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Lee DH, Lee K, Kim YS, Cha CJ. Comprehensive genomic landscape of antibiotic resistance in Staphylococcus epidermidis. mSystems 2024; 9:e0022624. [PMID: 38727238 PMCID: PMC11237394 DOI: 10.1128/msystems.00226-24] [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: 02/15/2024] [Accepted: 04/04/2024] [Indexed: 06/19/2024] Open
Abstract
Staphylococcus epidermidis, a common commensal bacterium found on human skin, can cause infections in clinical settings, and the presence of antibiotic resistance genes (ARGs) impedes the treatment of S. epidermidis infections. However, studies characterizing the ARGs in S. epidermidis with regard to genomic and ecological diversities are limited. Thus, we performed a comprehensive and comparative analysis of 405 high-quality S. epidermidis genomes, including those of 35 environmental isolates from the Han River, to investigate the genomic diversity of antibiotic resistance in this pathogen. Comparative genomic analysis revealed the prevalence of ARGs in S. epidermidis genomes associated with multi-locus sequence types. The genes encoding dihydrofolate reductase (dfrC) and multidrug efflux pump (norA) were genome-wide core ARGs. β-Lactam class ARGs were also highly prevalent in the S. epidermidis genomes, which was consistent with the resistance phenotype observed in river isolates. Furthermore, we identified chloramphenicol acetyltransferase genes (cat) in the plasmid-like sequences of the six river isolates, which have not been reported previously in S. epidermidis genomes. These genes were identical to those harbored by the Enterococcus faecium plasmids and associated with the insertion sequence 6 family transposases, homologous to those found in Staphylococcus aureus plasmids, suggesting the possibility of horizontal gene transfer between these Gram-positive pathogens. Comparison of the ARG and virulence factor profiles between S. epidermidis and S. aureus genomes revealed that these two species were clearly distinguished, suggesting genomic demarcation despite ecological overlap. Our findings provide a comprehensive understanding of the genomic diversity of antibiotic resistance in S. epidermidis. IMPORTANCE A comprehensive understanding of the antibiotic resistance gene (ARG) profiles of the skin commensal bacterium and opportunistic pathogen Staphylococcus epidermidis needs to be documented from a genomic point of view. Our study encompasses a comparative analysis of entire S. epidermidis genomes from various habitats, including those of 35 environmental isolates from the Han River sequenced in this study. Our results shed light on the distribution and diversity of ARGs within different S. epidermidis multi-locus sequence types, providing valuable insights into the ecological and genetic factors associated with antibiotic resistance. A comparison between S. epidermidis and Staphylococcus aureus revealed marked differences in ARG and virulence factor profiles, despite their overlapping ecological niches.
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Affiliation(s)
- Do-Hoon Lee
- Department of Systems Biotechnology and Center for Antibiotic Resistome, Chung-Ang University, Anseong, South Korea
| | - Kihyun Lee
- Department of Systems Biotechnology and Center for Antibiotic Resistome, Chung-Ang University, Anseong, South Korea
| | - Yong-Seok Kim
- Department of Systems Biotechnology and Center for Antibiotic Resistome, Chung-Ang University, Anseong, South Korea
| | - Chang-Jun Cha
- Department of Systems Biotechnology and Center for Antibiotic Resistome, Chung-Ang University, Anseong, South Korea
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Morales-Durán N, León-Buitimea A, Morones-Ramírez JR. Unraveling resistance mechanisms in combination therapy: A comprehensive review of recent advances and future directions. Heliyon 2024; 10:e27984. [PMID: 38510041 PMCID: PMC10950705 DOI: 10.1016/j.heliyon.2024.e27984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 03/07/2024] [Accepted: 03/08/2024] [Indexed: 03/22/2024] Open
Abstract
Antimicrobial resistance is a global health threat. Misuse and overuse of antimicrobials are the main drivers in developing drug-resistant bacteria. The emergence of the rapid global spread of multi-resistant bacteria requires urgent multisectoral action to generate novel treatment alternatives. Combination therapy offers the potential to exploit synergistic effects for enhanced antibacterial efficacy of drugs. Understanding the complex dynamics and kinetics of drug interactions in combination therapy is crucial. Therefore, this review outlines the current advances in antibiotic resistance's evolutionary and genetic dynamics in combination therapies-exposed bacteria. Moreover, we also discussed four pivotal future research areas to comprehend better the development of antibiotic resistance in bacteria treated with combination strategies.
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Affiliation(s)
- Nami Morales-Durán
- Facultad de Ciencias Químicas, Universidad Autónoma de Nuevo León (UANL), San Nicolás de los Garza, 66455, Mexico
- Centro de Investigación en Biotecnología y Nanotecnología, Facultad de Ciencias Químicas, Universidad Autónoma de Nuevo León, Parque de Investigación e Innovación Tecnológica, Apodaca, 66628, Mexico
| | - Angel León-Buitimea
- Facultad de Ciencias Químicas, Universidad Autónoma de Nuevo León (UANL), San Nicolás de los Garza, 66455, Mexico
- Centro de Investigación en Biotecnología y Nanotecnología, Facultad de Ciencias Químicas, Universidad Autónoma de Nuevo León, Parque de Investigación e Innovación Tecnológica, Apodaca, 66628, Mexico
| | - José R. Morones-Ramírez
- Facultad de Ciencias Químicas, Universidad Autónoma de Nuevo León (UANL), San Nicolás de los Garza, 66455, Mexico
- Centro de Investigación en Biotecnología y Nanotecnología, Facultad de Ciencias Químicas, Universidad Autónoma de Nuevo León, Parque de Investigación e Innovación Tecnológica, Apodaca, 66628, Mexico
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3
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Abdulkadir N, Saraiva JP, Zhang J, Stolte S, Gillor O, Harms H, Rocha U. Genome-centric analyses of 165 metagenomes show that mobile genetic elements are crucial for the transmission of antimicrobial resistance genes to pathogens in activated sludge and wastewater. Microbiol Spectr 2024; 12:e0291823. [PMID: 38289113 PMCID: PMC10913551 DOI: 10.1128/spectrum.02918-23] [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: 07/28/2023] [Accepted: 11/25/2023] [Indexed: 03/06/2024] Open
Abstract
Wastewater is considered a reservoir of antimicrobial resistance genes (ARGs), where the abundant antimicrobial-resistant bacteria and mobile genetic elements facilitate horizontal gene transfer. However, the prevalence and extent of these phenomena in different taxonomic groups that inhabit wastewater are still not fully understood. Here, we determined the presence of ARGs in metagenome-assembled genomes (MAGs) and evaluated the risks of MAG-carrying ARGs in potential human pathogens. The potential of these ARGs to be transmitted horizontally or vertically was also determined. A total of 5,916 MAGs (completeness >50%, contamination <10%) were recovered, covering 68 phyla and 279 genera. MAGs were dereplicated into 1,204 genome operational taxonomic units (gOTUs) as a proxy for species ( average nucleotide identity >0.95). The dominant ARG classes detected were bacitracin, multi-drug, macrolide-lincosamide-streptogramin (MLS), glycopeptide, and aminoglycoside, and 10.26% of them were located on plasmids. The main hosts of ARGs belonged to Escherichia, Klebsiella, Acinetobacter, Gresbergeria, Mycobacterium, and Thauera. Our data showed that 253 MAGs carried virulence factor genes (VFGs) divided into 44 gOTUs, of which 45 MAGs were carriers of ARGs, indicating that potential human pathogens carried ARGs. Alarmingly, the MAG assigned as Escherichia coli contained 159 VFGs, of which 95 were located on chromosomes and 10 on plasmids. In addition to shedding light on the prevalence of ARGs in individual genomes recovered from activated sludge and wastewater, our study demonstrates a workflow that can identify antimicrobial-resistant pathogens in complex microbial communities. IMPORTANCE Antimicrobial resistance (AMR) threatens the health of humans, animals, and natural ecosystems. In our study, an analysis of 165 metagenomes from wastewater revealed antibiotic-targeted alteration, efflux, and inactivation as the most prevalent AMR mechanisms. We identified several genera correlated with multiple ARGs, including Klebsiella, Escherichia, Acinetobacter, Nitrospira, Ottowia, Pseudomonas, and Thauera, which could have significant implications for AMR transmission. The abundance of bacA, mexL, and aph(3")-I in the genomes calls for their urgent management in wastewater. Our approach could be applied to different ecosystems to assess the risk of potential pathogens containing ARGs. Our findings highlight the importance of managing AMR in wastewater and can help design measures to reduce the transmission and evolution of AMR in these systems.
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Affiliation(s)
- Nafi’u Abdulkadir
- Department of Environmental Microbiology, Helmholtz Center for Environmental Research-UFZ, Leipzig, Germany
- Department of Biochemistry, Faculty of Natural Science, University of Leipzig, Leipzig, Germany
| | - Joao Pedro Saraiva
- Department of Environmental Microbiology, Helmholtz Center for Environmental Research-UFZ, Leipzig, Germany
| | - Junya Zhang
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Stefan Stolte
- Institute of Water Chemistry, Technical University of Dresden, Dresden, Germany
| | - Osnat Gillor
- Zuckerberg Institute for Water Research, J. Blaustein Institutes for Desert Research, Ben Gurion University, Midreshet Ben Gurion, Israel
| | - Hauke Harms
- Department of Environmental Microbiology, Helmholtz Center for Environmental Research-UFZ, Leipzig, Germany
- Department of Biochemistry, Faculty of Natural Science, University of Leipzig, Leipzig, Germany
| | - Ulisses Rocha
- Department of Environmental Microbiology, Helmholtz Center for Environmental Research-UFZ, Leipzig, Germany
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Lee JH, Kim NH, Jang KM, Jin H, Shin K, Jeong BC, Kim DW, Lee SH. Prioritization of Critical Factors for Surveillance of the Dissemination of Antibiotic Resistance in Pseudomonas aeruginosa: A Systematic Review. Int J Mol Sci 2023; 24:15209. [PMID: 37894890 PMCID: PMC10607276 DOI: 10.3390/ijms242015209] [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: 09/18/2023] [Revised: 10/13/2023] [Accepted: 10/13/2023] [Indexed: 10/29/2023] Open
Abstract
Pseudomonas aeruginosa is the primary opportunistic human pathogen responsible for a range of acute and chronic infections; it poses a significant threat to immunocompromised patients and is the leading cause of morbidity and mortality for nosocomial infections. Its high resistance to a diverse array of antimicrobial agents presents an urgent health concern. Among the mechanisms contributing to resistance in P. aeruginosa, the horizontal acquisition of antibiotic resistance genes (ARGs) via mobile genetic elements (MGEs) has gained recognition as a substantial concern in clinical settings, thus indicating that a comprehensive understanding of ARG dissemination within the species is strongly required for surveillance. Here, two approaches, including a systematic literature analysis and a genome database survey, were employed to gain insights into ARG dissemination. The genome database enabled scrutinizing of all the available sequence information and various attributes of P. aeruginosa isolates, thus providing an extensive understanding of ARG dissemination within the species. By integrating both approaches, with a primary focus on the genome database survey, mobile ARGs that were linked or correlated with MGEs, important sequence types (STs) carrying diverse ARGs, and MGEs responsible for ARG dissemination were identified as critical factors requiring strict surveillance. Although human isolates play a primary role in dissemination, the importance of animal and environmental isolates has also been suggested. In this study, 25 critical mobile ARGs, 45 critical STs, and associated MGEs involved in ARG dissemination within the species, are suggested as critical factors. Surveillance and management of these prioritized factors across the One Health sectors are essential to mitigate the emergence of multidrug-resistant (MDR) and extensively resistant (XDR) P. aeruginosa in clinical settings.
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Affiliation(s)
- Jung Hun Lee
- National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University, Yongin 17058, Republic of Korea; (J.H.L.); (K.-M.J.); (H.J.); (K.S.); (B.C.J.)
| | - Nam-Hoon Kim
- Division of Life Sciences, Jeonbuk National University, Jeonju 54896, Republic of Korea;
| | - Kyung-Min Jang
- National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University, Yongin 17058, Republic of Korea; (J.H.L.); (K.-M.J.); (H.J.); (K.S.); (B.C.J.)
| | - Hyeonku Jin
- National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University, Yongin 17058, Republic of Korea; (J.H.L.); (K.-M.J.); (H.J.); (K.S.); (B.C.J.)
| | - Kyoungmin Shin
- National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University, Yongin 17058, Republic of Korea; (J.H.L.); (K.-M.J.); (H.J.); (K.S.); (B.C.J.)
| | - Byeong Chul Jeong
- National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University, Yongin 17058, Republic of Korea; (J.H.L.); (K.-M.J.); (H.J.); (K.S.); (B.C.J.)
| | - Dae-Wi Kim
- Division of Life Sciences, Jeonbuk National University, Jeonju 54896, Republic of Korea;
| | - Sang Hee Lee
- National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University, Yongin 17058, Republic of Korea; (J.H.L.); (K.-M.J.); (H.J.); (K.S.); (B.C.J.)
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5
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Kim YS, Hwang EM, Jeong CM, Cha CJ. Flavobacterium psychrotrophum sp. nov. and Flavobacterium panacagri sp. nov., Isolated from Freshwater and Soil. J Microbiol 2023; 61:891-901. [PMID: 37851309 DOI: 10.1007/s12275-023-00081-1] [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: 06/28/2023] [Revised: 09/06/2023] [Accepted: 09/08/2023] [Indexed: 10/19/2023]
Abstract
Two novel bacterial strains CJ74T and CJ75T belonging to the genus Flavobacterium were isolated from freshwater of Han River and ginseng soil, South Korea, respectively. Strain CJ74T was Gram-stain-negative, aerobic, rod-shaped, non-motile, and non-flagellated, and did not produce flexirubin-type pigments. Strain CJ75T was Gram-stain-negative, aerobic, rod-shaped, motile by gliding, and non-flagellated, and produced flexirubin-type pigments. Both strains were shown to grow optimally at 30 °C in the absence of NaCl on R2A medium. Phylogenetic analysis based on 16S rRNA gene sequences showed that strains CJ74T and CJ75T belonged to the genus Flavobacterium and were most closely related to Flavobacterium niveum TAPW14T and Flavobacterium foetidum CJ42T with 96.17% and 97.29% 16S rRNA sequence similarities, respectively. Genomic analyses including the reconstruction of phylogenomic tree, average nucleotide identity, and digital DNA-DNA hybridization suggested that they were novel species of the genus Flavobacterium. Both strains contained menaquinone 6 (MK-6) as the primary respiratory quinone and phosphatidylethanolamine as a major polar lipid. The predominant fatty acids of both strains were iso-C15:0 and summed feature 3 (C16:1 ω7c and/or C16:1 ω6c). Based on the polyphasic taxonomic study, strains CJ74T and CJ75T represent novel species of the genus Flavobacterium, for which names Flavobacterium psychrotrophum sp. nov. and Flavobacterium panacagri sp. nov. are proposed, respectively. The type strains are CJ74T (=KACC 19819T =JCM 32889T) and CJ75T (=KACC 23149T =JCM 36132T).
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Affiliation(s)
- Yong-Seok Kim
- Department or Systems Biotechnology, Chung-Ang University, Anseong, 17546, Republic of Korea
| | - Eun-Mi Hwang
- Department or Systems Biotechnology, Chung-Ang University, Anseong, 17546, Republic of Korea
| | - Chang-Myeong Jeong
- Department or Systems Biotechnology, Chung-Ang University, Anseong, 17546, Republic of Korea
| | - Chang-Jun Cha
- Department or Systems Biotechnology, Chung-Ang University, Anseong, 17546, Republic of Korea.
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6
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Theophilus RJ, Taft DH. Antimicrobial Resistance Genes (ARGs), the Gut Microbiome, and Infant Nutrition. Nutrients 2023; 15:3177. [PMID: 37513595 PMCID: PMC10383493 DOI: 10.3390/nu15143177] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 07/14/2023] [Accepted: 07/14/2023] [Indexed: 07/30/2023] Open
Abstract
The spread of antimicrobial resistance genes (ARGs) is a major public health crisis, with the ongoing spread of ARGs leading to reduced efficacy of antibiotic treatments. The gut microbiome is a key reservoir for ARGs, and because diet shapes the gut microbiome, diet also has the potential to shape the resistome. This diet-gut microbiome-resistome relationship may also be important in infants and young children. This narrative review examines what is known about the interaction between the infant gut microbiome, the infant resistome, and infant nutrition, including exploring the potential of diet to mitigate infant ARG carriage. While more research is needed, diet has the potential to reduce infant and toddler carriage of ARGs, an important goal as part of maintaining the efficacy of available antibiotics and preserving infant and toddler health.
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Affiliation(s)
- Rufus J Theophilus
- Food Science and Human Nutrition Department, University of Florida, Gainesville, FL 32611, USA
| | - Diana Hazard Taft
- Food Science and Human Nutrition Department, University of Florida, Gainesville, FL 32611, USA
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Tripathi A, Kumar D, Chavda P, Rathore DS, Pandit R, Blake D, Tomley F, Joshi M, Joshi CG, Dubey SK. Resistome profiling reveals transmission dynamics of antimicrobial resistance genes from poultry litter to soil and plant. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 327:121517. [PMID: 36990341 DOI: 10.1016/j.envpol.2023.121517] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Revised: 02/26/2023] [Accepted: 03/25/2023] [Indexed: 06/19/2023]
Abstract
Poultry farming is a major livelihood in South and Southeast Asian economies where it is undergoing rapid intensification to meet the growing human demand for dietary protein. Intensification of poultry production systems is commonly supported by increased antimicrobial drug use, risking greater selection and dissemination of antimicrobial resistance genes (ARGs). Transmission of ARGs through food chains is an emerging threat. Here, we investigated transmission of ARGs from chicken (broiler and layer) litter to soil and Sorghum bicolor (L.) Moench plants based on field and pot experiments. The results demonstrate ARGs transmission from poultry litter to plant systems under field as well as experimental pot conditions. The most common ARGs could be tracked for transmission from litter to soil to plants were identified as detected were cmx, ErmX, ErmF, lnuB, TEM-98 and TEM-99, while common microorganisms included Escherichia coli, Staphylococcus aureus, Enterococcus faecium, Pseudomonas aeruginosa, and Vibrio cholerae. Using next generation sequencing and digital PCR assays we detected ARGs transmitted from poultry litter in both the roots and stems of S. bicolor (L.) Moench plants. Poultry litter is frequently used as a fertiliser because of its high nitrogen content; our studies show that ARGs can transmit from litter to plants and illustrates the risks posed to the environment by antimicrobial treatment of poultry. This knowledge is useful for formulating intervention strategies that can reduce or prevent ARGs transmission from one value chain to another, improving understanding of impacts on human and environmental health. The research outcome will help in further understanding the transmission and risks posed by ARGs from poultry to environmental and human/animal health.
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Affiliation(s)
- Animesh Tripathi
- Department of Botany, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh, 221005, India
| | - Dinesh Kumar
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology; (DST), Government of Gujarat, Gandhinagar, Gujarat, 382011, India
| | - Priyank Chavda
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology; (DST), Government of Gujarat, Gandhinagar, Gujarat, 382011, India
| | - Dalip Singh Rathore
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology; (DST), Government of Gujarat, Gandhinagar, Gujarat, 382011, India
| | - Ramesh Pandit
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology; (DST), Government of Gujarat, Gandhinagar, Gujarat, 382011, India
| | - Damer Blake
- Pathobiology and Population Sciences, The Royal Veterinary College, Hawkshead Lane, North Mymms, Hertfordshire, UK
| | - Fiona Tomley
- Pathobiology and Population Sciences, The Royal Veterinary College, Hawkshead Lane, North Mymms, Hertfordshire, UK
| | - Madhvi Joshi
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology; (DST), Government of Gujarat, Gandhinagar, Gujarat, 382011, India
| | - Chaitanya G Joshi
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology; (DST), Government of Gujarat, Gandhinagar, Gujarat, 382011, India
| | - Suresh Kumar Dubey
- Department of Botany, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh, 221005, India.
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Yu T, Fu Y, He J, Zhang J, Xianyu Y. Identification of Antibiotic Resistance in ESKAPE Pathogens through Plasmonic Nanosensors and Machine Learning. ACS NANO 2023; 17:4551-4563. [PMID: 36867448 DOI: 10.1021/acsnano.2c10584] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Antibiotic-resistant ESKAPE pathogens cause nosocomial infections that lead to huge morbidity and mortality worldwide. Rapid identification of antibiotic resistance is vital for the prevention and control of nosocomial infections. However, current techniques like genotype identification and antibiotic susceptibility testing are generally time-consuming and require large-scale equipment. Herein, we develop a rapid, facile, and sensitive technique to determine the antibiotic resistance phenotype among ESKAPE pathogens through plasmonic nanosensors and machine learning. Key to this technique is the plasmonic sensor array that contains gold nanoparticles functionalized with peptides differing in hydrophobicity and surface charge. The plasmonic nanosensors can interact with pathogens to generate bacterial fingerprints that alter the surface plasmon resonance (SPR) spectra of nanoparticles. In combination with machine learning, it enables the identification of antibiotic resistance among 12 ESKAPE pathogens in less than 20 min with an overall accuracy of 89.74%. This machine-learning-based approach allows for the identification of antibiotic-resistant pathogens from patients and holds great promise as a clinical tool for biomedical diagnosis.
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Affiliation(s)
- Ting Yu
- State Key Laboratory of Fluid Power and Mechatronic Systems, College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, People's Republic of China
| | - Ying Fu
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou 310016, People's Republic of China
| | - Jintao He
- College of Animal Sciences, Zhejiang University, Hangzhou 310058, People's Republic of China
| | - Jun Zhang
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou 310016, People's Republic of China
| | - Yunlei Xianyu
- State Key Laboratory of Fluid Power and Mechatronic Systems, College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, People's Republic of China
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou 310016, People's Republic of China
- Future Food Laboratory, Innovation Center of Yangtze River Delta, Zhejiang University, Jiaxing 314100, People's Republic of China
- Ningbo Research Institute, Zhejiang University, Ningbo 315100, People's Republic of China
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O’Connor L, Heyderman R. The challenges of defining the human nasopharyngeal resistome. Trends Microbiol 2023:S0966-842X(23)00056-2. [DOI: 10.1016/j.tim.2023.02.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 02/16/2023] [Accepted: 02/20/2023] [Indexed: 04/03/2023]
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Tan YC, Lahiri C. Promising Acinetobacter baumannii Vaccine Candidates and Drug Targets in Recent Years. Front Immunol 2022; 13:900509. [PMID: 35720310 PMCID: PMC9204607 DOI: 10.3389/fimmu.2022.900509] [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: 03/20/2022] [Accepted: 04/26/2022] [Indexed: 12/14/2022] Open
Abstract
In parallel to the uncontrolled use of antibiotics, the emergence of multidrug-resistant bacteria, like Acinetobacter baumannii, has posed a severe threat. A. baumannii predominates in the nosocomial setting due to its ability to persist in hospitals and survive antibiotic treatment, thereby eventually leading to an increasing prevalence and mortality due to its infection. With the increasing spectra of drug resistance and the incessant collapse of newly discovered antibiotics, new therapeutic countermeasures have been in high demand. Hence, recent research has shown favouritism towards the long-term solution of designing vaccines. Therefore, being a realistic alternative strategy to combat this pathogen, anti-A. Baumannii vaccines research has continued unearthing various antigens with variable results over the last decade. Again, other approaches, including pan-genomics, subtractive proteomics, and reverse vaccination strategies, have shown promise for identifying promiscuous core vaccine candidates that resulted in chimeric vaccine constructs. In addition, the integration of basic knowledge of the pathobiology of this drug-resistant bacteria has also facilitated the development of effective multiantigen vaccines. As opposed to the conventional trial-and-error approach, incorporating the in silico methods in recent studies, particularly network analysis, has manifested a great promise in unearthing novel vaccine candidates from the A. baumannii proteome. Some studies have used multiple A. baumannii data sources to build the co-functional networks and analyze them by k-shell decomposition. Additionally, Whole Genomic Protein Interactome (GPIN) analysis has utilized a rational approach for identifying essential proteins and presenting them as vaccines effective enough to combat the deadly pathogenic threats posed by A. baumannii. Others have identified multiple immune nodes using network-based centrality measurements for synergistic antigen combinations for different vaccination strategies. Protein-protein interactions have also been inferenced utilizing structural approaches, such as molecular docking and molecular dynamics simulation. Similar workflows and technologies were employed to unveil novel A. baumannii drug targets, with a similar trend in the increasing influx of in silico techniques. This review integrates the latest knowledge on the development of A. baumannii vaccines while highlighting the in silico methods as the future of such exploratory research. In parallel, we also briefly summarize recent advancements in A. baumannii drug target research.
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Affiliation(s)
- Yong Chiang Tan
- School of Postgraduate Studies, International Medical University, Kuala Lumpur, Malaysia
| | - Chandrajit Lahiri
- Department of Biological Sciences, Sunway University, Petaling Jaya, Malaysia
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Gold nanoparticle-DNA aptamer-assisted delivery of antimicrobial peptide effectively inhibits Acinetobacter baumannii infection in mice. J Microbiol 2021; 60:128-136. [PMID: 34964948 DOI: 10.1007/s12275-022-1620-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 12/09/2021] [Accepted: 12/13/2021] [Indexed: 12/19/2022]
Abstract
Acinetobacter baumannii causes multidrug resistance, leading to fatal infections in humans. In this study, we showed that Lys AB2 P3-His-a hexahistidine-tagged form of an antimicrobial peptide (AMP) loaded onto DNA aptamer-functionalized gold nanoparticles (AuNP-Apt)-can effectively inhibit A. baumannii infection in mice. When A. baumannii-infected mice were intraperitoneally injected with AuNP-Apt loaded with Lys AB2 P3-His, a marked reduction in A. baumannii colonization was observed in the mouse organs, leading to prominently increased survival time and rate of the mice compared to those of the control mice treated with AuNP-Apt or Lys AB2 P3-His only. This study shows that AMPs loaded onto AuNP-Apt could be an effective therapeutic tool against infections caused by multidrug-resistant pathogenic bacteria in humans.
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Datar R, Orenga S, Pogorelcnik R, Rochas O, Simner PJ, van Belkum A. Recent Advances in Rapid Antimicrobial Susceptibility Testing. Clin Chem 2021; 68:91-98. [DOI: 10.1093/clinchem/hvab207] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 09/17/2021] [Indexed: 12/30/2022]
Abstract
Abstract
Background
Antimicrobial susceptibility testing (AST) is classically performed using growth-based techniques that essentially require viable bacterial matter to become visible to the naked eye or a sophisticated densitometer.
Content
Technologies based on the measurement of bacterial density in suspension have evolved marginally in accuracy and rapidity over the 20th century, but assays expanded for new combinations of bacteria and antimicrobials have been automated, and made amenable to high-throughput turn-around. Over the past 25 years, elevated AST rapidity has been provided by nucleic acid-mediated amplification technologies, proteomic and other “omic” methodologies, and the use of next-generation sequencing. In rare cases, AST at the level of single-cell visualization was developed. This has not yet led to major changes in routine high-throughput clinical microbiological detection of antimicrobial resistance.
Summary
We here present a review of the new generation of methods and describe what is still urgently needed for their implementation in day-to-day management of the treatment of infectious diseases.
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Affiliation(s)
- Rucha Datar
- bioMérieux, Microbiology Research, La Balme Les Grottes, France
| | - Sylvain Orenga
- bioMérieux, Microbiology Research, La Balme Les Grottes, France
| | | | - Olivier Rochas
- bioMérieux, Corporate Business Development, Marcy l'Etoile, France
| | - Patricia J Simner
- Department of Pathology, Bacteriology, Division of Medical Microbiology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Alex van Belkum
- bioMérieux, Open Innovation and Partnerships, La Balme Les Grottes, France
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13
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Santoro F, Fox V, Romeo A, Lazzeri E, Pozzi G, Iannelli F. Chromosomal integration of Tn5253 occurs downstream of a conserved 11-bp sequence of the rbgA gene in Streptococcus pneumoniae and in all the other known hosts of this integrative conjugative element (ICE). Mob DNA 2021; 12:25. [PMID: 34740368 PMCID: PMC8571831 DOI: 10.1186/s13100-021-00253-z] [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: 09/02/2021] [Accepted: 10/20/2021] [Indexed: 01/07/2023] Open
Abstract
Background Tn5253, a composite Integrative Conjugative Element (ICE) of Streptococcus pneumoniae carrying tet(M) and cat resistance determinants, was found to (i) integrate at specific 83-bp integration site (attB), (ii) produce circular forms joined by a 84-bp sequence (attTn), and (iii) restore the chromosomal integration site. The purpose of this study is to functionally characterize the attB in S. pneumoniae strains with different genetic backgrounds and in other bacterial species, and to investigate the presence of Tn5253 attB site into bacterial genomes. Results Analysis of representative Tn5253-carryng transconjugants obtained in S. pneumoniae strains with different genetic backgrounds and in other bacterial species, namely Streptococcus agalactiae, Streptococcus gordonii, Streptococcus pyogenes, and Enterococcus faecalis showed that: (i) Tn5253 integrates in rbgA of S. pneumoniae and in orthologous rbgA genes of other bacterial species, (ii) integration occurs always downstream of a 11-bp sequence conserved among streptococcal and enterococcal hosts, (iii) length of the attB site corresponds to length of the duplication after Tn5253 integration, (iv) attB duplication restores rbgA CDS, (v) Tn5253 produced circular forms containing the attTn site at a concentration ranging between 2.0 × 10−5 to 1.2 × 10−2 copies per chromosome depending on bacterial species and strain, (vi) reconstitution of attB sites occurred at 3.7 × 10−5 to 1.7 × 10−2 copies per chromosome. A database search of complete microbial genomes using Tn5253 attB as a probe showed that (i) thirteen attB variants were present in the 85 complete pneumococcal genomes, (ii) in 75 pneumococcal genomes (88.3 %), the attB site was 83 or 84 nucleotides in length, while in 10 (11.7 %) it was 41 nucleotides, (iii) in other 19 bacterial species attB was located in orthologous rbgA genes and its size ranged between 17 and 84 nucleotides, (iv) the 11-bp sequence, which correspond to the last 11 nucleotides of attB sites, is conserved among the different bacterial species and can be considered the core of the Tn5253 integration site. Conclusions A functional characterization of the Tn5253 attB integration site combined with genome analysis contributed to elucidating the potential of Tn5253 horizontal gene transfer among different bacterial species. Supplementary Information The online version contains supplementary material available at 10.1186/s13100-021-00253-z.
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Affiliation(s)
- Francesco Santoro
- Laboratory of Molecular Microbiology and Biotechnology (LAMMB), Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Valeria Fox
- Laboratory of Molecular Microbiology and Biotechnology (LAMMB), Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Alessandra Romeo
- Laboratory of Molecular Microbiology and Biotechnology (LAMMB), Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Elisa Lazzeri
- Laboratory of Molecular Microbiology and Biotechnology (LAMMB), Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Gianni Pozzi
- Laboratory of Molecular Microbiology and Biotechnology (LAMMB), Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Francesco Iannelli
- Laboratory of Molecular Microbiology and Biotechnology (LAMMB), Department of Medical Biotechnologies, University of Siena, Siena, Italy.
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14
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Abstract
Microbial ecology is the study of microorganisms present in nature. It particularly focuses on microbial interactions with any biota and with surrounding environments. Microbial ecology is entering its golden age with innovative multi-omics methods triggered by next-generation sequencing technologies. However, the extraction of ecologically relevant information from ever-increasing omics data remains one of the most challenging tasks in microbial ecology. This special issue includes 11 review articles that provide an overview of the state of the art of omics-based approaches in the field of microbial ecology, with particular emphasis on the interpretation of omics data, environmental pollution tracking, interactions in microbiomes, and viral ecology.
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