfa/focDE was only detected in highly virulent strains. The bacteremic UTI group had a significantly higher prevalence of papGII (belonging to P fimbriae) than the UTI group (55.8% vs 37.3%; p=0.026). In addition, the P fimbriae gene cluster, including papC, papEF, and papGII, was predominant in highly virulent strains. Notably, our results show that multidrug-resistant (MDR) strains were significantly less virulent than non MDR strains. Conclusion Taken together, our results provide insights into the contributing factors in patients with UTI and urinary bacteremia.
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Affiliation(s)
- Chih-Yen Hsiao
- Division of Nephrology, Department of Internal Medicine, Ditmanson Medical Foundation Chia-Yi Christian Hospital, Chiayi, Taiwan
| | - Yi-Chien Lee
- Department of Internal Medicine, Fu Jen Catholic University Hospital, Fu Jen Catholic University, New Taipei City, Taiwan
- School of Medicine, College of Medicine, Fu Jen Catholic University, New Taipei City, Taiwan
| | - Douglas J H Shyu
- Department of Biological Science and Technology, National Pingtung University of Science and Technology, Neipu, Pingtung, Taiwan
| | - Che-Ping Su
- Department of Biochemical Science and Technology, National Chiayi University, Chiayi, Taiwan
| | - Man-Yi Lin
- Department of Biochemical Science and Technology, National Chiayi University, Chiayi, Taiwan
| | - Nai-Yu Guo
- Department of Respiratory Care, Chang-Gung University of Science and Technology, Chiayi, Taiwan
| | - Cheng-Lun Chiang
- Division of Nephrology, Department of Internal Medicine, Ditmanson Medical Foundation Chia-Yi Christian Hospital, Chiayi, Taiwan
| | - Yih-Yuan Chen
- Department of Biochemical Science and Technology, National Chiayi University, Chiayi, Taiwan
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Breen SKJ, Harper M, López-Causapé C, Rogers KE, Tait JR, Smallman TR, Lang Y, Lee WL, Zhou J, Zhang Y, Bulitta JB, Nation RL, Oliver A, Boyce JD, Landersdorfer CB. Synergistic effects of inhaled aztreonam plus tobramycin on hypermutable cystic fibrosis Pseudomonas aeruginosa isolates in a dynamic biofilm model evaluated by mechanism-based modelling and whole genome sequencing. Int J Antimicrob Agents 2024; 63:107161. [PMID: 38561094 DOI: 10.1016/j.ijantimicag.2024.107161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 03/19/2024] [Accepted: 03/22/2024] [Indexed: 04/04/2024]
Abstract
OBJECTIVE Hypermutable Pseudomonas aeruginosa strains are highly prevalent in chronic lung infections of patients with cystic fibrosis (CF). Acute exacerbations of these infections have limited treatment options. This study aimed to investigate inhaled aztreonam and tobramycin against clinical hypermutable P. aeruginosa strains using the CDC dynamic in vitro biofilm reactor (CBR), mechanism-based mathematical modelling (MBM) and genomic studies. METHODS Two CF multidrug-resistant strains were investigated in a 168 h CBR (n = 2 biological replicates). Regimens were inhaled aztreonam (75 mg 8-hourly) and tobramycin (300 mg 12-hourly) in monotherapies and combination. The simulated pharmacokinetic profiles of aztreonam and tobramycin (t1/2 = 3 h) were based on published lung fluid concentrations in patients with CF. Total viable and resistant counts were determined for planktonic and biofilm bacteria. MBM of total and resistant bacterial counts and whole genome sequencing were completed. RESULTS Both isolates showed reproducible bacterial regrowth and resistance amplification for the monotherapies by 168 h. The combination performed synergistically, with minimal resistant subpopulations compared to the respective monotherapies at 168 h. Mechanistic synergy appropriately described the antibacterial effects of the combination regimen in the MBM. Genomic analysis of colonies recovered from monotherapy regimens indicated noncanonical resistance mechanisms were likely responsible for treatment failure. CONCLUSION The combination of aztreonam and tobramycin was required to suppress the regrowth and resistance of planktonic and biofilm bacteria in all biological replicates of both hypermutable multidrug-resistant P. aeruginosa CF isolates. The developed MBM could be utilised for future investigations of this promising inhaled combination.
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Affiliation(s)
- Siobhonne K J Breen
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
| | - Marina Harper
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia
| | - Carla López-Causapé
- Servicio de Microbiología, Hospital Universitario Son Espases-IdISBa, Palma de Mallorca, Spain; CIBER Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain
| | - Kate E Rogers
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
| | - Jessica R Tait
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
| | - Thomas R Smallman
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia
| | - Yinzhi Lang
- Department of Pharmacotherapy and Translational Research, College of Pharmacy, University of Florida, Orlando, Florida, USA
| | - Wee L Lee
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
| | - Jieqiang Zhou
- Department of Pharmacotherapy and Translational Research, College of Pharmacy, University of Florida, Orlando, Florida, USA
| | - Yongzhen Zhang
- Department of Pharmacotherapy and Translational Research, College of Pharmacy, University of Florida, Orlando, Florida, USA
| | - Jurgen B Bulitta
- Department of Pharmacotherapy and Translational Research, College of Pharmacy, University of Florida, Orlando, Florida, USA
| | - Roger L Nation
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
| | - Antonio Oliver
- Servicio de Microbiología, Hospital Universitario Son Espases-IdISBa, Palma de Mallorca, Spain; CIBER Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain
| | - John D Boyce
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia
| | - Cornelia B Landersdorfer
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia.
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Yasin A, Mandato A, Hofmann L, Igbaria-Jaber Y, Shenberger Y, Gevorkyan-Airapetov L, Saxena S, Ruthstein S. The Dynamic Plasticity of P. aeruginosa CueR Copper Transcription Factor upon Cofactor and DNA Binding. Chembiochem 2024:e202400279. [PMID: 38776258 DOI: 10.1002/cbic.202400279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 05/17/2024] [Accepted: 05/22/2024] [Indexed: 05/24/2024]
Abstract
Bacteria use specialized proteins, like transcription factors, to rapidly control metal ion balance. CueR is a Gram-negative bacterial copper regulator. The structure of E. coli CueR complexed with Cu(I) and DNA was published, since then many studies have shed light on its function. However, P. aeruginosa CueR, which shows high sequence similarity to E. coli CueR, has been less studied. Here, we applied room-temperature electron paramagnetic resonance (EPR) measurements to explore changes in dynamics of P. aeruginosa CueR in dependency of copper concentrations and interaction with two different DNA promoter regions. We showed that P. aeruginosa CueR is less dynamic than the E. coli CueR protein and exhibits much higher sensitivity to DNA binding as compared to its E. coli CueR homolog. Moreover, a difference in dynamical behavior was observed when P. aeruginosa CueR binds to the copZ2 DNA promoter sequence compared to the mexPQ-opmE promoter sequence. Such dynamical differences may affect the expression levels of CopZ2 and MexPQ-OpmE proteins in P. aeruginosa. Overall, such comparative measurements of protein-DNA complexes derived from different bacterial systems reveal insights about how structural and dynamical differences between two highly homologous proteins lead to quite different DNA sequence-recognition and mechanistic properties.
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Affiliation(s)
- Ameer Yasin
- Department of Chemistry and the Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan, Israel, 5290002
| | - Alysia Mandato
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, 15260
| | - Lukas Hofmann
- Department of Chemistry and the Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan, Israel, 5290002
| | - Yasmin Igbaria-Jaber
- Department of Chemistry and the Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan, Israel, 5290002
| | - Yulia Shenberger
- Department of Chemistry and the Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan, Israel, 5290002
| | - Lada Gevorkyan-Airapetov
- Department of Chemistry and the Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan, Israel, 5290002
| | - Sunil Saxena
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, 15260
| | - Sharon Ruthstein
- Department of Chemistry and the Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan, Israel, 5290002
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Stehling EG, Furlan JPR, Lopes R, Chodkowski J, Stopnisek N, Savazzi EA, Shade A. The relationship between water quality and the microbial virulome and resistome in urban streams in Brazil. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 348:123849. [PMID: 38522607 DOI: 10.1016/j.envpol.2024.123849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 02/23/2024] [Accepted: 03/21/2024] [Indexed: 03/26/2024]
Abstract
Urban streams that receive untreated domestic and hospital waste can transmit infectious diseases and spread drug residues, including antimicrobials, which can then increase the selection of antimicrobial-resistant bacteria. Here, water samples were collected from three different urban streams in the state of São Paulo, Brazil, to relate their range of Water Quality Indices (WQIs) to the diversity and composition of aquatic microbial taxa, virulence genes (virulome), and antimicrobial resistance determinants (resistome), all assessed using untargeted metagenome sequencing. There was a predominance of phyla Proteobacteria, Actinobacteria, and Bacteroidetes in all samples, and Pseudomonas was the most abundant detected genus. Virulence genes associated with motility, adherence, and secretion systems were highly abundant and mainly associated with Pseudomonas aeruginosa. Furthermore, some opportunistic pathogenic genera had negative correlations with WQI. Many clinically relevant antimicrobial resistance genes (ARGs) and efflux pump-encoding genes that confer resistance to critically important antimicrobials were detected. The highest relative abundances of ARGs were β-lactams and macrolide-lincosamide-streptogramin. No statistically supported relationship was detected between the abundance of virulome/resistome and collection type/WQI. On the other hand, total solids were a weak predictor of gene abundance patterns. These results provide insights into various microbial outcomes given urban stream quality and point to its ecological complexity. In addition, this study suggests potential consequences for human health as mediated by aquatic microbial communities responding to typical urban outputs.
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Affiliation(s)
- Eliana Guedes Stehling
- Department of Clinical Analyses, Toxicology and Food Science, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Brazil.
| | - João Pedro Rueda Furlan
- Department of Clinical Analyses, Toxicology and Food Science, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Brazil.
| | - Ralf Lopes
- Department of Clinical Analyses, Toxicology and Food Science, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Brazil.
| | - John Chodkowski
- Department of Microbiology and Molecular Genetics, Michigan State University (MSU) - East Lansing, United States.
| | - Nejc Stopnisek
- Department of Microbiology and Molecular Genetics, Michigan State University (MSU) - East Lansing, United States; National Laboratory of Health, Environment and Food - Maribor, Slovenia.
| | | | - Ashley Shade
- Universite Claude Bernard Lyon 1, Laboratoire d'Ecologie Microbienne, UMR CNRS 5557, UMR INRAE 1418, VetAgro Sup, 69622, Villeurbanne, France.
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Gondal AJ, Choudhry N, Niaz A, Yasmin N. Molecular Analysis of Carbapenem and Aminoglycoside Resistance Genes in Carbapenem-Resistant Pseudomonas aeruginosa Clinical Strains: A Challenge for Tertiary Care Hospitals. Antibiotics (Basel) 2024; 13:191. [PMID: 38391577 PMCID: PMC10886086 DOI: 10.3390/antibiotics13020191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Revised: 01/09/2024] [Accepted: 01/23/2024] [Indexed: 02/24/2024] Open
Abstract
Carbapenem-resistant Pseudomonas aeruginosa (P. aeruginosa) strains have become a global threat due to their remarkable capability to survive and disseminate successfully by the acquisition of resistance genes. As a result, the treatment strategies have been severely compromised. Due to the insufficient available data regarding P. aeruginosa resistance from Pakistan, we aimed to investigate the resistance mechanisms of 249 P. aeruginosa strains by antimicrobial susceptibility testing, polymerase chain reaction for the detection of carbapenemases, aminoglycoside resistance genes, extended-spectrum beta-lactamases (ESBLs), sequence typing and plasmid typing. Furthermore, we tested silver nanoparticles (AgNPs) to evaluate their in vitro sensitivity against antimicrobial-resistant P. aeruginosa strains. We observed higher resistance against antimicrobials in the general surgery ward, general medicine ward and wound samples. Phenotypic carbapenemase-producer strains comprised 80.7% (201/249) with 89.0% (179/201) demonstrating genes encoding carbapenemases: blaNDM-1 (32.96%), blaOXA48 (37.43%), blaIMP (7.26%), blaVIM (5.03%), blaKPC-2 (1.12%), blaNDM-1/blaOXA48 (13.97%), blaOXA-48/blaVIM (1.68%) and blaVIM/blaIMP (0.56%). Aminoglycoside-modifying enzyme genes and 16S rRNA methylase variants were detected in 43.8% (109/249) strains: aac(6')-lb (12.8%), aac(3)-lla (12.0%), rmtB (21.1%), rmtC (11.0%), armA (12.8%), rmtD (4.6%), rmtF (6.4%), rmtB/aac(3)-lla (8.2%), rmtB/aac(6')-lla (7.3%) and rmtB/armA (3.6%). In total, 43.0% (77/179) of the strains coharbored carbapenemases and aminoglycoside resistance genes with 83.1% resistant to at least 1 agent in 3 or more classes and 16.9% resistant to every class of antimicrobials tested. Thirteen sequence types (STs) were identified: ST235, ST277, ST234, ST170, ST381, ST175, ST1455, ST1963, ST313, ST207, ST664, ST357 and ST348. Plasmid replicon types IncFI, IncFII, IncA/C, IncL/M, IncN, IncX, IncR and IncFIIK and MOB types F11, F12, H121, P131 and P3 were detected. Meropenem/AgNPs and Amikacin/AgNPs showed enhanced antibacterial activity. We reported the coexistence of carbapenemases and aminoglycoside resistance genes among carbapenem-resistant P. aeruginosa with diverse clonal lineages from Pakistan. Furthermore, we highlighted AgNP's potential role in handling future antimicrobial resistance concerns.
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Affiliation(s)
- Aamir Jamal Gondal
- Department of Biomedical Sciences, King Edward Medical University, Lahore 54000, Pakistan
| | - Nakhshab Choudhry
- Department of Biochemistry, King Edward Medical University, Lahore 54000, Pakistan
| | - Ammara Niaz
- Department of Biochemistry, King Edward Medical University, Lahore 54000, Pakistan
| | - Nighat Yasmin
- Department of Biomedical Sciences, King Edward Medical University, Lahore 54000, Pakistan
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Ventero MP, Haro-Moreno JM, Molina-Pardines C, Sánchez-Bautista A, García-Rivera C, Boix V, Merino E, López-Pérez M, Rodríguez JC. Role of Relebactam in the Antibiotic Resistance Acquisition in Pseudomonas aeruginosa: In Vitro Study. Antibiotics (Basel) 2023; 12:1619. [PMID: 37998821 PMCID: PMC10668777 DOI: 10.3390/antibiotics12111619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 10/30/2023] [Accepted: 11/08/2023] [Indexed: 11/25/2023] Open
Abstract
BACKGROUND Pseudomonas aeruginosa shows resistance to several antibiotics and often develops such resistance during patient treatment. OBJECTIVE Develop an in vitro model, using clinical isolates of P. aeruginosa, to compare the ability of the imipenem and imipenem/relebactam to generate resistant mutants to imipenem and to other antibiotics. Perform a genotypic analysis to detect how the selective pressure changes their genomes. METHODS The antibiotics resistance was studied by microdilution assays and e-test, and the genotypic study was performed by NGS. RESULTS The isolates acquired resistance to imipenem in an average of 6 days, and to imipenem/relebactam in 12 days (p value = 0.004). After 30 days of exposure, 75% of the isolates reached a MIC > 64 mg/L for imipenem and 37.5% for imipenem/relebactam (p value = 0.077). The 37.5% and the 12.5% imipenem/relebactam mutants developed resistance to piperacillin/tazobactam and ceftazidime, respectively, while the 87.5% and 37.5% of the imipenem mutants showed resistance to these drugs (p value = 0.003, p value = 0.015). The main biological processes altered by the SNPs were the glycosylation pathway, transcriptional regulation, histidine kinase response, porins, and efflux pumps. DISCUSSION The addition of relebactam delays the generation of resistance to imipenem and limits the cross-resistance to other beta-lactams. The clinical relevance of this phenomenon, which has the limitation that it has been performed in vitro, should be evaluated by stewardship programs in clinical practice, as it could be useful in controlling multi-drug resistance in P. aeruginosa.
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Affiliation(s)
- Maria Paz Ventero
- Microbiology Department, Dr. Balmis University General Hospital, Alicante Institute for Health and Biomedical Research (ISABIAL), 03010 Alicante, Spain; (M.P.V.); (A.S.-B.); (C.G.-R.); (J.C.R.)
| | - Jose M. Haro-Moreno
- Evolutionary Genomics Group, División de Microbiología, Universidad Miguel Hernández, Apartado 18, 03550 San Juan de Alicante, Spain
- Institut de Biologie Structurale J.-P. Ebel, Université Grenoble Alpes, 38000 Grenoble, France
| | - Carmen Molina-Pardines
- Microbiology Department, Dr. Balmis University General Hospital, Alicante Institute for Health and Biomedical Research (ISABIAL), 03010 Alicante, Spain; (M.P.V.); (A.S.-B.); (C.G.-R.); (J.C.R.)
- Evolutionary Genomics Group, División de Microbiología, Universidad Miguel Hernández, Apartado 18, 03550 San Juan de Alicante, Spain
| | - Antonia Sánchez-Bautista
- Microbiology Department, Dr. Balmis University General Hospital, Alicante Institute for Health and Biomedical Research (ISABIAL), 03010 Alicante, Spain; (M.P.V.); (A.S.-B.); (C.G.-R.); (J.C.R.)
| | - Celia García-Rivera
- Microbiology Department, Dr. Balmis University General Hospital, Alicante Institute for Health and Biomedical Research (ISABIAL), 03010 Alicante, Spain; (M.P.V.); (A.S.-B.); (C.G.-R.); (J.C.R.)
| | - Vicente Boix
- Infectious Diseases Unit, Dr. Balmis University General Hospital, Alicante Institute for Health and Biomedical Research (ISABIAL), 03010 Alicante, Spain
| | - Esperanza Merino
- Infectious Diseases Unit, Dr. Balmis University General Hospital, Alicante Institute for Health and Biomedical Research (ISABIAL), 03010 Alicante, Spain
| | - Mario López-Pérez
- Evolutionary Genomics Group, División de Microbiología, Universidad Miguel Hernández, Apartado 18, 03550 San Juan de Alicante, Spain
| | - Juan Carlos Rodríguez
- Microbiology Department, Dr. Balmis University General Hospital, Alicante Institute for Health and Biomedical Research (ISABIAL), 03010 Alicante, Spain; (M.P.V.); (A.S.-B.); (C.G.-R.); (J.C.R.)
- Evolutionary Genomics Group, División de Microbiología, Universidad Miguel Hernández, Apartado 18, 03550 San Juan de Alicante, Spain
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Alghamdi M, Al-Judaibi E, Al-Rashede M, Al-Judaibi A. Comparative De Novo and Pan-Genome Analysis of MDR Nosocomial Bacteria Isolated from Hospitals in Jeddah, Saudi Arabia. Microorganisms 2023; 11:2432. [PMID: 37894090 PMCID: PMC10609288 DOI: 10.3390/microorganisms11102432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 09/14/2023] [Accepted: 09/26/2023] [Indexed: 10/29/2023] Open
Abstract
Multidrug-resistant (MDR) bacteria are one of the most serious threats to public health, and one of the most important types of MDR bacteria are those that are acquired in a hospital, known as nosocomial. This study aimed to isolate and identify MDR bacteria from selected hospitals in Jeddah and analyze their antibiotic-resistant genes. Bacteria were collected from different sources and wards of hospitals in Jeddah City. Phoenix BD was used to identify the strains and perform susceptibility testing. Identification of selected isolates showing MDR to more than three classes on antibiotics was based on 16S rRNA gene and whole genome sequencing. Genes conferring resistance were characterized using de novo and pan-genome analyses. In total, we isolated 108 bacterial strains, of which 75 (69.44%) were found to be MDR. Taxonomic identification revealed that 24 (32%) isolates were identified as Escherichia coli, 19 (25.3%) corresponded to Klebsiella pneumoniae, and 17 (22.67%) were methicillin-resistant Staphylococcus aureus (MRSA). Among the Gram-negative bacteria, K. pneumoniae isolates showed the highest resistance levels to most antibiotics. Of the Gram-positive bacteria, S. aureus (MRSA) strains were noticed to exhibit the uppermost degree of resistance to the tested antibiotics, which is higher than that observed for K. pneumoniae isolates. Taken together, our results illustrated that MDR Gram-negative bacteria are the most common cause of nosocomial infections, while MDR Gram-positive bacteria are characterized by a wider antibiotic resistance spectrum. Whole genome sequencing found the appearance of antibiotic resistance genes, including SHV, OXA, CTX-M, TEM-1, NDM-1, VIM-1, ere(A), ermA, ermB, ermC, msrA, qacA, qacB, and qacC.
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Affiliation(s)
- Molook Alghamdi
- Department of Biological Sciences, Microbiology Section, Faculty of Science, Jeddah University, Jeddah 21959, Saudi Arabia; (M.A.); (E.A.-J.)
| | - Effat Al-Judaibi
- Department of Biological Sciences, Microbiology Section, Faculty of Science, Jeddah University, Jeddah 21959, Saudi Arabia; (M.A.); (E.A.-J.)
| | | | - Awatif Al-Judaibi
- Department of Biological Sciences, Microbiology Section, Faculty of Science, Jeddah University, Jeddah 21959, Saudi Arabia; (M.A.); (E.A.-J.)
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Tomaś N, Myszka K, Wolko Ł. Potassium Chloride, Sodium Lactate and Sodium Citrate Impaired the Antimicrobial Resistance and Virulence of Pseudomonas aeruginosa NT06 Isolated from Fish. Molecules 2023; 28:6654. [PMID: 37764430 PMCID: PMC10536532 DOI: 10.3390/molecules28186654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 09/11/2023] [Accepted: 09/15/2023] [Indexed: 09/29/2023] Open
Abstract
Sodium chloride (NaCl) is a commonly used additive in minimally processed fish-based products. The addition of NaCl to fish products and packaging in a modified atmosphere is usually efficient with regard to limiting the occurrence of the aquatic environmental pathogen Pseudomonas aeruginosa. Given the negative effects of excess NaCl in the diet, there is a growing demand to reduce NaCl in food products with safer substituents, but the knowledge of their impact on antibiotic resistant P. aeruginosa is limited. This study aimed to evaluate the physiological and transcriptome characteristics of P. aeruginosa NT06 isolated from fish and to determine the effect of selected concentrations of alternative NaCl compounds (KCl/NaL/NaC) on the P. aeruginosa NT06 virulence phenotype and genotype. In the study, among the isolated microorganisms, P. aeruginosa NT06 showed the highest antibiotic resistance (to ampicillin, ceftriaxone, nalidixic acid, and norfloxacin) and the ability to grow at 4 °C. The Comprehensive Antibiotic Resistance Database (CARD) and the Virulence Factor Database (VFDB) revealed the presence of 24 and 134 gene products assigned to AMR and VF in the P. aeruginosa NT06 transcriptome, respectively. KCl, KCl/NaL and KCl/NaL/NaC inhibited pyocyanin biosynthesis, elastase activity, and protease activity from 40 to 77%. The above virulence phenotypic observations were confirmed via RT-qPCR analyses, which showed that all tested AMR and VF genes were the most downregulated due to KCl/NaL/NaC treatment. In conclusion, this study provides insight into the potential AMR and VF among foodborne P. aeruginosa and the possible impairment of those features by KCl, NaL, and NaC, which exert synergistic effects and can be used in minimally processed fish-based products.
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Affiliation(s)
- Natalia Tomaś
- Department of Biotechnology and Food Microbiology, Poznan University of Life Sciences, Wojska Polskiego 48, 60-637 Poznań, Poland
| | - Kamila Myszka
- Department of Biotechnology and Food Microbiology, Poznan University of Life Sciences, Wojska Polskiego 48, 60-637 Poznań, Poland
| | - Łukasz Wolko
- Department of Biochemistry and Biotechnology, Poznan University of Life Sciences, Dojazd 11, 60-632 Poznań, Poland;
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Chauhan M, Kimothi A, Sharma A, Pandey A. Cold adapted Pseudomonas: ecology to biotechnology. Front Microbiol 2023; 14:1218708. [PMID: 37529326 PMCID: PMC10388556 DOI: 10.3389/fmicb.2023.1218708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 06/26/2023] [Indexed: 08/03/2023] Open
Abstract
The cold adapted microorganisms, psychrophiles/psychrotolerants, go through several modifications at cellular and biochemical levels to alleviate the influence of low temperature stress conditions. The low temperature environments depend on these cold adapted microorganisms for various ecological processes. The ability of the microorganisms to function in cold environments depends on the strategies directly associated with cell metabolism, physicochemical constrains, and stress factors. Pseudomonas is one among such group of microorganisms which is predominant in cold environments with a wide range of ecological and biotechnological applications. Bioformulations of Pseudomonas spp., possessing plant growth promotion and biocontrol abilities for application under low temperature environments, are well documented. Further, recent advances in high throughput sequencing provide essential information regarding the prevalence of Pseudomonas in rhizospheres and their role in plant health. Cold adapted species of Pseudomonas are also getting recognition for their potential in biodegradation and bioremediation of environmental contaminants. Production of enzymes and bioactive compounds (primarily as an adaptation mechanism) gives way to their applications in various industries. Exopolysaccharides and various biotechnologically important enzymes, produced by cold adapted species of Pseudomonas, are making their way in food, textiles, and pharmaceuticals. The present review, therefore, aims to summarize the functional versatility of Pseudomonas with particular reference to its peculiarities along with the ecological and biotechnological applications.
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Affiliation(s)
- Mansi Chauhan
- Department of Microbiology, Graphic Era (Deemed to be University), Dehradun, Uttarakhand, India
| | - Ayushi Kimothi
- Department of Microbiology, Graphic Era (Deemed to be University), Dehradun, Uttarakhand, India
| | - Avinash Sharma
- National Centre for Cell Science, Pune, Maharashtra, India
| | - Anita Pandey
- Department of Biotechnology, Graphic Era (Deemed to be University), Dehradun, Uttarakhand, India
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12
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Yasuda N, Fujita T, Fujioka T, Tagawa M, Kohira N, Torimaru K, Shiota S, Kumagai T, Morita D, Ogawa W, Tsuchiya T, Kuroda T. Effects of the order of exposure to antimicrobials on the incidence of multidrug-resistant Pseudomonas aeruginosa. Sci Rep 2023; 13:8826. [PMID: 37258635 DOI: 10.1038/s41598-023-35256-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 05/15/2023] [Indexed: 06/02/2023] Open
Abstract
Multidrug-resistant Pseudomonas aeruginosa (MDRP) is one of the most important pathogens in clinical practice. To clarify the mechanisms contributing to its emergence, we isolated MDRPs using the P. aeruginosa PAO1, the whole genome sequence of which has already been elucidated. Mutant strains resistant to carbapenems, aminoglycosides, and new quinolones, which are used to treat P. aeruginosa infections, were isolated; however, none met the criteria for MDRPs. Then, PAO1 strains were exposed to these antimicrobial agents in various orders and the appearance rate of MDRP varied depending on the order of exposure; MDRPs more frequently appeared when gentamicin was applied before ciprofloxacin, but were rarely isolated when ciprofloxacin was applied first. Exposure to ciprofloxacin followed by gentamicin increased the expression of MexCD-OprJ, an RND-type multidrug efflux pump, due to the NfxB mutation. In contrast, exposure to gentamicin followed by ciprofloxacin resulted in more mutations in DNA gyrase. These results suggest that the type of quinolone resistance mechanism is related to the frequency of MDRP and that the risk of MDRP incidence is highly dependent on the order of exposure to gentamicin and ciprofloxacin.
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Affiliation(s)
- Nami Yasuda
- Department of Microbiology, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, 1-1-1, Tsushima-Naka, Kita-ku, Okayama, 700-8530, Japan
| | - Tomoko Fujita
- Department of Microbiology, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, 1-1-1, Tsushima-Naka, Kita-ku, Okayama, 700-8530, Japan
| | - Takahiro Fujioka
- Department of Microbiology, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, 1-1-1, Tsushima-Naka, Kita-ku, Okayama, 700-8530, Japan
| | - Mei Tagawa
- Department of Microbiology, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, 1-1-1, Tsushima-Naka, Kita-ku, Okayama, 700-8530, Japan
| | - Naoki Kohira
- Department of Microbiology, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, 1-1-1, Tsushima-Naka, Kita-ku, Okayama, 700-8530, Japan
| | - Kensho Torimaru
- Department of Microbiology, Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3, Kasumi, Minami-ku, Hiroshima, 734-8553, Japan
| | - Sumiko Shiota
- Department of Molecular Biology, School of Pharmacy, Shujitsu University, 1-6-1 Nishigawara, Naka-ku, Okayama, 703-8516, Japan
| | - Takanori Kumagai
- Department of Microbiology, Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3, Kasumi, Minami-ku, Hiroshima, 734-8553, Japan
| | - Daichi Morita
- Department of Microbiology, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, 1-1-1, Tsushima-Naka, Kita-ku, Okayama, 700-8530, Japan
- Department of Microbiology, Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3, Kasumi, Minami-ku, Hiroshima, 734-8553, Japan
| | - Wakano Ogawa
- Department of Microbiology, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, 1-1-1, Tsushima-Naka, Kita-ku, Okayama, 700-8530, Japan
- Department of Microbiology and Biochemistry, Daiichi University of Pharmacy, 22-1, Tamagawa-Machi, Minami-ku, Fukuoka, 815-8511, Japan
| | - Tomofusa Tsuchiya
- Department of Microbiology, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, 1-1-1, Tsushima-Naka, Kita-ku, Okayama, 700-8530, Japan
| | - Teruo Kuroda
- Department of Microbiology, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, 1-1-1, Tsushima-Naka, Kita-ku, Okayama, 700-8530, Japan.
- Department of Microbiology, Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3, Kasumi, Minami-ku, Hiroshima, 734-8553, Japan.
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Hafiz TA, Bin Essa EA, Alharbi SR, Alyami AS, Alkudmani ZS, Mubaraki MA, Alturki NA, Alotaibi F. Epidemiological, Microbiological, and Clinical Characteristics of Multi-Resistant Pseudomonas aeruginosa Isolates in King Fahad Medical City, Riyadh, Saudi Arabia. Trop Med Infect Dis 2023; 8:tropicalmed8040205. [PMID: 37104331 PMCID: PMC10145365 DOI: 10.3390/tropicalmed8040205] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 03/27/2023] [Accepted: 03/28/2023] [Indexed: 04/03/2023] Open
Abstract
Increasing rates of serious multi-drug resistant (MDR) Pseudomonas aeruginosa infections have been reported globally, including in Saudi Arabia. This retrospective study investigates the epidemiological, microbiological, and clinical characteristics of multi-resistant P. aeruginosa (n3579 clinical isolates) in King Fahad Medical City, Riyadh, Saudi Arabia (2019–2021). Information on antimicrobial susceptibility and medical history was collected from the hospital database. P. aeruginosa infections occurred in 55.6% of males and 44.4% of females, and P. aeruginosa was more prevalent in children than in adults. Our analysis showed that P. aeruginosa had the highest sensitivity to amikacin (92.6%) and greatest resistance to aztreonam (29.8%), imipenem (29.5%), ceftazidime (26.1%), meropenem (25.6%), and cefepime (24.3%). MDR and extensively drug resistant (XDR) strains were more prevalent in male than female patients. Female patients showed higher rates of infection with pan-drug resistant (PDR) strains. Respiratory samples contained the majority of resistant isolates. Septic shock and liver disease were strongly correlated with mortality in the ICU patient group after analysing the relative risk associated with mortality. Our study emphasises the threat of multi-resistant P. aeruginosa in Saudi Arabia (and potentially the Middle East) and highlights important sources and contexts of infection that inhibit its effective control and clinical management.
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Affiliation(s)
- Taghreed A. Hafiz
- Clinical Laboratory Sciences Department, College of Applied Medical Sciences, King Saud University, Riyadh 12372, Saudi Arabia
- Correspondence: ; Tel.: +966-11-805-2575
| | - Eman A. Bin Essa
- Clinical Laboratory Sciences Department, College of Applied Medical Sciences, King Saud University, Riyadh 12372, Saudi Arabia
| | - Sarah R. Alharbi
- Clinical Laboratory Sciences Department, College of Applied Medical Sciences, King Saud University, Riyadh 12372, Saudi Arabia
| | - Ahmed S. Alyami
- Pathology and Clinical Laboratory Medicine, King Fahad Medical City, Riyadh 11525, Saudi Arabia
| | - Zeina S. Alkudmani
- Clinical Laboratory Sciences Department, College of Applied Medical Sciences, King Saud University, Riyadh 12372, Saudi Arabia
| | - Murad A. Mubaraki
- Clinical Laboratory Sciences Department, College of Applied Medical Sciences, King Saud University, Riyadh 12372, Saudi Arabia
| | - Norah A. Alturki
- Clinical Laboratory Sciences Department, College of Applied Medical Sciences, King Saud University, Riyadh 12372, Saudi Arabia
| | - Fawzia Alotaibi
- Pathology Department, College of Medicine, King Saud University, Riyadh 12372, Saudi Arabia
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14
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Food for Thought: Proteomics for Meat Safety. Life (Basel) 2023; 13:life13020255. [PMID: 36836616 PMCID: PMC9966529 DOI: 10.3390/life13020255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 01/13/2023] [Accepted: 01/14/2023] [Indexed: 01/18/2023] Open
Abstract
Foodborne bacteria interconnect food and human health. Despite significant progress in food safety regulation, bacterial contamination is still a serious public health concern and the reason for significant commercial losses. The screening of the microbiome in meals is one of the main aspects of food production safety influencing the health of the end-consumers. Our research provides an overview of proteomics findings in the field of food safety made over the last decade. It was believed that proteomics offered an accurate snapshot of the complex networks of the major biological machines called proteins. The proteomic methods for the detection of pathogens were armed with bioinformatics algorithms, allowing us to map the data onto the genome and transcriptome. The mechanisms of the interaction between bacteria and their environment were elucidated with unprecedented sensitivity, specificity, and depth. Using our web-based tool ScanBious for automated publication analysis, we analyzed over 48,000 scientific articles on antibiotic and disinfectant resistance and highlighted the benefits of proteomics for the food safety field. The most promising approach to studying safety in food production is the combination of classical genomic and metagenomic approaches and the advantages provided by proteomic methods with the use of panoramic and targeted mass spectrometry.
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15
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Comparison of Virulence-Factor-Encoding Genes and Genotype Distribution amongst Clinical Pseudomonas aeruginosa Strains. Int J Mol Sci 2023; 24:ijms24021269. [PMID: 36674786 PMCID: PMC9863696 DOI: 10.3390/ijms24021269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 12/29/2022] [Accepted: 01/04/2023] [Indexed: 01/11/2023] Open
Abstract
Pseudomonas aeruginosa is an opportunistic pathogen encoding several virulence factors in its genome, which is well-known for its ability to cause severe and life-threatening infections, particularly among cystic fibrosis patients. The organism is also a major cause of nosocomial infections, mainly affecting patients with immune deficiencies and burn wounds, ventilator-assisted patients, and patients affected by other malignancies. The extensively reported emergence of multidrug-resistant (MDR) P. aeruginosa strains poses additional challenges to the management of infections. The aim of this study was to compare the incidence rates of selected virulence-factor-encoding genes and the genotype distribution amongst clinical multidrug-sensitive (MDS) and MDR P. aeruginosa strains. The study involved 74 MDS and 57 MDR P. aeruginosa strains and the following virulence-factor-encoding genes: lasB, plC H, plC N, exoU, nan1, pilA, and pilB. The genotype distribution, with respect to the antimicrobial susceptibility profiles of the strains, was also analyzed. The lasB and plC N genes were present amongst several P. aeruginosa strains, including all the MDR P. aeruginosa, suggesting that their presence might be used as a marker for diagnostic purposes. A wide variety of genotype distributions were observed among the investigated isolates, with the MDS and MDR strains exhibiting, respectively, 18 and 9 distinct profiles. A higher prevalence of genes determining the virulence factors in the MDR strains was observed in this study, but more research is needed on the prevalence and expression levels of these genes in additional MDR strains.
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New Variants of Pseudomonas aeruginosa High-Risk Clone ST233 Associated with an Outbreak in a Mexican Paediatric Hospital. Microorganisms 2022; 10:microorganisms10081533. [PMID: 36013951 PMCID: PMC9414371 DOI: 10.3390/microorganisms10081533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 07/23/2022] [Accepted: 07/23/2022] [Indexed: 02/01/2023] Open
Abstract
Recent multidrug resistance in Pseudomonas aeruginosa has favoured the adaptation and dissemination of worldwide high-risk strains. In June 2018, 15 P. aeruginosa strains isolated from patients and a contaminated multi-dose meropenem vial were characterized to assess their association to an outbreak in a Mexican paediatric hospital. The strains were characterized by antibiotic susceptibility profiling, virulence factors’ production, and biofilm formation. The clonal relationship among isolates was determined with pulse-field gel electrophoresis (PFGE) and multi-locus sequence typing (MLST) sequencing. Repressor genes for the MexAB-OprM efflux pump were sequenced for haplotype identification. Of the strains, 60% were profiled as extensively drug-resistant (XDR), 33% as multidrug-resistant (MDR), and 6.6% were classified as sensitive (S). All strains presented intermediate resistance to colistin, and 80% were sensitive to aztreonam. Pyoverdine was the most produced virulence factor. The PFGE technique was performed for the identification of the outbreak, revealing eight strains with the same electrophoretic pattern. ST235 and ten new sequence types (STs) were identified, all closely related to ST233. ST3241 predominated in 26.66% of the strains. Twenty-five synonymous and seventeen nonsynonymous substitutions were identified in the regulatory genes of the MexAB-OprM efflux pump, and nalC was the most variable gene. Six different haplotypes were identified. Strains from the outbreak were metallo-β-lactamases and phylogenetically related to the high-risk clone ST233.
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Comparison of Ceftolozane/Tazobactam Infusion Regimens in a Hollow-Fiber Infection Model against Extensively Drug-Resistant Pseudomonas aeruginosa Isolates. Microbiol Spectr 2022; 10:e0089222. [PMID: 35695526 PMCID: PMC9241897 DOI: 10.1128/spectrum.00892-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
The aim of this study was to compare the efficacy of intermittent (1-h), extended (4-h), and continuous ceftolozane-tazobactam (C/T) infusion against three extensively drug-resistant (XDR) sequence type (ST) 175 P. aeruginosa isolates with different susceptibilities to C/T (MIC = 2 to 16 mg/L) in a 7-day hollow-fiber infection model (HFIM). C/T in continuous infusion achieved the largest reduction in total number of bacterial colonies in the overall treatment arms for both C/T-susceptible and -resistant isolates. It was also the only regimen with bactericidal activity against all three isolates. These data suggest that continuous C/T infusion should be considered a potential treatment for infections caused by XDR P. aeruginosa isolates, including nonsusceptible ones. Proper use of C/T dosing regimens may lead to better clinical management of XDR P. aeruginosa infections. IMPORTANCE Ceftolozane-tazobactam (C/T) is an antipseudomonal antibiotic with a high clinical impact in treating infection caused by extensively drug-resistant (XDR) Pseudomonas aeruginosa isolates, but resistance is emerging. Given its time-dependent behavior, C/T continuous infusion can improve exposure and therefore the pharmacokinetic/pharmacodynamic target attainment. We compared the efficacy of intermittent, extended, and continuous C/T infusion against three XDR ST175 P. aeruginosa isolates with different C/T MICs by means of an in vitro dynamic hollow-fiber model. We demonstrated that C/T in continuous infusion achieved the largest reduction in bacterial density in the overall treatment arms for both susceptible and resistant isolates. It was also the only regimen with bactericidal activity against all three isolates. Through this study, we want to demonstrate that developing individually tailored antimicrobial treatments is becoming essential. Our results support the role of C/T level monitoring and of dose adjustments for better clinical management and outcomes.
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Royal Jelly as a Nutraceutical Natural Product with a Focus on Its Antibacterial Activity. Pharmaceutics 2022; 14:pharmaceutics14061142. [PMID: 35745715 PMCID: PMC9227439 DOI: 10.3390/pharmaceutics14061142] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 05/20/2022] [Accepted: 05/25/2022] [Indexed: 02/06/2023] Open
Abstract
Royal jelly (RJ) is one of the most valued natural products and is known for its health-promoting properties. Due to its therapeutic effects, it has been used in medicine since antiquity. Nowadays, several studies indicate that RJ acts as a powerful antimicrobial agent. Indeed, researchers shed light on its antioxidant and anticancer activity. RJ’s biological properties are related to its bioactive compounds, such as proteins, peptides, phenolic, and fatty acids. The aim of this review is to highlight recent findings on RJ’s main bioactive compounds correlated with its health-promoting properties. The available literature suggests that these bioactive compounds can be used as an alternative approach in order to enhance human health. Moreover, throughout this paper, we underline the prominent antibacterial effect of RJ against several target bacterial strains. In addition, we briefly discuss other therapeutic activities, such as antioxidative and anticancer effects, of this outstanding natural product.
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Koçak E, Nigiz Ş, Özkan E, Erdoğan Kablan S, Hazirolan G, Nemutlu E, Kır S, Sağıroğlu M, Özkul C. Exometabolomic Analysis of Susceptible and Multi-Drug Resistant Pseudomonas aeruginosa. Lett Appl Microbiol 2022; 75:234-242. [PMID: 35419823 DOI: 10.1111/lam.13719] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Revised: 03/10/2022] [Accepted: 04/01/2022] [Indexed: 11/30/2022]
Abstract
Multidrug resistant (MDR) Pseudomonas aeruginosa strains have recently become one of the major public health concerns worldwide leading to difficulties in selecting appropriate antibiotic treatment. Thus, it is important to elucidate the characteristics of MDR isolates. Herein, we aimed to determine the unique exometabolome profile of P. aeruginosa clinical isolates in monocultures that comprise high resistance to multiple antibiotics, and compare the differential metabolite profiles obtained from susceptible isolates by using GC/MS. Our results showed that partial least square-discriminant analysis (PLS-DA) score plot clearly discriminated the MDR and susceptible isolates indicating the altered exometabolite profiles, and highlighted the significantly enriched levels of trehalose and glutamic acid in MDR isolates. Expression of trehalose synthase (treS) was also 1.5 fold higher in MDR isolates, relatively to susceptible isolates. Overall, our study provides insights into the distinct footprints of MDR P. aeruginosa isolates in mono-culture.
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Affiliation(s)
- Engin Koçak
- Department of Analytical Chemistry, Faculty of Gulhane Pharmacy, Health Sciences University, Ankara, Turkey
| | - Şeyma Nigiz
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Hacettepe University, Ankara, Turkey
| | - Ece Özkan
- Department of Analytical Chemistry, Faculty of Pharmacy, Başkent University, Ankara, Turkey
| | - Sevilay Erdoğan Kablan
- Department of Analytical Chemistry, Faculty of Pharmacy, Hacettepe University, Ankara, Turkey
| | - Gülşen Hazirolan
- Department of Clinical Microbiology, Faculty of Medicine, Hacettepe University, Ankara, Turkey
| | - Emirhan Nemutlu
- Department of Analytical Chemistry, Faculty of Pharmacy, Hacettepe University, Ankara, Turkey
| | - Sedef Kır
- Department of Analytical Chemistry, Faculty of Pharmacy, Hacettepe University, Ankara, Turkey
| | - Meral Sağıroğlu
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Hacettepe University, Ankara, Turkey
| | - Ceren Özkul
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Hacettepe University, Ankara, Turkey
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Oliveira Monteiro LM, Saraiva JP, Brizola Toscan R, Stadler PF, Silva-Rocha R, Nunes da Rocha U. PredicTF: prediction of bacterial transcription factors in complex microbial communities using deep learning. ENVIRONMENTAL MICROBIOME 2022; 17:7. [PMID: 35135629 PMCID: PMC8822659 DOI: 10.1186/s40793-021-00394-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 12/03/2021] [Indexed: 06/14/2023]
Abstract
BACKGROUND Transcription factors (TFs) are proteins controlling the flow of genetic information by regulating cellular gene expression. A better understanding of TFs in a bacterial community context may open novel revenues for exploring gene regulation in ecosystems where bacteria play a key role. Here we describe PredicTF, a platform supporting the prediction and classification of novel bacterial TF in single species and complex microbial communities. PredicTF is based on a deep learning algorithm. RESULTS To train PredicTF, we created a TF database (BacTFDB) by manually curating a total of 11,961 TF distributed in 99 TF families. Five model organisms were used to test the performance and the accuracy of PredicTF. PredicTF was able to identify 24-62% of the known TFs with an average precision of 88% in our five model organisms. We demonstrated PredicTF using pure cultures and a complex microbial community. In these demonstrations, we used (meta)genomes for TF prediction and (meta)transcriptomes for determining the expression of putative TFs. CONCLUSION PredicTF demonstrated high accuracy in predicting transcription factors in model organisms. We prepared the pipeline to be easily implemented in studies profiling TFs using (meta)genomes and (meta)transcriptomes. PredicTF is an open-source software available at https://github.com/mdsufz/PredicTF .
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Affiliation(s)
- Lummy Maria Oliveira Monteiro
- Helmholtz Center for Environmental Research (UFZ), Leipzig, Germany
- Bioinformatics Group, Institute of Computer Science, Universität Leipzig, Leipzig, Germany
- Ribeirão Preto Medical School (FMRP), University of São Paulo (USP), Ribeirão Prêto, Brazil
| | | | | | - Peter F. Stadler
- Bioinformatics Group, Institute of Computer Science, Universität Leipzig, Leipzig, Germany
| | - Rafael Silva-Rocha
- Ribeirão Preto Medical School (FMRP), University of São Paulo (USP), Ribeirão Prêto, Brazil
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Contribution of Governance and Socioeconomic Factors to the P. aeruginosa MDR in Europe. Antibiotics (Basel) 2022; 11:antibiotics11020212. [PMID: 35203815 PMCID: PMC8868180 DOI: 10.3390/antibiotics11020212] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Revised: 11/19/2021] [Accepted: 01/05/2022] [Indexed: 12/20/2022] Open
Abstract
This work aims to explain the behavior of the multi-drug resistance (MDR) percentage of Pseudomonas aeruginosa in Europe, through multivariate statistical analysis and machine learning validation, using data from the European Antimicrobial Resistance Surveillance System, the World Health Organization, and the World Bank. We ran a multidimensional data panel regression analysis and used machine learning techniques to validate a pooling panel data case. The results of our analysis showed that the most important variables explaining the MDR phenomena across European countries are governance variables, such as corruption control and the rule of law. The models proposed in this study showed the complexity of the antibiotic drugs resistance problem. The efforts controlling MDR P. aeruginosa, as a well-known Healthcare-Associated Infection (HCAI), should be focused on solving national governance problems that impact resource distribution, in addition to individual guidelines, such as promoting the appropriate use of antibiotics.
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THYROID GLAND PARENCHYMA MORPHOLOGICAL ABNORMALITIES IN RATS ON THE THIRD DAY AFTER SKIN THERMAL BURNING. WORLD OF MEDICINE AND BIOLOGY 2022. [DOI: 10.26724/2079-8334-2022-3-81-231-235] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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23
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Leontyev АE, Pavlenko IV, Kovalishena ОV, Saperkin NV, Tulupov АА, Beschastnov VV. Application of Phagotherapy in the Treatment of Burn Patients (Review). Sovrem Tekhnologii Med 2021; 12:95-103. [PMID: 34795985 PMCID: PMC8596250 DOI: 10.17691/stm2020.12.3.12] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Indexed: 12/22/2022] Open
Abstract
Treatment of patients with a burn injury is a complex process involving multicomponent multidirectional intensive therapy of the majority of organs and systems damaged by thermal effects on the skin, alternating with repeated surgical interventions aimed at removing nonviable tissues with subsequent plastic closure of wound defects. After the recovery from the burn shock, local infectious complications are considered to be the leading problem that decelerates the process of recovery and is the main cause of lethal outcomes. Since the skin integrity is broken, microorganisms penetrate readily into the internal environment of the human organism resulting in a septic state with multiple organ failure. A widespread and often uncontrollable use of antibacterial drugs in medical practice has led to the emergence of multiple drug resistance (MDR) in microorganisms. Introduction of drugs made on the basis of bacteriophages into practice is presently becoming increasingly important. This is confirmed by the growing interest in this field of pharmacology, the development of special programs aimed at studying the processes of phage and bacterial cell interaction. This review presents the main types of bacteria pertaining to MDR pathogens, principles of their classification, and the risk factors for infecting patients. The mechanisms of the selective action of phage particles on a bacterial cell and the possibility of using phage therapy in the treatment of burn injury (experimental and clinical data) based on the analysis of foreign literature are demonstrated as well as new positive properties of phages related to the changes in the macroorganism immune status caused by the interaction with bacteriophage particles.
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Affiliation(s)
- А E Leontyev
- Researcher, Group for Thermal Trauma Study, University Clinic; Privolzhsky Research Medical University, 10/1 Minin and Pozharsky Square, Nizhny Novgorod, 603005, Russia
| | - I V Pavlenko
- Junior Researcher, Group for Thermal Trauma Study, University Clinic; Privolzhsky Research Medical University, 10/1 Minin and Pozharsky Square, Nizhny Novgorod, 603005, Russia
| | - О V Kovalishena
- Professor, Head of the Department of Epidemiology, Microbiology, and Evidence-Based Medicine; Privolzhsky Research Medical University, 10/1 Minin and Pozharsky Square, Nizhny Novgorod, 603005, Russia
| | - N V Saperkin
- Associate Professor, Department of Epidemiology, Microbiology, and Evidence-Based Medicine
| | - А А Tulupov
- Junior Researcher, Group for Thermal Trauma Study, University Clinic; Privolzhsky Research Medical University, 10/1 Minin and Pozharsky Square, Nizhny Novgorod, 603005, Russia
| | - V V Beschastnov
- Researcher, Group for Thermal Trauma Study, University Clinic Privolzhsky Research Medical University, 10/1 Minin and Pozharsky Square, Nizhny Novgorod, 603005, Russia
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24
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Montero MM, Domene-Ochoa S, López-Causapé C, Luque S, Sorlí L, Campillo N, Padilla E, Prim N, Ferrer-Alapont L, Angulo-Brunet A, Grau S, Oliver A, Horcajada JP. Impact of ceftolozane/tazobactam concentrations in continuous infusion against extensively drug-resistant Pseudomonas aeruginosa isolates in a hollow-fiber infection model. Sci Rep 2021; 11:22178. [PMID: 34773066 PMCID: PMC8589991 DOI: 10.1038/s41598-021-01784-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 11/03/2021] [Indexed: 11/20/2022] Open
Abstract
Ceftolozane/tazobactam (C/T) has emerged as a potential agent for the treatment of extensively drug-resistant (XDR) Pseudomonas aeruginosa infections. As it is a time-dependent antimicrobial, prolonged infusion may help achieve pharmacokinetic/pharmacodynamic (PK/PD) targets. To compare alternative steady-state concentrations (Css) of C/T in continuous infusion (CI) against three XDR P. aeruginosa ST175 isolates with C/T minimum inhibitory concentration (MIC) values of 2 to 16 mg/L in a hollow-fiber infection model (HFIM). Duplicate 10-day HFIM assays were performed to evaluate Css of C/T in CI: one compared 20 and 45 mg/L against the C/T-susceptible isolate while the other compared 45 and 80 mg/L against the two C/T-non-susceptible isolates. C/T resistance emerged when C/T-susceptible isolate was treated with C/T in CI at a Css of 20 mg/L; which showed a deletion in the gene encoding AmpC β-lactamase. The higher dosing regimen (80 mg/L) showed a slight advantage in effectiveness. The higher dosing regimen has the greatest bactericidal effect, regardless of C/T MIC. Exposure to the suboptimal Css of 20 mg/L led to the emergence of C/T resistance in the susceptible isolate. Antimicrobial regimens should be optimized through C/T levels monitoring and dose adjustments to improve clinical management.
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Affiliation(s)
- María M Montero
- Infectious Diseases Service, Hospital del Mar, Infectious Pathology and Antimicrobials Research Group (IPAR), Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), Universitat Autònoma de Barcelona (UAB), CEXS-Universitat Pompeu Fabra, Passeig Marítim 25-29, 08003, Barcelona, Spain.
| | - Sandra Domene-Ochoa
- Infectious Diseases Service, Hospital del Mar, Infectious Pathology and Antimicrobials Research Group (IPAR), Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), Universitat Autònoma de Barcelona (UAB), CEXS-Universitat Pompeu Fabra, Passeig Marítim 25-29, 08003, Barcelona, Spain
| | - Carla López-Causapé
- Servicio de Microbiología y Unidad de Investigación, Hospital Son Espases, IdISBa, Palma de Mallorca, Spain
| | - Sonia Luque
- Infectious Diseases Service, Hospital del Mar, Infectious Pathology and Antimicrobials Research Group (IPAR), Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), Universitat Autònoma de Barcelona (UAB), CEXS-Universitat Pompeu Fabra, Passeig Marítim 25-29, 08003, Barcelona, Spain.,Pharmacy Service, Hospital del Mar, Barcelona, Spain
| | - Luisa Sorlí
- Infectious Diseases Service, Hospital del Mar, Infectious Pathology and Antimicrobials Research Group (IPAR), Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), Universitat Autònoma de Barcelona (UAB), CEXS-Universitat Pompeu Fabra, Passeig Marítim 25-29, 08003, Barcelona, Spain
| | | | | | - Núria Prim
- Laboratori de Referència de Catalunya, Barcelona, Spain
| | - Lorena Ferrer-Alapont
- Infectious Diseases Service, Hospital del Mar, Infectious Pathology and Antimicrobials Research Group (IPAR), Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), Universitat Autònoma de Barcelona (UAB), CEXS-Universitat Pompeu Fabra, Passeig Marítim 25-29, 08003, Barcelona, Spain
| | - Ariadna Angulo-Brunet
- Psychology and Education Science Studies, Universitat Oberta de Catalunya, Barcelona, Spain
| | - Santiago Grau
- Infectious Diseases Service, Hospital del Mar, Infectious Pathology and Antimicrobials Research Group (IPAR), Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), Universitat Autònoma de Barcelona (UAB), CEXS-Universitat Pompeu Fabra, Passeig Marítim 25-29, 08003, Barcelona, Spain.,Pharmacy Service, Hospital del Mar, Barcelona, Spain
| | - Antonio Oliver
- Servicio de Microbiología y Unidad de Investigación, Hospital Son Espases, IdISBa, Palma de Mallorca, Spain
| | - Juan P Horcajada
- Infectious Diseases Service, Hospital del Mar, Infectious Pathology and Antimicrobials Research Group (IPAR), Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), Universitat Autònoma de Barcelona (UAB), CEXS-Universitat Pompeu Fabra, Passeig Marítim 25-29, 08003, Barcelona, Spain
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25
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Ham SY, Kim HS, Jo MJ, Lee JH, Byun Y, Ko GJ, Park HD. Combined Treatment of 6-Gingerol Analog and Tobramycin for Inhibiting Pseudomonas aeruginosa Infections. Microbiol Spectr 2021; 9:e0019221. [PMID: 34704784 PMCID: PMC8549756 DOI: 10.1128/spectrum.00192-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 09/10/2021] [Indexed: 11/20/2022] Open
Abstract
Pseudomonas aeruginosa is a ubiquitous human pathogen that causes severe infections. Although antibiotics, such as tobramycin, are currently used for infection therapy, their antibacterial activity has resulted in the emergence of multiple antibiotic-resistant bacteria. The 6-gingerol analog, a structural derivative of the main component of ginger, is a quorum sensing (QS) inhibitor. However, it has a lower biofilm inhibitory activity than antibiotics and the possibility to cause toxicity in humans. Therefore, novel and more effective approaches for decreasing dosing concentration and increasing biofilm inhibitory activity are required to alleviate P. aeruginosa infections. In this study, a 6-gingerol analog was combined with tobramycin to treat P. aeruginosa infections. The combined treatment of 6-gingerol analog and tobramycin showed strong inhibitory activities on biofilm formation and the production of QS-related virulence factors of P. aeruginosa compared to single treatments. Furthermore, the combined treatment alleviated the infectivity of P. aeruginosa in an insect model using Tenebrio molitor larvae without inducing any cytotoxic effects in human lung epithelial cells. The 6-gingerol analog showed these inhibitory activities at much lower concentrations when used in combination with tobramycin. Adjuvant effects were observed through increased QS-disrupting processes rather than through antibacterial action. In particular, improved RhlR inactivation by this combination is a possible target for therapeutic development in LasR-independent chronic infections. Therefore, the combined treatment of 6-gingerol analog and tobramycin may be considered an effective method for treating P. aeruginosa infections. IMPORTANCE Pseudomonas aeruginosa is a pathogen that causes various infectious diseases through quorum-sensing regulation. Although antibiotics are mainly used to treat P. aeruginosa infections, they cause the emergence of resistant bacteria in humans. To compensate for the disadvantages of antibiotics and increase their effectiveness, natural products were used in combination with antibiotics in this study. We discovered that combined treatment with 6-gingerol analog from naturally-derived ginger substances and tobramycin resulted in more effective reductions of biofilm formation and virulence factor production in P. aeruginosa than single treatments. Our findings support the notion that when 6-gingerol analog is combined with tobramycin, the effects of the analog can be exerted at much lower concentrations. Furthermore, its improved LasR-independent RhlR inactivation may serve as a key target for therapeutic development in chronic infections. Therefore, the combined treatment of 6-gingerol analog and tobramycin is suggested as a novel alternative for treating P. aeruginosa infections.
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Affiliation(s)
- So-Young Ham
- School of Civil, Environmental and Architectural Engineering, Korea University, Seoul, Republic of Korea
| | - Han-Shin Kim
- Korean Peninsula Infrastructure Cooperation Team, Korea Institute of Civil Engineering and Building Technology (KICT), Goyang-si, Gyeonggi-do, Republic of Korea
| | - Min Jee Jo
- Department of Internal Medicine, College of Medicine, Korea University, Seoul, Republic of Korea
| | - Jeong-Hoon Lee
- School of Civil, Environmental and Architectural Engineering, Korea University, Seoul, Republic of Korea
| | - Youngjoo Byun
- College of Pharmacy, Korea University, Sejong, Republic of Korea
- Biomedical Research Center, Korea University Guro Hospital, Seoul, Republic of Korea
| | - Gang-Jee Ko
- Department of Internal Medicine, College of Medicine, Korea University, Seoul, Republic of Korea
| | - Hee-Deung Park
- School of Civil, Environmental and Architectural Engineering, Korea University, Seoul, Republic of Korea
- KU-KIST Graduate School of Converging Science and Technology, Korea University, Seoul, Republic of Korea
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Mancuso G, Midiri A, Gerace E, Biondo C. Bacterial Antibiotic Resistance: The Most Critical Pathogens. Pathogens 2021; 10. [PMID: 34684258 DOI: 10.3390/pathogens10101310/s1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 10/02/2021] [Accepted: 10/08/2021] [Indexed: 05/20/2023] Open
Abstract
Antibiotics have made it possible to treat bacterial infections such as meningitis and bacteraemia that, prior to their introduction, were untreatable and consequently fatal. Unfortunately, in recent decades overuse and misuse of antibiotics as well as social and economic factors have accelerated the spread of antibiotic-resistant bacteria, making drug treatment ineffective. Currently, at least 700,000 people worldwide die each year due to antimicrobial resistance (AMR). Without new and better treatments, the World Health Organization (WHO) predicts that this number could rise to 10 million by 2050, highlighting a health concern not of secondary importance. In February 2017, in light of increasing antibiotic resistance, the WHO published a list of pathogens that includes the pathogens designated by the acronym ESKAPE (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species) to which were given the highest "priority status" since they represent the great threat to humans. Understanding the resistance mechanisms of these bacteria is a key step in the development of new antimicrobial drugs to tackle drug-resistant bacteria. In this review, both the mode of action and the mechanisms of resistance of commonly used antimicrobials will be examined. It also discusses the current state of AMR in the most critical resistant bacteria as determined by the WHO's global priority pathogens list.
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Affiliation(s)
- Giuseppe Mancuso
- Department of Human Pathology, University of Messina, 98125 Messina, Italy
| | - Angelina Midiri
- Department of Human Pathology, University of Messina, 98125 Messina, Italy
| | | | - Carmelo Biondo
- Department of Human Pathology, University of Messina, 98125 Messina, Italy
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27
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Mancuso G, Midiri A, Gerace E, Biondo C. Bacterial Antibiotic Resistance: The Most Critical Pathogens. Pathogens 2021; 10:pathogens10101310. [PMID: 34684258 PMCID: PMC8541462 DOI: 10.3390/pathogens10101310] [Citation(s) in RCA: 293] [Impact Index Per Article: 97.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 10/02/2021] [Accepted: 10/08/2021] [Indexed: 02/05/2023] Open
Abstract
Antibiotics have made it possible to treat bacterial infections such as meningitis and bacteraemia that, prior to their introduction, were untreatable and consequently fatal. Unfortunately, in recent decades overuse and misuse of antibiotics as well as social and economic factors have accelerated the spread of antibiotic-resistant bacteria, making drug treatment ineffective. Currently, at least 700,000 people worldwide die each year due to antimicrobial resistance (AMR). Without new and better treatments, the World Health Organization (WHO) predicts that this number could rise to 10 million by 2050, highlighting a health concern not of secondary importance. In February 2017, in light of increasing antibiotic resistance, the WHO published a list of pathogens that includes the pathogens designated by the acronym ESKAPE (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species) to which were given the highest "priority status" since they represent the great threat to humans. Understanding the resistance mechanisms of these bacteria is a key step in the development of new antimicrobial drugs to tackle drug-resistant bacteria. In this review, both the mode of action and the mechanisms of resistance of commonly used antimicrobials will be examined. It also discusses the current state of AMR in the most critical resistant bacteria as determined by the WHO's global priority pathogens list.
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Affiliation(s)
- Giuseppe Mancuso
- Department of Human Pathology, University of Messina, 98125 Messina, Italy; (G.M.); (A.M.)
| | - Angelina Midiri
- Department of Human Pathology, University of Messina, 98125 Messina, Italy; (G.M.); (A.M.)
| | | | - Carmelo Biondo
- Department of Human Pathology, University of Messina, 98125 Messina, Italy; (G.M.); (A.M.)
- Correspondence: ; Tel.: +39-090-221-33-22
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28
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Grishin SY, Dzhus UF, Glukhov AS, Selivanova OM, Surin AK, Galzitskaya OV. Identification of Amyloidogenic Regions in Pseudomonas aeruginosa Ribosomal S1 Protein. Int J Mol Sci 2021; 22:ijms22147291. [PMID: 34298910 PMCID: PMC8305250 DOI: 10.3390/ijms22147291] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 06/24/2021] [Accepted: 07/01/2021] [Indexed: 12/13/2022] Open
Abstract
Bacterial S1 protein is a functionally important ribosomal protein. It is a part of the 30S ribosomal subunit and is also able to interact with mRNA and tmRNA. An important feature of the S1 protein family is a strong tendency towards aggregation. To study the amyloidogenic properties of S1, we isolated and purified the recombinant ribosomal S1 protein of Pseudomonas aeruginosa. Using the FoldAmyloid, Waltz, Pasta 2.0, and AGGRESCAN programs, amyloidogenic regions of the protein were predicted, which play a key role in its aggregation. The method of limited proteolysis in combination with high performance liquid chromatography and mass spectrometric analysis of the products, made it possible to identify regions of the S1 protein from P. aeruginosa that are protected from the action of proteinase K, trypsin, and chymotrypsin. Sequences of theoretically predicted and experimentally identified amyloidogenic regions were used to synthesize four peptides, three of which demonstrated the ability to form amyloid-like fibrils, as shown by electron microscopy and fluorescence spectroscopy. The identified amyloidogenic sites can further serve as a basis for the development of new antibacterial peptides against the pathogenic microorganism P. aeruginosa.
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Affiliation(s)
- Sergei Y. Grishin
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia; (S.Y.G.); (U.F.D.); (A.S.G.); (O.M.S.); (A.K.S.)
| | - Ulyana F. Dzhus
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia; (S.Y.G.); (U.F.D.); (A.S.G.); (O.M.S.); (A.K.S.)
| | - Anatoly S. Glukhov
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia; (S.Y.G.); (U.F.D.); (A.S.G.); (O.M.S.); (A.K.S.)
| | - Olga M. Selivanova
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia; (S.Y.G.); (U.F.D.); (A.S.G.); (O.M.S.); (A.K.S.)
| | - Alexey K. Surin
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia; (S.Y.G.); (U.F.D.); (A.S.G.); (O.M.S.); (A.K.S.)
- The Branch of the Institute of Bioorganic Chemistry, Russian Academy of Sciences, 142290 Pushchino, Russia
- State Research Center for Applied Microbiology and Biotechnology, 142279 Obolensk, Russia
| | - Oxana V. Galzitskaya
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia; (S.Y.G.); (U.F.D.); (A.S.G.); (O.M.S.); (A.K.S.)
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, 142290 Pushchino, Russia
- Correspondence:
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Hwang W, Yong JH, Min KB, Lee KM, Pascoe B, Sheppard SK, Yoon SS. Genome-wide association study of signature genetic alterations among pseudomonas aeruginosa cystic fibrosis isolates. PLoS Pathog 2021; 17:e1009681. [PMID: 34161396 PMCID: PMC8274868 DOI: 10.1371/journal.ppat.1009681] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 07/12/2021] [Accepted: 05/31/2021] [Indexed: 12/18/2022] Open
Abstract
Pseudomonas aeruginosa (PA) is an opportunistic pathogen that causes diverse human infections including chronic airway infection in patients with cystic fibrosis (CF). Comparing the genomes of CF and non-CF PA isolates has great potential to identify the genetic basis of pathogenicity. To gain a deeper understanding of PA adaptation in CF airways, we performed a genome-wide association study (GWAS) on 1,001 PA genomes. Genetic variations identified among CF isolates were categorized into (i) alterations in protein-coding regions, either large- or small-scale, and (ii) polymorphic variation in intergenic regions. We introduced each CF-associated genetic alteration into the genome of PAO1, a prototype PA strain, and validated the outcomes experimentally. Loci readily mutated among CF isolates included genes encoding a probable sulfatase, a probable TonB-dependent receptor (PA2332~PA2336), L-cystine transporter (YecS, PA0313), and a probable transcriptional regulator (PA5438). A promoter region of a heme/hemoglobin uptake outer membrane receptor (PhuR, PA4710) was also different between the CF and non-CF isolate groups. Our analysis highlights ways in which the PA genome evolves to survive and persist within the context of chronic CF infection.
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Affiliation(s)
- Wontae Hwang
- Department of Microbiology and Immunology, Seoul, Republic of Korea
- Brain Korea 21 PLUS Project for Medical Sciences, Seoul, Republic of Korea
| | - Ji Hyun Yong
- Department of Microbiology and Immunology, Seoul, Republic of Korea
- Brain Korea 21 PLUS Project for Medical Sciences, Seoul, Republic of Korea
| | - Kyung Bae Min
- Department of Microbiology and Immunology, Seoul, Republic of Korea
- Brain Korea 21 PLUS Project for Medical Sciences, Seoul, Republic of Korea
| | - Kang-Mu Lee
- Department of Microbiology and Immunology, Seoul, Republic of Korea
- Brain Korea 21 PLUS Project for Medical Sciences, Seoul, Republic of Korea
| | - Ben Pascoe
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, United Kingdom
| | - Samuel K Sheppard
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, United Kingdom
| | - Sang Sun Yoon
- Department of Microbiology and Immunology, Seoul, Republic of Korea
- Brain Korea 21 PLUS Project for Medical Sciences, Seoul, Republic of Korea
- Institute for Immunology and Immunological Diseases, Seoul, Republic of Korea
- Severance Biomedical Science Institute, Yonsei University College of Medicine, Seoul, Republic of Korea
- * E-mail:
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Overexpression of the MexXY Multidrug Efflux System Correlates with Deficient Pyoverdine Production in Pseudomonas aeruginosa. Antibiotics (Basel) 2021; 10:antibiotics10060658. [PMID: 34073068 PMCID: PMC8226967 DOI: 10.3390/antibiotics10060658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 05/29/2021] [Accepted: 05/31/2021] [Indexed: 12/02/2022] Open
Abstract
Multidrug-resistant Pseudomonas aeruginosa poses a serious problem due to hospital- and healthcare-associated infections. A major drug resistance mechanism of P. aeruginosa involves active efflux via resistance nodulation cell division (RND)-type multidrug efflux pumps of which MexXY is increasingly recognized as a primary determinant of aminoglycoside resistance in P. aeruginosa. MexXY overexpression is often observed in drug-resistant P. aeruginosa clinical isolates. MexXY deficiency increased pyoverdine production in all four P. aeruginosa strains we tested. MexXY-overproducing multidrug-resistant P. aeruginosa PA7 exhibited the greatest effect among the strains. Complementation with a MexXY-expressing plasmid restored low-level pyoverdine production in a MexXY-deficient P. aeruginosa mutant from PA7, indicating that MexXY expression decreases pyoverdine production. Because P. aeruginosa produces pyoverdine to acquire iron, MexXY-deficient mutants might be more susceptible to iron deficiency than MexXY-producing strains or might require extra iron. High-risk clones of multidrug-resistant P. aeruginosa reportedly tend to be MexXY overproducers but defective pyoverdine producers. This study suggests that P. aeruginosa reduces production of a virulence factor after acquiring a drug resistance factor.
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31
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Pseudomonas aeruginosa adaptation and evolution in patients with cystic fibrosis. Nat Rev Microbiol 2021; 19:331-342. [PMID: 33214718 DOI: 10.1038/s41579-020-00477-5] [Citation(s) in RCA: 189] [Impact Index Per Article: 63.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/09/2020] [Indexed: 01/29/2023]
Abstract
Intense genome sequencing of Pseudomonas aeruginosa isolates from cystic fibrosis (CF) airways has shown inefficient eradication of the infecting bacteria, as well as previously undocumented patient-to-patient transmission of adapted clones. However, genome sequencing has limited potential as a predictor of chronic infection and of the adaptive state during infection, and thus there is increasing interest in linking phenotypic traits to the genome sequences. Phenotypic information ranges from genome-wide transcriptomic analysis of patient samples to determination of more specific traits associated with metabolic changes, stress responses, antibiotic resistance and tolerance, biofilm formation and slow growth. Environmental conditions in the CF lung shape both genetic and phenotypic changes of P. aeruginosa during infection. In this Review, we discuss the adaptive and evolutionary trajectories that lead to early diversification and late convergence, which enable P. aeruginosa to succeed in this niche, and we point out how knowledge of these biological features may be used to guide diagnosis and therapy.
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Pérez-Garza J, Franco-Frías E, García-Heredia A, García S, Leon JS, Jaykus LA, Heredia N. The Cantaloupe Farm Environment Has a Diverse Genetic Pool of Antibiotic-Resistance and Virulence Genes. Foodborne Pathog Dis 2021; 18:469-476. [PMID: 33900863 DOI: 10.1089/fpd.2020.2900] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Cantaloupes contaminated with pathogens have led to many high-profile outbreaks and illnesses. Since bacterial virulence genes (VGs) can act in tandem with antibiotic-resistance and mobile genetic elements, there is a need to evaluate these gene reservoirs in fresh produce, such as cantaloupes. The goal of this study was to assess the distribution of antibiotic-resistance, virulence, and mobile genetic elements genes (MGEGs) in cantaloupe farm environments. A total of 200 samples from cantaloupe melons (n = 99), farm workers' hands (n = 66), and production water (n = 35) were collected in México. Each sample was assayed for the presence of 14 antibiotic-resistance genes, 15 VGs, and 5 MGEGs by polymerase chain reaction. Our results indicated that tetracycline (tetA and tetB) (18% of cantaloupe, 45% of hand samples) and sulfonamide (sul1) (30% of cantaloupe, 71% of hand samples) resistance genes were frequently detected. The colistin resistance gene (mcr1) was detected in 10% of cantaloupe and 23% of farm workers' hands. Among VGs, Salmonella genes invA and spiA were the most abundant. There was a significantly higher likelihood of detecting antibiotic-resistance, virulence, and MGEGs on hands compared with water samples. These results demonstrate a diverse pool of antibiotic-resistance and VGs in cantaloupe production.
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Affiliation(s)
- Janeth Pérez-Garza
- Laboratorio de Bioquímica y Genética de Microorganismos, Departamento de Microbiologia e Inmunología, Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, San Nicolas de los Garza, México
| | - Eduardo Franco-Frías
- Laboratorio de Bioquímica y Genética de Microorganismos, Departamento de Microbiologia e Inmunología, Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, San Nicolas de los Garza, México
| | - Alam García-Heredia
- Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst, Massachusetts, USA
| | - Santos García
- Laboratorio de Bioquímica y Genética de Microorganismos, Departamento de Microbiologia e Inmunología, Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, San Nicolas de los Garza, México
| | - Juan S Leon
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, Georgia, USA
| | - Lee-Ann Jaykus
- Department of Food Science, North Carolina State University, Raleigh, North Carolina, USA
| | - Norma Heredia
- Laboratorio de Bioquímica y Genética de Microorganismos, Departamento de Microbiologia e Inmunología, Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, San Nicolas de los Garza, México
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Harada LK, Júnior WB, Silva EC, Oliveira TJ, Moreli FC, Júnior JMO, Tubino M, Vila MMDC, Balcão VM. Bacteriophage-Based Biosensing of Pseudomonas aeruginosa: An Integrated Approach for the Putative Real-Time Detection of Multi-Drug-Resistant Strains. BIOSENSORS-BASEL 2021; 11:bios11040124. [PMID: 33921071 PMCID: PMC8071457 DOI: 10.3390/bios11040124] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 04/03/2021] [Accepted: 04/13/2021] [Indexed: 12/19/2022]
Abstract
During the last decennium, it has become widely accepted that ubiquitous bacterial viruses, or bacteriophages, exert enormous influences on our planet’s biosphere, killing between 4–50% of the daily produced bacteria and constituting the largest genetic diversity pool on our planet. Currently, bacterial infections linked to healthcare services are widespread, which, when associated with the increasing surge of antibiotic-resistant microorganisms, play a major role in patient morbidity and mortality. In this scenario, Pseudomonas aeruginosa alone is responsible for ca. 13–15% of all hospital-acquired infections. The pathogen P. aeruginosa is an opportunistic one, being endowed with metabolic versatility and high (both intrinsic and acquired) resistance to antibiotics. Bacteriophages (or phages) have been recognized as a tool with high potential for the detection of bacterial infections since these metabolically inert entities specifically attach to, and lyse, bacterial host cells, thus, allowing confirmation of the presence of viable cells. In the research effort described herein, three different phages with broad lytic spectrum capable of infecting P. aeruginosa were isolated from environmental sources. The isolated phages were elected on the basis of their ability to form clear and distinctive plaques, which is a hallmark characteristic of virulent phages. Next, their structural and functional stabilization was achieved via entrapment within the matrix of porous alginate, biopolymeric, and bio-reactive, chromogenic hydrogels aiming at their use as sensitive matrices producing both color changes and/or light emissions evolving from a reaction with (released) cytoplasmic moieties, as a bio-detection kit for P. aeruginosa cells. Full physicochemical and biological characterization of the isolated bacteriophages was the subject of a previous research paper.
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Affiliation(s)
- Liliam K. Harada
- PhageLab—Laboratory of Biofilms and Bacteriophages, University of Sorocaba, Sorocaba, SP 18023-000, Brazil; (L.K.H.); (E.C.S.); (T.J.O.); (F.C.M.); (J.M.O.J.); (M.M.D.C.V.)
| | | | - Erica C. Silva
- PhageLab—Laboratory of Biofilms and Bacteriophages, University of Sorocaba, Sorocaba, SP 18023-000, Brazil; (L.K.H.); (E.C.S.); (T.J.O.); (F.C.M.); (J.M.O.J.); (M.M.D.C.V.)
| | - Thais J. Oliveira
- PhageLab—Laboratory of Biofilms and Bacteriophages, University of Sorocaba, Sorocaba, SP 18023-000, Brazil; (L.K.H.); (E.C.S.); (T.J.O.); (F.C.M.); (J.M.O.J.); (M.M.D.C.V.)
| | - Fernanda C. Moreli
- PhageLab—Laboratory of Biofilms and Bacteriophages, University of Sorocaba, Sorocaba, SP 18023-000, Brazil; (L.K.H.); (E.C.S.); (T.J.O.); (F.C.M.); (J.M.O.J.); (M.M.D.C.V.)
| | - José M. Oliveira Júnior
- PhageLab—Laboratory of Biofilms and Bacteriophages, University of Sorocaba, Sorocaba, SP 18023-000, Brazil; (L.K.H.); (E.C.S.); (T.J.O.); (F.C.M.); (J.M.O.J.); (M.M.D.C.V.)
| | - Matthieu Tubino
- Institute of Chemistry, University of Campinas, Campinas, SP 13083-970, Brazil;
| | - Marta M. D. C. Vila
- PhageLab—Laboratory of Biofilms and Bacteriophages, University of Sorocaba, Sorocaba, SP 18023-000, Brazil; (L.K.H.); (E.C.S.); (T.J.O.); (F.C.M.); (J.M.O.J.); (M.M.D.C.V.)
| | - Victor M. Balcão
- PhageLab—Laboratory of Biofilms and Bacteriophages, University of Sorocaba, Sorocaba, SP 18023-000, Brazil; (L.K.H.); (E.C.S.); (T.J.O.); (F.C.M.); (J.M.O.J.); (M.M.D.C.V.)
- Department of Biology and CESAM, University of Aveiro, Campus Universitário de Santiago, P-3810-193 Aveiro, Portugal
- Correspondence: ; Tel.: +55-(15)-2101-7029
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Hosu MC, Vasaikar SD, Okuthe GE, Apalata T. Detection of extended spectrum beta-lactamase genes in Pseudomonas aeruginosa isolated from patients in rural Eastern Cape Province, South Africa. Sci Rep 2021; 11:7110. [PMID: 33782509 PMCID: PMC8007629 DOI: 10.1038/s41598-021-86570-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Accepted: 02/24/2021] [Indexed: 01/01/2023] Open
Abstract
The proliferation of extended spectrum beta-lactamase (ESBL) producing Pseudomonas aeruginosa represent a major public health threat. In this study, we evaluated the antimicrobial resistance patterns of P. aeruginosa strains and characterized the ESBLs and Metallo- β-lactamases (MBL) produced. Strains of P. aeruginosa cultured from patients who attended Nelson Mandela Academic Hospital and other clinics in the four district municipalities of the Eastern Cape between August 2017 and May 2019 were identified; antimicrobial susceptibility testing was carried out against thirteen clinically relevant antibiotics using the BioMérieux VITEK 2 and confirmed by Beckman autoSCAN-4 System. Real-time PCR was done using Roche Light Cycler 2.0 to detect the presence of ESBLs; blaSHV, blaTEM and blaCTX-M genes; and MBLs; blaIMP, blaVIM. Strains of P. aeruginosa demonstrated resistance to wide-ranging clinically relevant antibiotics including piperacillin (64.2%), followed by aztreonam (57.8%), cefepime (51.5%), ceftazidime (51.0%), piperacillin/tazobactam (50.5%), and imipenem (46.6%). A total of 75 (36.8%) multidrug-resistant (MDR) strains were observed of the total pool of isolates. The blaTEM, blaSHV and blaCTX-M was detected in 79.3%, 69.5% and 31.7% isolates (n = 82), respectively. The blaIMP was detected in 1.25% while no blaVIM was detected in any of the strains tested. The study showed a high rate of MDR P. aeruginosa in our setting. The vast majority of these resistant strains carried blaTEM and blaSHV genes. Continuous monitoring of antimicrobial resistance and strict compliance towards infection prevention and control practices are the best defence against spread of MDR P. aeruginosa.
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Affiliation(s)
- Mojisola C Hosu
- Division of Medical Microbiology, Department of Laboratory Medicine and Pathology, Faculty of Health Sciences, Walter Sisulu University and National Health Laboratory Services, Mthatha, Eastern Cape, South Africa
| | - Sandeep D Vasaikar
- Division of Medical Microbiology, Department of Laboratory Medicine and Pathology, Faculty of Health Sciences, Walter Sisulu University and National Health Laboratory Services, Mthatha, Eastern Cape, South Africa
| | - Grace E Okuthe
- Department of Biological and Environmental Sciences, Walter Sisulu University, Mthatha, Eastern Cape, South Africa
| | - Teke Apalata
- Division of Medical Microbiology, Department of Laboratory Medicine and Pathology, Faculty of Health Sciences, Walter Sisulu University and National Health Laboratory Services, Mthatha, Eastern Cape, South Africa.
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Hofmann L, Hirsch M, Ruthstein S. Advances in Understanding of the Copper Homeostasis in Pseudomonas aeruginosa. Int J Mol Sci 2021; 22:2050. [PMID: 33669570 PMCID: PMC7922089 DOI: 10.3390/ijms22042050] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Revised: 02/10/2021] [Accepted: 02/15/2021] [Indexed: 12/12/2022] Open
Abstract
Thirty-five thousand people die as a result of more than 2.8 million antibiotic-resistant infections in the United States of America per year. Pseudomonas aeruginosa (P. aeruginosa) is classified a serious threat, the second-highest threat category of the U.S. Department of Health and Human Services. Among others, the World Health Organization (WHO) encourages the discovery and development of novel antibiotic classes with new targets and mechanisms of action without cross-resistance to existing classes. To find potential new target sites in pathogenic bacteria, such as P. aeruginosa, it is inevitable to fully understand the molecular mechanism of homeostasis, metabolism, regulation, growth, and resistances thereof. P. aeruginosa maintains a sophisticated copper defense cascade comprising three stages, resembling those of public safety organizations. These stages include copper scavenging, first responder, and second responder. Similar mechanisms are found in numerous pathogens. Here we compare the copper-dependent transcription regulators cueR and copRS of Escherichia coli (E. coli) and P. aeruginosa. Further, phylogenetic analysis and structural modelling of mexPQ-opmE reveal that this efflux pump is unlikely to be involved in the copper export of P. aeruginosa. Altogether, we present current understandings of the copper homeostasis in P. aeruginosa and potential new target sites for antimicrobial agents or a combinatorial drug regimen in the fight against multidrug resistant pathogens.
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Affiliation(s)
| | | | - Sharon Ruthstein
- Institute of Nanotechnology and Advanced Materials & Department of Chemistry, Faculty of Exact Sciences, Bar-Ilan University, Ramat-Gan 5290002, Israel; (L.H.); (M.H.)
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Fattah RAFA, Fathy FEZY, Mohamed TAH, Elsayed MS. Effect of chitosan nanoparticles on quorum sensing-controlled virulence factors and expression of LasI and RhlI genes among Pseudomonas aeruginosa clinical isolates. AIMS Microbiol 2021; 7:415-430. [PMID: 35071940 PMCID: PMC8712529 DOI: 10.3934/microbiol.2021025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Accepted: 10/20/2021] [Indexed: 12/25/2022] Open
Abstract
<abstract>
<p>Antibiotic-resistant strains of <italic>Pseudomonas aeruginosa (P. aeruginosa</italic>) pose a major threat for healthcare-associated and community-acquired infections. <italic>P. aeruginosa</italic> is recognized as an opportunistic pathogen using quorum sensing (QS) system to regulate the expression of virulence factors and biofilm development. Thus, meddling with the QS system would give alternate methods of controlling the pathogenicity. This study aimed to assess the inhibitory impact of chitosan nanoparticles (CS-NPs) on <italic>P. aeruginosa</italic> virulence factors regulated by QS (e.g., motility and biofilm formation) and <italic>LasI</italic> and <italic>RhlI</italic> gene expression. Minimum inhibitory concentration (MIC) of CS-NPs against 30 isolates of <italic>P. aeruginosa</italic> was determined. The CS-NPs at sub-MIC were utilized to assess their inhibitory effect on motility, biofilm formation, and the expression levels of <italic>LasI</italic> and <italic>RhlI</italic> genes. CS-NPs remarkably inhibited the tested virulence factors as compared to the controls grown without the nanoparticles. The mean (±SD) diameter of swimming motility was decreased from 3.93 (±1.5) to 1.63 (±1.02) cm, and the mean of the swarming motility was reduced from 3.5 (±1.6) to 1.9 (±1.07) cm. All isolates became non-biofilm producers, and the mean percentage rate of biofilm inhibition was 84.95% (±6.18). Quantitative real-time PCR affirmed the opposition of QS activity by lowering the expression levels of <italic>LasI</italic> and <italic>RhlI</italic> genes; the expression level was decreased by 90- and 100-folds, respectively. In conclusion, the application of CS-NPs reduces the virulence factors significantly at both genotypic and phenotypic levels. These promising results can breathe hope in the fight against resistant <italic>P. aeruginosa</italic> by repressing its QS-regulated virulence factors.</p>
</abstract>
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Thioether-linked dihydropyrrol-2-one analogues as PqsR antagonists against antibiotic resistant Pseudomonas aeruginosa. Bioorg Med Chem 2021; 31:115967. [PMID: 33434766 DOI: 10.1016/j.bmc.2020.115967] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Revised: 12/15/2020] [Accepted: 12/18/2020] [Indexed: 02/07/2023]
Abstract
The Pseudomonas quinolone system (pqs) is one of the key quorum sensing systems in antibiotic-resistant P. aeruginosa and is responsible for the production of virulence factors and biofilm formation. Thus, synthetic small molecules that can target the PqsR (MvfR) receptor can be utilized as quorum sensing inhibitors to treat P. aeruginosa infections. In this study, we report the synthesis of novel thioether-linked dihydropyrrol-2-one (DHP) analogues as PqsR antagonists. Compound 7g containing a 2-mercaptopyridyl linkage effectively inhibited the pqs system with an IC50 of 32 µM in P. aeruginosa PAO1. Additionally, these inhibitors significantly reduced bacterial aggregation and biofilm formation without affecting planktonic growth. The molecular docking study suggest that these inhibitors bind with the ligand binding domain of the MvfR as a competitive antagonist.
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Gene Loss and Acquisition in Lineages of Pseudomonas aeruginosa Evolving in Cystic Fibrosis Patient Airways. mBio 2020; 11:mBio.02359-20. [PMID: 33109761 PMCID: PMC7593970 DOI: 10.1128/mbio.02359-20] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Bacterial airway infections, predominantly caused by P. aeruginosa, are a major cause of mortality and morbidity of CF patients. While short insertions and deletions as well as point mutations occurring during infection are well studied, there is a lack of understanding of how gene loss and acquisition play roles in bacterial adaptation to the human airways. Here, we investigated P. aeruginosa within-host evolution with regard to gene loss and acquisition. We show that during long-term infection P. aeruginosa genomes tend to lose genes, in particular, genes related to virulence. This adaptive strategy allows reduction of the genome size and evasion of the host’s immune response. This knowledge is crucial to understand the basic mutational steps that, on the timescale of years, diversify lineages and adds to the identification of bacterial genetic determinants that have implications for CF disease. Genome analyses have documented that there are differences in gene repertoire between evolutionary distant lineages of the same bacterial species; however, less is known about microevolutionary dynamics of gene loss and acquisition within bacterial lineages as they evolve over years. Here, we analyzed the genomes of 45 Pseudomonas aeruginosa lineages evolving in the lungs of cystic fibrosis (CF) patients to identify genes that are lost or acquired during the first years of infection. On average, lineage genome content changed by 88 genes (range, 0 to 473). Genes were more often lost than acquired, and prophage genes were more variable than bacterial genes. We identified convergent loss or acquisition of the same genes across lineages, suggesting selection for loss and acquisition of certain genes in the host environment. We found that a notable proportion of such genes are associated with virulence; a trait previously shown to be important for adaptation. Furthermore, we also compared the genomes across lineages to show that the within-lineage variable genes (i.e., genes that had been lost or acquired during the infection) often belonged to genomic content not shared across all lineages. In sum, our analysis adds to the knowledge on the pace and drivers of gene loss and acquisition in bacteria evolving over years in a human host environment and provides a basis to further understand how gene loss and acquisition play roles in lineage differentiation and host adaptation.
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Kula BE, Hudson D, Sligl WI. Pseudomonas aeruginosa infection in intensive care: Epidemiology, outcomes, and antimicrobial susceptibilities. JOURNAL OF THE ASSOCIATION OF MEDICAL MICROBIOLOGY AND INFECTIOUS DISEASE CANADA = JOURNAL OFFICIEL DE L'ASSOCIATION POUR LA MICROBIOLOGIE MEDICALE ET L'INFECTIOLOGIE CANADA 2020; 5:130-138. [PMID: 36341317 PMCID: PMC9608728 DOI: 10.3138/jammi-2020-0003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2020] [Accepted: 06/05/2020] [Indexed: 06/16/2023]
Abstract
BACKGROUND Pseudomonas aeruginosa (PA) infection in the intensive care unit (ICU) contributes to substantial mortality. In this study, we describe the epidemiology, antimicrobial susceptibilities, and outcomes of ICU patients with pseudomonal infection. METHODS ICU patients with PA were identified and classified as colonized or infected. Infected patients were reviewed for source, patient characteristics, antimicrobial susceptibilities, appropriateness of empiric antimicrobial therapy, and 30-day mortality. Independent predictors of mortality were identified using multivariable logistic regression. RESULTS One hundred forty (71%) patients with PA were infected. Mean patient age was 55 (SD 18) years; 62% were male. Admission categories included medical (71%), surgical (20%), and trauma or neurological (9%). Mean Acute Physiology and Chronic Health Evaluation (APACHE) II score was 19 (SD 10). One hundred twenty-six (90%) patients were mechanically ventilated, 102 (73%) required vasopressors, and 27 (19%) received renal replacement; 32 (23%) died within 30 days. Infection was nosocomial in 101 (72%) cases. Sources were respiratory (66%), skin-soft tissue (11%), urinary (10%), blood (5%), surgical (5%), gastrointestinal (2%), or unknown (1%). Twenty (14%) isolates were multi-drug resistant; 6 (4%) were extensively drug resistant. Empiric antimicrobial therapy was effective in 97 (69%) cases. Liver disease (adjusted OR [aOR] 6.2, 95% CI 1.5 to 25.7; p = 0.01), malignancy (aOR 5.0, 95% CI 1.5 to 17.3; p = 0.01), and higher APACHE II score (aOR 1.1, 95% CI 1.0 to 1.1; p = 0.02) were independently associated with 30-day mortality. CONCLUSIONS PA infection in ICU is most commonly respiratory and associated with substantial mortality. Existing malignancy, liver disease, and higher APACHE II score were independently associated with mortality.
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Affiliation(s)
- Brittany E Kula
- Division of Internal Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Darren Hudson
- Department of Critical Care Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Wendy I Sligl
- Department of Critical Care Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
- Division of Infectious Diseases, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
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Biogenic Preparation and Characterization of ZnO Nanoparticles from Natural Polysaccharide Azadirachta indica .L. (neem gum) and its Clinical Implications. J CLUST SCI 2020. [DOI: 10.1007/s10876-020-01863-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Malburet C, Leclercq L, Cotte JF, Thiebaud J, Cottet H. Study of Interactions between Antigens and Polymeric Adjuvants in Vaccines by Frontal Analysis Continuous Capillary Electrophoresis. Biomacromolecules 2020; 21:3364-3373. [PMID: 32609507 DOI: 10.1021/acs.biomac.0c00782] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Vaccine adjuvants are used to enhance the immune response induced by antigens that have insufficient immunostimulatory capabilities. The present work aims at developing a frontal analysis continuous capillary electrophoresis (FACCE) methodology for the study of antigen-adjuvant interactions in vaccine products. After method optimization using three cationic model proteins, namely lysozyme, cytochrome c, and ribonuclease A, FACCE was successfully implemented to quantify the free antigen and thus to determine the interaction parameters (stoichiometry and binding constant) between an anionic polymeric adjuvant (polyacrylic acid, SPA09) and a cationic vaccine antigen in development for the treatment for Staphylococcus aureus. The influence of the ionic strength of the medium on the interactions was investigated. A strong dependence of the binding parameters with the ionic strength was observed. The concentration of the polymeric adjuvant was also found to significantly modify the ionic strength of the formulation, the extent of which could be estimated and corrected.
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Affiliation(s)
- Camille Malburet
- IBMM, University of Montpellier, CNRS, ENSCM, Montpellier, France.,Analytical Sciences, Sanofi Pasteur, 1541 Avenue Marcel Mérieux, Marcy-l'Étoile 69280, France
| | - Laurent Leclercq
- IBMM, University of Montpellier, CNRS, ENSCM, Montpellier, France
| | - Jean-François Cotte
- Analytical Sciences, Sanofi Pasteur, 1541 Avenue Marcel Mérieux, Marcy-l'Étoile 69280, France
| | - Jérôme Thiebaud
- Analytical Sciences, Sanofi Pasteur, 1541 Avenue Marcel Mérieux, Marcy-l'Étoile 69280, France
| | - Hervé Cottet
- IBMM, University of Montpellier, CNRS, ENSCM, Montpellier, France
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do Nascimento APB, Medeiros Filho F, Pauer H, Antunes LCM, Sousa H, Senger H, Albano RM, Trindade Dos Santos M, Carvalho-Assef APD, da Silva FAB. Characterization of a SPM-1 metallo-beta-lactamase-producing Pseudomonas aeruginosa by comparative genomics and phenotypic analysis. Sci Rep 2020; 10:13192. [PMID: 32764694 PMCID: PMC7413544 DOI: 10.1038/s41598-020-69944-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 07/16/2020] [Indexed: 11/17/2022] Open
Abstract
Pseudomonas aeruginosa is one of the most common pathogens related to healthcare-associated infections. The Brazilian isolate, named CCBH4851, is a multidrug-resistant clone belonging to the sequence type 277. The antimicrobial resistance mechanisms of the CCBH4851 strain are associated with the presence of the bla\documentclass[12pt]{minimal}
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\begin{document}$$_\text {SPM-1}$$\end{document}SPM-1 gene, encoding a metallo-beta-lactamase, in combination with other exogenously acquired genes. Whole-genome sequencing studies focusing on emerging pathogens are essential to identify key features of their physiology that may lead to the identification of new targets for therapy. Using both Illumina and PacBio sequencing data, we obtained a single contig representing the CCBH4851 genome with annotated features that were consistent with data reported for the species. However, comparative analysis with other Pseudomonas aeruginosa strains revealed genomic differences regarding virulence factors and regulatory proteins. In addition, we performed phenotypic assays that revealed CCBH4851 is impaired in bacterial motilities and biofilm formation. On the other hand, CCBH4851 genome contained acquired genomic islands that carry transcriptional factors, virulence and antimicrobial resistance-related genes. Presence of single nucleotide polymorphisms in the core genome, mainly those located in resistance-associated genes, suggests that these mutations may also influence the multidrug-resistant behavior of CCBH4851. Overall, characterization of Pseudomonas aeruginosa CCBH4851 complete genome revealed the presence of features that strongly relates to the virulence and antibiotic resistance profile of this important infectious agent.
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Affiliation(s)
| | | | - Heidi Pauer
- Centro de Desenvolvimento Tecnológico em Saúde, Fundação Oswaldo Cruz, Rio de Janeiro, 21040-361, Brazil
| | - Luis Caetano Martha Antunes
- Centro de Desenvolvimento Tecnológico em Saúde, Fundação Oswaldo Cruz, Rio de Janeiro, 21040-361, Brazil.,Escola Nacional de Saúde Pública Sergio Arouca, Fundação Oswaldo Cruz, Rio de Janeiro, 21041-210, Brazil
| | - Hério Sousa
- Departamento de Computação, Universidade Federal de São Carlos, São Carlos, 13565-905, Brazil
| | - Hermes Senger
- Departamento de Computação, Universidade Federal de São Carlos, São Carlos, 13565-905, Brazil
| | - Rodolpho Mattos Albano
- Departamento de Bioquímica, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, 21941-909, Brazil
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Dehbashi S, Pourmand MR, Alikhani MY, Asl SS, Arabestani MR. Coordination of las regulated virulence factors with Multidrug-Resistant and extensively drug-resistant in superbug strains of P. aeruginosa. Mol Biol Rep 2020; 47:4131-4143. [PMID: 32474845 DOI: 10.1007/s11033-020-05559-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Accepted: 05/26/2020] [Indexed: 12/21/2022]
Abstract
Successful pathogenicity often resulted from a complicated association between virulence and antibiotic resistance in Pseudomonas aeruginosa infections. Therefore, the current study aimed to investigate the relationship between the las system and antibiotic resistance. Seventy-three (73) P. aeruginosa isolates were collected from burn wounds (26.02%), blood cultures (30.13%), catheters (12.32%), and urine culture (31.50%). Among the 73 collected isolates, 22 isolates were considered as multi-drug resistant (MDR) and 11 isolates as extensively-drug resistant (XDR). Furthermore, phenazines and LasA protease were detected among 21.91% and 32.87% of isolates, respectively. Quantitative real-time PCR assessment of KPC, MBL, and lasI/R indicated that resistance and virulence factors are more expressed in XDR strains than MDR strains. Also, the expression level of KPC and MBL reduced in non-biofilm forming strains. However, increased expression levels of lasI, lasR, and the KPC genes were observed in LasA and LasB protease producing strains. Interestingly, 16 known sequence types (including ST108, ST260, ST217) and three novel STs (ST2452, ST2427, and ST2542) were characterized among the collected isolates, which are related to the virulence and resistance. In MDR-XDR strains, a strong correlation between lasI/R and the variants of antibiotic resistance genes was found. In conclusion, the pathogenicity of P. aeruginosa may increase the prevalence of antibiotic-resistant strains.
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Affiliation(s)
- Sanaz Dehbashi
- Department of Microbiology, Faculty of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Mohammad Reza Pourmand
- Department of Pathobiology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad Yousef Alikhani
- Department of Microbiology, Faculty of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Sara Soleimani Asl
- Department of Anatomy, Faculty of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Mohammad Reza Arabestani
- Department of Microbiology, Faculty of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran.
- Nutrition Health Research Center, Hamadan University of Medical Sciences, Hamadan, Iran.
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Ipe DS, Kumar PTS, Love RM, Hamlet SM. Silver Nanoparticles at Biocompatible Dosage Synergistically Increases Bacterial Susceptibility to Antibiotics. Front Microbiol 2020; 11:1074. [PMID: 32670214 PMCID: PMC7326045 DOI: 10.3389/fmicb.2020.01074] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 04/29/2020] [Indexed: 12/21/2022] Open
Abstract
Antibiotics used to treat bacterial infections can become ineffective over time or result in the emergence of antibiotic resistant pathogens. With the advent of nanotechnology, silver nanoparticles (AgNPs) have gained significant attention as a therapeutic agent due to the well-known antimicrobial properties of silver. However, there are concerns and limited literature on the potential cytotoxicity of nanoparticles at effective antimicrobial concentrations. AgNPs prepared from silver nitrate with glucose reduction were characterized by surface plasmon resonance, dynamic light scattering, zeta potential analysis and transmission electron microscopy. The cytotoxicity of AgNPs towards human gingival fibroblasts over 7 days was determined using cell proliferation assays and confocal microscopy. AgNP MIC and antibacterial effects alone and in combination with 11 antibiotics were determined against a panel of nine microbial species including gram-positive and gram-negative bacterial species. AgNPs concentrations ≤ 1 μg/mL were non-cytotoxic but also showed no antibacterial effects. However, when combined with each of eleven antibiotics, the biocompatible concentration of AgNPs (1 μg/mL) resulted in significant inhibition of bacterial growth for multiple bacterial species that were resistant to either the antibiotics or AgNPs alone. This study presents a promising strategy with further testing in vivo, to develop novel antimicrobial agents and strategies to confront emerging antimicrobial resistance.
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Affiliation(s)
- Deepak S Ipe
- School of Dentistry and Oral Health, Griffith University, Gold Coast, QLD, Australia.,Menzies Health Institute Queensland, Griffith University, Gold Coast, QLD, Australia
| | - P T Sudheesh Kumar
- School of Dentistry and Oral Health, Griffith University, Gold Coast, QLD, Australia
| | - Robert M Love
- School of Dentistry and Oral Health, Griffith University, Gold Coast, QLD, Australia
| | - Stephen M Hamlet
- School of Dentistry and Oral Health, Griffith University, Gold Coast, QLD, Australia.,Menzies Health Institute Queensland, Griffith University, Gold Coast, QLD, Australia
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45
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Drought-tolerant and plant growth-promoting endophytic Staphylococcus sp. having synergistic effect with silicate supplementation. Arch Microbiol 2020; 202:1899-1906. [PMID: 32448960 DOI: 10.1007/s00203-020-01911-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 03/11/2020] [Accepted: 05/11/2020] [Indexed: 10/24/2022]
Abstract
Endophytic bacteria have been reported to have symbiotic, mutualistic, commensalistic or trophobiotic relationships with various plant parts. As part of its adaptation, many endophytic organisms are known to exhibit properties with multiple beneficial effects to the plant system. Even though many bacterial genera have been identified to have endophytic association, isolation of those which were previously demonstrated well for human association is quite interesting. In the study, endophytic bacteria Ceb1 isolated from the rhizome of Curcuma longa was identified by 16S rDNA sequencing as Staphylococcus sp. Further, Ceb1 was observed to have the ability to tolerate drought stress. While screening for the plant growth-promoting traits, Ceb1 was found to be positive for IAA production both under drought-stressed and normal conditions as confirmed by HPLC. The Ceb1 priming with Vigna unguiculata was observed to enhance the growth parameters of the plant. Analysis of Ceb1-treated plants by ICP-MS further showed modulation of both macro- and micronutrients. Upon drought stress induction in Vigna unguiculata, Ceb1 was found to provide synergistic plant growth-promoting effect to the plant along with the supplemented silicate sources. Under the changing agroclimatic conditions, exploring the plant stress-alleviating effects of endophytes is highly significant.
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46
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Efficacy of Ceftolozane-Tazobactam in Combination with Colistin against Extensively Drug-Resistant Pseudomonas aeruginosa, Including High-Risk Clones, in an In Vitro Pharmacodynamic Model. Antimicrob Agents Chemother 2020; 64:AAC.02542-19. [PMID: 32041712 DOI: 10.1128/aac.02542-19] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 01/30/2020] [Indexed: 12/11/2022] Open
Abstract
Combination therapy is an attractive therapeutic option for extensively drug-resistant (XDR) Pseudomonas aeruginosa infections. Colistin has been the only treatment available for these infections for many years, but its results are suboptimal. Ceftolozane-tazobactam (C/T) is a newly available therapeutic option that has shown good antipseudomonal activity, even against a number of XDR P. aeruginosa strains. However, data about combinations containing C/T are scarce. The aim of this study was to analyze the activity of C/T and colistin alone and in combination against a collection of XDR P. aeruginosa strains containing 24 representative clinical isolates from a multicentre Spanish study. Twenty-four time-kill experiments performed over 24 h were conducted in duplicate to determine the effects of colistin and C/T alone and combined. An in vitro pharmacodynamic chemostat model then was used to validate this combination against three selected XDR P. aeruginosa ST175 isolates with different susceptibility levels to C/T. Static time-kill assays demonstrated superior synergistic or additive effect for C/T plus colistin against 21 of the 24 isolates studied. In the in vitro dynamic pharmacokinetic/pharmacodynamic (PK/PD) model, the C/T regimen of 2/1 g every 8 h with a steady-state concentration of 2 mg/liter colistin effectively suppressed the bacterial growth at 24 h. Additive or synergistic interactions were observed for C/T plus colistin against XDR P. aeruginosa strains and particularly against C/T-resistant strains. C/T plus colistin may be a useful treatment for XDR P. aeruginosa infections, including those caused by high risk-clones resistant to C/T.
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Dave A, Samarth A, Karolia R, Sharma S, Karunakaran E, Partridge L, MacNeil S, Monk PN, Garg P, Roy S. Characterization of Ocular Clinical Isolates of Pseudomonas aeruginosa from Non-Contact Lens Related Keratitis Patients from South India. Microorganisms 2020; 8:microorganisms8020260. [PMID: 32075262 PMCID: PMC7074794 DOI: 10.3390/microorganisms8020260] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 02/10/2020] [Accepted: 02/13/2020] [Indexed: 12/25/2022] Open
Abstract
P. aeruginosa is the most common Gram-negative organism causing bacterial keratitis. Pseudomonas utilizes various virulence mechanisms to adhere and colonize in the host tissue. In the present study, we examined virulence factors associated with thirty-four clinical P. aeruginosa isolates collected from keratitis patients seeking care at L V Prasad Eye Institute, Hyderabad. The virulence-associated genes in all the isolates were genotyped and characteristics such as antibiotic susceptibility, biofilm formation, swarming motility, pyoverdine production and cell cytotoxicity were analyzed. All the isolates showed the presence of genes related to biofilm formation, alkaline proteases and elastases; however, there was a difference in the presence of genes related to the type III secretion system (T3SS). A higher prevalence of exoU+ genotype was noted in the drug-resistant isolates. All the isolates were capable of forming biofilms and more than 70% of the isolates showed good swarming motility. Pyoverdine production was not associated with the T3SS genotype. In the cytotoxicity assay, the presence of exoS,exoU or both resulted in higher cytotoxicity compared to the absence of both the genes. Overall, our results suggest that the T3SS profile is a good indicator of P. aeruginosa virulence characteristics and the isolates lacking the effector genes may have evolved alternate mechanisms of colonization in the host.
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Affiliation(s)
- Alpana Dave
- Prof. Brien Holden Eye Research Centre, LV Prasad Eye Institute, Hyderabad 500034, India; (A.D.); (A.S.); (P.G.)
| | - Apurwa Samarth
- Prof. Brien Holden Eye Research Centre, LV Prasad Eye Institute, Hyderabad 500034, India; (A.D.); (A.S.); (P.G.)
| | - Roshni Karolia
- Jhaveri Microbiology Centre, LV Prasad Eye Institute, Hyderabad 500034, India; (R.K.); (S.S.)
| | - Savitri Sharma
- Jhaveri Microbiology Centre, LV Prasad Eye Institute, Hyderabad 500034, India; (R.K.); (S.S.)
| | - Esther Karunakaran
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield S102TG, UK;
| | - Lynda Partridge
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S102TG, UK;
| | - Sheila MacNeil
- Department of Material Science and Engineering, University of Sheffield, Sheffield S102TG, UK;
| | - Peter N. Monk
- Department of Infection Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield S102RX, UK;
| | - Prashant Garg
- Prof. Brien Holden Eye Research Centre, LV Prasad Eye Institute, Hyderabad 500034, India; (A.D.); (A.S.); (P.G.)
| | - Sanhita Roy
- Prof. Brien Holden Eye Research Centre, LV Prasad Eye Institute, Hyderabad 500034, India; (A.D.); (A.S.); (P.G.)
- Correspondence: ; Tel.: +91-40-30612529; Fax: +91-40-30612535
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Min KB, Yoon SS. Transcriptome analysis reveals that the RNA polymerase-binding protein DksA1 has pleiotropic functions in Pseudomonas aeruginosa. J Biol Chem 2020; 295:3851-3864. [PMID: 32047111 DOI: 10.1074/jbc.ra119.011692] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 02/09/2020] [Indexed: 12/20/2022] Open
Abstract
The stringent response (SR) is a highly conserved stress response in bacteria. It is composed of two factors, (i) a nucleotide alarmone, guanosine tetra- and pentaphosphate ((p)ppGpp), and (ii) an RNA polymerase-binding protein, DksA, that regulates various phenotypes, including bacterial virulence. The clinically significant opportunistic bacterial pathogen Pseudomonas aeruginosa possesses two genes, dksA1 and dksA2, that encode DksA proteins. It remains elusive, however, which of these two genes plays a more important role in SR regulation. In this work, we compared genome-wide, RNA-Seq-based transcriptome profiles of ΔdksA1, ΔdksA2, and ΔdksA1ΔdksA2 mutants to globally assess the effects of these gene deletions on transcript levels coupled with phenotypic analyses. The ΔdksA1 mutant exhibited substantial defects in a wide range of phenotypes, including quorum sensing (QS), anaerobiosis, and motility, whereas the ΔdksA2 mutant exhibited no significant phenotypic changes, suggesting that the dksA2 gene may not have an essential function in P. aeruginosa under the conditions used here. Of note, the ΔdksA1 mutants displayed substantially increased transcription of genes involved in polyamine biosynthesis, and we also detected increased polyamine levels in these mutants. Because SAM is a shared precursor for the production of both QS autoinducers and polyamines, these findings suggest that DksA1 deficiency skews the flow of SAM toward polyamine production rather than to QS signaling. Together, our results indicate that DksA1, but not DksA2, controls many important phenotypes in P. aeruginosa We conclude that DksA1 may represent a potential target whose inhibition may help manage recalcitrant P. aeruginosa infections.
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Affiliation(s)
- Kyung Bae Min
- Department of Microbiology and Immunology, Yonsei University College of Medicine, Seoul 03722, Korea.,Brain Korea 21 PLUS Project for Medical Sciences, Yonsei University College of Medicine, Seoul 03722, Korea
| | - Sang Sun Yoon
- Department of Microbiology and Immunology, Yonsei University College of Medicine, Seoul 03722, Korea .,Brain Korea 21 PLUS Project for Medical Sciences, Yonsei University College of Medicine, Seoul 03722, Korea.,Institute for Immunology and Immunological Diseases, Yonsei University College of Medicine, Seoul 03722, Korea
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49
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Badawy MSEM, Riad OKM, Taher FA, Zaki SA. Chitosan and chitosan-zinc oxide nanocomposite inhibit expression of LasI and RhlI genes and quorum sensing dependent virulence factors of Pseudomonas aeruginosa. Int J Biol Macromol 2020; 149:1109-1117. [PMID: 32032711 DOI: 10.1016/j.ijbiomac.2020.02.019] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 01/15/2020] [Accepted: 02/03/2020] [Indexed: 02/08/2023]
Abstract
The great ability of Pseudomonas aeruginosa to cause chronic infection is attributed to several virulence factors, biofilm formation, intrinsic and acquired resistance to many antibiotics. Anti-quorum sensing (QS) and anti-virulence therapy are promising alternatives to the existing antibiotic therapy. In this study, the effect of chitosan and the prepared chitosan-zinc oxide (CH/ZnO) nanocomposite on QS-dependent virulence factors and acyl homoserine lactone "AHL" production was studied. The chemical structure of the prepared CH/ZnO nanocomposite was characterized by FT-IR spectrum and XRD. The thermal stability and particle size were determined. Chitosan causes a significant decrease in AHL, biofilm, pyocyanin production and motility of P. aeruginosa. CH/ZnO nanocomposite augments the inhibitory activity of chitosan in both phenotypic and genotypic levels. Both chitosan and CH/ZnO nanocomposite downregulate the expression of LasI and RhlI genes using quantitative real-time PCR. The expression of RhlI gene in PAO1 is reduced by 1240 folds after treatment with CH/ZnO nanocomposite. The expression of LasI and RhlI genes in clinical isolates is reduced by 1778.07 and 627.29 folds upon treatment with CH/ZnO. These promising results may find a rescue in the battle of fighting P. aeruginosa by repressing its QS-dependent virulence factors.
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Affiliation(s)
- Mona Shaban E M Badawy
- Department of Microbiology and Immunology, Faculty of Pharmacy, Al-Azhar University, Cairo, Egypt
| | - Omnia Karem M Riad
- Department of Microbiology and Immunology, Faculty of Pharmacy, Al-Azhar University, Cairo, Egypt.
| | - F A Taher
- Applied Physical Chemistry, Faculty of Science (Girls), Al-Azhar University, Cairo, Egypt; Al-Azhar Technology Incubator (ATI), Al-Azhar University, Cairo, Egypt
| | - Samar A Zaki
- Department of Microbiology and Immunology, Faculty of Pharmacy, Al-Azhar University, Cairo, Egypt
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50
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Nguyen XTK, Pinyakong O, Thayanukul P. Bacterial community structures and biodegradation kinetic of Tiamulin antibiotic degrading enriched consortia from swine wastewater. JOURNAL OF ENVIRONMENTAL HEALTH SCIENCE & ENGINEERING 2019; 17:1121-1130. [PMID: 32030179 PMCID: PMC6985375 DOI: 10.1007/s40201-019-00426-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 12/04/2019] [Indexed: 05/05/2023]
Abstract
The antibiotic tiamulin (TIA) is common and widely used medication for dysentery eradication in swine productions. Tiamulin persists in livestock manure, and its residues have been found in various environment. This work obtained four tiamulin-degrading enriched bacterial consortia from a covered anaerobic lagoon system and a stabilized pond system of swine farms. Tiamulin was efficiently removed by the enriched cultures at the concentrations between 2.5 and 200 mg/L, with a removal of 60.1-99.9% during 16 h and a degradation half-life of 4.5-15.7 h. The stabilized pond system cultured with taimulin solely could eliminate tiamulin at the highest rates. The logistic substrate degradation model fit most of the experimental data. Next-generation amplicon sequencing was conducted, and it was found that the bacterial community was significantly impacted by the inoculum source, nutrient addition, and high tiamulin concentrations. Principal coordinate analysis (PCoA) indicated the similarity of bacterial communities in the original enriched samples and the 2.5 mg/L tiamulin-removed cultures. The 200 mg/L consortia were rather different and became similar to the other 200 mg/L consortia from different sources and cultures without nutrient supplementation. Shannon and Simpson indices suggested a reduction in bacterial diversity at high concentrations. The microbes that had high growth in the most efficient enriched culture, or which were abundant in all samples, or which increased with higher tiamulin concentrations were likely to be the major tiamulin-degrading bacteria. This is the first report suggested the possible roles of Achromobacter, Delftia, Flavobacterium, Pseudomonas, and Stenotrophomonas in tiamulin degradation.
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Affiliation(s)
- Xuan Thi Kim Nguyen
- International Program in Hazardous Substance and Environmental Management, Graduate School, Chulalongkorn University, Bangkok, 10330 Thailand
- Department of Natural Science, Faculty of Education, Bac Lieu University, Bac Lieu, 260000 Vietnam
| | - Onruthai Pinyakong
- Microbial Technology for Marine Pollution Treatment Research Unit, Department of Microbiology, Faculty of Science, Chulalongkorn University, Bangkok, 10330 Thailand
- Center of Excellences on Hazardous Substance Management (HSM), Chulalongkorn University, Bangkok, 10330 Thailand
| | - Parinda Thayanukul
- Center of Excellences on Hazardous Substance Management (HSM), Chulalongkorn University, Bangkok, 10330 Thailand
- Faculty of Engineering, Department of Environmental Engineering, King Mongkut’s University of Technology, Thonburi, 10140 Thailand
- Department of Biology, Faculty of Science, Mahidol University, Bangkok, 10400 Thailand
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