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Godinho O, Devos DP, Quinteira S, Lage OM. The influence of the phylum Planctomycetota in the environmental resistome. Res Microbiol 2024; 175:104196. [PMID: 38467354 DOI: 10.1016/j.resmic.2024.104196] [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: 09/08/2023] [Revised: 02/28/2024] [Accepted: 03/06/2024] [Indexed: 03/13/2024]
Abstract
Antimicrobial resistance is one of the leading causes of death worldwide and research on this topic has been on the spotlight for a long time. More recently and in agreement with the One Health Approach, the focus has moved towards the environmental resistome. Members of the phylum Planctomycetota are ubiquitously present in the environment including in hotspots for antimicrobial resistance selection and dissemination. Furthermore, phenotypic broad-range resistance has been observed in diverse members of this phylum. Here we review the evidence available on antimicrobial resistance in the underexploited Planctomycetota and highlight key aspects for future studies.
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Affiliation(s)
- Ofélia Godinho
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal; CIMAR/CIIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Porto, Portugal.
| | - Damien P Devos
- Centro Andaluz de Biología del Desarrollo, Consejo Superior de Investigaciones Científicas, Junta de Andalucía, Universidad Pablo de Olavide, Seville, Spain
| | - Sandra Quinteira
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal; CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO, Rede de Investigação em Biodiversidade e Biologia Evolutiva, Laboratório Associado, Universidade do Porto, 4485-6661 Vairão, Portugal; BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal; 1H-TOXRUN - One Health Toxicology Research Unit, University Institute of Health Sciences (IUCS), CESPU, CRL, 4585-116 Gandra, Portugal
| | - Olga M Lage
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal; CIMAR/CIIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Porto, Portugal
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2
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Laborda P, Molin S, Johansen HK, Martínez JL, Hernando-Amado S. Role of bacterial multidrug efflux pumps during infection. World J Microbiol Biotechnol 2024; 40:226. [PMID: 38822187 DOI: 10.1007/s11274-024-04042-7] [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: 04/03/2024] [Accepted: 05/29/2024] [Indexed: 06/02/2024]
Abstract
Multidrug efflux pumps are protein complexes located in the cell envelope that enable bacteria to expel, not only antibiotics, but also a wide array of molecules relevant for infection. Hence, they are important players in microbial pathogenesis. On the one hand, efflux pumps can extrude exogenous compounds, including host-produced antimicrobial molecules. Through this extrusion, pathogens can resist antimicrobial agents and evade host defenses. On the other hand, efflux pumps also have a role in the extrusion of endogenous compounds, such as bacterial intercommunication signaling molecules, virulence factors or metabolites. Therefore, efflux pumps are involved in the modulation of bacterial behavior and virulence, as well as in the maintenance of the bacterial homeostasis under different stresses found within the host. This review delves into the multifaceted roles that efflux pumps have, shedding light on their impact on bacterial virulence and their contribution to bacterial infection. These observations suggest that strategies targeting bacterial efflux pumps could both reinvigorate the efficacy of existing antibiotics and modulate the bacterial pathogenicity to the host. Thus, a comprehensive understanding of bacterial efflux pumps can be pivotal for the development of new effective strategies for the management of infectious diseases.
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Affiliation(s)
- Pablo Laborda
- Department of Clinical Microbiology, Rigshospitalet, Copenhagen, 9301, Denmark.
| | - Søren Molin
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Helle Krogh Johansen
- Department of Clinical Microbiology, Rigshospitalet, Copenhagen, 9301, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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3
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Ren Z, Li H, Luo W. Unraveling the mystery of antibiotic resistance genes in green and red Antarctic snow. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 915:170148. [PMID: 38246373 DOI: 10.1016/j.scitotenv.2024.170148] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Revised: 01/09/2024] [Accepted: 01/11/2024] [Indexed: 01/23/2024]
Abstract
Antarctic snow is a thriving habitat for a diverse array of complex microorganisms, and can present in different colors due to algae blooms. However, the potential role of Antarctic snow as reservoirs for antibiotic resistance genes (ARGs) has not been studied. Using metagenomic sequencing, we studied ARGs in green-snow and red-snow on the Fildes Peninsula, Antarctica. Alpha and beta diversities of ARGs, as well as co-occurrence between ARGs and bacteria were assessed. The results showed that a total of 525 ARGs conferring resistance to 30 antibiotic classes were detected across the samples, with half of the ARGs presented in all samples. Green-snow exhibited a higher number of ARGs compared to red-snow. The most abundant ARGs conferring resistance to commonly used antibiotics, including disinfecting agents and antiseptics, peptide, isoniazid, MLS, fluoroquinolone, aminocoumarin, etc. Multidrug resistance genes stood out as the most diverse and abundant, with antibiotic efflux emerging as the dominant resistance mechanism. Interestingly, the composition of ARGs in green-snow markedly differed from that in red-snow, highlighting distinct ARG profiles. Beta-diversity partitioning showed a higher contribution of nestedness for ARG's variation in green-snow, while higher contribution of turnover in red-snow. Furthermore, the co-occurrence analysis between ARGs and bacteria unveiled intricate relationships, indicating that certain ARGs may have multiple potential hosts. The observed differences in co-occurrence networks between green-snow and red-snow suggested distinct host relationships between ARGs and bacteria in these colored snows. Given the increasing appearance of the colored snow around the world due to the climate change, the results shed light on the mystery and potential implication of ARGs in green and red Antarctic snow.
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Affiliation(s)
- Ze Ren
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Huirong Li
- Key Laboratory for Polar Science, Polar Research Institute of China, Ministry of Natural Resources, Shanghai 200136, China; Key Laboratory of Polar Ecosystem and Climate Change, Shanghai Jiao Tong University, Ministry of Education, Shanghai 200030, China; Shanghai Key Laboratory of Polar Life and Environment Sciences, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Wei Luo
- Key Laboratory for Polar Science, Polar Research Institute of China, Ministry of Natural Resources, Shanghai 200136, China; Key Laboratory of Polar Ecosystem and Climate Change, Shanghai Jiao Tong University, Ministry of Education, Shanghai 200030, China; Shanghai Key Laboratory of Polar Life and Environment Sciences, Shanghai Jiao Tong University, Shanghai 200030, China.
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4
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Ren Z, Zhang C, Li X, Luo W. Thermokarst lakes are hotspots of antibiotic resistance genes in permafrost regions on the Qinghai-Tibet Plateau. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 344:123334. [PMID: 38218544 DOI: 10.1016/j.envpol.2024.123334] [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: 08/18/2023] [Revised: 11/02/2023] [Accepted: 01/07/2024] [Indexed: 01/15/2024]
Abstract
Antibiotic resistance genes (ARGs) are natural products and emerging pollutants in remote environments, including permafrost regions that are rapidly thawing due to climate warming. We investigated the role of thermokarst lakes (including sediment and water) in reserving ARGs compared to permafrost soils across the permafrost regions on the Qinghai-Tibet Plateau. As intrinsically connected distinct environments, permafrost soil, lake sediment, and lake water harbored 1239 ARGs in total, while a considerable number of same ARGs (683 out of 1239) concurrently presented in all these environments. Soil and sediment had a higher number of ARGs than water. Multidrug resistance genes were the most diverse and abundant in all three environments, where cls, ropB, mdfA, fabI, and macB were the top five most abundant ARGs while with different orders. Soil and sediment had similar ARG profiles, and the alpha and beta diversity of ARGs in sediment were positively correlated with that in soil. The beta diversity of ARG profiles between sediment and soil was highly contributed by turnover component (89%). However, turnover and nestedness components were almost equality contributed (46%-54%) to the beta diversity of ARG profiles between soil and water as well as between sediment and water. The results suggested that thermokarst lake sediments might inherit the ARGs in permafrost soils. Water ARGs are the subset of soil ARGs and sediment ARGs to a certain degree with species turnover playing a significant role. When accounting the ARGs in sediment and water together, thermokarst lakes had a significantly higher number of ARGs than permafrost soils, suggesting that thermokarst lakes act as the hotspots of ARGs in permafrost regions. These findings are disturbing especially due to the fact that tremendous number of thermokarst lakes are forming under accelerating climate change.
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Affiliation(s)
- Ze Ren
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Cheng Zhang
- Advanced Institute of Natural Sciences, Beijing Normal University, Zhuhai, 519087, China; School of Engineering Technology, Beijing Normal University, Zhuhai, 519087, China
| | - Xia Li
- Advanced Institute of Natural Sciences, Beijing Normal University, Zhuhai, 519087, China
| | - Wei Luo
- Key Laboratory for Polar Science, Polar Research Institute of China, Ministry of Natural Resources, Shanghai, 200136, China; Key Laboratory of Polar Ecosystem and Climate Change (Shanghai Jiao Tong University), Ministry of Education, Shanghai, 200030, China; The Technology and Equipment Engineering Centre for Polar Observations, Zhejiang University, Zhoushan, 316000, China.
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Shi X, Dai Y, Lan Z, Wang S, Cui L, Xiao C, Zhao K, Li X, Liu W, Zhang Q. Interplay between the β-lactam side chain and an active-site mobile loop of NDM-1 in penicillin hydrolysis as a potential target for mechanism-based inhibitor design. Int J Biol Macromol 2024; 262:130041. [PMID: 38336327 DOI: 10.1016/j.ijbiomac.2024.130041] [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: 10/09/2023] [Revised: 02/04/2024] [Accepted: 02/06/2024] [Indexed: 02/12/2024]
Abstract
Metallo-β-lactamases (MβLs) stand as significant resistant mechanism against β-lactam antibiotics in Gram-negative bacteria. The worldwide dissemination of New Delhi metallo-β-lactamases (NDMs) intensifies antimicrobial resistance, posing severe threats to human health due to the absence of inhibitors available in clinical therapy. L3, a flexible β-hairpin loop flanking the active site in MβLs, has been proven to wield influence over the reaction process by assuming a crucial role in substrate recognition and intermediate stabilization. In principle, it potentially retards product release from the enzyme, consequently reducing the overall turnover rate although the details regarding this aspect remain inadequately elucidated. In this study, we crystallized NDM-1 in complex with three penicillin substrates, conducted molecular dynamics simulations, and measured the steady-state kinetic parameters. These analyses consistently unveiled substantial disparities in their interactions with loop L3. We further synthesized a penicillin V derivative with increased hydrophobicity in the R1 side chain and co-crystallized it with NDM-1. Remarkably, this compound exhibited much stronger dynamic interplay with L3 during molecular dynamics simulation, showed much lower Km and kcat values, and demonstrated moderate inhibitory capacity to NDM-1 catalyzed meropenem hydrolysis. The data presented here may provide a strategic approach for designing mechanism-based MβL inhibitors focusing on structural elements external to the enzyme's active center.
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Affiliation(s)
- Xiangrui Shi
- Department of Obstetrics and Gynecology, Daping Hospital, Army Medical University, Chongqing 400042, China
| | - Yujie Dai
- Department of Obstetrics and Gynecology, Daping Hospital, Army Medical University, Chongqing 400042, China
| | - Zhu Lan
- Institute of Immunology, Army Medical University, Chongqing 400038, China
| | - Sheng Wang
- College of Life Science and Technology, Huazhong University of Science and Technology, 1037 Luoyu Avenue, Wuhan, Hubei 430074, China
| | - Liwei Cui
- Institute of Immunology, Army Medical University, Chongqing 400038, China
| | - Chengliang Xiao
- College of Life Science and Technology, Huazhong University of Science and Technology, 1037 Luoyu Avenue, Wuhan, Hubei 430074, China
| | - Kunhong Zhao
- Key Laboratory of Green Pesticide and Agricultural Bioengineering, Minister of Education, Guizhou University, Guiyang 550025, China
| | - Xiangyang Li
- Key Laboratory of Green Pesticide and Agricultural Bioengineering, Minister of Education, Guizhou University, Guiyang 550025, China.
| | - Wei Liu
- Institute of Immunology, Army Medical University, Chongqing 400038, China.
| | - Qinghua Zhang
- Department of Obstetrics and Gynecology, Daping Hospital, Army Medical University, Chongqing 400042, China.
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Otun SO, Graca R, Achilonu I. Combating Aminoglycoside Resistance: From Structural and Functional Characterisation to Therapeutic Challenges with RKAAT. Curr Protein Pept Sci 2024; 25:454-468. [PMID: 38314602 DOI: 10.2174/0113892037278814231226104509] [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: 09/18/2023] [Revised: 12/04/2023] [Accepted: 12/07/2023] [Indexed: 02/06/2024]
Abstract
A comprehensive knowledge of aminoglycoside-modifying enzymes (AMEs) and their role in bacterial resistance mechanisms is urgently required due to the rising incidence of antibiotic resistance, particularly in Klebsiella pneumoniae infections. This study explores the essential features of AMEs, including their structural and functional properties, the processes by which they contribute to antibiotic resistance, and the therapeutic importance of aminoglycosides. The study primarily examines the Recombinant Klebsiella pneumoniae Aminoglycoside Adenylyl Transferase (RKAAT), particularly emphasizing its biophysical characteristics and the sorts of resistance it imparts. Furthermore, this study examines the challenges presented by RKAAT-mediated resistance, an evaluation of treatment methods and constraints, and options for controlling infection. The analysis provides a prospective outlook on strategies to address and reduce antibiotic resistance. This extensive investigation seeks to provide vital insights into the continuing fight against bacterial resistance, directing future research efforts and medicinal approaches.
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Affiliation(s)
- Sarah Oluwatobi Otun
- Department of Molecular and Cell Biology, Protein Structure-function Unit, University of Witwatersrand, Johannesburg, South Africa
| | - Richard Graca
- Department of Molecular and Cell Biology, Protein Structure-function Unit, University of Witwatersrand, Johannesburg, South Africa
| | - Ikechukwu Achilonu
- Department of Molecular and Cell Biology, Protein Structure-function Unit, University of Witwatersrand, Johannesburg, South Africa
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Lee C, Zaheer R, Munns K, Holman DB, Van Domselaar G, Zovoilis A, McAllister TA. Effect of Antimicrobial Use in Conventional Versus Natural Cattle Feedlots on the Microbiome and Resistome. Microorganisms 2023; 11:2982. [PMID: 38138126 PMCID: PMC10745953 DOI: 10.3390/microorganisms11122982] [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: 11/06/2023] [Revised: 12/08/2023] [Accepted: 12/12/2023] [Indexed: 12/24/2023] Open
Abstract
Antimicrobial use (AMU) in the livestock industry has been associated with increased levels of antimicrobial resistance. Recently, there has been an increase in the number of "natural" feedlots in the beef cattle sector that raise cattle without antibiotics. Shotgun metagenomics was employed to characterize the impact of AMU in feedlot cattle on the microbiome, resistome, and mobilome. Sequenced fecal samples identified a decline (q < 0.01) in the genera Methanobrevibacter and Treponema in the microbiome of naturally vs. conventionally raised feedlot cattle, but this difference was not (q > 0.05) observed in catch basin samples. No differences (q > 0.05) were found in the class-level resistome between feedlot practices. In fecal samples, decreases from conventional to natural (q < 0.05) were noted in reads for the antimicrobial-resistant genes (ARGs) mefA, tet40, tetO, tetQ, and tetW. Plasmid-associated ARGs were more common in feces from conventional than natural feedlot cattle. Interestingly, more chromosomal- than plasmid-associated macrolide resistance genes were observed in both natural and conventional feedlots, suggesting that they were more stably conserved than the predominately plasmid-associated tetracycline resistance genes. This study suggests that generationally selected resistomes through decades of AMU persist even after AMU ceases in natural production systems.
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Affiliation(s)
- Catrione Lee
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Government of Canada, 5403 1st Avenue South, Lethbridge, AB T1J 4B1, Canada; (C.L.); (R.Z.); (K.M.)
- Southern Alberta Genomic Sciences Centre, Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, AB T1K 3M4, Canada;
| | - Rahat Zaheer
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Government of Canada, 5403 1st Avenue South, Lethbridge, AB T1J 4B1, Canada; (C.L.); (R.Z.); (K.M.)
| | - Krysty Munns
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Government of Canada, 5403 1st Avenue South, Lethbridge, AB T1J 4B1, Canada; (C.L.); (R.Z.); (K.M.)
| | - Devin B. Holman
- Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, Government of Canada, 6000 C and E Trail, Lacombe, AB T4L 1W1, Canada;
| | - Gary Van Domselaar
- National Microbiology Laboratory, Public Health Agency of Canada, Government of Canada, 1015 Arlington Street, Winnipeg, MB R3E 3R2, Canada;
| | - Athanasios Zovoilis
- Southern Alberta Genomic Sciences Centre, Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, AB T1K 3M4, Canada;
| | - Tim A. McAllister
- Southern Alberta Genomic Sciences Centre, Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, AB T1K 3M4, Canada;
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Obanor O, Afegbua SL, Ameh JB. Sanitary status and water quality of some drinking water sources and antibiogram of Shiga toxin-producing Escherichia coli O157:H7 isolated from Shika, Zaria, Nigeria. INTERNATIONAL JOURNAL OF ENVIRONMENTAL HEALTH RESEARCH 2023; 33:1604-1616. [PMID: 35984757 DOI: 10.1080/09603123.2022.2111409] [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: 02/14/2022] [Accepted: 08/04/2022] [Indexed: 06/15/2023]
Abstract
This study assessed the sanitary condition and quality of selected wells and boreholes in Shika, Zaria Nigeria. Fifty samples each were collected during the dry and wet seasons. This involved sanitary survey, water quality assessment, isolation and characterization of Shiga toxin-producing Escherichia coli O157:H7 (STEC) and, antibiogram assay. Based on the risk of contamination, wells (72%) had a high risk of contamination, while boreholes (44%) had low risk of contamination. Their physicochemical quality varied with season and location, and mean total coliform (TC) and faecal coliform (FC) were significantly lower in the dry season (p < 0.05). STEC were isolated from only wells with a prevalence of 4%, and exhibited a multidrug resistance pattern (amoxicillin, erythromycin and tetracycline). There was a strong positive correlation between sanitary status and water quality. The high- and very high-risk categories (wells) were strongly correlated with TC, FC, BOD, phosphate, turbidity and pH. .
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Affiliation(s)
- Osayande Obanor
- Department of Microbiology, Faculty of Life Sciences, Ahmadu Bello University, Zaria, Nigeria
| | - Seniyat Larai Afegbua
- Department of Microbiology, Faculty of Life Sciences, Ahmadu Bello University, Zaria, Nigeria
| | - Joseph Baba Ameh
- Department of Microbiology, Faculty of Life Sciences, Ahmadu Bello University, Zaria, Nigeria
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Sanz-García F, Gil-Gil T, Laborda P, Blanco P, Ochoa-Sánchez LE, Baquero F, Martínez JL, Hernando-Amado S. Translating eco-evolutionary biology into therapy to tackle antibiotic resistance. Nat Rev Microbiol 2023; 21:671-685. [PMID: 37208461 DOI: 10.1038/s41579-023-00902-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/19/2023] [Indexed: 05/21/2023]
Abstract
Antibiotic resistance is currently one of the most important public health problems. The golden age of antibiotic discovery ended decades ago, and new approaches are urgently needed. Therefore, preserving the efficacy of the antibiotics currently in use and developing compounds and strategies that specifically target antibiotic-resistant pathogens is critical. The identification of robust trends of antibiotic resistance evolution and of its associated trade-offs, such as collateral sensitivity or fitness costs, is invaluable for the design of rational evolution-based, ecology-based treatment approaches. In this Review, we discuss these evolutionary trade-offs and how such knowledge can aid in informing combination or alternating antibiotic therapies against bacterial infections. In addition, we discuss how targeting bacterial metabolism can enhance drug activity and impair antibiotic resistance evolution. Finally, we explore how an improved understanding of the original physiological function of antibiotic resistance determinants, which have evolved to reach clinical resistance after a process of historical contingency, may help to tackle antibiotic resistance.
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Affiliation(s)
- Fernando Sanz-García
- Departamento de Microbiología, Medicina Preventiva y Salud Pública, Universidad de Zaragoza, Zaragoza, Spain
| | - Teresa Gil-Gil
- Centro Nacional de Biotecnología, CSIC, Darwin 3, Madrid, Spain
- Programa de Doctorado en Biociencias Moleculares, Universidad Autónoma de Madrid, Madrid, Spain
| | - Pablo Laborda
- Centro Nacional de Biotecnología, CSIC, Darwin 3, Madrid, Spain
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
- Department of Clinical Microbiology, 9301, Rigshospitalet, Copenhagen, Denmark
| | - Paula Blanco
- Molecular Basis of Adaptation, Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid, Spain
- VISAVET Health Surveillance Centre, Universidad Complutense Madrid, Madrid, Spain
| | | | - Fernando Baquero
- Department of Microbiology, Hospital Universitario Ramón y Cajal (IRYCIS), CIBER en Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
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Singh S, Verma T, Khamari B, Bulagonda EP, Nandi D, Umapathy S. Antimicrobial Resistance Studies Using Raman Spectroscopy on Clinically Relevant Bacterial Strains. Anal Chem 2023. [PMID: 37463121 DOI: 10.1021/acs.analchem.3c01453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2023]
Abstract
There has been a steep rise in the emergence of antibiotic-resistant bacteria in the past few years. A timely diagnosis can help in initiating appropriate antibiotic therapy. However, conventional techniques for diagnosing antibiotic resistance are time-consuming and labor-intensive. Therefore, we investigated the potential of Raman spectroscopy as a rapid surveillance technology for tracking the emergence of antibiotic resistance. In this study, we used Raman spectroscopy to differentiate clinical isolates of antibiotic-resistant and -sensitive bacteria of Escherichia coli, Acinetobacter baumannii, and Enterobacter species. The spectra were collected with or without exposure to various antibiotics (ciprofloxacin, gentamicin, meropenem, and nitrofurantoin), each having a distinct mechanism of action. Ciprofloxacin- and meropenem-treated sensitive strains showed a decrease in the intensity of Raman bands associated with DNA (667, 724, 785, 1378, 1480, and 1575 cm-1) and proteins (640 and 1662 cm-1), coupled with an increase in the intensity of lipid bands (891, 960, and 1445 cm-1). Gentamicin- and nitrofurantoin-treated sensitive strains showed an increase in the intensity of nucleic acid bands (668, 724, 780, 810, 1378, 1480, and 1575 cm-1) while a decrease in the intensity of protein bands (640, 1003, 1606, and 1662 cm-1) and the lipid band (1445 cm-1). The Raman spectral changes observed in the antibiotic-resistant strains were opposite to that of antibiotic-sensitive strains. The Raman spectral data correlated well with the antimicrobial susceptibility test results. The Raman spectral dataset was used for partial least-squares (PLS) analysis to validate the biomarkers obtained from the univariate analysis. Overall, this study showcases the potential of Raman spectroscopy for detecting antibiotic-resistant and -sensitive bacteria.
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Affiliation(s)
- Saumya Singh
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore 560012, Karnataka, India
| | - Taru Verma
- Centre for Biosystems Science and Engineering, Indian Institute of Science, Bangalore 560012, Karnataka, India
| | - Balaram Khamari
- Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Puttaparthi 515134, Andhra Pradesh, India
| | - Eswarappa Pradeep Bulagonda
- Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Puttaparthi 515134, Andhra Pradesh, India
| | - Dipankar Nandi
- Centre for Biosystems Science and Engineering, Indian Institute of Science, Bangalore 560012, Karnataka, India
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, Karnataka, India
| | - Siva Umapathy
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore 560012, Karnataka, India
- Centre for Biosystems Science and Engineering, Indian Institute of Science, Bangalore 560012, Karnataka, India
- Department of Instrumentation and Applied Physics, Indian Institute of Science, Bangalore 560012, Karnataka, India
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11
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Junaid M, Thirapanmethee K, Khuntayaporn P, Chomnawang MT. CRISPR-Based Gene Editing in Acinetobacter baumannii to Combat Antimicrobial Resistance. Pharmaceuticals (Basel) 2023; 16:920. [PMID: 37513832 PMCID: PMC10384873 DOI: 10.3390/ph16070920] [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: 05/25/2023] [Revised: 06/19/2023] [Accepted: 06/20/2023] [Indexed: 07/30/2023] Open
Abstract
Antimicrobial resistance (AMR) poses a significant threat to the health, social, environment, and economic sectors on a global scale and requires serious attention to addressing this issue. Acinetobacter baumannii was given top priority among infectious bacteria because of its extensive resistance to nearly all antibiotic classes and treatment options. Carbapenem-resistant A. baumannii is classified as one of the critical-priority pathogens on the World Health Organization (WHO) priority list of antibiotic-resistant bacteria for effective drug development. Although available genetic manipulation approaches are successful in A. baumannii laboratory strains, they are limited when employed on newly acquired clinical strains since such strains have higher levels of AMR than those used to select them for genetic manipulation. Recently, the CRISPR-Cas (Clustered regularly interspaced short palindromic repeats/CRISPR-associated protein) system has emerged as one of the most effective, efficient, and precise methods of genome editing and offers target-specific gene editing of AMR genes in a specific bacterial strain. CRISPR-based genome editing has been successfully applied in various bacterial strains to combat AMR; however, this strategy has not yet been extensively explored in A. baumannii. This review provides detailed insight into the progress, current scenario, and future potential of CRISPR-Cas usage for AMR-related gene manipulation in A. baumannii.
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Affiliation(s)
- Muhammad Junaid
- Department of Microbiology, Faculty of Pharmacy, Mahidol University, Bangkok 10400, Thailand
- Antimicrobial Resistance Interdisciplinary Group (AmRIG), Faculty of Pharmacy, Mahidol University, Bangkok 10400, Thailand
| | - Krit Thirapanmethee
- Department of Microbiology, Faculty of Pharmacy, Mahidol University, Bangkok 10400, Thailand
- Antimicrobial Resistance Interdisciplinary Group (AmRIG), Faculty of Pharmacy, Mahidol University, Bangkok 10400, Thailand
| | - Piyatip Khuntayaporn
- Department of Microbiology, Faculty of Pharmacy, Mahidol University, Bangkok 10400, Thailand
- Antimicrobial Resistance Interdisciplinary Group (AmRIG), Faculty of Pharmacy, Mahidol University, Bangkok 10400, Thailand
| | - Mullika Traidej Chomnawang
- Department of Microbiology, Faculty of Pharmacy, Mahidol University, Bangkok 10400, Thailand
- Antimicrobial Resistance Interdisciplinary Group (AmRIG), Faculty of Pharmacy, Mahidol University, Bangkok 10400, Thailand
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12
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Cheng Q, Ma Z, Gong Z, Liang Y, Guo J, Ye X, Han Z, Yao Z. Whole-genome sequencing analysis of Klebsiella aerogenes among men who have sex with men in Guangzhou, China. Front Microbiol 2023; 14:1102907. [PMID: 37333657 PMCID: PMC10272549 DOI: 10.3389/fmicb.2023.1102907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Accepted: 05/09/2023] [Indexed: 06/20/2023] Open
Abstract
Klebsiella aerogenes is a common infectious bacterium that poses a threat to human health. Nevertheless, there are limited data on the population structure, genetic diversity, and pathogenicity of K. aerogenes, especially among men who have sex with men (MSM). The present study aimed to clarify the sequence types (STs), clonal complexes (CCs), resistance genes, and virulence factors of popular strains. Multilocus sequence typing was used to describe the population structure of K. aerogenes. The Virulence Factor Database and Comprehensive Antibiotic Resistance Database were used to assess the virulence and resistance profiles. In this study, next-generation sequencing was performed on nasal swabs specimens collected in an HIV Voluntary Counseling Testing outpatient department in Guangzhou, China, from April to August 2019. The identification results showed that a total of 258 K. aerogenes isolates were collected from 911 participants. We found that the isolates were most resistant to furantoin (89.53%, 231/258) and ampicillin (89.15%, 230/258), followed by imipenem (24.81%, 64/258) and cefotaxime (18.22%, 47/258). The most common STs in carbapenem-resistant K. aerogenes were ST4, ST93, and ST14. The population has at least 14 CCs, including several novel ones identified in this study (CC11-CC16). The main mechanism of drug resistance genes was antibiotic efflux. Based on the presence of the iron carrier production genes irp and ybt, we identified two clusters according to virulence profiles. In cluster A, CC3 and CC4 carry the clb operator encoding the toxin. Increased monitoring is needed for the three main ST type strains carried by MSM. The main clone group CC4 has a large number of toxin genes, and it spreads among MSM. Caution is needed to prevent further spread of this clone group in this population. In sum, our results may provide a foundation for the development of new therapeutic and surveillance strategies for treating MSM.
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Affiliation(s)
- Qi Cheng
- Department of Epidemiology and Health Statistics, School of Public Health, Guangdong Pharmaceutical University, Guangzhou, China
| | - Zheng Ma
- The Sixth People's Hospital of Dongguan, Dongguan, China
| | - Zijun Gong
- Department of Epidemiology and Health Statistics, School of Public Health, Guangdong Pharmaceutical University, Guangzhou, China
| | - Yuelang Liang
- Department of Epidemiology and Health Statistics, School of Public Health, Guangdong Pharmaceutical University, Guangzhou, China
| | - Jiajia Guo
- Department of Epidemiology and Health Statistics, School of Public Health, Guangdong Pharmaceutical University, Guangzhou, China
| | - Xiaohua Ye
- Department of Epidemiology and Health Statistics, School of Public Health, Guangdong Pharmaceutical University, Guangzhou, China
| | - Zhigang Han
- Department of Acquired Immune Deficiency Syndrome/Sexually Transmitted Disease Control and Prevention, Guangzhou Center for Disease Control and Prevention, Guangzhou, China
| | - Zhenjiang Yao
- Department of Epidemiology and Health Statistics, School of Public Health, Guangdong Pharmaceutical University, Guangzhou, China
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13
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Liang H, Zhang J, Hu J, Li X, Li B. Fluoroquinolone Residues in the Environment Rapidly Induce Heritable Fluoroquinolone Resistance in Escherichia coli. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:4784-4795. [PMID: 36917150 DOI: 10.1021/acs.est.2c04999] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Extensive antibiotic use increases the environmental presence of their residues and may accelerate the development of antibiotic resistance, although this remains poorly understood at environmentally relevant concentrations. Herein, susceptible Escherichia coli K12 was continuously exposed to five antibiotics at such concentrations for 100 days. The de novo-evolved mutants rapidly obtained fluoroquinolone resistance within 10 days, as indicated by the 4- and 16-fold augmentation of minimum inhibitory concentrations against enrofloxacin and ciprofloxacin, respectively. Moreover, the mutants maintained heritable fluoroquinolone resistance after the withdrawal of antibiotics for 30 days. Genomic analysis identified Asp87Gly or Ser83Leu substitutions in the gyrA gene in the mutants. Transcriptomics data showed that the transcriptional response of the mutants to fluoroquinolones was primarily involved in biofilm formation, cellular motility, porin, oxidative stress defense, and energy metabolism. Homologous recombination and molecular docking revealed that mutations of gyrA primarily mainly conferred fluoroquinolone resistance, while mutations at different positions of gyrA likely endowed different fluoroquinolone resistance levels. Collectively, this study revealed that environmentally relevant concentrations of antibiotics could rapidly induce heritable antibiotic resistance; therefore, the discharge of antibiotics into the environment should be rigorously controlled to prevent the development of antibiotic resistance.
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Affiliation(s)
- Hebin Liang
- State Environmental Protection Key Laboratory of Microorganism Application and Risk Control,Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
- Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
- Shenzhen Engineering Research Laboratory for Sludge and Food Waste Treatment and Resource Recovery, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
| | - Jiayu Zhang
- State Environmental Protection Key Laboratory of Microorganism Application and Risk Control,Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
- Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
- Shenzhen Engineering Research Laboratory for Sludge and Food Waste Treatment and Resource Recovery, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
| | - Jiahui Hu
- School of Environment, Tsinghua University, Beijing 100084, China
| | - Xiaoyan Li
- State Environmental Protection Key Laboratory of Microorganism Application and Risk Control,Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
- Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
- Shenzhen Engineering Research Laboratory for Sludge and Food Waste Treatment and Resource Recovery, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
| | - Bing Li
- State Environmental Protection Key Laboratory of Microorganism Application and Risk Control,Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
- Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
- Shenzhen Engineering Research Laboratory for Sludge and Food Waste Treatment and Resource Recovery, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
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14
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Kot M, Kalińska A, Jaworski S, Wierzbicki M, Smulski S, Gołębiewski M. In Vitro Studies of Nanoparticles as a Potentially New Antimicrobial Agent for the Prevention and Treatment of Lameness and Digital Dermatitis in Cattle. Int J Mol Sci 2023; 24:ijms24076146. [PMID: 37047119 PMCID: PMC10094334 DOI: 10.3390/ijms24076146] [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: 02/06/2023] [Revised: 03/17/2023] [Accepted: 03/22/2023] [Indexed: 04/14/2023] Open
Abstract
Digital dermatitis (DD) is the second most prevalent disease in dairy cattle. It causes significant losses for dairy breeders and negatively impacts cows' welfare and milk yield. Despite this, its etiology has not been entirely identified, and available data are limited. Antibiotic therapy is a practical method for managing animal health, but overuse has caused the evolution of antibiotic-resistant bacteria, leading to a loss in antimicrobial efficacy. The antimicrobial properties of metal nanoparticles (NPs) may be a potential alternative to antibiotics. The aim of this study was to determine the biocidal properties of AgNPs, CuNPs, AuNPs, PtNPs, FeNPs, and their nanocomposites against pathogens isolated from cows suffering from hoof diseases, especially DD. The isolated pathogens included Sphingomonas paucimobilis, Ochrobactrum intermedium I, Ochrobactrum intermedium II, Ochrobactrum gallinifaecis, and Actinomyces odontolyticus. Cultures were prepared in aerobic and anaerobic environments. The viability of the pathogens was then determined after applying nanoparticles at various concentrations. The in vitro experiment showed that AgNPs and CuNPs, and their complexes, had the highest biocidal effect on pathogens. The NPs' biocidal properties and their synergistic effects were confirmed, which may forecast their use in the future treatment and the prevention of lameness in cows, especially DD.
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Affiliation(s)
- Magdalena Kot
- Animal Breeding Department, Warsaw University of Life Sciences, 02-786 Warszawa, Poland
| | - Aleksandra Kalińska
- Animal Breeding Department, Warsaw University of Life Sciences, 02-786 Warszawa, Poland
| | - Sławomir Jaworski
- Department of Nanobiotechnology, Warsaw University of Life Sciences, 02-786 Warszawa, Poland
| | - Mateusz Wierzbicki
- Department of Nanobiotechnology, Warsaw University of Life Sciences, 02-786 Warszawa, Poland
| | - Sebastian Smulski
- Department of Internal Diseases and Diagnostics, Poznań University of Life Sciences, 60-637 Poznań, Poland
| | - Marcin Gołębiewski
- Animal Breeding Department, Warsaw University of Life Sciences, 02-786 Warszawa, Poland
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15
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Kundar R, Gokarn K. CRISPR-Cas System: A Tool to Eliminate Drug-Resistant Gram-Negative Bacteria. Pharmaceuticals (Basel) 2022; 15:1498. [PMID: 36558949 PMCID: PMC9781512 DOI: 10.3390/ph15121498] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 11/18/2022] [Accepted: 11/24/2022] [Indexed: 12/04/2022] Open
Abstract
Rapidly emerging drug-resistant superbugs, especially Gram-negative bacteria, pose a serious threat to healthcare systems all over the globe. Newer strategies are being developed to detect and overcome the arsenal of weapons that these bacteria possess. The development of antibiotics is time-consuming and may not provide full proof of action on evolving drug-resistant pathogens. The clustered regularly interspaced short palindromic repeats/CRISPR-associated protein (CRISPR/Cas) systems are promising in curbing drug-resistant bacteria. This review focuses on the pathogenesis of Gram-negative bacteria, emergence of antimicrobial drug resistance, and their treatment failures. It also draws attention to the present status of the CRISPR-Cas system in diagnosisand treatment of Gram-negative bacterial infections.
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Affiliation(s)
- Rajeshwari Kundar
- Department of Microbiology, Sir H.N. Medical Research Society, Sir H.N. Reliance Foundation Hospital & Research Centre, Mumbai 400004, Maharashtra, India
| | - Karuna Gokarn
- Department of Microbiology, Sir H.N. Medical Research Society, Sir H.N. Reliance Foundation Hospital & Research Centre, Mumbai 400004, Maharashtra, India
- Department of Microbiology, St. Xavier’s College, 5- Mahapalika Marg, Mumbai 400001, Maharashtra, India
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16
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Laborda P, Sanz-García F, Ochoa-Sánchez LE, Gil-Gil T, Hernando-Amado S, Martínez JL. Wildlife and Antibiotic Resistance. Front Cell Infect Microbiol 2022; 12:873989. [PMID: 35646736 PMCID: PMC9130706 DOI: 10.3389/fcimb.2022.873989] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 04/14/2022] [Indexed: 11/27/2022] Open
Abstract
Antibiotic resistance is a major human health problem. While health care facilities are main contributors to the emergence, evolution and spread of antibiotic resistance, other ecosystems are involved in such dissemination. Wastewater, farm animals and pets have been considered important contributors to the development of antibiotic resistance. Herein, we review the impact of wildlife in such problem. Current evidence supports that the presence of antibiotic resistance genes and/or antibiotic resistant bacteria in wild animals is a sign of anthropic pollution more than of selection of resistance. However, once antibiotic resistance is present in the wild, wildlife can contribute to its transmission across different ecosystems. Further, the finding that antibiotic resistance genes, currently causing problems at hospitals, might spread through horizontal gene transfer among the bacteria present in the microbiomes of ubiquitous animals as cockroaches, fleas or rats, supports the possibility that these organisms might be bioreactors for the horizontal transfer of antibiotic resistance genes among human pathogens. The contribution of wildlife in the spread of antibiotic resistance among different hosts and ecosystems occurs at two levels. Firstly, in the case of non-migrating animals, the transfer will take place locally; a One Health problem. Paradigmatic examples are the above mentioned animals that cohabit with humans and can be reservoirs and vehicles for antibiotic resistance dissemination. Secondly, migrating animals, such as gulls, fishes or turtles may participate in the dissemination of antibiotic resistance across different geographic areas, even between different continents, which constitutes a Global Health issue.
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Affiliation(s)
- Pablo Laborda
- Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
- Programa de Doctorado en Biociencias Moleculares, Universidad Autónoma de Madrid, Madrid, Spain
| | - Fernando Sanz-García
- Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
- Departamento de Microbiología, Medicina Preventiva y Salud Pública, Universidad de Zaragoza, Zaragoza, Spain
| | - Luz Edith Ochoa-Sánchez
- Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Teresa Gil-Gil
- Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
- Programa de Doctorado en Biociencias Moleculares, Universidad Autónoma de Madrid, Madrid, Spain
| | - Sara Hernando-Amado
- Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - José Luis Martínez
- Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
- *Correspondence: José Luis Martínez,
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17
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Nagy K, Dukic B, Hodula O, Ábrahám Á, Csákvári E, Dér L, Wetherington MT, Noorlag J, Keymer JE, Galajda P. Emergence of Resistant Escherichia coli Mutants in Microfluidic On-Chip Antibiotic Gradients. Front Microbiol 2022; 13:820738. [PMID: 35391738 PMCID: PMC8981919 DOI: 10.3389/fmicb.2022.820738] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 02/23/2022] [Indexed: 11/13/2022] Open
Abstract
Spatiotemporal structures and heterogeneities are common in natural habitats, yet their role in the evolution of antibiotic resistance is still to be uncovered. We applied a microfluidic gradient generator device to study the emergence of resistant bacteria in spatial ciprofloxacin gradients. We observed biofilm formation in regions with sub-inhibitory concentrations of antibiotics, which quickly expanded into the high antibiotic regions. In the absence of an explicit structure of the habitat, this multicellular formation led to a spatial structure of the population with local competition and limited migration. Therefore, such structures can function as amplifiers of selection and aid the spread of beneficial mutations. We found that the physical environment itself induces stress-related mutations that later prove beneficial when cells are exposed to antibiotics. This shift in function suggests that exaptation occurs in such experimental scenarios. The above two processes pave the way for the subsequent emergence of highly resistant specific mutations.
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Affiliation(s)
- Krisztina Nagy
- Institute of Biophysics, Biological Research Centre, Szeged, Hungary
- Department of Biotechnology, University of Szeged, Szeged, Hungary
- *Correspondence: Krisztina Nagy,
| | - Barbara Dukic
- Institute of Biophysics, Biological Research Centre, Szeged, Hungary
| | - Orsolya Hodula
- Institute of Biophysics, Biological Research Centre, Szeged, Hungary
| | - Ágnes Ábrahám
- Institute of Biophysics, Biological Research Centre, Szeged, Hungary
- Doctoral School of Multidisciplinary Medical Sciences, University of Szeged, Szeged, Hungary
| | - Eszter Csákvári
- Institute of Biophysics, Biological Research Centre, Szeged, Hungary
| | - László Dér
- Institute of Biophysics, Biological Research Centre, Szeged, Hungary
| | | | - Janneke Noorlag
- Department of Natural Sciences and Technology, University of Aysén, Coyhaique, Chile
| | - Juan E. Keymer
- Department of Natural Sciences and Technology, University of Aysén, Coyhaique, Chile
| | - Péter Galajda
- Institute of Biophysics, Biological Research Centre, Szeged, Hungary
- Péter Galajda,
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18
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Salmonella spp. Response to Lytic Bacteriophage and Lactic Acid on Marinated and Tenderized Raw Pork Loins. Foods 2022; 11:foods11060879. [PMID: 35327301 PMCID: PMC8951642 DOI: 10.3390/foods11060879] [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] [Received: 02/24/2022] [Revised: 03/16/2022] [Accepted: 03/17/2022] [Indexed: 11/17/2022] Open
Abstract
Bacterial food poisoning cases due to Salmonella have been linked with a variety of pork products. This study evaluated the effects of a Salmonella-specific lytic bacteriophage and lactic acid (LA) on Salmonella Enteritidis, Salmonella Montevideo, and Salmonella Heidelberg growth on raw pork loins. Pork loins were cut into approximately 4 cm thick slices. Pork slices were randomly assigned to five treatment groups (control, DI water, LA 2.5%, phage 5%, and LA 2.5% + phage 5%) with six slices per group per replication. Pork loins were inoculated with 106 CFU/mL of Salmonella spp. and stored at 4 °C for 30 min. After 1 h of treatment application and marination, phage 5% significantly (p < 0.05) reduced the surface bacterial population by 2.30 logs when compared with the control group. Moreover, the combined treatment of LA 2.5% + phage 5% significantly (p < 0.05) reduced the surface bacterial population by more than 2.36 logs after 1 h of marination. In the post-tenderization surface samples, the combination of both phage and LA showed a significant reduction (p < 0.05) when compared with the control group. However, the treatments had no effect (p > 0.05) when analyzing the translocation of pathogens on pork loins.
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19
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Deatherage Kaiser BL, Birdsell DN, Hutchison JR, Thelaus J, Jenson SC, Andrianaivoarimanana V, Byström M, Myrtennäs K, McDonough RF, Nottingham RD, Sahl JW, Schweizer HP, Rajerison M, Forsman M, Wunschel DS, Wagner DM. Proteomic Signatures of Antimicrobial Resistance in Yersinia pestis and Francisella tularensis. Front Med (Lausanne) 2022; 9:821071. [PMID: 35223919 PMCID: PMC8866660 DOI: 10.3389/fmed.2022.821071] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 01/10/2022] [Indexed: 11/20/2022] Open
Abstract
Antimicrobial resistance (AMR) is a well-recognized, widespread, and growing issue of concern. With increasing incidence of AMR, the ability to respond quickly to infection with or exposure to an AMR pathogen is critical. Approaches that could accurately and more quickly identify whether a pathogen is AMR also are needed to more rapidly respond to existing and emerging biological threats. We examined proteins associated with paired AMR and antimicrobial susceptible (AMS) strains of Yersinia pestis and Francisella tularensis, causative agents of the diseases plague and tularemia, respectively, to identify whether potential existed to use proteins as signatures of AMR. We found that protein expression was significantly impacted by AMR status. Antimicrobial resistance-conferring proteins were expressed even in the absence of antibiotics in growth media, and the abundance of 10–20% of cellular proteins beyond those that directly confer AMR also were significantly changed in both Y. pestis and F. tularensis. Most strikingly, the abundance of proteins involved in specific metabolic pathways and biological functions was altered in all AMR strains examined, independent of species, resistance mechanism, and affected cellular antimicrobial target. We have identified features that distinguish between AMR and AMS strains, including a subset of features shared across species with different resistance mechanisms, which suggest shared biological signatures of resistance. These features could form the basis of novel approaches to identify AMR phenotypes in unknown strains.
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Affiliation(s)
- Brooke L Deatherage Kaiser
- Pacific Northwest National Laboratory, Chemical and Biological Signatures Group, Richland, WA, United States
| | - Dawn N Birdsell
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, United States
| | - Janine R Hutchison
- Pacific Northwest National Laboratory, Chemical and Biological Signatures Group, Richland, WA, United States
| | - Johanna Thelaus
- Swedish Defence Research Agency, Chemical, Biological, Radioactive, and Nuclear (CBRN) - Defence and Security, Umeå, Sweden
| | - Sarah C Jenson
- Pacific Northwest National Laboratory, Chemical and Biological Signatures Group, Richland, WA, United States
| | | | - Mona Byström
- Swedish Defence Research Agency, Chemical, Biological, Radioactive, and Nuclear (CBRN) - Defence and Security, Umeå, Sweden
| | - Kerstin Myrtennäs
- Swedish Defence Research Agency, Chemical, Biological, Radioactive, and Nuclear (CBRN) - Defence and Security, Umeå, Sweden
| | - Ryelan F McDonough
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, United States
| | - Roxanne D Nottingham
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, United States
| | - Jason W Sahl
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, United States
| | - Herbert P Schweizer
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, United States
| | - Minoarisoa Rajerison
- Plague Unit, Central Laboratory for Plague, Institut Pasteur de Madagascar, Antananarivo, Madagascar
| | - Mats Forsman
- Swedish Defence Research Agency, Chemical, Biological, Radioactive, and Nuclear (CBRN) - Defence and Security, Umeå, Sweden
| | - David S Wunschel
- Pacific Northwest National Laboratory, Chemical and Biological Signatures Group, Richland, WA, United States
| | - David M Wagner
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, United States
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20
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Suhadolnik MLS, Costa PS, Paiva MC, Salim ACDM, Barbosa FAR, Lobo FP, Nascimento AMA. Spatiotemporal dynamics of the resistome and virulome of riverine microbiomes disturbed by a mining mud tsunami. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 806:150936. [PMID: 34678365 DOI: 10.1016/j.scitotenv.2021.150936] [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: 08/09/2021] [Revised: 10/05/2021] [Accepted: 10/08/2021] [Indexed: 06/13/2023]
Abstract
Aquatic ecosystems are highly vulnerable to anthropogenic activities. However, it remains unclear how the microbiome responds to press disturbance events in these ecosystems. We examined the impact of the world's largest mining disaster (Brazil, 2015) on sediment microbiomes in two disturbed rivers compared to an undisturbed river during 390 days post-disturbance. The diversity and structure of the virulome and microbiome, and of antibiotic and metal resistomes, consistently differed between the disturbed and undisturbed rivers, particularly at day 7 post-disturbance. 684 different ARGs were predicted, 38% were exclusive to the disturbed rivers. Critical antibiotic resistance genes (ARGs), e.g., mcr and ereA2, were significantly more common in the disturbed microbiomes. 401 different ARGs were associated with mobile genetic elements (MGEs), 95% occurred in the disturbed rivers. While plasmids were the most common MGEs with a broad spectrum of ARGs, spanning 16 antibiotic classes, integrative conjugative elements (ICEs) and integrons disseminated ARGs associated with aminoglycoside and tetracycline, and aminoglycoside and beta-lactam, respectively. A significant increase in the relative abundance of class 1 integrons, ICEs, and pathogens was identified at day 7 in the disturbed microbiomes, 72-, 14- and 3- fold higher, respectively, compared with the undisturbed river. Mobile ARGs associated with ESKAPEE group pathogens, while metal resistance genes and virulence factor genes in nonpathogenic hosts predominated in all microbiomes. Network analysis showed highly interconnected ARGs in the disturbed communities, including genes targeting antibiotics of last resort. Interactions between copper and beta-lactam/aminoglycoside/macrolide resistance genes, mostly mobile and critical, were also uncovered. We conclude that the mud tsunami resulted in resistome expansion, enrichment of pathogens, and increases in promiscuous and mobile ARGs. From a One Health perspective, mining companies need to move toward more environmentally friendly and socially responsible mining practices to reduce risks associated with pathogens and critical and mobile ARGs.
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Affiliation(s)
- Maria Luíza Soares Suhadolnik
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Brazil
| | - Patrícia Silva Costa
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Brazil
| | | | | | | | - Francisco Pereira Lobo
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Brazil
| | - Andréa Maria Amaral Nascimento
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Brazil.
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21
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Mulpuru V, Mishra N. Antimicrobial Peptides from Human Microbiome Against Multidrug Efflux Pump of Pseudomonas aeruginosa: a Computational Study. Probiotics Antimicrob Proteins 2022; 14:180-188. [PMID: 35040024 DOI: 10.1007/s12602-022-09910-y] [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] [Accepted: 01/09/2022] [Indexed: 01/04/2023]
Abstract
The excess use of antibiotics has led to the evolution of multidrug-resistant pathogenic strains causing worldwide havoc. These multidrug-resistant strains require potent inhibitors. Pseudomonas aeruginosa is a lead cause of nosocomial infections and also feature in the critical priority list of the world health organization (WHO) for the development of new antibiotics against their antimicrobial resistance. Antimicrobial peptides (AMPs) found in almost every life form from microorganisms to humans are known to defend their hosts against various pathogens. Owing to the diversity of the human microbiome, in this study, we have identified the cell-penetrating AMPs from the human microbiome and studied their inhibitory activity against the outer membrane protein OprM of the MexAB-OprM, a constitutively expressed multidrug efflux pump of the Ps. aeruginosa. Screening of the AMPs from the human microbiome resulted in the identification of 147 cell-penetrating AMPs (CPAMPs). The virtual screening of these CPAMPs against the OprM protein showed significant inhibitory results with the top docked AMP showing binding affinity exceeding -30 kcal/mol. The molecular dynamic simulation determined the interaction stabilities between the AMPs and the OprM at the binding site. Further, the residue interaction networks (RINs) are analyses to identify the inhibitory patterns. Later, these patterns were confirmed by MM-PBSA analysis suggesting that the AMPs are majorly stabilized by electrostatic interactions at the binding site. Thus, the high binding affinity and insights from the molecular interaction signify that the identified CPAMPs from the human microbiome can be further explored as inhibitory agents against multidrug-resistant Ps. aeruginosa.
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Affiliation(s)
- Viswajit Mulpuru
- Department of Applied Sciences, Indian Institute of Information Technology Allahabad, Prayagraj, India
| | - Nidhi Mishra
- Department of Applied Sciences, Indian Institute of Information Technology Allahabad, Prayagraj, India.
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22
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Alaidaroos BA. Rare Actinomycetes from Undiscovered Sources as a Source of Novel Antimicrobial Agents to Control Multidrug-Resistant Bacteria. INTERNATIONAL JOURNAL OF PHARMACEUTICAL RESEARCH AND ALLIED SCIENCES 2022. [DOI: 10.51847/dpfaj9fiep] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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Rodríguez-Molina D, Berglund F, Blaak H, Flach CF, Kemper M, Marutescu L, Gradisteanu GP, Popa M, Spießberger B, Weinmann T, Wengenroth L, Chifiriuc MC, Larsson DGJ, Nowak D, Radon K, de Roda Husman AM, Wieser A, Schmitt H. Carriage of ESBL-producing Enterobacterales in wastewater treatment plant workers and surrounding residents - the AWARE Study. Eur J Clin Microbiol Infect Dis 2021:10.1007/s10096-021-04387-z. [PMID: 34902088 PMCID: PMC8667530 DOI: 10.1007/s10096-021-04387-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 11/29/2021] [Indexed: 12/19/2022]
Abstract
To investigate whether wastewater treatment plant (WWTP) workers and residents living in close proximity to a WWTP have elevated carriage rates of ESBL-producing Enterobacterales, as compared to the general population. From 2018 to 2020, we carried out a cross-sectional study in Germany, the Netherlands, and Romania among WWTP workers (N = 344), nearby residents (living ≤ 300 m away from WWTPs; N = 431) and distant residents (living ≥ 1000 m away = reference group; N = 1165). We collected information on potential confounders via questionnaire. Culture of participants' stool samples was performed with ChromID®-ESBL agar plates and species identification with MALDI-TOF-MS. We used logistic regression to estimate the odds ratio (OR) for carrying ESBL-producing E. coli (ESBL-EC). Sensitivity analyses included stratification by country and interaction models using country as secondary exposure. Prevalence of ESBL-EC was 11% (workers), 29% (nearby residents), and 7% (distant residents), and higher in Romania (28%) than in Germany (7%) and the Netherlands (6%). Models stratified by country showed that within the Romanian population, WWTP workers are about twice as likely (aOR = 2.34, 95% CI: 1.22-4.50) and nearby residents about three times as likely (aOR = 3.17, 95% CI: 1.80-5.59) to be ESBL-EC carriers, when compared with distant residents. In stratified analyses by country, we found an increased risk for carriage of ESBL-EC in Romanian workers and nearby residents. This effect was higher for nearby residents than for workers, which suggests that, for nearby residents, factors other than the local WWTP could contribute to the increased carriage.
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Affiliation(s)
- Daloha Rodríguez-Molina
- Occupational and Environmental Epidemiology and NetTeaching Unit, Institute and Clinic for Occupational, Social and Environmental Medicine, University Hospital, LMU Munich, Ziemssenstr. 5, 80336, Munich, Germany.
- Institute for Medical Information Processing, Biometry, and Epidemiology - IBE, LMU Munich, Munich, Germany.
- Pettenkofer School of Public Health, Munich, Germany.
| | - Fanny Berglund
- Department of Infectious Diseases, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden
| | - Hetty Blaak
- Centre of Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Carl-Fredrik Flach
- Department of Infectious Diseases, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden
| | - Merel Kemper
- Centre of Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Luminita Marutescu
- Department of Microbiology and Immunology, Faculty of Biology, University of Bucharest and the Academy of Romanian Scientists, Bucharest, Romania
- Earth, Environmental and Life Sciences Section, Research Institute of the University of Bucharest, University of Bucharest, Bucharest, Romania
| | - Gratiela Pircalabioru Gradisteanu
- Department of Microbiology and Immunology, Faculty of Biology, University of Bucharest and the Academy of Romanian Scientists, Bucharest, Romania
- Earth, Environmental and Life Sciences Section, Research Institute of the University of Bucharest, University of Bucharest, Bucharest, Romania
| | - Marcela Popa
- Department of Microbiology and Immunology, Faculty of Biology, University of Bucharest and the Academy of Romanian Scientists, Bucharest, Romania
- Earth, Environmental and Life Sciences Section, Research Institute of the University of Bucharest, University of Bucharest, Bucharest, Romania
| | - Beate Spießberger
- German Centre for Infection Research (DZIF) Partner Site Munich, Munich, Germany
- Max Von Pettenkofer Institute, Faculty of Medicine, LMU Munich, Munich, Germany
- Department of Infectious Diseases and Tropical Medicine, LMU University Hospital Munich, Munich, Germany
| | - Tobias Weinmann
- Occupational and Environmental Epidemiology and NetTeaching Unit, Institute and Clinic for Occupational, Social and Environmental Medicine, University Hospital, LMU Munich, Ziemssenstr. 5, 80336, Munich, Germany
| | - Laura Wengenroth
- Occupational and Environmental Epidemiology and NetTeaching Unit, Institute and Clinic for Occupational, Social and Environmental Medicine, University Hospital, LMU Munich, Ziemssenstr. 5, 80336, Munich, Germany
| | - Mariana Carmen Chifiriuc
- Department of Microbiology and Immunology, Faculty of Biology, University of Bucharest and the Academy of Romanian Scientists, Bucharest, Romania
- Earth, Environmental and Life Sciences Section, Research Institute of the University of Bucharest, University of Bucharest, Bucharest, Romania
| | - D G Joakim Larsson
- Department of Infectious Diseases, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden
| | - Dennis Nowak
- Occupational and Environmental Epidemiology and NetTeaching Unit, Institute and Clinic for Occupational, Social and Environmental Medicine, University Hospital, LMU Munich, Ziemssenstr. 5, 80336, Munich, Germany
- German Center for Lung Research (DZL), Comprehensive Pneumology Center Munich (CPC-M), Munich, Germany
| | - Katja Radon
- Occupational and Environmental Epidemiology and NetTeaching Unit, Institute and Clinic for Occupational, Social and Environmental Medicine, University Hospital, LMU Munich, Ziemssenstr. 5, 80336, Munich, Germany
| | - Ana Maria de Roda Husman
- Centre of Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Andreas Wieser
- German Centre for Infection Research (DZIF) Partner Site Munich, Munich, Germany
- Max Von Pettenkofer Institute, Faculty of Medicine, LMU Munich, Munich, Germany
- Department of Infectious Diseases and Tropical Medicine, LMU University Hospital Munich, Munich, Germany
| | - Heike Schmitt
- Centre of Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
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Transcriptional Response of Multidrug-Resistant Klebsiella pneumoniae Clinical Isolates to Ciprofloxacin Stress. THE CANADIAN JOURNAL OF INFECTIOUS DISEASES & MEDICAL MICROBIOLOGY = JOURNAL CANADIEN DES MALADIES INFECTIEUSES ET DE LA MICROBIOLOGIE MEDICALE 2021; 2021:5570963. [PMID: 34876946 PMCID: PMC8645360 DOI: 10.1155/2021/5570963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 11/01/2021] [Indexed: 11/17/2022]
Abstract
Background The term “persisters” refers to a small bacterial population that persists during treatment with high antibiotic concentration or dose in the absence of genetic resistance. The present study was designed to investigate the transcriptional response in indigenous Klebsiella pneumoniae under the ciprofloxacin stress. Methods Isolation and identification of K. pneumoniae were carried out through standard microbiological protocols. The characterization of quinolone resistance was performed by estimating the quinolone susceptibility testing, MIC estimation, and detecting the QRDR and PMQR. Transcriptional response of the isolates to ciprofloxacin was determined using qPCR. Results Among 34 isolates, 23 (67%) were resistant to ciprofloxacin. Both QRDR (gyrA and gyrB) and PMQR (qnrA, qnrB, and qnrS) were detected in the isolates, and all were found resistant to ciprofloxacin. The mRNA levels of both mutS and euTu under the influence of ciprofloxacin were significantly increased. On ciprofloxacin exposure, the mRNA levels of the DNA damage response element (mutS) were raised in a time-dependent fashion. K. pneumoniae showed high-level resistance to ciprofloxacin in the presence of mutations in QRDR and PMQR genes. Conclusion The transcriptional response revealed the upregulation of DNA repair and protein folding elements (mutS and euTu) in ciprofloxacin stress and delayed cell division. The ciprofloxacin was found to trigger various stress responses in a time- and concentration-dependent manner.
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Umar A, Haque A, Alghamdi YS, Mashraqi MM, Rehman A, Shahid F, Khurshid M, Ashfaq UA. Development of a Candidate Multi-Epitope Subunit Vaccine against Klebsiella aerogenes: Subtractive Proteomics and Immuno-Informatics Approach. Vaccines (Basel) 2021; 9:vaccines9111373. [PMID: 34835304 PMCID: PMC8624419 DOI: 10.3390/vaccines9111373] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Revised: 11/03/2021] [Accepted: 11/11/2021] [Indexed: 12/17/2022] Open
Abstract
Klebsiella aerogenes is a Gram-negative bacterium which has gained considerable importance in recent years. It is involved in 10% of nosocomial and community-acquired urinary tract infections and 12% of hospital-acquired pneumonia. This organism has an intrinsic ability to produce inducible chromosomal AmpC beta-lactamases, which confer high resistance. The drug resistance in K. aerogenes has been reported in China, Israel, Poland, Italy and the United States, with a high mortality rate (~50%). This study aims to combine immunological approaches with molecular docking approaches for three highly antigenic proteins to design vaccines against K. aerogenes. The synthesis of the B-cell, T-cell (CTL and HTL) and IFN-γ epitopes of the targeted proteins was performed and most conserved epitopes were chosen for future research studies. The vaccine was predicted by connecting the respective epitopes, i.e., B cells, CTL and HTL with KK, AAY and GPGPG linkers and all these were connected with N-terminal adjuvants with EAAAK linker. The humoral response of the constructed vaccine was measured through IFN-γ and B-cell epitopes. Before being used as vaccine candidate, all identified B-cell, HTL and CTL epitopes were tested for antigenicity, allergenicity and toxicity to check the safety profiles of our vaccine. To find out the compatibility of constructed vaccine with receptors, MHC-I, followed by MHC-II and TLR4 receptors, was docked with the vaccine. Lastly, in order to precisely certify the proper expression and integrity of our construct, in silico cloning was carried out. Further studies are needed to confirm the safety features and immunogenicity of the vaccine.
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Affiliation(s)
- Ahitsham Umar
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad 38000, Pakistan; (A.U.); (A.H.); (A.R.); (F.S.)
| | - Asma Haque
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad 38000, Pakistan; (A.U.); (A.H.); (A.R.); (F.S.)
| | - Youssef Saeed Alghamdi
- Department of Biology, Turabah University College, Taif University, Taif 21944, Saudi Arabia;
| | - Mutaib M Mashraqi
- Department of Clinical Laboratory Sciences, College of Applied Medical Science, Najran University, Najran 61441, Saudi Arabia;
| | - Abdur Rehman
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad 38000, Pakistan; (A.U.); (A.H.); (A.R.); (F.S.)
| | - Farah Shahid
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad 38000, Pakistan; (A.U.); (A.H.); (A.R.); (F.S.)
| | - Mohsin Khurshid
- Department of Microbiology, Government College University Faisalabad, Faisalabad 38000, Pakistan;
| | - Usman Ali Ashfaq
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad 38000, Pakistan; (A.U.); (A.H.); (A.R.); (F.S.)
- Correspondence:
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Farooq A, Kim J, Raza S, Jang J, Han D, Sadowsky MJ, Unno T. A hybrid DNA sequencing approach is needed to properly link genotype to phenotype in multi-drug resistant bacteria. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 289:117856. [PMID: 34330011 DOI: 10.1016/j.envpol.2021.117856] [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: 03/25/2021] [Revised: 06/30/2021] [Accepted: 07/25/2021] [Indexed: 06/13/2023]
Abstract
Antibiotic resistance genes (ARGs) are now viewed as emerging contaminants posing a potential worldwide human health risk. The degree to which ARGs are transferred to other bacteria via mobile genetic elements (MGEs), including insertion sequences (ISs), plasmids, and phages, has a strong association with their likelihood to function as resistance transfer determinants. Consequently, understanding the structure and function of MGEs is paramount to assessing future health risks associated with ARGs in an environment subjected to strong antibiotic pressure. In this study we used whole genome sequencing, done using MinION and HiSeq platforms, to examine antibiotic resistance determinants among four multidrug resistant bacteria isolated from fish farm effluent in Jeju, South Korea. The combined data was used to ascertain the association between ARGs and MGEs. Hybrid assembly using HiSeq and MinION reads revealed the presence of IncFIB(K) and pVPH2 plasmids, whose sizes were verified using pulsed field gel electrophoresis. Twenty four ARGs and 95 MGEs were identified among the 955 coding sequences annotated on these plasmids. More importantly, 22 of 24 ARGs conferring resistance to various antibiotics were found to be located near MGEs, whereas about a half of the ARGs (11 out of 21) were so in chromosomes. Our results also suggest that the total phenotypic resistance exhibited by the isolates was mainly contributed by these putatively mobilizable ARGs. The study gives genomic insights into the origins of putatively mobilizable ARGs in bacteria subjected to selection pressure.
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Affiliation(s)
- Adeel Farooq
- Faculty of Biotechnology, School of Life Sciences, SARI, Jeju National University, Jeju, 63243, Republic of Korea
| | - Jungman Kim
- Research Institute for Basic Sciences (RIBS), Jeju National University, Jeju, 63243, Republic of Korea
| | - Shahbaz Raza
- Faculty of Biotechnology, School of Life Sciences, SARI, Jeju National University, Jeju, 63243, Republic of Korea
| | - Jeonghwan Jang
- Division of Biotechnology, Jeonbuk National University, Iksan, 54596, Republic of Korea
| | - Dukki Han
- Department of Marine Molecular Bioscience, Gangneung-Wonju National University, Gangneung, 25457, Republic of Korea
| | - Michael J Sadowsky
- BioTechnology Institute, University of Minnesota, St. Paul, MN, USA; Department of Soil, Water & Climate, and Department of Microbial and Plant Biology, University of Minnesota, St. Paul, MN, USA
| | - Tatsuya Unno
- Faculty of Biotechnology, School of Life Sciences, SARI, Jeju National University, Jeju, 63243, Republic of Korea.
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Her HL, Lin PT, Wu YW. PangenomeNet: a pan-genome-based network reveals functional modules on antimicrobial resistome for Escherichia coli strains. BMC Bioinformatics 2021; 22:548. [PMID: 34758735 PMCID: PMC8579557 DOI: 10.1186/s12859-021-04459-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 10/19/2021] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Discerning genes crucial to antimicrobial resistance (AMR) mechanisms is becoming more and more important to accurately and swiftly identify AMR pathogenic strains. Pangenome-wide association studies (e.g. Scoary) identified numerous putative AMR genes. However, only a tiny proportion of the putative resistance genes are annotated by AMR databases or Gene Ontology. In addition, many putative resistance genes are of unknown function (termed hypothetical proteins). An annotation tool is crucially needed in order to reveal the functional organization of the resistome and expand our knowledge of the AMR gene repertoire. RESULTS We developed an approach (PangenomeNet) for building co-functional networks from pan-genomes to infer functions for hypothetical genes. Using Escherichia coli as an example, we demonstrated that it is possible to build co-functional network from its pan-genome using co-inheritance, domain-sharing, and protein-protein-interaction information. The investigation of the network revealed that it fits the characteristics of biological networks and can be used for functional inferences. The subgraph consisting of putative meropenem resistance genes consists of clusters of stress response genes and resistance gene acquisition pathways. Resistome subgraphs also demonstrate drug-specific AMR genes such as beta-lactamase, as well as functional roles shared among multiple classes of drugs, mostly in the stress-related pathways. CONCLUSIONS By demonstrating the idea of pan-genome-based co-functional network on the E. coli species, we showed that the network can infer functional roles of the genes, including those without functional annotations, and provides holistic views on the putative antimicrobial resistomes. We hope that the pan-genome network idea can help formulate hypothesis for targeted experimental works.
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Affiliation(s)
- Hsuan-Lin Her
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, 92093, USA
| | - Po-Ting Lin
- Department of Mechanical Engineering, National Taiwan University of Science and Technology, No.43, Keelung Rd., Sec.4, Da'an Dist., Taipei City, 10609, Taiwan.
- Center for Cyber-Physical System Innovation, National Taiwan University of Science and Technology, Taipei, 10609, Taiwan.
| | - Yu-Wei Wu
- Graduate Institute of Biomedical Informatics, College of Medical Science and Technology, Taipei Medical University, 250, Wuxing St., Sinyi District, Taipei, 11031, Taiwan.
- Clinical Big Data Research Center, Taipei Medical University Hospital, Taipei, 11031, Taiwan.
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Brauner A, Balaban NQ. Quantitative biology of survival under antibiotic treatments. Curr Opin Microbiol 2021; 64:139-145. [PMID: 34715469 DOI: 10.1016/j.mib.2021.10.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 08/14/2021] [Accepted: 10/08/2021] [Indexed: 01/21/2023]
Abstract
The mathematical formulation for the dynamics of growth reduction and/or killing under antibiotic treatments has a long history. Even before the extensive use of antibiotics, attempts to model the killing dynamics of biocides were made [1]. Here, we review relatively simple quantitative formulations of the two main modes of survival under antibiotics, resistance and tolerance, as well as their heterogeneity in bacterial populations. We focus on the two main types of heterogeneity that have been described: heteroresistance and antibiotic persistence, each linked to the variation in a different parameter of the antibiotic response dynamics. Finally, we review the effects on survival of combining resistance and tolerance mutations as well as on the mode and tempo of evolution under antibiotic treatments.
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Affiliation(s)
- Asher Brauner
- Racah Institute of Physics, Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel
| | - Nathalie Q Balaban
- Racah Institute of Physics, Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel.
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Distribution and Influence on the Microbial Ecological Relationship of Antibiotic Resistance Genes in Soil at a Watershed Scale. SUSTAINABILITY 2021. [DOI: 10.3390/su13179748] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Antibiotic resistance genes (ARGs) are ubiquitous in the environment, with previous studies mainly focusing on the terrestrial ecosystem, which is prone to higher antibiotic application. However, the characteristics, distribution pattern, and driving factors of soil ARGs at the macro scale are still unclear. In this study, the soil ARGs, antibiotics, mobile genetic elements (MGEs), soil properties, toxic metals, polycyclic aromatic hydrocarbons (PAHs), and bacterial community in the Taipu River Basin were analyzed to investigate the distribution and dissemination of ARGs at a watershed scale. The results revealed that ARGs were widespread in the soils along the Taipu River, and that ARG profiles varied greatly with different types of land use, but showed regional similarities. The characteristics were mainly determined by antibiotic input and the ARG transmission mediated by MGEs. The order of the contribution of environmental factors to ARG distribution was toxic metals > PAHs > soil properties. Toxic metal pollution was coupled with ARGs through MGE mediation, while PAHs and soil properties were most likely to affect the ARG distribution by shifting the bacterial community. The microbial–ecological relationship changed significantly with the enrichment of ARGs, and its impact may extend to the watershed scale. Transposon IS1247 can be used as an indicator of the ARGs impact on the microbial ecological relationship in the soils of the Taipu River Basin.
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El-Gendy AO, Samir A, Ahmed E, Enwemeka CS, Mohamed T. The antimicrobial effect of 400 nm femtosecond laser and silver nanoparticles on gram-positive and gram-negative bacteria. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2021; 223:112300. [PMID: 34455353 DOI: 10.1016/j.jphotobiol.2021.112300] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 08/13/2021] [Accepted: 08/23/2021] [Indexed: 10/20/2022]
Abstract
Silver nanoparticles are well-known for their antimicrobial effect. However, they are potentially toxic in high doses. We explored the possibility of enhancing the bactericidal effect of low concentrations of silver nanoparticles with blue light femtosecond laser irradiation, since such concentrations are less toxic. The growth dynamics of Pseudomonas aeruginosa, Listeria monocytogenes and methicillin-resistant Staphylococcus aureus grown in pre-synthesized silver nanoparticles were measured with or without pre-irradiation with 50 mW and 400 nm femtosecond laser irradiation. With each bacterium, combined treatment with laser and silver nanoparticles significantly reduced bacterial growth, indicating that this form of treatment could be beneficial in the ongoing efforts to reduce the deleterious effects of antibiotic resistant Gram-positive and Gram-negative bacteria. The combined treatment was more antimicrobial than treatment with silver nanoparticles alone or photo-irradiation alone. P. aeruginosa and L. monocytogenes were more susceptible to the bactericidal effects of silver nanoparticles, and the combination of laser treatment and silver nanoparticles than MRSA.
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Affiliation(s)
- Ahmed O El-Gendy
- Laser Institute for Research and Applications LIRA, Beni-Suef University, Beni-Suef 62511, Egypt; Faculty of Pharmacy, Department of Microbiology and Immunology, Beni-Suef University, Beni-Suef 62514, Egypt
| | - Ahmed Samir
- Laser Institute for Research and Applications LIRA, Beni-Suef University, Beni-Suef 62511, Egypt
| | - Esraa Ahmed
- Laser Institute for Research and Applications LIRA, Beni-Suef University, Beni-Suef 62511, Egypt
| | - Chukuka S Enwemeka
- College of Health and Human Services, San Diego State University, San Diego, CA 92182, USA
| | - Tarek Mohamed
- Laser Institute for Research and Applications LIRA, Beni-Suef University, Beni-Suef 62511, Egypt.
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Sanz-García F, Gil-Gil T, Laborda P, Ochoa-Sánchez LE, Martínez JL, Hernando-Amado S. Coming from the Wild: Multidrug Resistant Opportunistic Pathogens Presenting a Primary, Not Human-Linked, Environmental Habitat. Int J Mol Sci 2021; 22:8080. [PMID: 34360847 PMCID: PMC8347278 DOI: 10.3390/ijms22158080] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 07/22/2021] [Accepted: 07/24/2021] [Indexed: 12/24/2022] Open
Abstract
The use and misuse of antibiotics have made antibiotic-resistant bacteria widespread nowadays, constituting one of the most relevant challenges for human health at present. Among these bacteria, opportunistic pathogens with an environmental, non-clinical, primary habitat stand as an increasing matter of concern at hospitals. These organisms usually present low susceptibility to antibiotics currently used for therapy. They are also proficient in acquiring increased resistance levels, a situation that limits the therapeutic options for treating the infections they cause. In this article, we analyse the most predominant opportunistic pathogens with an environmental origin, focusing on the mechanisms of antibiotic resistance they present. Further, we discuss the functions, beyond antibiotic resistance, that these determinants may have in the natural ecosystems that these bacteria usually colonize. Given the capacity of these organisms for colonizing different habitats, from clinical settings to natural environments, and for infecting different hosts, from plants to humans, deciphering their population structure, their mechanisms of resistance and the role that these mechanisms may play in natural ecosystems is of relevance for understanding the dissemination of antibiotic resistance under a One-Health point of view.
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Affiliation(s)
| | | | | | | | - José L. Martínez
- Centro Nacional de Biotecnología, CSIC, 28049 Madrid, Spain; (F.S.-G.); (T.G.-G.); (P.L.); (L.E.O.-S.); (S.H.-A.)
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Zhou L, Alcalde RE, Deng J, Zuniga B, Sanford RA, Fouke BW, Werth CJ. Impact of antibiotic concentration gradients on nitrate reduction and antibiotic resistance in a microfluidic gradient chamber. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 779:146503. [PMID: 34030234 DOI: 10.1016/j.scitotenv.2021.146503] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 03/05/2021] [Accepted: 03/11/2021] [Indexed: 06/12/2023]
Abstract
In order to explore the impact of antibiotics on the bacterial metabolic cycling of nitrate within contaminated soil and groundwater environments, we compared the effects of polymyxin B (PMB) and ciprofloxacin (CIP) concentration gradients on the distribution and activity of a wild type (WT) and a flagella deficient mutant (Δflag) of Shewanella oneidensis MR-1 in a microfluidic gradient chamber (MGC). Complementary batch experiments were performed to measure bacteriostatic versus bactericidal concentrations of the two antibiotics, as well as their effect on nitrate reduction. Prior work demonstrated that PMB disrupts cell membranes while CIP inhibits DNA synthesis. Consistent with these modes of action, batch results from this work show that PMB is bactericidal at lower concentrations than CIP relative to their respective minimum inhibitory concentrations (MICs) (≥5× MICPMB vs. ≥20× MICCIP). Concentration gradients from 0 to 50× the MIC of both antibiotics were established in the MGC across a 2-cm interconnected pore network, with nutrients injected at both concentration boundaries. The WT cells could only access and reduce nitrate in regions of the MGC with PMB at <18× MICPMB, whereas this occurred with CIP up to 50× MICCIP; and cells extracted from these MGCs showed no antibiotic resistance. The distribution of Δflag cells was further limited to lower antibiotic concentrations (≤1× MICPMB, ≤43× MICCIP) due to inability of movement. These results indicate that S. oneidensis access and reduce nitrate in bactericidal regions via chemotactic migration without development of antibiotic resistance, and that this migration is inhibited by acutely lethal bactericidal levels of antibiotics.
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Affiliation(s)
- Lang Zhou
- Department of Civil, Architectural and Environmental Engineering, University of Texas at Austin, Austin, TX 78712, USA
| | - Reinaldo E Alcalde
- Department of Civil, Architectural and Environmental Engineering, University of Texas at Austin, Austin, TX 78712, USA
| | - Jinzi Deng
- Carl R. Woese Institute of Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Baltazar Zuniga
- College of Natural Sciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Robert A Sanford
- Department of Geology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Bruce W Fouke
- Carl R. Woese Institute of Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA; Department of Geology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA; Department of Microbiology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Charles J Werth
- Department of Civil, Architectural and Environmental Engineering, University of Texas at Austin, Austin, TX 78712, USA.
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Chouker MA, Abdallah H, Zeiz A, El-Dakdouki MH. Host-quest inclusion complex of quinoxaline-1,4-dioxide derivative with 2-hydroxypropyl-β-cyclodextrin: Preparation, characterization, and antibacterial activity. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.130273] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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Matthews A, Majeed A, Barraclough TG, Raymond B. Function is a better predictor of plant rhizosphere community membership than 16S phylogeny. Environ Microbiol 2021; 23:6089-6103. [PMID: 34190398 DOI: 10.1111/1462-2920.15652] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 06/23/2021] [Accepted: 06/28/2021] [Indexed: 11/26/2022]
Abstract
Rhizobacterial communities are important for plant health but we still have limited understanding of how they are constructed or how they can be manipulated. High-throughput 16S rRNA sequencing provides good information on taxonomic composition but remains an unreliable proxy for phenotypes. In this study, we tested the hypothesis that experimentally observed functional traits would be better predictors of community membership than phylogenetic origin. To test this hypothesis, we sampled communities on four plant species grown in two soil types and characterized 593 bacterial isolates in terms of antibiotic susceptibility, carbon metabolism, resource use and plant growth-promoting traits. In support of our hypothesis we found that three of the four plant species had phylogenetically diverse, but functionally constrained communities. Notably, communities did not grow best on complex media mimicking their host of origin but were distinguished by variation in overall growth characteristics (copiotrophy/oligotrophy) and antibiotic susceptibility. These data, combined with variation in phylogenetic structure, suggest that different classes of traits (antagonistic competition or resource-based) are more important in different communities. This culture-based approach supports and complements the findings of a previous high-throughput 16S rRNA analysis of this experiment and provides functional insights into the patterns observed with culture-independent methods.
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Affiliation(s)
- Andrew Matthews
- College of Life and Environmental Sciences, University of Exeter, Penryn, UK.,Department of Life Sciences, Imperial College London, Ascot, UK
| | - Afshan Majeed
- Department of Soil and Environmental Sciences, University of the Poonch, Rawalakot, Azad Jammu and Kashmir, Pakistan
| | | | - Ben Raymond
- College of Life and Environmental Sciences, University of Exeter, Penryn, UK.,Department of Life Sciences, Imperial College London, Ascot, UK
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Gil-Gil T, Ochoa-Sánchez LE, Baquero F, Martínez JL. Antibiotic resistance: Time of synthesis in a post-genomic age. Comput Struct Biotechnol J 2021; 19:3110-3124. [PMID: 34141134 PMCID: PMC8181582 DOI: 10.1016/j.csbj.2021.05.034] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 05/13/2021] [Accepted: 05/20/2021] [Indexed: 12/20/2022] Open
Abstract
Antibiotic resistance has been highlighted by international organizations, including World Health Organization, World Bank and United Nations, as one of the most relevant global health problems. Classical approaches to study this problem have focused in infected humans, mainly at hospitals. Nevertheless, antibiotic resistance can expand through different ecosystems and geographical allocations, hence constituting a One-Health, Global-Health problem, requiring specific integrative analytic tools. Antibiotic resistance evolution and transmission are multilayer, hierarchically organized processes with several elements (from genes to the whole microbiome) involved. However, their study has been traditionally gene-centric, each element independently studied. The development of robust-economically affordable whole genome sequencing approaches, as well as other -omic techniques as transcriptomics and proteomics, is changing this panorama. These technologies allow the description of a system, either a cell or a microbiome as a whole, overcoming the problems associated with gene-centric approaches. We are currently at the time of combining the information derived from -omic studies to have a more holistic view of the evolution and spread of antibiotic resistance. This synthesis process requires the accurate integration of -omic information into computational models that serve to analyse the causes and the consequences of acquiring AR, fed by curated databases capable of identifying the elements involved in the acquisition of resistance. In this review, we analyse the capacities and drawbacks of the tools that are currently in use for the global analysis of AR, aiming to identify the more useful targets for effective corrective interventions.
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Affiliation(s)
- Teresa Gil-Gil
- Centro Nacional de Biotecnología, CSIC, Darwin 3, 28049 Madrid, Spain
| | | | - Fernando Baquero
- Department of Microbiology, Hospital Universitario Ramón y Cajal (IRYCIS), Madrid, Spain
- CIBER en Epidemiología y Salud Pública (CIBER-ESP), Madrid, Spain
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Wengenroth L, Berglund F, Blaak H, Chifiriuc MC, Flach CF, Pircalabioru GG, Larsson DGJ, Marutescu L, van Passel MWJ, Popa M, Radon K, de Roda Husman AM, Rodríguez-Molina D, Weinmann T, Wieser A, Schmitt H. Antibiotic Resistance in Wastewater Treatment Plants and Transmission Risks for Employees and Residents: The Concept of the AWARE Study. Antibiotics (Basel) 2021; 10:478. [PMID: 33919179 PMCID: PMC8143112 DOI: 10.3390/antibiotics10050478] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 04/14/2021] [Accepted: 04/17/2021] [Indexed: 11/18/2022] Open
Abstract
Antibiotic resistance has become a serious global health threat. Wastewater treatment plants may become unintentional collection points for bacteria resistant to antimicrobials. Little is known about the transmission of antibiotic resistance from wastewater treatment plants to humans, most importantly to wastewater treatment plant workers and residents living in the vicinity. We aim to deliver precise information about the methods used in the AWARE (Antibiotic Resistance in Wastewater: Transmission Risks for Employees and Residents around Wastewater Treatment Plants) study. Within the AWARE study, we gathered data on the prevalence of two antibiotic resistance phenotypes, ESBL-producing E. coli and carbapenemase-producing Enterobacteriaceae, as well as on their corresponding antibiotic resistance genes isolated from air, water, and sewage samples taken from inside and outside of different wastewater treatment plants in Germany, the Netherlands, and Romania. Additionally, we analysed stool samples of wastewater treatment plant workers, nearby residents, and members of a comparison group living ≥1000 m away from the closest WWTP. To our knowledge, this is the first study investigating the potential spread of ESBL-producing E. coli, carbapenemase-producing Enterobacteriaceae, and antibiotic resistance genes from WWTPs to workers, the environment, and nearby residents. Quantifying the contribution of different wastewater treatment processes to the removal efficiency of ESBL-producing E. coli, carbapenemase-producing Enterobacteriaceae, and antibiotic resistance genes will provide us with evidence-based support for possible mitigation strategies.
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Affiliation(s)
- Laura Wengenroth
- Institute and Clinic for Occupational, Social and Environmental Medicine, University Hospital, LMU (Ludwig-Maximilians-Universität) Munich, 80336 Munich, Germany; (K.R.); (D.R.-M.); (T.W.)
| | - Fanny Berglund
- Centre for Antibiotic Resistance Research at University of Gothenburg, Department of Infectious Diseases, Institute of Biomedicine, University of Gothenburg, 405 30 Gothenburg, Sweden; (F.B.); (C.-F.F.); (D.G.J.L.)
| | - Hetty Blaak
- Centre Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), 3721 MA Bilthoven, The Netherlands; (H.B.); (M.W.J.v.P.); (A.M.d.R.H.); (H.S.)
| | - Mariana Carmen Chifiriuc
- Earth, Environment and Life Sciences Division, Research Institute, University of Bucharest, 050657 Bucharest, Romania; (M.C.C.); (G.G.P.); (L.M.); (M.P.)
| | - Carl-Fredrik Flach
- Centre for Antibiotic Resistance Research at University of Gothenburg, Department of Infectious Diseases, Institute of Biomedicine, University of Gothenburg, 405 30 Gothenburg, Sweden; (F.B.); (C.-F.F.); (D.G.J.L.)
| | - Gratiela Gradisteanu Pircalabioru
- Earth, Environment and Life Sciences Division, Research Institute, University of Bucharest, 050657 Bucharest, Romania; (M.C.C.); (G.G.P.); (L.M.); (M.P.)
| | - D. G. Joakim Larsson
- Centre for Antibiotic Resistance Research at University of Gothenburg, Department of Infectious Diseases, Institute of Biomedicine, University of Gothenburg, 405 30 Gothenburg, Sweden; (F.B.); (C.-F.F.); (D.G.J.L.)
| | - Luminita Marutescu
- Earth, Environment and Life Sciences Division, Research Institute, University of Bucharest, 050657 Bucharest, Romania; (M.C.C.); (G.G.P.); (L.M.); (M.P.)
| | - Mark W. J. van Passel
- Centre Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), 3721 MA Bilthoven, The Netherlands; (H.B.); (M.W.J.v.P.); (A.M.d.R.H.); (H.S.)
- Directorate of International Affairs, Ministry of Health, Welfare and Sport, 2500 EJ The Hague, The Netherlands
| | - Marcela Popa
- Earth, Environment and Life Sciences Division, Research Institute, University of Bucharest, 050657 Bucharest, Romania; (M.C.C.); (G.G.P.); (L.M.); (M.P.)
| | - Katja Radon
- Institute and Clinic for Occupational, Social and Environmental Medicine, University Hospital, LMU (Ludwig-Maximilians-Universität) Munich, 80336 Munich, Germany; (K.R.); (D.R.-M.); (T.W.)
| | - Ana Maria de Roda Husman
- Centre Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), 3721 MA Bilthoven, The Netherlands; (H.B.); (M.W.J.v.P.); (A.M.d.R.H.); (H.S.)
| | - Daloha Rodríguez-Molina
- Institute and Clinic for Occupational, Social and Environmental Medicine, University Hospital, LMU (Ludwig-Maximilians-Universität) Munich, 80336 Munich, Germany; (K.R.); (D.R.-M.); (T.W.)
- Institute for Medical Information Processing, Biometry, and Epidemiology—IBE, LMU (Ludwig-Maximilians-Universität) Munich, 81377 Munich, Germany
- Pettenkofer School of Public Health, 81377 Munich, Germany
| | - Tobias Weinmann
- Institute and Clinic for Occupational, Social and Environmental Medicine, University Hospital, LMU (Ludwig-Maximilians-Universität) Munich, 80336 Munich, Germany; (K.R.); (D.R.-M.); (T.W.)
| | - Andreas Wieser
- Division of Infectious Diseases and Tropical Medicine, LMU (Ludwig-Maximilians-Universität) University Hospital, 80802 Munich, Germany;
- Faculty of Medicine, Max von Pettenkofer Institute, LMU (Ludwig-Maximilians-Universität), 80336 Munich, Germany
| | - Heike Schmitt
- Centre Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), 3721 MA Bilthoven, The Netherlands; (H.B.); (M.W.J.v.P.); (A.M.d.R.H.); (H.S.)
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Hashmi SZH, Dhiman TK, Chaudhary N, Singh AK, Kumar R, Sharma JG, Kumar A, Solanki PR. Levofloxacin Detection Using l-Cysteine Capped MgS Quantum Dots via the Photoinduced Electron Transfer Process. FRONTIERS IN NANOTECHNOLOGY 2021. [DOI: 10.3389/fnano.2021.616186] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Antibiotics resistance is becoming one of the biggest problems of the 21st century. The prior detection of antibiotics resistance can help human beings in better treatment of diseases. Here, we have used l-Cysteine capped magnesium sulfide quantum dots (L-Cyst-MgS QDs) to detect Levofloxacin antibiotic. L-Cyst-MgS QDs were synthesized using the hydrothermal method. Transmission electron microscopy study showed monodispersed L-Cyst-MgS QDs of 2–4 nm in size. Energy dispersive x-ray photoemission spectroscopy study confirmed the elemental composition of the L-Cyst-MgS QDs without any impurity. UV-vis absorption study showed a peak centered around 340 nm. The photoluminescence study exhibited the maximum peak at 410 nm for 340 nm of excitation wavelength. L-Cyst-MgS QDs were studied with thirteen antibiotics, namely Thiamphenicol, Gentamicin, Erythromycin, Ofloxacin, Ampicillin, Ciprofloxacin, Tetracycline, Chloramphenicol, Florfenicol, Amoxicillin, Moxifloxacin, Norfloxacin, and Levofloxacin. Among these, Levofloxacin showed the most significant change in the peaks’ intensity and was further used for the interaction study. In the interaction study, the peak corresponding to MgS showed a continuous decrease, while the peak corresponding to Levofloxacin showed an increase with the increased concentrations (0–100 μg/ml) of Levofloxacin. Linear behavior was obtained in the range of 1–90 μg/ml. FT-IR study confirmed the interaction of the Levofloxacin with L-Cyst-MgS QDs. The Time-resolved fluorescence spectroscopy showed identical lifetime for both the samples and no spectral overlap confirm the FRET free system. The underlying mechanism is explained based on the electron transfer from the conduction band of the L-Cyst-MgS QDs to the HOMO of Levofloxacin. The limit of detection was found to be 0.21 μg/ml.
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Kumar M, Sarma DK, Shubham S, Kumawat M, Verma V, Nina PB, JP D, Kumar S, Singh B, Tiwari RR. Futuristic Non-antibiotic Therapies to Combat Antibiotic Resistance: A Review. Front Microbiol 2021; 12:609459. [PMID: 33574807 PMCID: PMC7870489 DOI: 10.3389/fmicb.2021.609459] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 01/04/2021] [Indexed: 12/26/2022] Open
Abstract
The looming problem of resistance to antibiotics in microorganisms is a global health concern. The drug-resistant microorganisms originating from anthropogenic sources and commercial livestock farming have posed serious environmental and health challenges. Antibiotic-resistant genes constituting the environmental "resistome" get transferred to human and veterinary pathogens. Hence, deciphering the origin, mechanism and extreme of transfer of these genetic factors into pathogens is extremely important to develop not only the therapeutic interventions to curtail the infections, but also the strategies to avert the menace of microbial drug-resistance. Clinicians, researchers and policymakers should jointly come up to develop the strategies to prevent superfluous exposure of pathogens to antibiotics in non-clinical settings. This article highlights the present scenario of increasing antimicrobial-resistance in pathogenic bacteria and the clinical importance of unconventional or non-antibiotic therapies to thwart the infectious pathogenic microorganisms.
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Affiliation(s)
- Manoj Kumar
- ICMR-National Institute for Research in Environmental Health, Bhopal, India
| | | | - Swasti Shubham
- ICMR-National Institute for Research in Environmental Health, Bhopal, India
| | - Manoj Kumawat
- ICMR-National Institute for Research in Environmental Health, Bhopal, India
| | - Vinod Verma
- Stem Cell Research Centre, Department of Hematology, SGPGIMS, Lucknow, India
| | | | - Devraj JP
- ICMR- National Institute of Nutrition, Hyderabad, India
| | - Santosh Kumar
- ICMR- National Institute of Nutrition, Hyderabad, India
| | - Birbal Singh
- ICAR-Indian Veterinary Research Institute, Regional Station, Palampur, India
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39
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Bolatchiev A. Antibacterial activity of human defensins against Staphylococcus aureus and Escherichia coli. PeerJ 2020; 8:e10455. [PMID: 33304659 PMCID: PMC7698690 DOI: 10.7717/peerj.10455] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 11/09/2020] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND The global problem of antibiotic resistance requires the search for and development of new methods of treatment. One of the promising strategies is the use of low doses of antimicrobial peptides, in particular, human defensins HNP-1, hBD-1, and hBD-3, in combination with antibacterial drugs already used in clinical practice. This approach may be used to increase the effectiveness of conventional antibiotics. However, this requires thorough study of the effectiveness of defensins in combination with antibiotics against a large number of bacterial strains with known phenotypes of antibiotic resistance. The aim of this work was to study the antibacterial effect of HNP-1, hBD-1 and hBD-3 in combination with rifampicin or amikacin against clinical isolates of Staphylococcus aureus (n = 27) and Escherichia coli (n = 24) collected from hospitalized patients. METHODS The standard checkerboard assay was used to determine minimum inhibitory concentrations (MICs) of antimicrobials. The combined microbicidal effects of two substances (defensin + conventional antibiotic) were assessed by the fractional inhibitory concentration index (FICI). RESULTS The highest anti-staphylococcal activity (including methicillin-resistant strains) among defensins was demonstrated by hBD-3 that had MIC of 1 (0.5-4) mg/L (hereinafter, MIC values are presented as median and interquartile range). The MIC of HNP-1 against S. aureus was 4 (2-8) mg/L; the MIC of hBD-1 was 8 (4-8) mg/L. Against E. coli, the most effective was also found to be hBD-3 that had MIC of 4 (4-8) mg/L; the MIC of HNP-1 was 12 (4-32) mg/L. The combinations of HNP-1 + rifampicin and hBD-3 + rifampicin demonstrated synergistic effects against S. aureus. Against E. coli, combinations of HNP-1 + amikacin and hBD-3 + amikacin also showed synergy of action.
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Affiliation(s)
- Albert Bolatchiev
- Department of Clinical Pharmacology, Stavropol State Medical University, Stavropol, Russian Federation
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40
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Barlow VL, Lai SJ, Chen CY, Tsai CH, Wu SH, Tsai YH. Effect of membrane fusion protein AdeT1 on the antimicrobial resistance of Escherichia coli. Sci Rep 2020; 10:20464. [PMID: 33235243 PMCID: PMC7687900 DOI: 10.1038/s41598-020-77339-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 11/10/2020] [Indexed: 01/03/2023] Open
Abstract
Acinetobacter baumannii is a prevalent pathogen that can rapidly acquire resistance to antibiotics. Indeed, multidrug-resistant A. baumannii is a major cause of hospital-acquired infections and has been recognised by the World Health Organization as one of the most threatening bacteria to our society. Resistance-nodulation-division (RND) type multidrug efflux pumps have been demonstrated to convey antibiotic resistance to a wide range of pathogens and are the primary resistance mechanism employed by A. baumannii. A component of an RND pump in A. baumannii, AdeT1, was previously demonstrated to enhance the antimicrobial resistance of Escherichia coli. Here, we report the results of experiments which demonstrate that wild-type AdeT1 does not confer antimicrobial resistance in E. coli, highlighting the importance of verifying protein production when determining minimum inhibitory concentrations (MICs) especially by broth dilution. Nevertheless, using an agar-based MIC assay, we found that propionylation of Lys280 on AdeT1 renders E. coli cells more resistant to erythromycin.
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Affiliation(s)
| | - Shu-Jung Lai
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan.,Research Center for Cancer Biology, China Medical University, Taichung, Taiwan.,Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Chia-Yu Chen
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Cheng-Han Tsai
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Shih-Hsiung Wu
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Yu-Hsuan Tsai
- School of Chemistry, Cardiff University, Cardiff, UK.
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41
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Thornton CN, Tanner WD, VanDerslice JA, Brazelton WJ. Localized effect of treated wastewater effluent on the resistome of an urban watershed. Gigascience 2020; 9:5992824. [PMID: 33215210 PMCID: PMC7677451 DOI: 10.1093/gigascience/giaa125] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Revised: 07/14/2020] [Indexed: 11/14/2022] Open
Abstract
Background Wastewater treatment is an essential tool for maintaining water quality in urban environments. While the treatment of wastewater can remove most bacterial cells, some will inevitably survive treatment to be released into natural environments. Previous studies have investigated antibiotic resistance within wastewater treatment plants, but few studies have explored how a river’s complete set of antibiotic resistance genes (the “resistome") is affected by the release of treated effluent into surface waters. Results Here we used high-throughput, deep metagenomic sequencing to investigate the effect of treated wastewater effluent on the resistome of an urban river and the downstream distribution of effluent-associated antibiotic resistance genes and mobile genetic elements. Treated effluent release was found to be associated with increased abundance and diversity of antibiotic resistance genes and mobile genetic elements. The impact of wastewater discharge on the river’s resistome diminished with increasing distance from effluent discharge points. The resistome at river locations that were not immediately downstream from any wastewater discharge points was dominated by a single integron carrying genes associated with resistance to sulfonamides and quaternary ammonium compounds. Conclusions Our study documents variations in the resistome of an urban watershed from headwaters to a major confluence in an urban center. Greater abundances and diversity of antibiotic resistance genes are associated with human fecal contamination in river surface water, but the fecal contamination effect seems to be localized, with little measurable effect in downstream waters. The diverse composition of antibiotic resistance genes throughout the watershed suggests the influence of multiple environmental and biological factors.
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Affiliation(s)
- Christopher N Thornton
- School of Biological Sciences, University of Utah, 257 South 1400 East, Rm. 201, 84112, Salt Lake City, UT, USA
| | - Windy D Tanner
- Department of Family and Preventive Medicine, University of Utah, 257 South 1400 East, Rm. 201, 84112, Salt Lake City, UT, USA
| | - James A VanDerslice
- Department of Family and Preventive Medicine, University of Utah, 257 South 1400 East, Rm. 201, 84112, Salt Lake City, UT, USA
| | - William J Brazelton
- School of Biological Sciences, University of Utah, 257 South 1400 East, Rm. 201, 84112, Salt Lake City, UT, USA
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Hernando-Amado S, Coque TM, Baquero F, Martínez JL. Antibiotic Resistance: Moving From Individual Health Norms to Social Norms in One Health and Global Health. Front Microbiol 2020; 11:1914. [PMID: 32983000 PMCID: PMC7483582 DOI: 10.3389/fmicb.2020.01914] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 07/21/2020] [Indexed: 12/16/2022] Open
Abstract
Antibiotic resistance is a problem for human health, and consequently, its study had been traditionally focused toward its impact for the success of treating human infections in individual patients (individual health). Nevertheless, antibiotic-resistant bacteria and antibiotic resistance genes are not confined only to the infected patients. It is now generally accepted that the problem goes beyond humans, hospitals, or long-term facility settings and that it should be considered simultaneously in human-connected animals, farms, food, water, and natural ecosystems. In this regard, the health of humans, animals, and local antibiotic-resistance-polluted environments should influence the health of the whole interconnected local ecosystem (One Health). In addition, antibiotic resistance is also a global problem; any resistant microorganism (and its antibiotic resistance genes) could be distributed worldwide. Consequently, antibiotic resistance is a pandemic that requires Global Health solutions. Social norms, imposing individual and group behavior that favor global human health and in accordance with the increasingly collective awareness of the lack of human alienation from nature, will positively influence these solutions. In this regard, the problem of antibiotic resistance should be understood within the framework of socioeconomic and ecological efforts to ensure the sustainability of human development and the associated human-natural ecosystem interactions.
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Affiliation(s)
- Sara Hernando-Amado
- Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Teresa M. Coque
- Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS) and Centro de Investigación Biomédica en Red Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Fernando Baquero
- Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS) and Centro de Investigación Biomédica en Red Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - José L. Martínez
- Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
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Zhou L, Lei D, Wang Q, Luo X, Chen Y. Biocompatible Polyphosphorylcholine Hydrogels with Inherent Antibacterial and Nonfouling Behavior Effectively Promote Skin Wound Healing. ACS APPLIED BIO MATERIALS 2020; 3:5357-5366. [DOI: 10.1021/acsabm.0c00666] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Liangqin Zhou
- College of Polymer Science and Engineering, Sichuan University, Chengdu 610065, P. R. China
| | - Dongqin Lei
- College of Polymer Science and Engineering, Sichuan University, Chengdu 610065, P. R. China
| | - Quan Wang
- College of Polymer Science and Engineering, Sichuan University, Chengdu 610065, P. R. China
| | - Xianglin Luo
- College of Polymer Science and Engineering, Sichuan University, Chengdu 610065, P. R. China
- State Key Lab of Polymer Materials Engineering, Sichuan University, Chengdu 610065, P. R. China
| | - Yuanwei Chen
- College of Polymer Science and Engineering, Sichuan University, Chengdu 610065, P. R. China
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Kumar S, Narayan KS, Shandilya S, Sood SK, Kapila S. Role of non-PTS dependent glucose permease (GlcU) in maintaining the fitness cost during acquisition of nisin resistance by Enterococcus faecalis. FEMS Microbiol Lett 2020; 366:5628326. [PMID: 31738414 DOI: 10.1093/femsle/fnz230] [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: 08/22/2019] [Accepted: 11/15/2019] [Indexed: 11/13/2022] Open
Abstract
Nisin is used for food preservation due to its antibacterial activity. However, some bacteria survive under the prevailing conditions owing to the acquisition of resistance. This study aimed to characterize nisin-resistant Enterococcus faecalis isolated from raw buffalo milk and investigate their fitness cost. FE-SEM, biofilm and cytochrome c assay were used for characterization. Growth kinetics, HPLC, qPCR and western blotting were performed to confer their fitness cost. Results revealed that nisin-resistant E. faecalis were morphologically different from sensitive strain and internalize more glucose. However, no significant difference was observed in the growth pattern of the resistant strain compared to that of the sensitive strain. A non-phosphotransferase glucose permease (GlcU) was found to be associated with enhanced glucose uptake. Conversely, Mpt, a major phosphotransferase system responsible for glucose uptake, did not play any role, as confirmed by gene expression studies and western blot analysis of HPr protein. The phosphorylation of His-15 residue of HPr phosphoprotein was reduced, while that of the Ser-46 residue increased with progression in nisin resistance, indicating that it may be involved in the regulation of pathogenicity. In conclusion, resistance imposes a significant fitness cost and GlcU plays a key role in maintaining the fitness cost in nisin-resistant variants.
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Affiliation(s)
- Sandeep Kumar
- Animal Biochemistry Division, National Dairy Research Institute, Karnal 132001, Haryana, India
| | - Kapil Singh Narayan
- Animal Biochemistry Division, National Dairy Research Institute, Karnal 132001, Haryana, India
| | - Shruti Shandilya
- Animal Biochemistry Division, National Dairy Research Institute, Karnal 132001, Haryana, India
| | - Shiv Kumar Sood
- Animal Biochemistry Division, National Dairy Research Institute, Karnal 132001, Haryana, India
| | - Suman Kapila
- Animal Biochemistry Division, National Dairy Research Institute, Karnal 132001, Haryana, India
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Hu D, Zou L, Yu W, Jia F, Han H, Yao K, Jin Q, Ji J. Relief of Biofilm Hypoxia Using an Oxygen Nanocarrier: A New Paradigm for Enhanced Antibiotic Therapy. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2020; 7:2000398. [PMID: 32596125 PMCID: PMC7312432 DOI: 10.1002/advs.202000398] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 03/10/2020] [Indexed: 06/01/2023]
Abstract
Biofilms are chief culprits of most intractable infections and pose great threats to human health. Conventional antibiotic therapies are hypodynamic to biofilms due to their strong drug resistance, closely related with biofilm hypoxia. A new strategy for enhanced antibiotic therapy by relieving biofilm hypoxia is reported here. A two-step sequential delivery strategy is fabricated using perfluorohexane (PFH)-loaded liposomes (lip) as oxygen (O2) carriers (denoted as lip@PFH@O2) and commercial antibiotics. The results indicate that the two-step sequential treatment exhibits much lower minimum bactericidal concentrations than the antibiotic treatment alone. In this design, the lip@PFH@O2 holds positively charged surface for better biofilm penetration. After penetrating into biofilm, oxygen can be released from lip@PFH@O2 by inches, which greatly relieves biofilm hypoxia. With the relief of hypoxia, the quorum sensing and the drug efflux pumps of bacteria are suppressed by restraining related gene expression, leading to the reduced antibiotic resistance. Furthermore, the in vivo experimental results also demonstrate that lip@PFH@O2 can effectively relieve biofilm hypoxia and enhance therapeutic efficacy of antibiotics. As a proof-of-concept, this research provides an innovative strategy for enhanced antibiotic therapy by relieving hypoxia, which may hold a bright future in combating biofilm-associated infections.
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Affiliation(s)
- Dengfeng Hu
- MOE Key Laboratory of Macromolecule Synthesis and Functionalization of Ministry of Education, Department of Polymer Science and EngineeringZhejiang UniversityHangzhouZhejiang Province310027P. R. China
| | - Lingyun Zou
- MOE Key Laboratory of Macromolecule Synthesis and Functionalization of Ministry of Education, Department of Polymer Science and EngineeringZhejiang UniversityHangzhouZhejiang Province310027P. R. China
| | - Weijiang Yu
- MOE Key Laboratory of Macromolecule Synthesis and Functionalization of Ministry of Education, Department of Polymer Science and EngineeringZhejiang UniversityHangzhouZhejiang Province310027P. R. China
| | - Fan Jia
- MOE Key Laboratory of Macromolecule Synthesis and Functionalization of Ministry of Education, Department of Polymer Science and EngineeringZhejiang UniversityHangzhouZhejiang Province310027P. R. China
| | - Haijie Han
- Eye CenterSecond Affiliated Hospital, School of MedicineZhejiang UniversityHangzhouZhejiang Province310027P. R. China
| | - Ke Yao
- Eye CenterSecond Affiliated Hospital, School of MedicineZhejiang UniversityHangzhouZhejiang Province310027P. R. China
| | - Qiao Jin
- MOE Key Laboratory of Macromolecule Synthesis and Functionalization of Ministry of Education, Department of Polymer Science and EngineeringZhejiang UniversityHangzhouZhejiang Province310027P. R. China
| | - Jian Ji
- MOE Key Laboratory of Macromolecule Synthesis and Functionalization of Ministry of Education, Department of Polymer Science and EngineeringZhejiang UniversityHangzhouZhejiang Province310027P. R. China
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Liu H, Li H, Liang Y, Du X, Yang C, Yang L, Xie J, Zhao R, Tong Y, Qiu S, Song H. Phage-delivered sensitisation with subsequent antibiotic treatment reveals sustained effect against antimicrobial resistant bacteria. Am J Cancer Res 2020; 10:6310-6321. [PMID: 32483454 PMCID: PMC7255016 DOI: 10.7150/thno.42573] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 04/25/2020] [Indexed: 12/31/2022] Open
Abstract
Temperate phages integrated with clustered regularly interspaced short palindromic repeat (CRISPR)/Cas systems have been gaining attention as potential strategies for combating bacteria resistant to antimicrobials. To further advance this technology, phage recombination procedure should be improved, and the bactericidal effect should be examined in detail and compared with conventional lytic phage strategy. The possibility of the emergence of mutational resistance, a phenomenon commonly observed with lytic phage therapy, should be illustrated. Methods: Here, we developed a novel one-step cloning method to fulfil the recombination of CRISPR/Cas9 system within the genome of a new isolated lysogenic Escherichia coli phage. Then, we proposed and developed a phage-delivered resistance eradication with subsequent antibiotic treatment (PRESA) strategy. The removal efficiency and antimicrobial effect of the plasmids were analysed. Long-term antimicrobial effect was evaluated by continued OD600 monitoring for 240 hours to illustrate the potential mutational resistance, compared with the lytic phage strategy. The treatment effect of PRESA was evaluated in vivo by determining bacterial loads in the skin and intestine of infected mice, in contrast with lytic phage therapy. Genome sequencing was performed to identify mutations in bacterial cells treated with phage strategies. Results: Phage-delivered CRISPR targeting efficiently eradicated and blocked the transfer of the antibiotic resistance plasmid. PRESA decreased the bacterial load by over 6- and 5-logs in vitro and in vivo, respectively. Importantly, while lytic phages induced mutational phage resistance at 24 h in vitro and 48 hours in vivo, PRESA demonstrated a constant effect and revealed no resistant mutants. Genes involved in DNA mismatch repair were upregulated in cells undergoing Cas9-based plasmid cleavage, which may reduce the development of mutations. Conclusion: The PRESA strategy for eradicating resistant bacteria showed high bactericidal efficacy and a sustained inhibition effect against resistant bacteria. By restoring the efficacy of low-cost antibiotics, PRESA could be developed as an efficient and economical therapy for infections of antibiotic resistant bacteria.
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Bhattarai K, Bastola R, Baral B. Antibiotic drug discovery: Challenges and perspectives in the light of emerging antibiotic resistance. ADVANCES IN GENETICS 2020; 105:229-292. [PMID: 32560788 DOI: 10.1016/bs.adgen.2019.12.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Amid a rising threat of antimicrobial resistance in a global scenario, our huge investments and high-throughput technologies injected for rejuvenating the key therapeutic scaffolds to suppress these rising superbugs has been diminishing severely. This has grasped world-wide attention, with increased consideration being given to the discovery of new chemical entities. Research has now proven that the relatively tiny and simpler microbes possess enhanced capability of generating novel and diverse chemical constituents with huge therapeutic leads. The usage of these beneficial organisms could help in producing new chemical scaffolds that govern the power to suppress the spread of obnoxious superbugs. Here in this review, we have explicitly focused on several appealing strategies employed for the generation of new chemical scaffolds. Also, efforts on providing novel insights on some of the unresolved questions in the production of metabolites, metabolic profiling and also the serendipity of getting "hit molecules" have been rigorously discussed. However, we are highly aware that biosynthetic pathway of different classes of secondary metabolites and their biosynthetic route is a vast topic, thus we have avoided discussion on this topic.
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Affiliation(s)
- Keshab Bhattarai
- University of Tübingen, Tübingen, Germany; Center for Natural and Applied Sciences (CENAS), Kathmandu, Nepal
| | - Rina Bastola
- Spinal Cord Injury Association-Nepal (SCIAN), Pokhara, Nepal
| | - Bikash Baral
- Spinal Cord Injury Association-Nepal (SCIAN), Pokhara, Nepal.
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Wang Y, Jiang Y, Deng Y, Yi C, Wang Y, Ding M, Liu J, Jin X, Shen L, He Y, Wu X, Chen X, Sun C, Zheng M, Zhang R, Ye H, An H, Wong A. Probiotic Supplements: Hope or Hype? Front Microbiol 2020; 11:160. [PMID: 32184760 PMCID: PMC7058552 DOI: 10.3389/fmicb.2020.00160] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2019] [Accepted: 01/22/2020] [Indexed: 12/17/2022] Open
Abstract
Probiotic bacteria have been associated with various health benefits and included in overwhelming number of foods. Today, probiotic supplements are consumed with increasing regularity and record a rapidly growing economic value. With billions of heterogeneous populations of probiotics per serving, probiotic supplements contain the largest quantity of probiotics across all functional foods. They often carry antibiotic-resistant determinants that can be transferred to and accumulate in resident bacteria of the gastrointestinal tract and risk their acquisitions by opportunistic pathogens. While the health benefits of probiotics have been widely publicized, this health risk, however, is underrepresented in both scientific studies and public awareness. On the other hand, the human gut presents conditions that are unfavorable for bacteria, including probiotics. It remains uncertain if probiotics from supplements can tolerate acids and bile salts that may undermine their effectiveness in conferring health benefits. Here, we put into perspective the perceived health benefits and the long-term safety of consuming probiotic supplements, specifically bringing intolerance to acids and bile salts, and the long-standing issue of antibiotic-resistant gene transfer into sharp focus. We report that probiotics from supplements examined in this study have poor tolerance to acids and bile salts while also displaying resistance to multiple antibiotics. They could also adapt and gain resistance to streptomycin in vitro. In an environment where consuming supplements is considered a norm, our results and that of others will put in perspective the persisting concerns surrounding probiotic supplements so that the current hype does not overpower the hope.
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Affiliation(s)
- Yuxuan Wang
- Department of Biology, College of Science and Technology, Wenzhou-Kean University, Wenzhou, China
| | - Yinyin Jiang
- Department of Biology, College of Science and Technology, Wenzhou-Kean University, Wenzhou, China
| | - Yuxin Deng
- Department of Biology, College of Science and Technology, Wenzhou-Kean University, Wenzhou, China
| | - Chen Yi
- Department of Biology, College of Science and Technology, Wenzhou-Kean University, Wenzhou, China
| | - Yangcan Wang
- Department of Biology, College of Science and Technology, Wenzhou-Kean University, Wenzhou, China
| | - Mengnan Ding
- Department of Biology, College of Science and Technology, Wenzhou-Kean University, Wenzhou, China
| | - Jie Liu
- Department of Biology, College of Science and Technology, Wenzhou-Kean University, Wenzhou, China
| | - Xuanjing Jin
- Department of Biology, College of Science and Technology, Wenzhou-Kean University, Wenzhou, China
| | - Lishan Shen
- Department of Biology, College of Science and Technology, Wenzhou-Kean University, Wenzhou, China
| | - Yue He
- Department of Biology, College of Science and Technology, Wenzhou-Kean University, Wenzhou, China
| | - Xinyun Wu
- Department of Biology, College of Science and Technology, Wenzhou-Kean University, Wenzhou, China
| | - Xuefei Chen
- Department of Biology, College of Science and Technology, Wenzhou-Kean University, Wenzhou, China
| | - Changyi Sun
- Department of Biology, College of Science and Technology, Wenzhou-Kean University, Wenzhou, China
| | - Min Zheng
- Department of Biology, College of Science and Technology, Wenzhou-Kean University, Wenzhou, China
| | - Ruijia Zhang
- Department of Biology, College of Science and Technology, Wenzhou-Kean University, Wenzhou, China
| | - Hailv Ye
- Department of Biology, College of Science and Technology, Wenzhou-Kean University, Wenzhou, China
| | - Huiting An
- Department of Biology, College of Science and Technology, Wenzhou-Kean University, Wenzhou, China
| | - Aloysius Wong
- Department of Biology, College of Science and Technology, Wenzhou-Kean University, Wenzhou, China
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Hernando-Amado S, Sanz-García F, Martínez JL. Antibiotic Resistance Evolution Is Contingent on the Quorum-Sensing Response in Pseudomonas aeruginosa. Mol Biol Evol 2020; 36:2238-2251. [PMID: 31228244 DOI: 10.1093/molbev/msz144] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Different works have explored independently the evolution toward antibiotic resistance and the role of eco-adaptive mutations in the adaptation to a new habitat (as the infected host) of bacterial pathogens. However, knowledge about the connection between both processes is still limited. We address this issue by comparing the evolutionary trajectories toward antibiotic resistance of a Pseudomonas aeruginosa lasR defective mutant and its parental wild-type strain, when growing in presence of two ribosome-targeting antibiotics. Quorum-sensing lasR defective mutants are selected in P. aeruginosa populations causing chronic infections. Further, we observed they are also selected in vitro as a first adaptation for growing in culture medium. By using experimental evolution and whole-genome sequencing, we found that the evolutionary trajectories of P. aeruginosa in presence of these antibiotics are different in lasR defective and in wild-type backgrounds, both at the phenotypic and the genotypic levels. Recreation of a set of mutants in both genomic backgrounds (either wild type or lasR defective) allowed us to determine the existence of negative epistatic interactions between lasR and antibiotic resistance determinants. These epistatic interactions could lead to mutual contingency in the evolution of antibiotic resistance when P. aeruginosa colonizes a new habitat in presence of antibiotics. If lasR mutants are selected first, this would constraint antibiotic resistance evolution. Conversely, when resistance mutations (at least those studied in the present work) are selected, lasR mutants may not be selected in presence of antibiotics. These results underlie the importance of contingency and epistatic interactions in modulating antibiotic resistance evolution.
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50
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Ben Maamar S, Glawe AJ, Brown TK, Hellgeth N, Hu J, Wang JP, Huttenhower C, Hartmann EM. Mobilizable antibiotic resistance genes are present in dust microbial communities. PLoS Pathog 2020; 16:e1008211. [PMID: 31971995 PMCID: PMC6977718 DOI: 10.1371/journal.ppat.1008211] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 11/13/2019] [Indexed: 11/23/2022] Open
Abstract
The decades-long global trend of urbanization has led to a population that spends increasing amounts of time indoors. Exposure to microbes in buildings, and specifically in dust, is thus also increasing, and has been linked to various health outcomes and to antibiotic resistance genes (ARGs). These are most efficiently screened using DNA sequencing, but this method does not determine which microbes are viable, nor does it reveal whether their ARGs can actually disseminate to other microbes. We have thus performed the first study to: 1) examine the potential for ARG dissemination in indoor dust microbial communities, and 2) validate the presence of detected mobile ARGs in viable dust bacteria. Specifically, we integrated 166 dust metagenomes from 43 different buildings. Sequences were assembled, annotated, and screened for potential integrons, transposons, plasmids, and associated ARGs. The same dust samples were further investigated using cultivation and isolate genome and plasmid sequencing. Potential ARGs were detected in dust isolate genomes, and we confirmed their placement on mobile genetic elements using long-read sequencing. We found 183 ARGs, of which 52 were potentially mobile (associated with a putative plasmid, transposon or integron). One dust isolate related to Staphylococcus equorum proved to contain a plasmid carrying an ARG that was detected metagenomically and confirmed through whole genome and plasmid sequencing. This study thus highlights the power of combining cultivation with metagenomics to assess the risk of potentially mobile ARGs for public health.
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Affiliation(s)
- Sarah Ben Maamar
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, Illinois, United States of America
| | - Adam J. Glawe
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, Illinois, United States of America
| | - Taylor K. Brown
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, Illinois, United States of America
| | - Nancy Hellgeth
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, Illinois, United States of America
| | - Jinglin Hu
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, Illinois, United States of America
| | - Ji-Ping Wang
- Department of Statistics, Northwestern University, Evanston, Illinois, United States of America
| | - Curtis Huttenhower
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Erica M. Hartmann
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, Illinois, United States of America
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