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Franklin AM, Weller DL, Durso LM, Bagley M, Davis BC, Frye JG, Grim CJ, Ibekwe AM, Jahne MA, Keely SP, Kraft AL, McConn BR, Mitchell RM, Ottesen AR, Sharma M, Strain EA, Tadesse DA, Tate H, Wells JE, Williams CF, Cook KL, Kabera C, McDermott PF, Garland JL. A one health approach for monitoring antimicrobial resistance: developing a national freshwater pilot effort. FRONTIERS IN WATER 2024; 6:10.3389/frwa.2024.1359109. [PMID: 38855419 PMCID: PMC11157689 DOI: 10.3389/frwa.2024.1359109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Antimicrobial resistance (AMR) is a world-wide public health threat that is projected to lead to 10 million annual deaths globally by 2050. The AMR public health issue has led to the development of action plans to combat AMR, including improved antimicrobial stewardship, development of new antimicrobials, and advanced monitoring. The National Antimicrobial Resistance Monitoring System (NARMS) led by the United States (U.S) Food and Drug Administration along with the U.S. Centers for Disease Control and U.S. Department of Agriculture has monitored antimicrobial resistant bacteria in retail meats, humans, and food animals since the mid 1990's. NARMS is currently exploring an integrated One Health monitoring model recognizing that human, animal, plant, and environmental systems are linked to public health. Since 2020, the U.S. Environmental Protection Agency has led an interagency NARMS environmental working group (EWG) to implement a surface water AMR monitoring program (SWAM) at watershed and national scales. The NARMS EWG divided the development of the environmental monitoring effort into five areas: (i) defining objectives and questions, (ii) designing study/sampling design, (iii) selecting AMR indicators, (iv) establishing analytical methods, and (v) developing data management/analytics/metadata plans. For each of these areas, the consensus among the scientific community and literature was reviewed and carefully considered prior to the development of this environmental monitoring program. The data produced from the SWAM effort will help develop robust surface water monitoring programs with the goal of assessing public health risks associated with AMR pathogens in surface water (e.g., recreational water exposures), provide a comprehensive picture of how resistant strains are related spatially and temporally within a watershed, and help assess how anthropogenic drivers and intervention strategies impact the transmission of AMR within human, animal, and environmental systems.
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Affiliation(s)
- Alison M. Franklin
- United States (U.S.) Environmental Protection Agency, Office of Research and Development, Cincinnati, OH, United States
| | - Daniel L. Weller
- U.S. Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Lisa M. Durso
- U.S. Department of Agriculture, Agricultural Research Service (USDA, ARS), Agroecosystem Management Research, Lincoln, NE, United States
| | - Mark Bagley
- United States (U.S.) Environmental Protection Agency, Office of Research and Development, Cincinnati, OH, United States
| | - Benjamin C. Davis
- United States (U.S.) Environmental Protection Agency, Office of Research and Development, Cincinnati, OH, United States
| | - Jonathan G. Frye
- USDA ARS, U.S. National Poultry Research Center, Poultry Microbiological Safety and Processing Research Unit, Athens, GA, United States
| | - Christopher J. Grim
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, MD, United States
| | - Abasiofiok M. Ibekwe
- USDA, ARS, Agricultural Water Efficiency and Salinity Research Unit, Riverside, CA, United States
| | - Michael A. Jahne
- United States (U.S.) Environmental Protection Agency, Office of Research and Development, Cincinnati, OH, United States
| | - Scott P. Keely
- United States (U.S.) Environmental Protection Agency, Office of Research and Development, Cincinnati, OH, United States
| | - Autumn L. Kraft
- Oak Ridge Institute for Science and Education, USDA, ARS, Beltsville, MD, United States
| | - Betty R. McConn
- Oak Ridge Institute for Science and Education, USDA, ARS, Beltsville, MD, United States
| | - Richard M. Mitchell
- Environmental Protection Agency, Office of Water, Washington, DC, United States
| | - Andrea R. Ottesen
- Center for Veterinary Medicine, National Antimicrobial Resistance Monitoring System (NARMS), U.S. Food and Drug Administration, Laurel, MD, United States
| | - Manan Sharma
- USDA, ARS Environmental Microbial and Food Safety Laboratory, Beltsville, MD, United States
| | - Errol A. Strain
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, MD, United States
| | - Daniel A. Tadesse
- Center for Veterinary Medicine, National Antimicrobial Resistance Monitoring System (NARMS), U.S. Food and Drug Administration, Laurel, MD, United States
| | - Heather Tate
- Center for Veterinary Medicine, National Antimicrobial Resistance Monitoring System (NARMS), U.S. Food and Drug Administration, Laurel, MD, United States
| | - Jim E. Wells
- USDA, ARS, U.S. Meat Animal Research Center, Meat Safety and Quality, Clay Center, NE, United States
| | - Clinton F. Williams
- USDA, ARS, US Arid-Land Agricultural Research Center, Maricopa, AZ, United States
| | - Kim L. Cook
- USDA, ARS Nutrition, Food Safety and Quality National Program Staff, Beltsville, MD, United States
| | - Claudine Kabera
- Center for Veterinary Medicine, National Antimicrobial Resistance Monitoring System (NARMS), U.S. Food and Drug Administration, Laurel, MD, United States
| | - Patrick F. McDermott
- Center for Veterinary Medicine, National Antimicrobial Resistance Monitoring System (NARMS), U.S. Food and Drug Administration, Laurel, MD, United States
| | - Jay L. Garland
- United States (U.S.) Environmental Protection Agency, Office of Research and Development, Cincinnati, OH, United States
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Malavez Y, Nieves-Miranda SM, Loperena Gonzalez PN, Padin-Lopez AF, Xiaoli L, Dudley EG. Exploring Antimicrobial Resistance Profiles of E. coli Isolates in Dairy Cattle: A Baseline Study across Dairy Farms with Varied Husbandry Practices in Puerto Rico. Microorganisms 2023; 11:2879. [PMID: 38138023 PMCID: PMC10745463 DOI: 10.3390/microorganisms11122879] [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: 09/14/2023] [Revised: 11/12/2023] [Accepted: 11/14/2023] [Indexed: 12/24/2023] Open
Abstract
Antimicrobial treatment in livestock can contribute to the emergence and spread of antimicrobial-resistant (AMR) microorganisms. Despite substantial surveillance of AMR bacteria in the continental United States, the prevalence of these AMR organisms in U.S. territories, such as Puerto Rico, remains understudied. The goals of this research included obtaining baseline data on the antimicrobial profile of E. coli isolates from Puerto Rico dairy farms with different husbandry practices. Seventy-nine fecal samples were collected from two types of conventional dairy farms: those that fed calves with tank milk and those that fed calves with waste milk. These samples were collected from the animals' rectums, culture, and subsequently confirmed through biochemical tests. Out of these samples, 32 isolates were analyzed phenotypically and genotypically to elucidate their AMR profiles. The results underscore a discrepancy in the occurrence of antimicrobial resistance genes between calves and adult cattle. Notably, waste milk-fed calves exhibited a significantly higher prevalence of antibiotic-resistant E. coli when compared to their tank milk-fed counterparts. These disparities emphasize the need for more comprehensive investigations to determine causative factors. These results underscore the urgency of comprehensive strategies to raise awareness about how management practices influence antimicrobial resistance, shifting the focus from treatment to prevention.
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Affiliation(s)
- Yadira Malavez
- Department of Natural Sciences, University of Puerto Rico, Aguadilla, PR 00603, USA; (S.M.N.-M.); (A.F.P.-L.)
- Department of Biology, Industrial Biotechnology Program, University of Puerto Rico, Mayagüez, PR 00681, USA
- Department of Animal Sciences, Agricultural Experimental Station, University of Puerto Rico, Mayagüez, PR 00681, USA
| | - Sharon M. Nieves-Miranda
- Department of Natural Sciences, University of Puerto Rico, Aguadilla, PR 00603, USA; (S.M.N.-M.); (A.F.P.-L.)
| | - Paola N. Loperena Gonzalez
- Department of Natural Sciences, University of Puerto Rico, Aguadilla, PR 00603, USA; (S.M.N.-M.); (A.F.P.-L.)
| | - Adrian F. Padin-Lopez
- Department of Natural Sciences, University of Puerto Rico, Aguadilla, PR 00603, USA; (S.M.N.-M.); (A.F.P.-L.)
| | - Lingzi Xiaoli
- Department of Food Science, The Pennsylvania State University, University Park, PA 16802, USA (E.G.D.)
| | - Edward G. Dudley
- Department of Food Science, The Pennsylvania State University, University Park, PA 16802, USA (E.G.D.)
- E. coli Reference Center, The Pennsylvania State University, University Park, PA 16802, USA
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Goodarzi Z, Asad S, Mehrshad M. Genome-resolved insight into the reservoir of antibiotic resistance genes in aquatic microbial community. Sci Rep 2022; 12:21047. [PMID: 36473884 PMCID: PMC9726936 DOI: 10.1038/s41598-022-25026-3] [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: 05/10/2022] [Accepted: 11/23/2022] [Indexed: 12/12/2022] Open
Abstract
Aquatic microbial communities are an important reservoir of antibiotic resistance genes (ARGs). However, distribution and diversity of different ARG categories in environmental microbes with different ecological strategies is not yet well studied. Despite the potential exposure of the southern part of the Caspian Sea to the release of antibiotics, little is known about its natural resistome profile. We used a combination of Hidden Markov model (HMM), homology alignment and a deep learning approach for comprehensive screening of the diversity and distribution of ARGs in the Caspian Sea metagenomes at genome resolution. Detected ARGs were classified into five antibiotic resistance categories including prevention of access to target (44%), modification/protection of targets (30%), direct modification of antibiotics (22%), stress resistance (3%), and metal resistance (1%). The 102 detected ARG containing metagenome-assembled genomes of the Caspian Sea were dominated by representatives of Acidimicrobiia, Gammaproteobacteria, and Actinobacteria classes. Comparative analysis revealed that the highly abundant, oligotrophic, and genome streamlined representatives of taxa Acidimicrobiia and Actinobacteria modify the antibiotic target via mutation to develop antibiotic resistance rather than carrying extra resistance genes. Our results help with understanding how the encoded resistance categories of each genome are aligned with its ecological strategies.
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Affiliation(s)
- Zahra Goodarzi
- grid.46072.370000 0004 0612 7950Department of Biotechnology, College of Science, University of Tehran, Tehran, Iran
| | - Sedigheh Asad
- grid.46072.370000 0004 0612 7950Department of Biotechnology, College of Science, University of Tehran, Tehran, Iran
| | - Maliheh Mehrshad
- grid.6341.00000 0000 8578 2742Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences (SLU), Box 7050, 75007 Uppsala, Sweden
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Bellato A, Robino P, Stella MC, Scarrone L, Scalas D, Nebbia P. Resistance to Critical Important Antibacterials in Staphylococcus pseudintermedius Strains of Veterinary Origin. Antibiotics (Basel) 2022; 11:antibiotics11121758. [PMID: 36551415 PMCID: PMC9774309 DOI: 10.3390/antibiotics11121758] [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: 10/21/2022] [Revised: 11/24/2022] [Accepted: 12/02/2022] [Indexed: 12/12/2022] Open
Abstract
Staphylococcal infections represent a challenge in companion animals and hospitalized patients. This study aimed to assess the resistance of Staphylococcus pseudintermedius isolates, against a broad panel of antibacterials, including exclusive to human medicine. A total of 40 S. pseudintermedius were collected from clinical specimens of dogs (n = 31) and cats (n = 5). All strains were tested for 20 antibacterials, namely 14 Critical Important and eight Highly Important Antibacterials (CIA and HIA, respectively), indicative for 18 antimicrobial classes. All strains were susceptible to seven antibiotics (daptomycin, fosfomycin, fusidic acid, linezolid, quinupristin-dalfopristin, teicoplanin/vancomycin, tigecycline). The highest resistance was against penicillin (97.5% Confidence Interval [CI]: 83.8-100.0), whereas the lowest against telavancin (2.5%, CI: 0.0-16.2). Resistance versus Highest Priority CIA was observed, namely against macrolides (70.0, CI: 52.1-84.3), quinolones (62.5, CI: 44.5-78.3), 5th generation cephalosporins (7.5, CI: 1.3-21.6), and glycopeptides (2.5%, CI: 0.0-14.2). Among High Priority CIA, strains were resistant only to aminoglycosides (65.0, CI: 47.0-80.4) and ansamycins (12.5, CI: 3.8-28.1). We observed the highest resistance against veterinary medicine antibacterials, but there was also resistance against antibacterials exclusive to human medicine, namely ceftaroline (7.5, CI: 1.0-23.8) and telavancin. S. pseudintermedius zoonotic potential and its rate of acquisition of new resistance should encourage surveillance on a broad spectrum of antibacterials.
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Ding M, Ye Z, Liu L, Wang W, Chen Q, Zhang F, Wang Y, Sjöling Å, Martín-Rodríguez AJ, Hu R, Chen W, Zhou Y. Subinhibitory antibiotic concentrations promote the horizontal transfer of plasmid-borne resistance genes from Klebsiellae pneumoniae to Escherichia coli. Front Microbiol 2022; 13:1017092. [PMID: 36419429 PMCID: PMC9678054 DOI: 10.3389/fmicb.2022.1017092] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 09/30/2022] [Indexed: 11/07/2023] Open
Abstract
Horizontal gene transfer plays an important role in the spread of antibiotic resistance, in which plasmid-mediated conjugation transfer is the most important mechanism. While sub-minimal inhibitory concentrations (sub-MIC) of antibiotics could promote conjugation frequency, the mechanism by which sub-MIC levels of antibiotics affect conjugation frequency is not clear. Here, we used Klebsiella pneumoniae SW1780 carrying the multi-drug resistance plasmid pSW1780-KPC as the donor strain, to investigate the effects of sub-MICs of meropenem (MEM), ciprofloxacin (CIP), cefotaxime (CTX), and amikacin (AK) on conjugational transfer of pSW1780-KPC from SW1780 to Escherichia coli J53. Our results showed that the transfer frequencies increased significantly by treating SW1780 strain with sub-MIC levels of MEM, CIP, CTX and AK. Transfer frequencies at sub-MIC conditions in a Galleria mellonella were significantly higher than in vitro. To investigate gene expression and metabolic effects, RT-qPCR and LC-MS-based metabolome sequencing were performed. Transcript levels of T4SS genes virB1, virB2, virB4, virB8, and conjugation-related genes traB, traK, traE, and traL were significantly upregulated by exposure to sub-MICs of MEM, CIP, CTX, and AK. Metabolome sequencing revealed nine differentially regulated metabolites. Our findings are an early warning for a wide assessment of the roles of sub-MIC levels of antibiotics in the spread of antibiotic resistance.
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Affiliation(s)
- Manlin Ding
- Department of Pathogenic Biology, School of Basic Medicine, Southwest Medical University, Luzhou, China
- Department of Clinical Laboratory, The Affiliated Traditional Chinese Medicine Hospital of Southwest Medical University, Luzhou, China
| | - Zi Ye
- Department of Pathogenic Biology, School of Basic Medicine, Southwest Medical University, Luzhou, China
| | - Lu Liu
- Department of Pathogenic Biology, School of Basic Medicine, Southwest Medical University, Luzhou, China
| | - Wei Wang
- Department of Pathogenic Biology, School of Basic Medicine, Southwest Medical University, Luzhou, China
| | - Qiao Chen
- Department of Pathogenic Biology, School of Basic Medicine, Southwest Medical University, Luzhou, China
| | - Feiyang Zhang
- Department of Pathogenic Biology, School of Basic Medicine, Southwest Medical University, Luzhou, China
| | - Ying Wang
- Department of Pathogenic Biology, School of Basic Medicine, Southwest Medical University, Luzhou, China
| | - Åsa Sjöling
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | | | - Renjing Hu
- Department of Laboratory Medicine, The Affiliated Wuxi No. 2 People’s Hospital of Nanjing Medical University, Wuxi, China
| | - Wenbi Chen
- Department of Pathogenic Biology, School of Basic Medicine, Southwest Medical University, Luzhou, China
| | - Yingshun Zhou
- Department of Pathogenic Biology, School of Basic Medicine, Southwest Medical University, Luzhou, China
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Silva DPD, Cardoso MS, Macedo AJ. Endophytic Fungi as a Source of Antibacterial Compounds-A Focus on Gram-Negative Bacteria. Antibiotics (Basel) 2022; 11:1509. [PMID: 36358164 PMCID: PMC9687006 DOI: 10.3390/antibiotics11111509] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 10/24/2022] [Accepted: 10/26/2022] [Indexed: 07/30/2023] Open
Abstract
Bacterial resistance has become one of the main motives in the worldwide race for undescribed antibacterial agents. The difficulties in the treatment of bacterial infections are a public health issue that increasingly highlights the need for antimicrobial agents. Endophytic microorganisms are a promising alternative in the search for drugs, due to the vast number of metabolites produced with unique characteristics and bioactive potential. This review highlights the importance of endophytic microorganisms as a source of secondary metabolites in the search for active molecules against bacteria of medical importance, with a special focus on gram-negative species. This fact is supported by the findings raised in this review, which brings an arsenal of 166 molecules with characterized chemical structures and their antibacterial activities. In addition, the low cost, ease of maintenance, and optimization-controlled fermentation conditions favor reproducibility in commercial scale. Given their importance, it is necessary to intensify the search for new molecules from endophytic microorganisms, and to increasingly invest in this very promising font.
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Effects of Sub-Minimum Inhibitory Concentrations of Imipenem and Colistin on Expression of Biofilm-Specific Antibiotic Resistance and Virulence Genes in Acinetobacter baumannii Sequence Type 1894. Int J Mol Sci 2022; 23:ijms232012705. [PMID: 36293559 PMCID: PMC9603859 DOI: 10.3390/ijms232012705] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Revised: 10/11/2022] [Accepted: 10/18/2022] [Indexed: 12/15/2022] Open
Abstract
Antibiotics at suboptimal doses promote biofilm formation and the development of antibiotic resistance. The underlying molecular mechanisms, however, were not investigated. Here, we report the effects of sub-minimum inhibitory concentrations (sub-MICs) of imipenem and colistin on genes associated with biofilm formation and biofilm-specific antibiotic resistance in a multidrug-tolerant clinical strain of Acinetobacter baumannii Sequence Type (ST) 1894. Comparative transcriptome analysis was performed in untreated biofilm and biofilm treated with sub-MIC doses of imipenem and colistin. RNA sequencing data showed that 78 and 285 genes were differentially expressed in imipenem and colistin-treated biofilm cells, respectively. Among the differentially expressed genes (DEGs), 48 and 197 genes were upregulated exclusively in imipenem and colistin-treated biofilm cells, respectively. The upregulated genes included those encoding matrix synthesis (pgaB), multidrug efflux pump (novel00738), fimbrial proteins, and homoserine lactone synthase (AbaI). Upregulation of biofilm-associated genes might enhance biofilm formation when treated with sub-MICs of antibiotics. The downregulated genes include those encoding DNA gyrase (novel00171), 30S ribosomal protein S20 (novel00584), and ribosome releasing factor (RRF) were downregulated when the biofilm cells were treated with imipenem and colistin. Downregulation of these genes affects protein synthesis, which in turn slows down cell metabolism and makes biofilm cells more tolerant to antibiotics. In this investigation, we also found that 5 of 138 small RNAs (sRNAs) were differentially expressed in biofilm regardless of antibiotic treatment or not. Of these, sRNA00203 showed the highest expression levels in biofilm. sRNAs regulate gene expression and are associated with biofilm formation, which may in turn affect the expression of biofilm-specific antibiotic resistance. In summary, when biofilm cells were exposed to sub-MIC doses of colistin and imipenem, coordinated gene responses result in increased biofilm production, multidrug efflux pump expression, and the slowdown of metabolism, which leads to drug tolerance in biofilm. Targeting antibiotic-induced or repressed biofilm-specific genes represents a new strategy for the development of innovative and effective treatments for biofilm-associated infections caused by A. baumannii.
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Mohapatra B, Malhotra H, Phale PS. Life Within a Contaminated Niche: Comparative Genomic Analyses of an Integrative Conjugative Element ICE nahCSV86 and Two Genomic Islands From Pseudomonas bharatica CSV86 T Suggest Probable Role in Colonization and Adaptation. Front Microbiol 2022; 13:928848. [PMID: 35875527 PMCID: PMC9298801 DOI: 10.3389/fmicb.2022.928848] [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: 04/26/2022] [Accepted: 06/08/2022] [Indexed: 11/26/2022] Open
Abstract
Comparative genomic and functional analyses revealed the presence of three genomic islands (GIs, >50 Kb size): ICEnahCSV86, Pseudomonas bharatica genomic island-1 (PBGI-1), and PBGI-2 in the preferentially aromatic-degrading soil bacterium, Pseudomonas bharatica CSV86T. Site-specific genomic integration at or near specific transfer RNAs (tRNAs), near-syntenic structural modules, and phylogenetic relatedness indicated their evolutionary lineage to the type-4 secretion system (T4SS) ICEclc family, thus predicting these elements to be integrative conjugative elements (ICEs). These GIs were found to be present as a single copy in the genome and the encoded phenotypic traits were found to be stable, even in the absence of selection pressure. ICEnahCSV86 harbors naphthalene catabolic (nah-sal) cluster, while PBGI-1 harbors Co-Zn-Cd (czc) efflux genes as cargo modules, whereas PBGI-2 was attributed to as a mixed-function element. The ICEnahCSV86 has been reported to be conjugatively transferred (frequency of 7 × 10–8/donor cell) to Stenotrophomonas maltophilia CSV89. Genome-wide comparative analyses of aromatic-degrading bacteria revealed nah-sal clusters from several Pseudomonas spp. as part of probable ICEs, syntenic to conjugatively transferable ICEnahCSV86 of strain CSV86T, suggesting it to be a prototypical element for naphthalene degradation. It was observed that the plasmids harboring nah-sal clusters were phylogenetically incongruent with predicted ICEs, suggesting genetic divergence of naphthalene metabolic clusters in the Pseudomonas population. Gene synteny, divergence estimates, and codon-based Z-test indicated that ICEnahCSV86 is probably derived from PBGI-2, while multiple recombination events masked the ancestral lineage of PBGI-1. Diversifying selection pressure (dN-dS = 2.27–4.31) imposed by aromatics and heavy metals implied the modular exchange-fusion of various cargo clusters through events like recombination, rearrangement, domain reshuffling, and active site optimization, thus allowing the strain to evolve, adapt, and maximize the metabolic efficiency in a contaminated niche. The promoters (Pnah and Psal) of naphthalene cargo modules (nah, sal) on ICEnahCSV86 were proved to be efficient for heterologous protein expression in Escherichia coli. GI-based genomic plasticity expands the metabolic spectrum and versatility of CSV86T, rendering efficient adaptation to the contaminated niche. Such isolate(s) are of utmost importance for their application in bioremediation and are the probable ideal host(s) for metabolic engineering.
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Affiliation(s)
- Balaram Mohapatra
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Harshit Malhotra
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Prashant S Phale
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
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HAM-ART: An optimised culture-free Hi-C metagenomics pipeline for tracking antimicrobial resistance genes in complex microbial communities. PLoS Genet 2022; 18:e1009776. [PMID: 35286304 PMCID: PMC8947609 DOI: 10.1371/journal.pgen.1009776] [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: 08/10/2021] [Revised: 03/24/2022] [Accepted: 02/07/2022] [Indexed: 11/19/2022] Open
Abstract
Shotgun metagenomics is a powerful tool to identify antimicrobial resistance (AMR) genes in microbiomes but has the limitation that extrachromosomal DNA, such as plasmids, cannot be linked with the host bacterial chromosome. Here we present a comprehensive laboratory and bioinformatics pipeline HAM-ART (Hi-C Assisted Metagenomics for Antimicrobial Resistance Tracking) optimised for the generation of metagenome-assembled genomes including both chromosomal and extrachromosomal AMR genes. We demonstrate the performance of the pipeline in a study comparing 100 pig faecal microbiomes from low- and high-antimicrobial use pig farms (organic and conventional farms). We found significant differences in the distribution of AMR genes between low- and high-antimicrobial use farms including a plasmid-borne lincosamide resistance gene exclusive to high-antimicrobial use farms in three species of Lactobacilli. The bioinformatics pipeline code is available at https://github.com/lkalmar/HAM-ART.
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Siebor E, de Curraize C, Varin V, Magallon A, Neuwirth C. Mobilisation of plasmid-mediated bla VEB-1 gene cassette into distinct genomic islands of Proteus mirabilis after ceftazidime exposure. J Glob Antimicrob Resist 2021; 27:26-30. [PMID: 34333164 DOI: 10.1016/j.jgar.2021.07.011] [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: 12/02/2019] [Revised: 05/31/2021] [Accepted: 07/11/2021] [Indexed: 10/20/2022] Open
Abstract
OBJECTIVES We sought to integrate a VEB-1-encoding gene cassette into the integron of the MDR region of genomic islands (GIs) harboured by Proteus mirabilis strains after antibiotic exposure. METHODS An IncP1 plasmid from Achromobacter xylosoxidans carrying the cassette array dfrA14-blaVEB-1-aadB was introduced by conjugation into five strains of P. mirabilis: PmBRI, PmABB, PmSCO and Pm2CHAMA harbouring Salmonella GI 1 and PmESC harbouring Proteus GI 1. Circular intermediates of the cassettes were amplified by PCR. blaVEB-harbouring P. mirabilis were exposed to increasing concentrations of ceftazidime each day. Presence of blaVEB-1 in the GI was assessed by PCR. The complete MDR regions were mapped and sequenced in positive clones. RESULTS Circular intermediates were detected for dfrA14 and blaVEB-1-aadB and dfrA14-blaVEB-1-aadB cassettes arrays in A. xylosoxidans, and for aadA2 in P. mirabilis. Insertion of blaVEB-1 into the GIs occurred under ceftazidime pressure. In all cases, the three cassettes from IncP1 were integrated. They replaced the cassette array of PmBRI, PmABB and PmSCO in which floRc, tet(A)G and blaPSE-1 were conserved, whereas they replaced an integron and the IS26-flanked region in Pm2CHAMA. In PmESC, they only replaced aadB, with aadA2 being conserved. blaVEB-1 integration occurred just after conjugation for Pm2CHAMA but required ceftazidime exposure for the other strains. CONCLUSION Homologous recombination of gene cassettes conferring resistance to clinically important antibiotics may occur under antibiotic pressure between an integron located on a plasmid and a co-resident GI. This feature participates in the acquisition, maintenance and spread of antibiotic resistance genes.
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Affiliation(s)
- Eliane Siebor
- Laboratory of Bacteriology, University Hospital of Dijon, Plateau technique de Biologie, BP 37013, 21070 Dijon Cedex, France; and UMR 6249, CNRS Chrono-environnement, Université de Bourgogne Franche-Comté, 25000, Besançon, France
| | - Claire de Curraize
- Laboratory of Bacteriology, University Hospital of Dijon, Plateau technique de Biologie, BP 37013, 21070 Dijon Cedex, France; and UMR 6249, CNRS Chrono-environnement, Université de Bourgogne Franche-Comté, 25000, Besançon, France
| | - Veronique Varin
- Laboratory of Bacteriology, University Hospital of Dijon, Plateau technique de Biologie, BP 37013, 21070 Dijon Cedex, France; and UMR 6249, CNRS Chrono-environnement, Université de Bourgogne Franche-Comté, 25000, Besançon, France
| | - Arnaud Magallon
- Laboratory of Bacteriology, University Hospital of Dijon, Plateau technique de Biologie, BP 37013, 21070 Dijon Cedex, France; and UMR 6249, CNRS Chrono-environnement, Université de Bourgogne Franche-Comté, 25000, Besançon, France
| | - Catherine Neuwirth
- Laboratory of Bacteriology, University Hospital of Dijon, Plateau technique de Biologie, BP 37013, 21070 Dijon Cedex, France; and UMR 6249, CNRS Chrono-environnement, Université de Bourgogne Franche-Comté, 25000, Besançon, France.
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Zhu H, Chen Y, Hang Y, Luo H, Fang X, Xiao Y, Cao X, Zou S, Hu X, Hu L, Zhong Q. Impact of inappropriate empirical antibiotic treatment on clinical outcomes of urinary tract infections caused by Escherichia coli: a retrospective cohort study. J Glob Antimicrob Resist 2021; 26:148-153. [PMID: 34118479 DOI: 10.1016/j.jgar.2021.05.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 05/01/2021] [Accepted: 05/30/2021] [Indexed: 11/26/2022] Open
Abstract
OBJECTIVES We aimed to determine the clinical impact of inappropriate empirical antibiotic treatment (IEAT) compared with appropriate empirical antibiotic treatment (AEAT) in hospitalised patients with urinary tract infections (UTIs) caused by Escherichia coli (E. coli). METHODS This retrospective cohort study included adult patients with a primary diagnosis of UTI who were treated with empirical antibiotics at a tertiary hospital in southern China over a 2-year period. Clinical data of patients who received IEAT were compared with those of patients receiving AEAT. We used multivariable logistic regression to identify the predictors for receiving IEAT and the risk factors affecting clinical outcomes. RESULTS A total of 213 patients were enrolled (median age, 61 years), of whom 103 (48.4%) received IEAT. IEAT was associated with empirical use of fluoroquinolones, male sex and age-adjusted Charlson comorbidity index (aCCI) score >6. Hospital length of stay (LOS) was longer for patients who received IEAT than for those who received AEAT (13.6 ± 8.6 days vs. 10.8 ± 7.9 days; P = 0.008). IEAT was an independent risk factor for longer LOS along with aCCI score ≥2, lung disease and cardiac disease. CONCLUSION Empirical use of fluoroquinolones for UTIs should be avoided, especially in male patients with aCCI score >6. Improved empirical antimicrobial therapy may have a beneficial impact in reducing bacterial resistance and healthcare costs by decreasing the LOS. Therefore, interventions to promote in-depth antibiotic stewardship programmes in China are needed.
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Affiliation(s)
- Hongying Zhu
- Jiangxi Provincial Key Laboratory of Medicine, Clinical Laboratory of the Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, People's Republic of China
| | - Yanhui Chen
- Jiangxi Provincial Key Laboratory of Medicine, Clinical Laboratory of the Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, People's Republic of China
| | - Yaping Hang
- Jiangxi Provincial Key Laboratory of Medicine, Clinical Laboratory of the Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, People's Republic of China
| | - Hong Luo
- Jiangxi Provincial Key Laboratory of Medicine, Clinical Laboratory of the Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, People's Republic of China
| | - Xueyao Fang
- Jiangxi Provincial Key Laboratory of Medicine, Clinical Laboratory of the Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, People's Republic of China
| | - Yanping Xiao
- Jiangxi Provincial Key Laboratory of Medicine, Clinical Laboratory of the Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, People's Republic of China
| | - Xingwei Cao
- Jiangxi Provincial Key Laboratory of Medicine, Clinical Laboratory of the Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, People's Republic of China
| | - Shan Zou
- Jiangxi Provincial Key Laboratory of Medicine, Clinical Laboratory of the Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, People's Republic of China
| | - Xiaoyan Hu
- Jiangxi Provincial Key Laboratory of Medicine, Clinical Laboratory of the Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, People's Republic of China
| | - Longhua Hu
- Jiangxi Provincial Key Laboratory of Medicine, Clinical Laboratory of the Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, People's Republic of China
| | - Qiaoshi Zhong
- Jiangxi Provincial Key Laboratory of Medicine, Clinical Laboratory of the Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, People's Republic of China.
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Subramaniam G, Girish M. Antibiotic Resistance - A Cause for Reemergence of Infections. Indian J Pediatr 2020; 87:937-944. [PMID: 32026301 DOI: 10.1007/s12098-019-03180-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 12/31/2019] [Indexed: 11/27/2022]
Abstract
This article can rightly be called 'the rise of the microbial phoenix'; for, all the microbial infections whose doomsday was predicted with the discovery of antibiotics, have thumbed their noses at mankind and reemerged phoenix like. The hubris generated by Sir Alexander Fleming's discovery of Penicillin in 1928, exemplified best by the comment by William H Stewart, the US Surgeon General in 1967, "It is time to close the books on infectious diseases" has been replaced by the realisation that the threat of antibiotic resistance is, in the words of the Chief Medical Officer of England, Dame Sally Davies, "just as important and deadly as climate change and international terrorism". Antimicrobial resistance threatens to negate all the major medical advances of the last century because antimicrobial use is linked to many other fields like organ transplantation and cancer chemotherapy. Antibiotic resistance genes have been there since ancient times in response to naturally occurring antibiotics. Modern medicine has only driven further evolution of antimicrobial resistance by use, misuse, overuse and abuse of antibiotics. Resistant bacteria proliferate by natural selection when their drug sensitive comrades are removed by antibiotics. In this article the authors discuss the various causes of antimicrobial resistance and dwell in some detail on antibiotic resistance in gram-positive and gram-negative organisms. Finally they stress on the important role clinicians have in limiting the development and spread of antimicrobial resistance.
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Affiliation(s)
- Girish Subramaniam
- Department of Pediatrics, Children Hospital, Midas Heights, Ramdaspeth, Nagpur, India.
| | - Meenakshi Girish
- Department of Pediatrics, All India Institute of Medical Sciences, Nagpur, India
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13
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Staneva D, Vasileva-Tonkova E, Grozdanov P, Vilhelmova-Ilieva N, Nikolova I, Grabchev I. Synthesis and photophysical characterisation of 3-bromo-4-dimethylamino-1,8-naphthalimides and their evaluation as agents for antibacterial photodynamic therapy. J Photochem Photobiol A Chem 2020. [DOI: 10.1016/j.jphotochem.2020.112730] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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14
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Majchrzak M, Zając E, Wawszczak M, Filipiak A, Głuszek S, Adamus-Białek W. Mathematical Analysis of Induced Antibiotic Resistance Among Uropathogenic Escherichia coli Strains. Microb Drug Resist 2020; 26:1236-1244. [DOI: 10.1089/mdr.2019.0292] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Michał Majchrzak
- Department of Surgical Medicine with the Laboratory of Medical Genetics, Collegium Medicum, The Jan Kochanowski University, Kielce, Poland
| | - Elżbieta Zając
- Department of Mathematics, The Jan Kochanowski University, Kielce, Poland
| | - Monika Wawszczak
- Department of Surgical Medicine with the Laboratory of Medical Genetics, Collegium Medicum, The Jan Kochanowski University, Kielce, Poland
| | - Aneta Filipiak
- Department of Surgical Medicine with the Laboratory of Medical Genetics, Collegium Medicum, The Jan Kochanowski University, Kielce, Poland
| | - Stanisław Głuszek
- Department of Surgical Medicine with the Laboratory of Medical Genetics, Collegium Medicum, The Jan Kochanowski University, Kielce, Poland
| | - Wioletta Adamus-Białek
- Department of Surgical Medicine with the Laboratory of Medical Genetics, Collegium Medicum, The Jan Kochanowski University, Kielce, Poland
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15
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Kojic M, Jovcic B, Miljkovic M, Novovic K, Begovic J, Studholme DJ. Large-scale chromosome flip-flop reversible inversion mediates phenotypic switching of expression of antibiotic resistance in lactococci. Microbiol Res 2020; 241:126583. [PMID: 32919223 DOI: 10.1016/j.micres.2020.126583] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 08/14/2020] [Accepted: 08/15/2020] [Indexed: 11/26/2022]
Abstract
Bacteria can gain resistance to antimicrobials by acquiring and expressing genetic elements that encode resistance determinants such as efflux pumps and drug-modifying enzymes, thus hampering treatment of infection. Previously we showed that acquisition of spectinomycin resistance in a lactococcal strain was correlated with a reversible genomic inversion, but the precise location and the genes affected were unknown. Here we use long-read whole-genome sequencing to precisely define the genomic inversion and we use quantitative PCR to identify associated changes in gene expression levels. The boundaries of the inversion fall within two identical copies of a prophage-like sequence, located on the left and right replichores; this suggests possible mechanisms for inversion through homologous recombination or prophage activity. The inversion is asymmetrical in respect of the axis between the origin and terminus of the replication and modulates the expression of a SAM-dependent methyltransferase, whose heterologous expression confers resistance to spectinomycin in lactococci and that is up-regulated on exposure to spectinomycin. This study provides one of the first examples of phase variation via large-scale chromosomal inversions that confers a switch in antimicrobial resistance in bacteria and the first outside of Staphylococcus aureus.
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Affiliation(s)
- Milan Kojic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia.
| | - Branko Jovcic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia; Faculty of Biology, University of Belgrade, Belgrade, Serbia
| | - Marija Miljkovic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Katarina Novovic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Jelena Begovic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - David J Studholme
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK
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Wu L, Xiao X, Chen F, Zhang H, Huang L, Rong L, Zou X. New parameters for the quantitative assessment of the proliferation of antibiotic resistance genes dynamic in the environment and its application: A case of sulfonamides and sulfonamide resistance genes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 726:138516. [PMID: 32305759 DOI: 10.1016/j.scitotenv.2020.138516] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 04/03/2020] [Accepted: 04/05/2020] [Indexed: 06/11/2023]
Abstract
Antibiotic resistance genes (ARGs) have been widely detected around the world and are generally viewed as emerging pollutants with environmental persistence. The proliferation of ARGs can be easily promoted by antibiotics. However, the dynamics of ARGs in the environment are still unable to be quantified using a single parameter, which is vital to evaluating the ability of ARGs to spread by antibiotics and effectively controlling ARGs. A new parameter, termed the relative area ratio of sample to control (ΔAR), was developed based on the quantitative features determined by ARG-time curves in soils contaminated with sulfonamides (SAs) and verified by quantitative structure-activity relationships (QSARs) models. The results showed that ΔAR can not only be used to accurately quantify the characteristics of SAs resistance genes (Suls) over time but also be applied to reveal the relationships between the proliferation of Suls and important factors (i.e., concentrations and chemical structures). Moreover, the ΔAR-based QSARs model indicated that bioavailability and the frequency of conjugative transfer, rather than the ability of induced mutations in bacteria, tend to be key processes of the characteristics of the proliferation of Suls. Therefore, ΔAR is a useful parameter to perform environmental risk assessments of ARG proliferation in the environment.
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Affiliation(s)
- Ligui Wu
- School of Life Science, Jinggangshan University, Ji'an 343009, China
| | - Xiaoyu Xiao
- School of Life Science, Jinggangshan University, Ji'an 343009, China
| | - Fen Chen
- School of Life Science, Jinggangshan University, Ji'an 343009, China; College of Environmental Science and Engineering, Guilin University of Technology, Guilin 541004, China
| | - Huan Zhang
- School of Life Science, Jinggangshan University, Ji'an 343009, China
| | - Liangliang Huang
- College of Environmental Science and Engineering, Guilin University of Technology, Guilin 541004, China
| | - Lingling Rong
- School of Life Science, Jinggangshan University, Ji'an 343009, China
| | - Xiaoming Zou
- School of Life Science, Jinggangshan University, Ji'an 343009, China; College of Environmental Science and Engineering, Guilin University of Technology, Guilin 541004, China.
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17
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Adamus-Białek W, Wawszczak M, Arabski M, Majchrzak M, Gulba M, Jarych D, Parniewski P, Głuszek S. Ciprofloxacin, amoxicillin, and aminoglycosides stimulate genetic and phenotypic changes in uropathogenic Escherichia coli strains. Virulence 2020; 10:260-276. [PMID: 30938219 PMCID: PMC6527016 DOI: 10.1080/21505594.2019.1596507] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Antibiotic therapy and its consequences in bacterial and human aspects are widely investigated. Despite this, the emergence of new multidrug resistant bacteria is still a current problem. The scope of our work included the observation of changes among uropathogenic Escherichia coli strains after the treatment with a subinhibitory concentration of different antibiotics. The sensitive strains with or without virulence factors were incubated with amoxicillin, ciprofloxacin, gentamycin, or tobramycin. After each passage, the E. coli derivatives were compared to their wild types based on their susceptibility profiles, virulence genes, biofilm formations and the fingerprint profiles of PCR products amplified with using the (N)(6)(CGG)(4) primer. It turned out that antibiotics caused significant changes in the repertoire of bacterial virulence and biofilm formation, corresponding to acquired cross-resistance. The genomic changes among the studied bacteria were reflected in the changed profiles of the CGG-PCR products. In conclusion, the inappropriate application of antibiotics may cause a rapid rise of Multidrug Resistant (MDR) strains and give bacteria a chance to modulate their own pathogenicity. This phenomenon has been easily observed among uropathogenic E. coli strains and it is one of the main reasons for recurrent infections of the urinary tract.
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Affiliation(s)
- Wioletta Adamus-Białek
- a Department of Surgery and Surgical Nursery with Laboratory of Genetics, Faculty of Medicine and Health Sciences , Jan Kochanowski University , Kielce , Poland
| | - Monika Wawszczak
- a Department of Surgery and Surgical Nursery with Laboratory of Genetics, Faculty of Medicine and Health Sciences , Jan Kochanowski University , Kielce , Poland
| | - Michał Arabski
- b Department of Biochemistry & Genetics , Jan Kochanowski University , Kielce , Poland
| | - Michał Majchrzak
- a Department of Surgery and Surgical Nursery with Laboratory of Genetics, Faculty of Medicine and Health Sciences , Jan Kochanowski University , Kielce , Poland
| | - Martyna Gulba
- a Department of Surgery and Surgical Nursery with Laboratory of Genetics, Faculty of Medicine and Health Sciences , Jan Kochanowski University , Kielce , Poland
| | - Dariusz Jarych
- c Institute of Medical Biology, Polish Academy of Sciences , Łódź , Poland
| | - Paweł Parniewski
- c Institute of Medical Biology, Polish Academy of Sciences , Łódź , Poland
| | - Stanisław Głuszek
- a Department of Surgery and Surgical Nursery with Laboratory of Genetics, Faculty of Medicine and Health Sciences , Jan Kochanowski University , Kielce , Poland
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18
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Maldonado-Carmona N, Ouk TS, Calvete MJF, Pereira MM, Villandier N, Leroy-Lhez S. Conjugating biomaterials with photosensitizers: advances and perspectives for photodynamic antimicrobial chemotherapy. Photochem Photobiol Sci 2020; 19:445-461. [PMID: 32104827 DOI: 10.1039/c9pp00398c] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Antimicrobial resistance is threatening to overshadow last century's medical advances. Previously eradicated infectious diseases are now resurgent as multi-drug resistant strains, leading to expensive, toxic and, in some cases, ineffective antimicrobial treatments. Given this outlook, researchers are willing to investigate novel antimicrobial treatments that may be able to deal with antimicrobial resistance, namely photodynamic therapy (PDT). PDT relies on the generation of toxic reactive oxygen species (ROS) in the presence of light and a photosensitizer (PS) molecule. PDT has been known for almost a century, but most of its applications have been directed towards the treatment of cancer and topical diseases. Unlike classical antimicrobial chemotherapy treatments, photodynamic antimicrobial chemotherapy (PACT) has a non-target specific mechanism of action, based on the generation of ROS, working against cellular membranes, walls, proteins, lipids and nucleic acids. This non-specific mechanism diminishes the chances of bacteria developing resistance. However, PSs usually are large molecules, prone to aggregation, diminishing their efficiency. This review will report the development of materials obtained from natural sources, as delivery systems for photosensitizing molecules against microorganisms. The present work emphasizes on the biological results rather than on the synthesis routes to prepare the conjugates. Also, it discusses the current state of the art, providing our perspective on the field.
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19
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Yang L, Wen Q, Zhao Y, Chen Z, Wang Q, Bürgmann H. New insight into effect of antibiotics concentration and process configuration on the removal of antibiotics and relevant antibiotic resistance genes. JOURNAL OF HAZARDOUS MATERIALS 2019; 373:60-66. [PMID: 30903957 DOI: 10.1016/j.jhazmat.2019.03.060] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 03/14/2019] [Accepted: 03/14/2019] [Indexed: 06/09/2023]
Abstract
To compare the performance and antibiotic-resistance character in different process configurations under different levels of antibiotics, anoxic/oxic-membrane bioreactors (MBR) 1#, MBR2# and a sequencing batch reactor (SBR) were operated with identical operating parameters. MBR1# and SBR were operated under high and increasing levels of antibiotics, MBR2# received constant and low concentration of antibiotics. Microbiological community and antibiotic resistance genes (ARGs) were investigated using 16S rDNA gene high-throughput sequencing and qPCR. More than 90% of penicillin and chlortetracycline were removed due to strong hydrolysis, followed by sulfamethoxazole (69.27%-86.25%) through biodegradation and norfloxacin (28.66%-53.86%) through adsorption. Process configuration affected total nitrogen removal more, while antibiotics concentration affected total phosphorus removal more. MBR1# outperformed SBR in reducing sulfamethoxazole, norfloxacin and ARGs due to the retention effect of the membrane module. Retention efficiency of ARGs in MBRs increased along the operation. Compared to the operational taxonomic unit (OTU) number before antibiotics addition, the OTU number in MBR1# and SBR decreased by 23.7% and 28.7%, while that in MBR2# kept relatively stable. Process configuration contributed to higher dissimilarity of microbial community than antibiotics concentration. The research provides an insight into the influence factors of antibiotics-containing wastewater treatment.
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Affiliation(s)
- Lian Yang
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology (SKLUWRE, HIT), Harbin, 150090, PR China
| | - Qinxue Wen
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology (SKLUWRE, HIT), Harbin, 150090, PR China
| | - Yaqi Zhao
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology (SKLUWRE, HIT), Harbin, 150090, PR China
| | - Zhiqiang Chen
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology (SKLUWRE, HIT), Harbin, 150090, PR China; School of Civil Engineering, Lanzhou University of Technology, Lanzhou, 730070, PR China.
| | - Qiong Wang
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology (SKLUWRE, HIT), Harbin, 150090, PR China
| | - Helmut Bürgmann
- Eawag Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Eawag, CH-6047, Switzerland
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20
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Ghosh P, Das S. Synthesis and Functionalization of 4-Quinolones - A Progressing Story. European J Org Chem 2019. [DOI: 10.1002/ejoc.201900452] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Prasanjit Ghosh
- Department of Chemistry; University of North Bengal; 734013 Darjeeling West Bengal India
| | - Sajal Das
- Department of Chemistry; University of North Bengal; 734013 Darjeeling West Bengal India
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21
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Abstract
Bacteria frequently encounter low concentrations of antibiotics. Active antibiotics are commonly detected in soil and water at concentrations much below lethal concentration. Although sub-MICs of antibiotics do not kill bacteria, they can have a major impact on bacterial populations by contributing to the development of antibiotic resistance through mutations in originally sensitive bacteria or acquisition of DNA from resistant bacteria. It was shown that concentrations as low as 100-fold below the MIC can actually lead to the selection of antibiotic-resistant cells. We seek to understand how bacterial cells react to such antibiotic concentrations using E. coli, the Gram-negative bacterial paradigm, and V. cholerae, the causative agent of cholera. Our findings shed light on the processes triggered at the DNA level by antibiotics targeting translation, how damage occurs, and what the bacterial strategies are to respond to such DNA damage. We have previously identified Vibrio cholerae mutants in which the stress response to subinhibitory concentrations of aminoglycoside is altered. One gene identified, VC1636, encodes a putative DNA/RNA helicase, recently named RadD in Escherichia coli. Here we combined extensive genetic characterization and high-throughput approaches in order to identify partners and molecular mechanisms involving RadD. We show that double-strand DNA breaks (DSBs) are formed upon subinhibitory tobramycin treatment in the absence of radD and recBCD and that formation of these DSBs can be overcome by RNase H1 overexpression. Loss of RNase H1, or of the transcription-translation coupling factor EF-P, is lethal in the radD deletion mutant. We propose that R-loops are formed upon sublethal aminoglycoside treatment, leading to the formation of DSBs that can be repaired by the RecBCD homologous recombination pathway, and that RadD counteracts such R-loop accumulation. We discuss how R-loops that can occur upon translation-transcription uncoupling could be the link between tobramycin treatment and DNA break formation.
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22
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Distribution of Virulence and Antimicrobial Resistance Genes in Phylogenetic Groups of Escherichia coli Strains Isolated from Mexican Patients with Urinary Infection. Jundishapur J Microbiol 2019. [DOI: 10.5812/jjm.83711] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
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23
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Manohar K, Peroumal D, Acharya N. TLS dependent and independent functions of DNA polymerase eta (Polη/Rad30) from Pathogenic Yeast Candida albicans. Mol Microbiol 2018; 110:707-727. [PMID: 29907984 DOI: 10.1111/mmi.14004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2018] [Revised: 06/03/2018] [Accepted: 06/06/2018] [Indexed: 02/06/2023]
Abstract
Polη, a unique TLS DNA polymerase that promotes efficient bypass of UV-induced CPDs and cisplatin adducts, has not been explored in Candida species yet. Here, we show that CaPolη plays a vital role in protecting Candida albicans genome from diverse array of DNA damaging agents, not limited to UV and cisplatin. Polη deficient strain did not exhibit any hyphal development in the presence of UV and cisplatin while the wild type strain profusely developed DNA damage induced filamentation. The polarized growth induced by HU and MMS was found to be Polη independent. No common regulatory pathway of morphogenesis operates in C. albicans due to genomic stress, rather Polη branches away from RAD53 dependent pathway to be specific to UV/cisplatin. Interestingly, serum that does not inflict any DNA damage also induces hyphal growth in C. albicans, and requires a functionally active Polη. Importantly, deletion of RAD30 sensitized the strain to amphotericin B; but its presence resulted in azole drug tolerance only in DNA damaging conditions. We suggest that the roles of CaPolη in genome stability and genotoxins induced filamentation are due to its TLS activities; whereas its TLS independent functions play a vital role in serum induced morphogenesis and amphotericin B resistance.
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Affiliation(s)
- Kodavati Manohar
- Laboratory of Genomic Instability and Diseases, Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, India
| | - Doureradjou Peroumal
- Laboratory of Genomic Instability and Diseases, Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, India
| | - Narottam Acharya
- Laboratory of Genomic Instability and Diseases, Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, India
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Stubenrauch CJ, Dougan G, Lithgow T, Heinz E. Constraints on lateral gene transfer in promoting fimbrial usher protein diversity and function. Open Biol 2018; 7:rsob.170144. [PMID: 29142104 PMCID: PMC5717340 DOI: 10.1098/rsob.170144] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 10/05/2017] [Indexed: 12/16/2022] Open
Abstract
Fimbriae are long, adhesive structures widespread throughout members of the family Enterobacteriaceae. They are multimeric extrusions, which are moved out of the bacterial cell through an integral outer membrane protein called usher. The complex folding mechanics of the usher protein were recently revealed to be catalysed by the membrane-embedded translocation and assembly module (TAM). Here, we examine the diversity of usher proteins across a wide range of extraintestinal (ExPEC) and enteropathogenic (EPEC) Escherichia coli, and further focus on a so far undescribed chaperone–usher system, with this usher referred to as UshC. The fimbrial system containing UshC is distributed across a discrete set of EPEC types, including model strains like E2348/67, as well as ExPEC ST131, currently the most prominent multi-drug-resistant uropathogenic E. coli strain worldwide. Deletion of the TAM from a naive strain of E. coli results in a drastic time delay in folding of UshC, which can be observed for a protein from EPEC as well as for two introduced proteins from related organisms, Yersinia and Enterobacter. We suggest that this models why the TAM machinery is essential for efficient folding of proteins acquired via lateral gene transfer.
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Affiliation(s)
- Christopher J Stubenrauch
- Infection and Immunity Program, Department of Microbiology, Monash University, Clayton 3800, Australia
| | - Gordon Dougan
- Infection Genomics Program, Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK
| | - Trevor Lithgow
- Infection and Immunity Program, Department of Microbiology, Monash University, Clayton 3800, Australia
| | - Eva Heinz
- Infection Genomics Program, Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK
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25
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Giebułtowicz J, Tyski S, Wolinowska R, Grzybowska W, Zaręba T, Drobniewska A, Wroczyński P, Nałęcz-Jawecki G. Occurrence of antimicrobial agents, drug-resistant bacteria, and genes in the sewage-impacted Vistula River (Poland). ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2018; 25:5788-5807. [PMID: 29235021 DOI: 10.1007/s11356-017-0861-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Accepted: 11/28/2017] [Indexed: 06/07/2023]
Abstract
Antimicrobial agents (antimicrobials) are a group of therapeutic and hygienic agents that either kill microorganisms or inhibit their growth. Their occurrence in surface water may reveal harmful effects on aquatic biota and challenge microbial populations. Recently, there is a growing concern over the contamination of surface water with both antimicrobial agents and multidrug-resistant bacteria. The aim of the study was the determination of the presence of selected antimicrobials at specific locations of the Vistula River (Poland), as well as in tap water samples originating from the Warsaw region. Analysis was performed using the liquid chromatography-electrospray ionization-tandem mass spectrometry method. In addition, the occurrence of drug-resistant bacteria and resistance genes was determined using standard procedures. This 2-year study is the first investigation of the simultaneous presence of antimicrobial agents, drug-resistant bacteria, and genes in Polish surface water. In Poland, relatively high concentrations of macrolides are observed in both surface and tap water. Simultaneous to the high macrolide levels in the environment, the presence of the erm B gene, coding the resistance to macrolides, lincosamides, and streptogramin, was detected in almost all sampling sites. Another ubiquitous gene was int1, an element of the 5'-conserved segment of class 1 integrons that encode site-specific integrase. Also, resistant isolates of Enterococcus faecium and Enterococcus faecalis and Gram-negative bacteria were recovered. Multidrug-resistant bacteria isolates of Gram-negative and Enterococcus were also detected. The results show that wastewater treatment plants (WWTP) are the main source of most antimicrobials, resistant bacteria, and genes in the aquatic environment, probably due to partial purification during wastewater treatment processes.
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Affiliation(s)
- Joanna Giebułtowicz
- Department of Bioanalysis and Drugs Analysis, Faculty of Pharmacy, Medical University of Warsaw, 1 Banacha Street, 02097, Warsaw, Poland.
| | - Stefan Tyski
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Medical University of Warsaw, 1 Banacha Street, 02097, Warsaw, Poland
- Department of Antibiotics and Microbiology, National Medicines Institute, 30/34 Chelmska Street, 00725, Warsaw, Poland
| | - Renata Wolinowska
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Medical University of Warsaw, 1 Banacha Street, 02097, Warsaw, Poland
| | - Wanda Grzybowska
- Department of Antibiotics and Microbiology, National Medicines Institute, 30/34 Chelmska Street, 00725, Warsaw, Poland
| | - Tomasz Zaręba
- Department of Antibiotics and Microbiology, National Medicines Institute, 30/34 Chelmska Street, 00725, Warsaw, Poland
| | - Agata Drobniewska
- Department of Environmental Health Sciences, Faculty of Pharmacy, Medical University of Warsaw, 1 Banacha Street, 02097, Warsaw, Poland
| | - Piotr Wroczyński
- Department of Bioanalysis and Drugs Analysis, Faculty of Pharmacy, Medical University of Warsaw, 1 Banacha Street, 02097, Warsaw, Poland
| | - Grzegorz Nałęcz-Jawecki
- Department of Environmental Health Sciences, Faculty of Pharmacy, Medical University of Warsaw, 1 Banacha Street, 02097, Warsaw, Poland
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The Current Case of Quinolones: Synthetic Approaches and Antibacterial Activity. Molecules 2016; 21:268. [PMID: 27043501 PMCID: PMC6274096 DOI: 10.3390/molecules21040268] [Citation(s) in RCA: 111] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Revised: 02/08/2016] [Accepted: 02/15/2016] [Indexed: 11/17/2022] Open
Abstract
Quinolones are broad-spectrum synthetic antibacterial drugs first obtained during the synthesis of chloroquine. Nalidixic acid, the prototype of quinolones, first became available for clinical consumption in 1962 and was used mainly for urinary tract infections caused by Escherichia coli and other pathogenic Gram-negative bacteria. Recently, significant work has been carried out to synthesize novel quinolone analogues with enhanced activity and potential usage for the treatment of different bacterial diseases. These novel analogues are made by substitution at different sites--the variation at the C-6 and C-8 positions gives more effective drugs. Substitution of a fluorine atom at the C-6 position produces fluroquinolones, which account for a large proportion of the quinolones in clinical use. Among others, substitution of piperazine or methylpiperazine, pyrrolidinyl and piperidinyl rings also yields effective analogues. A total of twenty six analogues are reported in this review. The targets of quinolones are two bacterial enzymes of the class II topoisomerase family, namely gyrase and topoisomerase IV. Quinolones increase the concentration of drug-enzyme-DNA cleavage complexes and convert them into cellular toxins; as a result they are bactericidal. High bioavailability, relative low toxicity and favorable pharmacokinetics have resulted in the clinical success of fluoroquinolones and quinolones. Due to these superior properties, quinolones have been extensively utilized and this increased usage has resulted in some quinolone-resistant bacterial strains. Bacteria become resistant to quinolones by three mechanisms: (1) mutation in the target site (gyrase and/or topoisomerase IV) of quinolones; (2) plasmid-mediated resistance; and (3) chromosome-mediated quinolone resistance. In plasmid-mediated resistance, the efflux of quinolones is increased along with a decrease in the interaction of the drug with gyrase (topoisomerase IV). In the case of chromosome-mediated quinolone resistance, there is a decrease in the influx of the drug into the cell.
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Michael CA, Dominey-Howes D, Labbate M. The antimicrobial resistance crisis: causes, consequences, and management. Front Public Health 2014; 2:145. [PMID: 25279369 PMCID: PMC4165128 DOI: 10.3389/fpubh.2014.00145] [Citation(s) in RCA: 429] [Impact Index Per Article: 42.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2014] [Accepted: 09/01/2014] [Indexed: 12/31/2022] Open
Abstract
The antimicrobial resistance (AMR) crisis is the increasing global incidence of infectious diseases affecting the human population, which are untreatable with any known antimicrobial agent. This crisis will have a devastating cost on human society as both debilitating and lethal diseases increase in frequency and scope. Three major factors determine this crisis: (1) the increasing frequency of AMR phenotypes among microbes is an evolutionary response to the widespread use of antimicrobials; (2) the large and globally connected human population allows pathogens in any environment access to all of humanity; and (3) the extensive and often unnecessary use of antimicrobials by humanity provides the strong selective pressure that is driving the evolutionary response in the microbial world. Of these factors, the size of the human population is least amenable to rapid change. In contrast, the remaining two factors may be affected, so offering a means of managing the crisis: the rate at which AMR, as well as virulence factors evolve in microbial world may be slowed by reducing the applied selective pressure. This may be accomplished by radically reducing the global use of current and prospective antimicrobials. Current management measures to legislate the use of antimicrobials and to educate the healthcare world in the issues, while useful, have not comprehensively addressed the problem of achieving an overall reduction in the human use of antimicrobials. We propose that in addition to current measures and increased research into new antimicrobials and diagnostics, a comprehensive education program will be required to change the public paradigm of antimicrobial usage from that of a first line treatment to that of a last resort when all other therapeutic options have failed.
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Affiliation(s)
- Carolyn Anne Michael
- School of Medical and Molecular Biosciences, University of Technology , Sydney, NSW , Australia
| | - Dale Dominey-Howes
- Asia - Pacific Natural Hazards Research Group, School of Geosciences, University of Sydney , Sydney, NSW , Australia
| | - Maurizio Labbate
- School of Medical and Molecular Biosciences, University of Technology , Sydney, NSW , Australia ; ithree Institute, University of Technology , Sydney, NSW , Australia
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Baharoglu Z, Mazel D. Influence of very short patch mismatch repair on SOS inducing lesions after aminoglycoside treatment in Escherichia coli. Res Microbiol 2014; 165:476-80. [PMID: 24946128 DOI: 10.1016/j.resmic.2014.05.039] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Revised: 05/22/2014] [Accepted: 05/28/2014] [Indexed: 10/25/2022]
Abstract
Low concentrations of aminoglycosides induce the SOS response in Vibrio cholerae but not in Escherichia coli. In order to determine whether a specific factor present in E. coli prevents this induction, we developed a genetic screen where only SOS inducing mutants are viable. We identified the vsr gene coding for the Vsr protein of the very short patch mismatch repair (VSPR) pathway. The effect of mismatch repair (MMR) mutants was also studied. We propose that lesions formed upon aminoglycoside treatment are preferentially repaired by VSPR without SOS induction in E. coli and by MMR when VSPR is impaired.
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Affiliation(s)
- Zeynep Baharoglu
- Institut Pasteur, Unité Plasticité du Génome Bactérien, Département Génomes et Génétique, 25 rue du docteur Roux, 75015 Paris, France; CNRS, UMR3525, Paris, France.
| | - Didier Mazel
- Institut Pasteur, Unité Plasticité du Génome Bactérien, Département Génomes et Génétique, 25 rue du docteur Roux, 75015 Paris, France; CNRS, UMR3525, Paris, France
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