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Williams MR, Telli AE, Telli N, Islam DT, Hashsham SA. Direct or DNA Extraction-Free Amplification and Quantification of Foodborne Pathogens. Methods Mol Biol 2025; 2852:3-17. [PMID: 39235733 DOI: 10.1007/978-1-0716-4100-2_1] [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] [Indexed: 09/06/2024]
Abstract
The use of direct nucleic acid amplification of pathogens from food matrices has the potential to reduce time to results over DNA extraction-based approaches as well as traditional culture-based approaches. Here we describe protocols for assay design and experiments for direct amplification of foodborne pathogens in food sample matrices using loop-mediated isothermal amplification (LAMP) and polymerase chain reaction (PCR). The examples provided include the detection of Escherichia coli in milk samples and Salmonella in pork meat samples. This protocol includes relevant reagents and methods including obtaining target sequences, assay design, sample processing, and amplification. These methods, though used for specific example matrices, could be applied to many other foodborne pathogens and sample types.
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Affiliation(s)
- Maggie R Williams
- School of Engineering & Technology, Institute for Great Lakes Research, Central Michigan University, Mt Pleasant, MI, USA
| | - Arife Ezgi Telli
- Department of Food Hygiene and Technology, Faculty of Veterinary Medicine, Selcuk University, Konya, Turkey
| | - Nihat Telli
- Department of Food Technology, Vocational School of Technical Sciences, Konya Technical University, Konya, Turkey
| | - Dar Tafazul Islam
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI, USA
| | - Syed A Hashsham
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI, USA.
- Center for Microbial Ecology, Michigan State University, East Lansing, MI, USA.
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2
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Arjun OK, Sethi M, Parida D, Dash J, Kumar Das S, Prakash T, Senapati S. Comprehensive physiological and genomic characterization of a potential probiotic strain, Lactiplantibacillus plantarum ILSF15, isolated from the gut of tribes of Odisha, India. Gene 2024; 931:148882. [PMID: 39182659 DOI: 10.1016/j.gene.2024.148882] [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: 03/18/2024] [Revised: 08/11/2024] [Accepted: 08/21/2024] [Indexed: 08/27/2024]
Abstract
Characterizing probiotic features of organisms isolated from diverse environments can lead to the discovery of novel strains with promising functional features and health attributes. The present study attempts to characterize a novel probiotic strain isolated from the gut of the tribal population of Odisha, India. Based on 16S rRNA-based phylogeny, the strain was identified as a species of the Lactiplantibacillus genus and was named Lactiplantibacillus plantarum strain ILSF15. The current investigation focuses on elucidating this strain's genetic and physiological properties associated with probiotic attributes such as biosafety risk, host adaptation/survival traits, and beneficial functional features. The novel strain was observed, in vitro, exhibiting features such as acid/bile tolerance, adhesion to the host enteric epithelial cells, cholesterol assimilation, and pathogen exclusion, indicating its ability to survive the harsh environment of the human GIT and resist the growth of harmful microorganisms. Additionally, the L. plantarum ILSF15 strain was found to harbor genes associated with the metabolism and synthesis of various bioactive molecules, including amino acids, carbohydrates, lipids, and vitamins, highlighting the organism's ability to efficiently utilize diverse resources and contribute to the host's nutrition and health. Several genes involved in host adaptation/survival strategies and host-microbe interactions were also identified from the ILSF15 genome. Moreover, L. plantarum strains, in general, were found to have an open pangenome characterized by high genetic diversity and the absence of specific lineages associated with particular habitats, signifying its versatile nature and potential applications in probiotic and functional food industries.
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Affiliation(s)
- O K Arjun
- School of Biosciences and Bioengineering, Indian Institute of Technology Mandi, Himachal Pradesh 175005, India
| | - Manisha Sethi
- Institute of Life Sciences, Nalco Square, Bhubaneswar, Odisha 751023, India
| | - Deepti Parida
- Institute of Life Sciences, Nalco Square, Bhubaneswar, Odisha 751023, India
| | - Jayalaxmi Dash
- Institute of Life Sciences, Nalco Square, Bhubaneswar, Odisha 751023, India
| | - Suraja Kumar Das
- Institute of Life Sciences, Nalco Square, Bhubaneswar, Odisha 751023, India
| | - Tulika Prakash
- School of Biosciences and Bioengineering, Indian Institute of Technology Mandi, Himachal Pradesh 175005, India.
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3
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Sivori F, Cavallo I, Truglio M, De Maio F, Sanguinetti M, Fabrizio G, Licursi V, Francalancia M, Fraticelli F, La Greca I, Lucantoni F, Camera E, Mariano M, Ascenzioni F, Cristaudo A, Pimpinelli F, Di Domenico EG. Staphylococcus aureus colonizing the skin microbiota of adults with severe atopic dermatitis exhibits genomic diversity and convergence in biofilm traits. Biofilm 2024; 8:100222. [PMID: 39381779 PMCID: PMC11460521 DOI: 10.1016/j.bioflm.2024.100222] [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: 08/04/2024] [Revised: 09/18/2024] [Accepted: 09/19/2024] [Indexed: 10/10/2024] Open
Abstract
Atopic dermatitis (AD) is a chronic inflammatory skin disorder exacerbated by Staphylococcus aureus colonization. The specific factors that drive S. aureus overgrowth and persistence in AD remain poorly understood. This study analyzed skin barrier functions and microbiome diversity in lesional (LE) and non-lesional (NL) forearm sites of individuals with severe AD compared to healthy control subjects (HS). Notable differences were found in transepidermal water loss, stratum corneum hydration, and microbiome composition. Cutibacterium was more prevalent in HS, while S. aureus and S. lugdunensis were predominantly found in AD LE skin. The results highlighted that microbial balance depends on inter-species competition. Specifically, network analysis at the genus level demonstrated that overall bacterial correlations were higher in HS, indicating a more stable microbial community. Notably, network analysis at the species level revealed that S. aureus engaged in competitive interactions in NL and LE but not in HS. Whole-genome sequencing (WGS) showed considerable genetic diversity among S. aureus strains from AD. Despite this variability, the isolates exhibited convergence in key phenotypic traits such as adhesion and biofilm formation, which are crucial for microbial persistence. These common phenotypes suggest an adaptive evolution, driven by competition in the AD skin microenvironment, of S. aureus and underscoring the interplay between genetic diversity and phenotypic convergence in microbial adaptation.
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Affiliation(s)
- Francesca Sivori
- Microbiology and Virology Unit, San Gallicano Dermatological Institute, IRCCS, Rome, Italy
| | - Ilaria Cavallo
- Microbiology and Virology Unit, San Gallicano Dermatological Institute, IRCCS, Rome, Italy
| | - Mauro Truglio
- Microbiology and Virology Unit, San Gallicano Dermatological Institute, IRCCS, Rome, Italy
| | - Flavio De Maio
- Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario “A. Gemelli” IRCSS, Rome, Italy
| | - Maurizio Sanguinetti
- Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario “A. Gemelli” IRCSS, Rome, Italy
| | - Giorgia Fabrizio
- Department of Biology and Biotechnology “C. Darwin” Sapienza University of Rome, Rome, Italy
| | - Valerio Licursi
- Institute of Molecular Biology and Pathology, National Research Council of Italy, Rome, Italy
| | - Massimo Francalancia
- Microbiology and Virology Unit, San Gallicano Dermatological Institute, IRCCS, Rome, Italy
| | - Fulvia Fraticelli
- Microbiology and Virology Unit, San Gallicano Dermatological Institute, IRCCS, Rome, Italy
| | - Ilenia La Greca
- Microbiology and Virology Unit, San Gallicano Dermatological Institute, IRCCS, Rome, Italy
| | - Federica Lucantoni
- Department of Biology and Biotechnology “C. Darwin” Sapienza University of Rome, Rome, Italy
| | - Emanuela Camera
- Laboratory of Cutaneous Physiopathology and Integrated Center of Metabolomics Research, San Gallicano Dermatological Institute, IRCCS, Rome, Italy
| | - Maria Mariano
- Clinical Dermatology, San Gallicano Dermatological Institute, IRCCS, Rome, Italy
| | - Fiorentina Ascenzioni
- Department of Biology and Biotechnology “C. Darwin” Sapienza University of Rome, Rome, Italy
| | - Antonio Cristaudo
- Clinical Dermatology, San Gallicano Dermatological Institute, IRCCS, Rome, Italy
| | - Fulvia Pimpinelli
- Microbiology and Virology Unit, San Gallicano Dermatological Institute, IRCCS, Rome, Italy
| | - Enea Gino Di Domenico
- Microbiology and Virology Unit, San Gallicano Dermatological Institute, IRCCS, Rome, Italy
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4
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Do DT, Yang MR, Vo TNS, Le NQK, Wu YW. Unitig-centered pan-genome machine learning approach for predicting antibiotic resistance and discovering novel resistance genes in bacterial strains. Comput Struct Biotechnol J 2024; 23:1864-1876. [PMID: 38707536 PMCID: PMC11067008 DOI: 10.1016/j.csbj.2024.04.035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 04/13/2024] [Accepted: 04/13/2024] [Indexed: 05/07/2024] Open
Abstract
In current genomic research, the widely used methods for predicting antimicrobial resistance (AMR) often rely on prior knowledge of known AMR genes or reference genomes. However, these methods have limitations, potentially resulting in imprecise predictions owing to incomplete coverage of AMR mechanisms and genetic variations. To overcome these limitations, we propose a pan-genome-based machine learning approach to advance our understanding of AMR gene repertoires and uncover possible feature sets for precise AMR classification. By building compacted de Brujin graphs (cDBGs) from thousands of genomes and collecting the presence/absence patterns of unique sequences (unitigs) for Pseudomonas aeruginosa, we determined that using machine learning models on unitig-centered pan-genomes showed significant promise for accurately predicting the antibiotic resistance or susceptibility of microbial strains. Applying a feature-selection-based machine learning algorithm led to satisfactory predictive performance for the training dataset (with an area under the receiver operating characteristic curve (AUC) of > 0.929) and an independent validation dataset (AUC, approximately 0.77). Furthermore, the selected unitigs revealed previously unidentified resistance genes, allowing for the expansion of the resistance gene repertoire to those that have not previously been described in the literature on antibiotic resistance. These results demonstrate that our proposed unitig-based pan-genome feature set was effective in constructing machine learning predictors that could accurately identify AMR pathogens. Gene sets extracted using this approach may offer valuable insights into expanding known AMR genes and forming new hypotheses to uncover the underlying mechanisms of bacterial AMR.
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Affiliation(s)
- Duyen Thi Do
- Graduate Institute of Biomedical Informatics, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
| | - Ming-Ren Yang
- Graduate Institute of Biomedical Informatics, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
- Department of Electrical Engineering, National Taiwan University of Science and Technology, Taipei, Taiwan
| | - Tran Nam Son Vo
- Department of Business Administration, College of Management, Lunghwa University of Science and Technology, Taoyuan City, Taiwan
| | - Nguyen Quoc Khanh Le
- Professional Master Program in Artificial Intelligence in Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Yu-Wei Wu
- Graduate Institute of Biomedical Informatics, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
- Clinical Big Data Research Center, Taipei Medical University Hospital, Taipei, Taiwan
- TMU Research Center for Digestive Medicine, Taipei Medical University, Taipei, Taiwan
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5
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Lee JH, Kim SG, Jang KM, Shin K, Jin H, Kim DW, Jeong BC, Lee SH. Elucidation of critical chemical moieties of metallo-β-lactamase inhibitors and prioritisation of target metallo-β-lactamases. J Enzyme Inhib Med Chem 2024; 39:2318830. [PMID: 38488135 PMCID: PMC10946278 DOI: 10.1080/14756366.2024.2318830] [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: 12/30/2023] [Accepted: 02/07/2024] [Indexed: 03/19/2024] Open
Abstract
The urgent demand for effective countermeasures against metallo-β-lactamases (MBLs) necessitates development of novel metallo-β-lactamase inhibitors (MBLIs). This study is dedicated to identifying critical chemical moieties within previously developed MBLIs, and critical MBLs should serve as the target in MBLI evaluations. Using the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA), a systematic literature analysis was conducted, and the NCBI RefSeq genome database was exploited to access the abundance profile and taxonomic distribution of MBLs and their variant types. Through the implementation of two distinct systematic approaches, we elucidated critical chemical moieties of MBLIs, providing pivotal information for rational drug design. We also prioritised MBLs and their variant types, highlighting the imperative need for comprehensive testing to ensure the potency and efficacy of the newly developed MBLIs. This approach contributes valuable information to advance the field of antimicrobial drug discovery.
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Affiliation(s)
- Jung Hun Lee
- National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University, Yongin, Republic of Korea
| | - Sang-Gyu Kim
- Division of Life Sciences, Jeonbuk National University, Jeonju, Republic of Korea
| | - Kyung-Min Jang
- National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University, Yongin, Republic of Korea
| | - Kyoungmin Shin
- National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University, Yongin, Republic of Korea
| | - Hyeonku Jin
- National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University, Yongin, Republic of Korea
| | - Dae-Wi Kim
- Division of Life Sciences, Jeonbuk National University, Jeonju, Republic of Korea
| | - Byeong Chul Jeong
- National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University, Yongin, Republic of Korea
| | - Sang Hee Lee
- National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University, Yongin, Republic of Korea
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Liu S, Yang X, Li R, Wang S, Han Z, Yang M, Zhang Y. IS6 family insertion sequences promote optrA dissemination between plasmids varying in transfer abilities. Appl Microbiol Biotechnol 2024; 108:132. [PMID: 38229329 DOI: 10.1007/s00253-023-12858-w] [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: 05/26/2023] [Revised: 09/25/2023] [Accepted: 11/13/2023] [Indexed: 01/18/2024]
Abstract
Plasmids are the primary vectors for intercellular transfer of the oxazolidinone and phenicol cross-resistance gene optrA, while insertion sequences (ISs) are mobile genetic elements that can mobilize plasmid-borne optrA intracellularly. However, little is known about how the IS-mediated intracellular mobility facilitates the dissemination of the optrA gene between plasmid categories that vary in transfer abilities, including non-mobilizable, mobilizable, and conjugative plasmids. Here, we performed a holistic genomic study of 52 optrA-carrying plasmids obtained from searches guided by the Comprehensive Antibiotic Resistance Database. Among the 132 ISs identified within 10 kbp from the optrA gene in the plasmids, IS6 family genes were the most prevalent (86/132). Homologous gene arrays containing IS6 family genes were shared between different plasmids, especially between mobilizable and conjugative plasmids. All these indicated the central role of IS6 family genes in disseminating plasmid-borne optrA. Thirty-three of the 52 plasmids were harbored by Enterococcus faecalis found mainly in humans and animals. By Nanopore sequencing and inverse PCR, the potential of the enterococcal optrA to be transmitted from a mobilizable plasmid to a conjugative plasmid mediated by IS6 family genes was further confirmed in Enterococcus faecalis strains recovered from the effluents of anaerobic digestion systems for treating chicken manure. Our findings highlight the increased intercellular transfer abilities and dissemination risk of plasmid-borne optrA gene caused by IS-mediated intracellular mobility, and underscore the importance of routinely monitoring the dynamic genetic contexts of clinically important antibiotic resistance genes to effectively control this critical public health threat. KEY POINTS: • IS6 was prevalent in optrA-plasmids varying in intercellular transfer abilities. • Enterococcal optrA-plasmids were widespread among human, animal, and the environment. • IS6 elevated the dissemination risk of enterococcal optrA-plasmids.
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Affiliation(s)
- Shihai Liu
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- National Engineering Research Center of Industrial Wastewater Detoxication and Resource Recovery, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaoxiao Yang
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Ruichao Li
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, Jiangsu, China
| | - Shaolin Wang
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China
| | - Ziming Han
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- National Engineering Research Center of Industrial Wastewater Detoxication and Resource Recovery, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Min Yang
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- National Engineering Research Center of Industrial Wastewater Detoxication and Resource Recovery, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yu Zhang
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.
- National Engineering Research Center of Industrial Wastewater Detoxication and Resource Recovery, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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7
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Yuan Q, Li W, Goh SG, Chen SL, Ng OT, He Y, Gin KYH. Genetic traits and transmission of antimicrobial resistance characteristics of cephalosporin resistant Escherichia coli in tropical aquatic environments. JOURNAL OF HAZARDOUS MATERIALS 2024; 479:135707. [PMID: 39236533 DOI: 10.1016/j.jhazmat.2024.135707] [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: 05/20/2024] [Revised: 08/08/2024] [Accepted: 08/29/2024] [Indexed: 09/07/2024]
Abstract
This study investigates the genetic traits and transmission mechanisms of cephalosporin-resistant Escherichia coli in tropical aquatic environments in Singapore. From 2016 to 2020, monthly samples were collected from wastewater treatment plants, marine niches, community sewage, beaches, reservoirs, aquaculture farms, and hospitals, yielding 557 isolates that were analyzed for antimicrobial resistance genes (ARGs) and mobile genetic elements (MGEs) using genomic methods. Findings reveal significant genotypic similarities between environmental and hospital-derived strains, particularly the pandemic E. coli ST131. Environmental strains exhibited high levels of intrinsic resistance mechanisms, including mutations in porins and efflux pumps, with key ARGs such as CMY-2 and NDM-9 predominantly carried by MGEs, which facilitate horizontal gene transfer. Notably, pathogenic EPEC and EHEC strains were detected in community sewage and aquaculture farms, posing substantial public health risks. This underscores the critical role of these environments as reservoirs for multidrug-resistant pathogens and emphasizes the interconnectedness of human activities and environmental health.
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Affiliation(s)
- Qiyi Yuan
- Department of Civil and Environmental Engineering, National University of Singapore, Singapore 117576, Singapore.
| | - Wenxuan Li
- NUS Environmental Research Institute, National University of Singapore, Singapore 117411, Singapore; State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China.
| | - Shin Giek Goh
- NUS Environmental Research Institute, National University of Singapore, Singapore 117411, Singapore.
| | - Swaine L Chen
- Genome Institute of Singapore, Singapore 138672, Singapore.
| | - Oon Tek Ng
- National Centre for Infectious Diseases, Singapore 308442, Singapore.
| | - Yiliang He
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Karina Yew-Hoong Gin
- Department of Civil and Environmental Engineering, National University of Singapore, Singapore 117576, Singapore; NUS Environmental Research Institute, National University of Singapore, Singapore 117411, Singapore.
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8
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Ancajas CMF, Oyedele AS, Butt CM, Walker AS. Advances, opportunities, and challenges in methods for interrogating the structure activity relationships of natural products. Nat Prod Rep 2024; 41:1543-1578. [PMID: 38912779 PMCID: PMC11484176 DOI: 10.1039/d4np00009a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Indexed: 06/25/2024]
Abstract
Time span in literature: 1985-early 2024Natural products play a key role in drug discovery, both as a direct source of drugs and as a starting point for the development of synthetic compounds. Most natural products are not suitable to be used as drugs without further modification due to insufficient activity or poor pharmacokinetic properties. Choosing what modifications to make requires an understanding of the compound's structure-activity relationships. Use of structure-activity relationships is commonplace and essential in medicinal chemistry campaigns applied to human-designed synthetic compounds. Structure-activity relationships have also been used to improve the properties of natural products, but several challenges still limit these efforts. Here, we review methods for studying the structure-activity relationships of natural products and their limitations. Specifically, we will discuss how synthesis, including total synthesis, late-stage derivatization, chemoenzymatic synthetic pathways, and engineering and genome mining of biosynthetic pathways can be used to produce natural product analogs and discuss the challenges of each of these approaches. Finally, we will discuss computational methods including machine learning methods for analyzing the relationship between biosynthetic genes and product activity, computer aided drug design techniques, and interpretable artificial intelligence approaches towards elucidating structure-activity relationships from models trained to predict bioactivity from chemical structure. Our focus will be on these latter topics as their applications for natural products have not been extensively reviewed. We suggest that these methods are all complementary to each other, and that only collaborative efforts using a combination of these techniques will result in a full understanding of the structure-activity relationships of natural products.
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Affiliation(s)
| | | | - Caitlin M Butt
- Department of Chemistry, Vanderbilt University, Nashville, TN, USA.
| | - Allison S Walker
- Department of Chemistry, Vanderbilt University, Nashville, TN, USA.
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
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9
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Chaudhari DN, Ahire JJ, Devkatte AN, Kulthe AA. Complete Genome Sequence and Probiotic Characterization of Lactobacillus delbrueckii subsp. Indicus DC-3 Isolated from Traditional Indigenous Fermented Milk. Probiotics Antimicrob Proteins 2024:10.1007/s12602-024-10385-2. [PMID: 39417972 DOI: 10.1007/s12602-024-10385-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/09/2024] [Indexed: 10/19/2024]
Abstract
In this study, Lactobacillus delbrueckii subsp. indicus DC-3 was isolated from Indian traditional indigenous fermented milk Dahi and identified using whole genome sequencing. The safety of the strain was evaluated using genetic and phenotypic analyses, such as the presence of virulence factors, mobile and insertion elements, plasmids, antibiotic resistance, etc. Besides this, the strain was comprehensively investigated for in vitro probiotic traits, biofilm formation, antibacterials, and exopolysaccharide (EPS) production. In results, the strain showed a single circular chromosome (3,145,837 bp) with a GC content of 56.73%, a higher number of accessory and unique genes, an open pan-genome, and the absence of mobile and insertion elements, plasmids, virulence, and transmissible antibiotic resistance genes. The strain was capable of surviving in gastric juice (83% viability at 3 h) and intestinal juice (71% viability at 6 h) and showed 42.5% autoaggregation, adhesion to mucin, 8.7% adhesion to xylene, and 8.3% adhesion to Caco-2 cells. The γ-hemolytic nature, usual antibiotic susceptibility profile, and negative results for mucin and gelatin degradation ensure the safety of the strain. The strain produced 10.5 g/L of D-lactic acid and hydrogen peroxide, capable of inhibiting and co-aggregating Escherichia coli MTCC 1687, Proteus mirabilis MTCC 425, and Candida albicans ATCC 14,053. In addition, the strain showed 90 mg/L EPS (48 h) and biofilm formation. In conclusion, this study demonstrates that L. delbrueckii subsp. indicus DC-3 is unique and different than previously reported L. delbrueckii subsp. indicus strains and is a safe potential probiotic candidate.
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Affiliation(s)
| | - Jayesh J Ahire
- Dr. Reddy's Laboratories Limited, Hyderabad, 500016, India.
| | | | - Amit A Kulthe
- MIT School of Food Technology, MIT-ADT University, Pune, 412201, India
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10
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Chen W, Zhou C, Su X, Yin X, Yuan W, Hu C, Zhao W. Revealing the Genetic Diversity of Chinese Chlamydia trachomatis Strains Directly From Clinical Samples Through Selective Whole Genome Amplification. J Infect Dis 2024; 230:857-867. [PMID: 38547503 DOI: 10.1093/infdis/jiae163] [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: 12/21/2023] [Accepted: 03/27/2024] [Indexed: 10/17/2024] Open
Abstract
BACKGROUND Chlamydia trachomatis is the causative agent of the most prevalent bacterial sexually transmitted infections globally. Whole genome sequencing is essential for molecular Chlamydia surveillance; however, its application is hampered by the pathogen's low abundance in clinical specimens and the expensive labor-intensive nature of existing enrichment methodologies for Chlamydia. METHODS We developed a targeted whole genome amplification tool termed SWITCH by integrating phi29 DNA polymerase-mediated amplification with meticulously designed primer sets to enrich the C trachomatis genome, followed by whole genome sequencing. This method underwent evaluation through testing synthetic and clinical specimens. RESULTS SWITCH demonstrated robust ability to achieve up to 98.3% genomic coverage of C trachomatis from as few as 26.4 genomic copies present in synthetic specimens, and it exhibited excellent performance across diverse C trachomatis serovars. Utilizing SWITCH, we directly generated 21 Chlamydia genomes from 26 clinical samples, enabling us to gain insights into the genetic relationships and phylogeny of current Chlamydia strains circulating in the country. Remarkably, this study marked the first instance of generating Chinese Chlamydia genomes directly from clinical samples. CONCLUSIONS SWITCH represents a practical cost-efficient approach to enrich the Chlamydia genome directly from clinical specimens, offering an efficient avenue for molecular surveillance of Chlamydia.
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Affiliation(s)
- Wentao Chen
- BSL-3 Laboratory (Guangdong), Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
- Dermatology Hospital, Southern Medical University, Guangzhou, China
| | - Chuchan Zhou
- Maoming People's Hospital, Southern Medical University, Maoming, China
| | - Xin Su
- Department of Clinical Laboratory, Guangdong Provincial Second Hospital of Traditional Chinese Medicine (Guangdong Provincial Engineering Technology Research Institute of Traditional Chinese Medicine), Guangzhou, China
| | - Xiaona Yin
- Dermatology Hospital, Southern Medical University, Guangzhou, China
| | - Weixi Yuan
- Department of Clinical Laboratory, Foshan Women and Children Hospital, Foshan, China
| | - Chuncai Hu
- Department of Clinical Laboratory, Lecong Hospital of Shunde, Foshan, China
| | - Wei Zhao
- BSL-3 Laboratory (Guangdong), Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
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11
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Contarin R, Drapeau A, François P, Madec JY, Haenni M, Dordet-Frisoni E. The interplay between mobilome and resistome in Staphylococcus aureus. mBio 2024; 15:e0242824. [PMID: 39287446 PMCID: PMC11481524 DOI: 10.1128/mbio.02428-24] [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: 08/08/2024] [Accepted: 08/26/2024] [Indexed: 09/19/2024] Open
Abstract
Antibiotic resistance genes (ARGs) in Staphylococcus aureus can disseminate vertically through successful clones, but also horizontally through the transfer of genes conveyed by mobile genetic elements (MGEs). Even though underexplored, MGE/ARG associations in S. aureus favor the emergence of multidrug-resistant clones, which are challenging therapeutic success in both human and animal health. This study investigated the interplay between the mobilome and the resistome of more than 10,000 S. aureus genomes from human and animal origin. The analysis revealed a remarkable diversity of MGEs and ARGs, with plasmids and transposons being the main carriers of ARGs. Numerous MGE/ARG associations were identified, suggesting that MGEs play a critical role in the dissemination of resistance. A high degree of similarity was observed in MGE/ARG associations between human and animal isolates, highlighting the potential for unrestricted spread of ARGs between hosts. Our results showed that in parallel to clonal expansion, MGEs and their associated ARGs can spread across different strain types sequence types (STs), favoring the evolution of these clones and their adaptation in selective environments. The high variability of MGE/ARG associations within individual STs and their spread across several STs highlight the crucial role of MGEs in shaping the S. aureus resistome. Overall, this study provides valuable insights into the complex interplay between MGEs and ARGs in S. aureus, emphasizing the need to elucidate the mechanisms governing the epidemic success of MGEs, particularly those implicated in ARG transfer.IMPORTANCEThe research presented in this article highlights the importance of understanding the interactions between mobile genetic elements (MGEs) and antibiotic resistance genes (ARGs) carried by Staphylococcus aureus, a versatile bacterium that can be both a harmless commensal and a dangerous pathogen for humans and animals. S. aureus has a great capacity to acquire and disseminate ARGs, enabling efficient adaption to various environmental or clinical conditions. By analyzing a large data set of S. aureus genomes, we highlighted the substantial role of MGEs, particularly plasmids and transposons, in disseminating ARGs within and between S. aureus populations, bypassing host barriers. Given that multidrug-resistant S. aureus strains are classified as a high-priority pathogen by global health organizations, this knowledge is crucial for understanding the complex dynamics of transmission of antibiotic resistance in this species.
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Affiliation(s)
- Rachel Contarin
- INTHERES, Université de Toulouse, INRAE, ENVT, Toulouse, France
- Anses—Université de Lyon, Unité Antibiorésistance et Virulence Bactériennes, Lyon, France
| | - Antoine Drapeau
- Anses—Université de Lyon, Unité Antibiorésistance et Virulence Bactériennes, Lyon, France
| | - Pauline François
- Anses—Université de Lyon, Unité Antibiorésistance et Virulence Bactériennes, Lyon, France
| | - Jean-Yves Madec
- Anses—Université de Lyon, Unité Antibiorésistance et Virulence Bactériennes, Lyon, France
| | - Marisa Haenni
- Anses—Université de Lyon, Unité Antibiorésistance et Virulence Bactériennes, Lyon, France
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Chu J, Choi J, Ji SK, Park C, Jung SH, Park SH, Lee DG. An outbreak of bla KPC-4- and bla VIM-1-producing Klebsiella pneumoniae and Klebsiella variicola at a single hospital in South Korea. Antimicrob Resist Infect Control 2024; 13:123. [PMID: 39394195 PMCID: PMC11470574 DOI: 10.1186/s13756-024-01478-2] [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: 05/15/2024] [Accepted: 10/01/2024] [Indexed: 10/13/2024] Open
Abstract
BACKGROUND The dissemination of Klebsiella spp. producing multiple carbapenemases has been increasingly recognized. Between July 2019 and August 2021, ten patients were found to carry Klebsiella spp. co-harboring blaKPC-4 and blaVIM-1 across multiple wards at a Korean hospital, and one isolate was recovered from a hand-washing sink, more than a year after the outbreak. This study aimed to investigate the outbreak and conduct a genomic study of these isolates. METHODS Whole-genome sequencing, including long-read sequencing, was performed to analyze plasmid structures and mobile genetic elements (MGEs). Bioinformatics analyses were performed to trace clonal transmission chains and horizontal gene transfer. RESULTS The findings suggested that the inter-ward spread of Klebsiella spp. seemed to be facilitated by healthcare worker contact or patient movement. Of the nine isolates collected (eight clinical and one environmental), seven (including the environmental isolate) were identified as K. pneumoniae (ST3680) and two were K. variicola (single-locus variant of ST5252). These isolates showed high genetic relatedness within their species and harbored the IncHI5B plasmid carrying both blaKPC-4 and blaVIM-1 (pKPCVIM.1). On this plasmid, blaVIM-1 was located in the Class 1 integron associated with IS1326::IS1353 (In2), and Tn4401b carrying blaKPC-4 was inserted into IS1326::IS1353, creating a novel MGE construct (In2_blaVIM-1-Tn4401b_blaKPC-4). CONCLUSION The hospital-wide spread of blaKPC-4 and blaVIM-1 was facilitated by clonal spread and horizontal plasmid transfer. The persistence of this strain in the hospital sink suggests a potential reservoir of the strain. Understanding the transmission mechanisms of persistent pathogens is important for improving infection control strategies in hospitals.
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Affiliation(s)
- Jiyon Chu
- Department of Medical Sciences, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Jaeki Choi
- Division of Infectious Diseases, Department of Internal Medicine, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
- Vaccine Bio Research Institute, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Seul Ki Ji
- Infection Prevention and Control Unit, Daejeon St. Mary's Hospital, The Catholic University of Korea, Daejeon, Republic of Korea
| | - Chulmin Park
- Vaccine Bio Research Institute, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Seung-Hyun Jung
- Department of Medical Sciences, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea.
- Integrated Research Center for Genome Polymorphism, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea.
- Department of Biochemistry, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea.
| | - Sun Hee Park
- Division of Infectious Diseases, Department of Internal Medicine, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea.
- Vaccine Bio Research Institute, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea.
| | - Dong-Gun Lee
- Division of Infectious Diseases, Department of Internal Medicine, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
- Vaccine Bio Research Institute, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
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13
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Lee JH, Tareen AR, Kim NH, Jeong C, Kang B, Lee G, Kim DW, Zahra R, Lee SH. Complete genome sequence of a high-risk Escherichia coli ST10 isolated from avian feces in Pakistan. Microbiol Resour Announc 2024:e0076924. [PMID: 39382271 DOI: 10.1128/mra.00769-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2024] [Accepted: 09/27/2024] [Indexed: 10/10/2024] Open
Abstract
We present the complete genome sequence of Escherichia coli strain PEC1009 isolated from avian feces in Pakistan. The strain belongs to sequence type (ST) 10, a high-risk clone. The strain possesses two plasmids, and various plasmid-borne antibiotic resistance genes and chromosome-borne virulence factor genes were identified in its genome.
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Affiliation(s)
- Jung Hun Lee
- National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University, Yongin, South Korea
| | - Abdul Rauf Tareen
- Department of Microbiology, Quaid-i-Azam University, Islamabad, Pakistan
| | - Nam-Hoon Kim
- Department of Life Sciences, Jeonbuk National University, Jeonju, South Korea
| | - Chanyeong Jeong
- National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University, Yongin, South Korea
| | - Byeonghyeon Kang
- National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University, Yongin, South Korea
| | - Gwangje Lee
- National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University, Yongin, South Korea
| | - Dae-Wi Kim
- Department of Life Sciences, Jeonbuk National University, Jeonju, South Korea
| | - Rabaab Zahra
- Department of Microbiology, Quaid-i-Azam University, Islamabad, Pakistan
| | - Sang Hee Lee
- National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University, Yongin, South Korea
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14
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Rao M, Teixeira JS, Flint A, Tamber S. Hazard characterization of antibiotic-resistant Aeromonas spp. isolated from mussel and oyster shellstock available for retail purchase in Canada. J Food Prot 2024:100374. [PMID: 39383948 DOI: 10.1016/j.jfp.2024.100374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2024] [Revised: 09/30/2024] [Accepted: 10/03/2024] [Indexed: 10/11/2024]
Abstract
Surveillance and monitoring of foods for the presence of antimicrobial-resistant (AMR) bacteria is required to assess the risks these bacteria pose to human health. Frequently consumed raw or lightly cooked, live bivalve shellfish such as mussels and oysters can be a source of exposure to AMR bacteria. This study sought to determine the prevalence of third generation cephalosporin (3GC) and carbapenem resistant bacteria in live mussel and oyster shellstock available for retail purchase through the course of one calendar year. Just over half of the 180 samples (52%) tested positive for the presence 3GC-resistant bacteria belonging to thirty distinct bacterial species. Speciation of the isolates was carried out using the Bruker MALDI Biotyper. Serratia spp., Aeromonas spp., and Rahnella spp. were the most frequently isolated groups of bacteria. Antibiotic resistance testing confirmed reduced susceptibility for 3GCs and/or carbapenems in 15 of the 29 Aeromonas isolates. Based on AMR patterns, and species identity, a sub-set of ten Aeromonas strains was chosen for further characterization by whole genome sequence analysis. Genomic analysis revealed the presence of multiple antibiotic resistance and virulence genes. A number of mobile genetic elements were also identified indicating the potential for horizontal gene transfer. Differences in gene detection by the bioinformatic tools and databases used (ResFinder. CARD RGI, PlasmidFinder, and MobSuite) are discussed. This study highlights the strengths and limitations of using genomics tools to perform hazard characterization of diverse foodborne bacterial species.
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Affiliation(s)
- Mary Rao
- Bureau of Microbial Hazards, Health Canada, 251 Sir Frederick Banting Driveway, A.L. 2204E, Ottawa, Ontario, Canada K1A 0K9
| | - Januana S Teixeira
- Bureau of Microbial Hazards, Health Canada, 251 Sir Frederick Banting Driveway, A.L. 2204E, Ottawa, Ontario, Canada K1A 0K9
| | - Annika Flint
- Bureau of Microbial Hazards, Health Canada, 251 Sir Frederick Banting Driveway, A.L. 2204E, Ottawa, Ontario, Canada K1A 0K9
| | - Sandeep Tamber
- Bureau of Microbial Hazards, Health Canada, 251 Sir Frederick Banting Driveway, A.L. 2204E, Ottawa, Ontario, Canada K1A 0K9.
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Ativi LAE, Adusei-Poku M, Boateng W, Owusu-Nyantantakyi C, Kwesi Danso J, Oclu A, Bortey A, Rabbi Amuasi G, Kofi Adu Tabi B, Paintsil E, Torpey K, Dzifa Dayie N, Egyir B. Antibiotic resistance and draft genome profiles of 10 Streptococcus pneumoniae and 3 Streptococcus pseudopneumoniae strains isolated from the nasopharynx of people living with human immunodeficiency virus in Ghana. Microbiol Resour Announc 2024:e0050524. [PMID: 39365088 DOI: 10.1128/mra.00505-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2024] [Accepted: 08/24/2024] [Indexed: 10/05/2024] Open
Abstract
Genomic data on clinically important bacteria species such as Streptococcus pneumoniae and Streptococcus pseudopneumoniae from low- and middle-income countries, including Ghana, are scarce. In this study, we provide data on antimicrobial resistance (AMR) and whole-genome profiles of a collection of streptococci species to support AMR surveillance efforts in the country.
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Affiliation(s)
| | - Mildred Adusei-Poku
- Department of Medical Microbiology, University of Ghana Medical School, Accra, Ghana
| | - William Boateng
- Department of Bacteriology, Noguchi Memorial Institute for Medical Research, Accra, Ghana
| | | | - Justice Kwesi Danso
- Department of Bacteriology, Noguchi Memorial Institute for Medical Research, Accra, Ghana
| | - Agnes Oclu
- Department of Bacteriology, Noguchi Memorial Institute for Medical Research, Accra, Ghana
| | - Alfred Bortey
- Department of Bacteriology, Noguchi Memorial Institute for Medical Research, Accra, Ghana
| | - Grebstad Rabbi Amuasi
- Department of Bacteriology, Noguchi Memorial Institute for Medical Research, Accra, Ghana
| | - Blessing Kofi Adu Tabi
- Department of Bacteriology, Noguchi Memorial Institute for Medical Research, Accra, Ghana
| | - Elijah Paintsil
- Department of Pediatrics, Yale School of Medicine, Yale University, New Haven, Connecticut, USA
| | - Kwasi Torpey
- Department of Population, Family and Reproductive Health, School of Public Health, University of Ghana, Accra, Ghana
| | - Nicholas Dzifa Dayie
- Department of Medical Microbiology, University of Ghana Medical School, Accra, Ghana
| | - Beverly Egyir
- Department of Bacteriology, Noguchi Memorial Institute for Medical Research, Accra, Ghana
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16
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Mejía-Limones I, Andrade-Molina D, Morey-León G, Hidalgo-Olmedo JC, Chang-Asinc JG, Fernández-Cadena JC, Rojas M. Whole-genome sequencing of Klebsiella pneumoniae MDR circulating in a pediatric hospital setting: a comprehensive genome analysis of isolates from Guayaquil, Ecuador. BMC Genomics 2024; 25:928. [PMID: 39367302 PMCID: PMC11451243 DOI: 10.1186/s12864-024-10835-9] [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: 09/25/2024] [Indexed: 10/06/2024] Open
Abstract
BACKGROUND Klebsiella pneumoniae is the major cause of nosocomial infections worldwide and is related to a worsening increase in Multidrug-Resistant Bacteria (MDR) and virulence genes that seriously affect immunosuppressed patients, long-stay intensive care patients, elderly individuals, and children. Whole-Genome Sequencing (WGS) has resulted in a useful strategy for characterizing the genomic components of clinically important bacteria, such as K. pneumoniae, enabling them to monitor genetic changes and understand transmission, highlighting the risk of dissemination of resistance and virulence associated genes in hospitals. In this study, we report on WGS 14 clinical isolates of K. pneumoniae from a pediatric hospital biobank of Guayaquil, Ecuador. RESULTS The main findings revealed pronounced genetic heterogeneity among the isolates. Multilocus sequencing type ST45 was the predominant lineage among non-KPC isolates, whereas ST629 was found more frequently among KPC isolates. Phylogenetic analysis suggested local transmission dynamics. Comparative genomic analysis revealed a core set of 3511 conserved genes and an open pangenome in neonatal isolates. The diversity of MLSTs and capsular types, and the high genetic diversity among these isolates indicate high intraspecific variability. In terms of virulence factors, we identified genes associated with adherence, biofilm formation, immune evasion, secretion systems, multidrug efflux pump transporters, and a notably high number of genes related to iron uptake. A large number of these genes were detected in the ST45 isolate, whereas iron uptake yersiniabactin genes were found exclusively in the non-KPC isolates. We observed high resistance to commonly used antibiotics and determined that these isolates exhibited multidrug resistance including β-lactams, aminoglycosides, fluoroquinolones, quinolones, trimetropins, fosfomycin and macrolides; additionally, resistance-associated point mutations and cross-resistance genes were identified in all the isolates. We also report the first K. pneumoniae KPC-3 gene producers in Ecuador. CONCLUSIONS Our WGS results for clinical isolates highlight the importance of MDR in neonatal K. pneumoniae infections and their genetic diversity. WGS will be an imperative strategy for the surveillance of K. pneumoniae in Ecuador, and will contribute to identifying effective treatment strategies for K. pneumoniae infections in critical units in patients at stratified risk.
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Affiliation(s)
- I Mejía-Limones
- Laboratorio de Ciencias Omicas, Facultad de Ciencias de La Salud, Universidad Espíritu Santo, Samborondón, Ecuador
| | - D Andrade-Molina
- Laboratorio de Ciencias Omicas, Facultad de Ciencias de La Salud, Universidad Espíritu Santo, Samborondón, Ecuador.
| | - G Morey-León
- Laboratorio de Ciencias Omicas, Facultad de Ciencias de La Salud, Universidad Espíritu Santo, Samborondón, Ecuador
| | - J C Hidalgo-Olmedo
- Hospital de Niños Dr. Roberto Gilbert E. Junta de Beneficencia de Guayaquil, Guayaquil, Ecuador
| | - J G Chang-Asinc
- Hospital de Niños Dr. Roberto Gilbert E. Junta de Beneficencia de Guayaquil, Guayaquil, Ecuador
| | - J C Fernández-Cadena
- African Genome Center, University Mohammed VI Polytechnic (UM6P), Ben Guerir, Morocco
| | - M Rojas
- Human Genomics Corporation S.A.S., Loja, Ecuador
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17
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Glen KA, Lamont IL. Characterization of acquired β-lactamases in Pseudomonas aeruginosa and quantification of their contributions to resistance. Microbiol Spectr 2024; 12:e0069424. [PMID: 39248479 PMCID: PMC11448201 DOI: 10.1128/spectrum.00694-24] [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: 03/15/2024] [Accepted: 07/25/2024] [Indexed: 09/10/2024] Open
Abstract
Pseudomonas aeruginosa is a highly problematic opportunistic pathogen that causes a range of different infections. Infections are commonly treated with β-lactam antibiotics, including cephalosporins, monobactams, penicillins, and carbapenems, with carbapenems regarded as antibiotics of last resort. Isolates of P. aeruginosa can contain horizontally acquired bla genes encoding β-lactamase enzymes, but the extent to which these contribute to β-lactam resistance in this species has not been systematically quantified. The overall aim of this research was to address this knowledge gap by quantifying the frequency of β-lactamase-encoding genes in P. aeruginosa and by determining the effects of β-lactamases on susceptibility of P. aeruginosa to β-lactams. Genome analysis showed that β-lactamase-encoding genes are present in 3% of P. aeruginosa but are enriched in carbapenem-resistant isolates (35%). To determine the substrate antibiotics, 10 β-lactamases were expressed from an integrative plasmid in the chromosome of P. aeruginosa reference strain PAO1. The β-lactamases reduced susceptibility to a variety of clinically used antibiotics, including carbapenems (meropenem, imipenem), penicillins (ticarcillin, piperacillin), cephalosporins (ceftazidime, cefepime), and a monobactam (aztreonam). Different enzymes acted on different β-lactams. β-lactamases encoded by the genomes of P. aeruginosa clinical isolates had similar effects to the enzymes expressed in strain PAO1. Genome engineering was used to delete β-lactamase-encoding genes from three carbapenem-resistant clinical isolates and increased susceptibility to substrate β-lactams. Our findings demonstrate that acquired β-lactamases play an important role in β-lactam resistance in P. aeruginosa, identifying substrate antibiotics for a range of enzymes and quantifying their contributions to resistance.IMPORTANCEPseudomonas aeruginosa is an extremely problematic pathogen, with isolates that are resistant to the carbapenem class of β-lactam antibiotics being in critical need of new therapies. Genes encoding β-lactamase enzymes that degrade β-lactam antibiotics can be present in P. aeruginosa, including carbapenem-resistant isolates. Here, we show that β-lactamase genes are over-represented in carbapenem-resistant isolates, indicating their key role in resistance. We also show that different β-lactamases alter susceptibility of P. aeruginosa to different β-lactam antibiotics and quantify the effects of selected enzymes on β-lactam susceptibility. This research significantly advances the understanding of the contributions of acquired β-lactamases to antibiotic resistance, including carbapenem resistance, in P. aeruginosa and by implication in other species. It has potential to expedite development of methods that use whole genome sequencing of infecting bacteria to inform antibiotic treatment, allowing more effective use of antibiotics, and facilitate the development of new antibiotics.
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Affiliation(s)
- Karl A Glen
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Iain L Lamont
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
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18
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Guo S, Liu Y, Yin Y, Chen Y, Jia S, Wu T, Liao J, Jiang X, Kareem HA, Li X, Pan J, Wang Y, Shen X. Unveiling the multifaceted potential of Pseudomonas khavaziana strain SR9: a promising biocontrol agent for wheat crown rot. Microbiol Spectr 2024; 12:e0071224. [PMID: 39162535 PMCID: PMC11448100 DOI: 10.1128/spectrum.00712-24] [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: 03/19/2024] [Accepted: 07/12/2024] [Indexed: 08/21/2024] Open
Abstract
Fusarium pseudograminearum, a soil-borne fungus, is the cause of the devastating wheat disease known as wheat crown rot (WCR). The persistence of this pathogen in the soil and crop residues contributes to the increased occurrence and severity of WCR. Therefore, developing effective strategies to prevent and manage WCR is of great importance. In this study, we isolated a bacterial strain, designated as SR9, from the stem of wheat, that exhibited potent antagonistic effects against F. pseudograminearum, as well as the biocontrol efficacy of SR9 on WCR was quantified at 83.99% ± 0.11%. We identified SR9 as Pseudomonas khavaziana and demonstrated its potential as a plant probiotic. SR9 displayed broad-spectrum antagonism against other fungal pathogens, including Neurospora dictyophora, Botrytis californica, and Botryosphaeria dothidea. Whole-genome sequencing analysis revealed that SR9 harbored genes encoding various cell wall-degrading enzymes, cellulases, and lipases, along with antifungal metabolites, which are responsible for its antagonistic activity. Gene knockout and quantitative PCR analyses reveal that phenazine is the essential factor for antagonism. SR9 possessed genes related to auxin synthesis, flagellar biosynthesis, biofilm adhesion, and the chemotaxis system, which play pivotal roles in plant colonization and growth promotion; we also evaluated the effects of SR9 on plant growth in wheat and Arabidopsis. Our findings strongly suggest that SR9 holds great promise as a biocontrol agent for WCR in sustainable agriculture.IMPORTANCEThe escalating prevalence of wheat crown rot, primarily attributed to Fusarium pseudograminearum, necessitates the development of cost-effective and eco-friendly biocontrol strategies. While plant endophytes are recognized for their biocontrol potential, reports on effective strains targeting wheat crown rot are sparse. This study introduces the Pseudomonas khavaziana SR9 strain as an efficacious antagonist to the wheat crown rot pathogen Fusarium pseudograminearum. Demonstrating a significant reduction in wheat crown rot incidence and notable plant growth promotion, SR9 emerges as a key contributor to plant health and agricultural sustainability. Our study outlines a biological approach to tackle wheat crown rot, establishing a groundwork for innovative sustainable agricultural practices.
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Affiliation(s)
- Shengzhi Guo
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Xianyang, Shaanxi, China
| | - Yuqi Liu
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Xianyang, Shaanxi, China
| | - Yanling Yin
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Xianyang, Shaanxi, China
- Xinjiang Production and Construction Crops Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin, College of Life Sciences, Tarim University, Xinjiang, China
| | - Yating Chen
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Xianyang, Shaanxi, China
| | - Siyu Jia
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Xianyang, Shaanxi, China
| | - Tong Wu
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Xianyang, Shaanxi, China
| | - Jun Liao
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Xianyang, Shaanxi, China
| | - Xinyan Jiang
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Xianyang, Shaanxi, China
| | - Hafiz Abdul Kareem
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Xianyang, Shaanxi, China
| | - Xuejun Li
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Agronomy, Northwest A&F University, Xianyang, Shaanxi, China
| | - Junfeng Pan
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Xianyang, Shaanxi, China
| | - Yao Wang
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Xianyang, Shaanxi, China
| | - Xihui Shen
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Xianyang, Shaanxi, China
- Xinjiang Production and Construction Crops Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin, College of Life Sciences, Tarim University, Xinjiang, China
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Wang L, Chen S, Xing M, Dong L, Zhu H, Lin Y, Li J, Sun T, Zhu X, Wang X. Genome characterization of Shewanella algae in Hainan Province, China. Front Microbiol 2024; 15:1474871. [PMID: 39417074 PMCID: PMC11480045 DOI: 10.3389/fmicb.2024.1474871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2024] [Accepted: 09/23/2024] [Indexed: 10/19/2024] Open
Abstract
Shewanella algae is an emerging marine zoonotic pathogen. In this study, we first reported the Shewanella algae infections in patients and animals in Hainan Province, China. Currently, there is still relatively little known about the whole-genome characteristics of Shewanella algae in most tropical regions, including in southern China. Here, we sequenced the 62 Shewanella algae strains isolated from Hainan Province and combined with the whole genomes sequences of 144 Shewanella algae genomes from public databases to analyze genomic features. Phylogenetic analysis revealed that Shewanella algae is widely distributed in the marine environments of both temperate and tropical countries, exhibiting close phylogenetic relationships with genomes isolated from patients, animals, and plants. Thereby confirming that exposure to marine environments is a risk factor for Shewanella algae infections. Average nucleotide identity analysis indicated that the clonally identical genomes could be isolated from patients with different sample types at different times. Pan-genome analysis identified a total of 21,909 genes, including 1,563 core genes, 8,292 strain-specific genes, and 12,054 accessory genes. Multiple putative virulence-associated genes were identified, encompassing 14 categories and 16 subcategories, with 171 distinct virulence factors. Three different plasmid replicon types were detected in 33 genomes. Eleven classes of antibiotic resistance genes and 352 integrons were identified. Antimicrobial susceptibility testing revealed a high resistance rate to imipenem and colistin among the strains studied, with 5 strains exhibiting multidrug resistance. However, they were all sensitive to amikacin, minocycline, and tigecycline. Our findings clarify the genomic characteristics and population structure of Shewanella algae in Hainan Province. The results offer insights into the genetic basis of pathogenicity in Shewanella algae and enhance our understanding of its global phylogeography.
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Affiliation(s)
- Licheng Wang
- Clinical & Central Laboratory of Sanya People’s Hospital, Sanya, China
| | - Shaojin Chen
- Clinical & Central Laboratory of Sanya People’s Hospital, Sanya, China
| | - Mei Xing
- Wenchang People’s Hospital, Wenchang, China
| | - Lingzhi Dong
- Clinical & Central Laboratory of Sanya People’s Hospital, Sanya, China
| | - Huaxiong Zhu
- Clinical & Central Laboratory of Sanya People’s Hospital, Sanya, China
| | - Yujin Lin
- Clinical & Central Laboratory of Sanya People’s Hospital, Sanya, China
| | - Jinyi Li
- Clinical & Central Laboratory of Sanya People’s Hospital, Sanya, China
| | - Tuo Sun
- Clinical & Central Laboratory of Sanya People’s Hospital, Sanya, China
| | - Xiong Zhu
- Clinical & Central Laboratory of Sanya People’s Hospital, Sanya, China
| | - Xiaoxia Wang
- Clinical & Central Laboratory of Sanya People’s Hospital, Sanya, China
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20
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Thorpe HA, Pesonen M, Corbella M, Pesonen H, Gaiarsa S, Boinett CJ, Tonkin-Hill G, Mäklin T, Pöntinen AK, MacAlasdair N, Gladstone RA, Arredondo-Alonso S, Kallonen T, Jamrozy D, Lo SW, Chaguza C, Blackwell GA, Honkela A, Schürch AC, Willems RJL, Merla C, Petazzoni G, Feil EJ, Cambieri P, Thomson NR, Bentley SD, Sassera D, Corander J. Pan-pathogen deep sequencing of nosocomial bacterial pathogens in Italy in spring 2020: a prospective cohort study. THE LANCET. MICROBE 2024; 5:100890. [PMID: 39178869 DOI: 10.1016/s2666-5247(24)00113-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 04/17/2024] [Accepted: 04/24/2024] [Indexed: 08/26/2024]
Abstract
BACKGROUND Nosocomial infections pose a considerable risk to patients who are susceptible, and this is particularly acute in intensive care units when hospital-associated bacteria are endemic. During the first wave of the COVID-19 pandemic, the surge of patients presented a significant obstacle to the effectiveness of infection control measures. We aimed to assess the risks and extent of nosocomial pathogen transmission under a high patient burden by designing a novel bacterial pan-pathogen deep-sequencing approach that could be integrated with standard clinical surveillance and diagnostics workflows. METHODS We did a prospective cohort study in a region of northern Italy that was severely affected by the first wave of the COVID-19 pandemic. Inpatients on both ordinary and intensive care unit (ICU) wards at the San Matteo hospital, Pavia were sampled on multiple occasions to identify bacterial pathogens from respiratory, nasal, and rectal samples. Diagnostic samples collected between April 7 and May 10, 2020 were cultured on six different selective media designed to enrich for Acinetobacter baumannii, Escherichia coli, Enterococcus faecium, Enterococcus faecalis, Klebsiella pneumoniae, Pseudomonas aeruginosa, Staphylococcus aureus, and Streptococcus pneumoniae, and DNA from each plate with positive growth was deep sequenced en masse. We used mSWEEP and mGEMS to bin sequencing reads by sequence cluster for each species, followed by mapping with snippy to generate high quality alignments. Antimicrobial resistance genes were detected by use of ARIBA and CARD. Estimates of hospital transmission were obtained from pairwise bacterial single nucleotide polymorphism distances, partitioned by within-patient and between-patient samples. Finally, we compared the accuracy of our binned Acinetobacter baumannii genomes with those obtained by single colony whole-genome sequencing of isolates from the same hospital. FINDINGS We recruited patients from March 1 to May 7, 2020. The pathogen population among the patients was large and diverse, with 2148 species detections overall among the 2418 sequenced samples from the 256 patients. In total, 55 sequence clusters from key pathogen species were detected at least five times. The antimicrobial resistance gene prevalence was correspondingly high, with key carbapenemase and extended spectrum ß-lactamase genes detected in at least 50 (40%) of 125 patients in ICUs. Using high-resolution mapping to infer transmission, we established that hospital transmission was likely to be a significant mode of acquisition for each of the pathogen species. Finally, comparison with single colony Acinetobacter baumannii genomes showed that the resolution offered by deep sequencing was equivalent to single-colony sequencing, with the additional benefit of detection of co-colonisation of highly similar strains. INTERPRETATION Our study shows that a culture-based deep-sequencing approach is a possible route towards improving future pathogen surveillance and infection control at hospitals. Future studies should be designed to directly compare the accuracy, cost, and feasibility of culture-based deep sequencing with single colony whole-genome sequencing on a range of bacterial species. FUNDING Wellcome Trust, European Research Council, Academy of Finland Flagship program, Trond Mohn Foundation, and Research Council of Norway.
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Affiliation(s)
- Harry A Thorpe
- Department of Biostatistics, Faculty of Medicine, University of Oslo, Oslo, Norway.
| | - Maiju Pesonen
- Department of Biostatistics, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Marta Corbella
- Microbiology and Virology Unit, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Henri Pesonen
- Department of Biostatistics, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Stefano Gaiarsa
- Microbiology and Virology Unit, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | | | - Gerry Tonkin-Hill
- Department of Biostatistics, Faculty of Medicine, University of Oslo, Oslo, Norway; Parasites and Microbes, Wellcome Sanger Institute, Cambridge, UK
| | - Tommi Mäklin
- Department of Computer Science, University of Helsinki, Helsinki, Finland
| | - Anna K Pöntinen
- Department of Biostatistics, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Neil MacAlasdair
- Department of Biostatistics, Faculty of Medicine, University of Oslo, Oslo, Norway; Parasites and Microbes, Wellcome Sanger Institute, Cambridge, UK
| | - Rebecca A Gladstone
- Department of Biostatistics, Faculty of Medicine, University of Oslo, Oslo, Norway
| | | | - Teemu Kallonen
- Institute of Biomedicine, University of Turku, Turku, Finland
| | - Dorota Jamrozy
- Parasites and Microbes, Wellcome Sanger Institute, Cambridge, UK
| | - Stephanie W Lo
- Parasites and Microbes, Wellcome Sanger Institute, Cambridge, UK
| | - Chrispin Chaguza
- Parasites and Microbes, Wellcome Sanger Institute, Cambridge, UK
| | | | - Antti Honkela
- Department of Computer Science, University of Helsinki, Helsinki, Finland
| | - Anita C Schürch
- Department of Medical Microbiology, Universitair Medisch Centrum Utrecht, Utrecht, Netherlands
| | - Rob J L Willems
- Department of Medical Microbiology, Universitair Medisch Centrum Utrecht, Utrecht, Netherlands
| | - Cristina Merla
- Microbiology and Virology Unit, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Greta Petazzoni
- Microbiology and Virology Unit, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy; Department of Medical, Surgical, Diagnostic and Pediatric Sciences, University of Pavia, Pavia, Italy
| | - Edward J Feil
- Milner Centre for Evolution, University of Bath, Claverton Down, Bath, UK
| | - Patrizia Cambieri
- Microbiology and Virology Unit, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | | | | | - Davide Sassera
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy; Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Jukka Corander
- Department of Biostatistics, Faculty of Medicine, University of Oslo, Oslo, Norway; Parasites and Microbes, Wellcome Sanger Institute, Cambridge, UK; Helsinki Institute for Information Technology, Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland.
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21
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Yadav A, Shinde PB, Mohan H, Dhar MS, Ponnusamy K, Marwal R, Radhakrishnan VS, Goyal S, Kedia S, Ahuja V, Sharma KK. Gut colonization with antibiotic-resistant Escherichia coli pathobionts leads to disease severity in ulcerative colitis. Int J Antimicrob Agents 2024; 64:107289. [PMID: 39084575 DOI: 10.1016/j.ijantimicag.2024.107289] [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: 03/17/2024] [Revised: 07/01/2024] [Accepted: 07/22/2024] [Indexed: 08/02/2024]
Abstract
BACKGROUND Escherichia coli is a Gram-negative commensal of human gut. Surprisingly, the role of E. coli in the pathogenesis of ulcerative colitis (UC) has not been explored until now. METHODS Human gut microbiota composition and meta-gut resistome were evaluated using metagenomics. Antibiotic susceptibility of E. coli isolates against different class of antibiotics was investigated. Further, the genome sequence analysis of E. coli isolates was performed to gain insight into the antimicrobial resistance (AMR) mechanism and virulence factors. Gut proteome of UC and non-UC was examined to understand the effect of resistant bacteria on host physiology. RESULTS In UC patients, meta-gut resistome was found to be dominated by AMR genes (829) compared to healthy controls (HC) [518]. The metagenome study revealed a higher prevalence of AMR genes in the rural population (378 in HC; 607 in UC) compared to the urban (340 in HC; 578 in UC). Approximately, 40% of all E. coli isolates were multi-drug resistant (MDR), with higher prevalence in UC (43.75%) compared to HC (33.33%). Up-regulated expression of antimicrobial human proteins (lactotransferrin, azurocidin, cathepsin G, neutrophil elastase, and neutrophil defensin 3) and inflammatory mediator (Protein S100-A9 and Protein S100-A8) suggest microbial infection in UC gut. CONCLUSIONS In addition to the conventional culturomics method, a multi-omics strategy provides deeper insights into the disease etiology, emergence of MDR pathobionts, and their roles in the disruption of the healthy gut environment in UC patients.
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Affiliation(s)
- Asha Yadav
- Laboratory of Enzymology and Gut Microbiology, Department of Microbiology, Maharshi Dayanand University, Rohtak, Haryana, India
| | - Pratik Balwant Shinde
- Laboratory of Enzymology and Gut Microbiology, Department of Microbiology, Maharshi Dayanand University, Rohtak, Haryana, India
| | - Hari Mohan
- Centre for Medical Biotechnology, Maharshi Dayanand University, Rohtak, Haryana, India
| | - Mahesh S Dhar
- Department of Biotechnology, National Centre for Disease Control, Delhi, India
| | | | - Robin Marwal
- Department of Biotechnology, National Centre for Disease Control, Delhi, India
| | - V S Radhakrishnan
- Department of Biotechnology, National Centre for Disease Control, Delhi, India
| | - Sandeep Goyal
- Department of Medicine, Pt. BD Sharma Post-graduate Institute of Medical Sciences, Rohtak, Haryana, India
| | - Saurabh Kedia
- Department of Gastroenterology and Human Nutrition, All India Institute of Medical Sciences, Ansari Nagar; New Delhi, India
| | - Vineet Ahuja
- Department of Gastroenterology and Human Nutrition, All India Institute of Medical Sciences, Ansari Nagar; New Delhi, India
| | - Krishna Kant Sharma
- Laboratory of Enzymology and Gut Microbiology, Department of Microbiology, Maharshi Dayanand University, Rohtak, Haryana, India.
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22
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Yagimoto K, Hosoda S, Sato M, Hamada M. Prediction of antibiotic resistance mechanisms using a protein language model. Bioinformatics 2024; 40:btae550. [PMID: 39254573 PMCID: PMC11464418 DOI: 10.1093/bioinformatics/btae550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Revised: 08/13/2024] [Accepted: 09/07/2024] [Indexed: 09/11/2024] Open
Abstract
MOTIVATION Antibiotic resistance has emerged as a major global health threat, with an increasing number of bacterial infections becoming difficult to treat. Predicting the underlying resistance mechanisms of antibiotic resistance genes (ARGs) is crucial for understanding and combating this problem. However, existing methods struggle to accurately predict resistance mechanisms for ARGs with low similarity to known sequences and lack sufficient interpretability of the prediction models. RESULTS In this study, we present a novel approach for predicting ARG resistance mechanisms using ProteinBERT, a protein language model (pLM) based on deep learning. Our method outperforms state-of-the-art techniques on diverse ARG datasets, including those with low homology to the training data, highlighting its potential for predicting the resistance mechanisms of unknown ARGs. Attention analysis of the model reveals that it considers biologically relevant features, such as conserved amino acid residues and antibiotic target binding sites, when making predictions. These findings provide valuable insights into the molecular basis of antibiotic resistance and demonstrate the interpretability of pLMs, offering a new perspective on their application in bioinformatics. AVAILABILITY AND IMPLEMENTATION The source code is available for free at https://github.com/hmdlab/ARG-BERT. The output results of the model are published at https://waseda.box.com/v/ARG-BERT-suppl.
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Affiliation(s)
- Kanami Yagimoto
- Department of Electrical Engineering and Bioscience, Graduate School of Advanced Science and Engineering, Waseda University, Tokyo 169-8555, Japan
| | - Shion Hosoda
- Center for Exploratory Research, Research and Development Group, Hitachi, Ltd, Tokyo 185-8601, Japan
| | - Miwa Sato
- Center for Exploratory Research, Research and Development Group, Hitachi, Ltd, Tokyo 185-8601, Japan
| | - Michiaki Hamada
- Department of Electrical Engineering and Bioscience, Graduate School of Advanced Science and Engineering, Waseda University, Tokyo 169-8555, Japan
- Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), National Institute of Advanced Industrial Science and Technology, Tokyo 169-8555, Japan
- Graduate School of Medicine, Nippon Medical School, Tokyo 113-8602, Japan
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23
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Merino N, Pagán E, Berdejo D, Worby CJ, Young M, Manson AL, Pagán R, Earl AM, García-Gonzalo D. Dynamics of microbiome and resistome in a poultry burger processing line. Food Res Int 2024; 193:114842. [PMID: 39160043 DOI: 10.1016/j.foodres.2024.114842] [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: 04/02/2024] [Revised: 07/04/2024] [Accepted: 07/26/2024] [Indexed: 08/21/2024]
Abstract
Traditionally, surveillance programs for food products and food processing environments have focused on targeted pathogens and resistance genes. Recent advances in high throughput sequencing allow for more comprehensive and untargeted monitoring. This study assessed the microbiome and resistome in a poultry burger processing line using culturing techniques and whole metagenomic sequencing (WMS). Samples included meat, burgers, and expired burgers, and different work surfaces. Microbiome analysis revealed spoilage microorganisms as the main microbiota, with substantial shifts observed during the shelf-life period. Core microbiota of meat and burgers included Pseudomonas spp., Psychrobacter spp., Shewanella spp. and Brochothrix spp., while expired burgers were dominated by Latilactobacillus spp. and Leuconostoc spp. Cleaning and disinfection (C&D) procedures altered the microbial composition of work surfaces, which still harbored Hafnia spp. and Acinetobacter spp. after C&D. Resistome analysis showed a low overall abundance of resistance genes, suggesting that effective interventions during processing may mitigate their transmission. However, biocide resistance genes were frequently found, indicating potential biofilm formation or inefficient C&D protocols. This study demonstrates the utility of combining culturing techniques and WMS for comprehensive of the microbiome and resistome characterization in food processing lines.
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Affiliation(s)
- Natalia Merino
- Departamento de Producción Animal Y Ciencia de Los Alimentos, Facultad de Veterinaria, Instituto Agroalimentario de Aragón-IA2 (Universidad de Zaragoza-CITA), 50013 Zaragoza, Spain; Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Elisa Pagán
- Departamento de Producción Animal Y Ciencia de Los Alimentos, Facultad de Veterinaria, Instituto Agroalimentario de Aragón-IA2 (Universidad de Zaragoza-CITA), 50013 Zaragoza, Spain
| | - Daniel Berdejo
- Departamento de Producción Animal Y Ciencia de Los Alimentos, Facultad de Veterinaria, Instituto Agroalimentario de Aragón-IA2 (Universidad de Zaragoza-CITA), 50013 Zaragoza, Spain
| | - Colin J Worby
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Mark Young
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Abigail L Manson
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Rafael Pagán
- Departamento de Producción Animal Y Ciencia de Los Alimentos, Facultad de Veterinaria, Instituto Agroalimentario de Aragón-IA2 (Universidad de Zaragoza-CITA), 50013 Zaragoza, Spain
| | - Ashlee M Earl
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Diego García-Gonzalo
- Departamento de Producción Animal Y Ciencia de Los Alimentos, Facultad de Veterinaria, Instituto Agroalimentario de Aragón-IA2 (Universidad de Zaragoza-CITA), 50013 Zaragoza, Spain.
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24
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Kim JI, Manuele A, Maguire F, Zaheer R, McAllister TA, Beiko RG. Identification of key drivers of antimicrobial resistance in Enterococcus using machine learning. Can J Microbiol 2024; 70:446-460. [PMID: 39079170 DOI: 10.1139/cjm-2024-0049] [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] [Indexed: 10/03/2024]
Abstract
With antimicrobial resistance (AMR) rapidly evolving in pathogens, quick and accurate identification of genetic determinants of phenotypic resistance is essential for improving surveillance, stewardship, and clinical mitigation. Machine learning (ML) models show promise for AMR prediction in diagnostics but require a deep understanding of internal processes to use effectively. Our study utilised AMR gene, pangenomic, and predicted plasmid features from 647 Enterococcus faecium and Enterococcus faecalis genomes across the One Health continuum, along with corresponding resistance phenotypes, to develop interpretive ML classifiers. Vancomycin resistance could be predicted with 99% accuracy with AMR gene features, 98% with pangenome features, and 96% with plasmid clusters. Top pangenome features overlapped with the resistance genes of the vanA operon, which are often laterally transmitted via plasmids. Doxycycline resistance prediction achieved approximately 92% accuracy with pangenome features, with the top feature being elements of Tn916 conjugative transposon, a tet(M) carrier. Erythromycin resistance prediction models achieved about 90% accuracy, but top features were negatively correlated with resistance due to the confounding effect of population structure. This work demonstrates the importance of reviewing ML models' features to discern biological relevance even when achieving high-performance metrics. Our workflow offers the potential to propose hypotheses for experimental testing, enhancing the understanding of AMR mechanisms, which are crucial for combating the AMR crisis.
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Affiliation(s)
- Jee In Kim
- Faculty of Computer Science, Dalhousie University, Halifax, NS, Canada
- Institute for Comparative Genomics, Dalhousie University, Halifax, NS, Canada
- Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | - Alexander Manuele
- Faculty of Computer Science, Dalhousie University, Halifax, NS, Canada
- Institute for Comparative Genomics, Dalhousie University, Halifax, NS, Canada
| | - Finlay Maguire
- Faculty of Computer Science, Dalhousie University, Halifax, NS, Canada
- Institute for Comparative Genomics, Dalhousie University, Halifax, NS, Canada
- Department of Community Health and Epidemiology, Dalhousie University, Faculty of Medicine, Halifax, NS, Canada
| | - Rahat Zaheer
- Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | | | - Robert G Beiko
- Faculty of Computer Science, Dalhousie University, Halifax, NS, Canada
- Institute for Comparative Genomics, Dalhousie University, Halifax, NS, Canada
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25
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Carpenter L, Miller S, Flynn E, Choo JM, Collins J, Shoubridge AP, Gordon D, Lynn DJ, Whitehead C, Leong LEX, Ivey KL, Wesselingh SL, Inacio MC, Crotty M, Papanicolas LE, Taylor SL, Rogers GB. Exposure to doxycycline increases risk of carrying a broad range of enteric antimicrobial resistance determinants in an elderly cohort. J Infect 2024; 89:106243. [PMID: 39142392 DOI: 10.1016/j.jinf.2024.106243] [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: 03/21/2024] [Revised: 08/04/2024] [Accepted: 08/05/2024] [Indexed: 08/16/2024]
Abstract
OBJECTIVES High rates of antibiotic prescription in residential aged care are likely to promote enteric carriage of antibiotic-resistant pathogens and increase the risk of antibiotic treatment failure. Despite their importance, relationships between antibiotic exposures and patterns of enteric resistance carriage in this population remain poorly understood. METHODS We conducted a cross-sectional metagenomic cohort analysis of stool samples from residents of five long-term aged-care facilities in South Australia. Taxonomic composition was determined, and enteric carriage of antibiotic resistance genes (ARGs) was identified and quantified against the Comprehensive Antibiotic Resistance Database. Both the detection and abundance of stool taxa and ARGs were related to antibiotic exposures up to 12 months prior. Factors associated with the abundance of ARGs of high clinical concern were identified. RESULTS Stool samples were provided by 164 participants (median age: 88 years, IQR 81-93; 72% female). Sixty-one percent (n = 100) of participants were prescribed antibiotics at least once in the prior 12 months (median prescriptions: 4, range: 1-52), most commonly a penicillin (n = 55, 33.5%), cephalosporin (n = 53, 32.3%), diaminopyrimidine (trimethoprim) (n = 36, 22%), or tetracycline (doxycycline) (n = 21, 12.8%). More than 1100 unique ARGs, conferring resistance to 38 antibiotic classes, were identified, including 20 ARGs of high clinical concern. Multivariate logistic regression showed doxycycline exposure to be the greatest risk factor for high ARG abundance (adjusted odds ratio [aOR]=14.8, q<0.001) and a significant contributor to inter-class selection, particularly for ARGs relating to penicillins (aOR=3.1, q=0.0004) and cephalosporins (aOR=3.4, q=0.003). High enteric ARG abundance was associated with the number of separate antibiotic exposures (aOR: 6.4, q<0.001), exposures within the prior 30 days (aOR: 4.6, q=0.008) and prior 30-100 days (aOR: 2.6, q=0.008), high duration of antibiotic exposure (aOR: 7.9, q<0.001), and exposure to 3 or more antibiotic classes (aOR: 7.4, q<0.001). Carriage of one or more ARGs of high clinical concern was identified in 99% of participants (n = 162, median: 3, IQR: 2-4), involving 11 ARGs conferring resistance to aminoglycosides, four to beta-lactams, one to glycopeptides, three to fluoroquinolones, and one to oxazolidinones. Carriage of ARGs of high clinical concern was positively associated with exposure to doxycycline (aminoglycoside, fluoroquinolone, and oxazolidinone ARGs) and trimethoprim (fluoroquinolone and beta-lactam ARGs). Analysis of doxycycline impact on microbiota composition suggested that observed resistome changes arose principally through direct ARG selection, rather than through the antibiotic depletion of sensitive bacterial populations. CONCLUSIONS The gut microbiome of aged care residents is a major reservoir of antibiotic resistance. As a critical antibiotic in medical practice, a comprehensive understanding of the impact of doxycycline exposure on the gut resistome is paramount for informed antibiotic use, particularly in an evolving landscape of prophylactic applications. Near-universal asymptomatic carriage of clinically critical resistance determinants is highly concerning and reinforces the urgent need for improved management of antibiotic use in long-term aged care.
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Affiliation(s)
- Lucy Carpenter
- Microbiome and Host Health Program, South Australian Health and Medical Research Institute, Adelaide, SA, Australia; Infection and Immunity, Flinders Health and Medical Research Institute, College of Medicine and Public Health, Flinders University, Bedford Park, SA, Australia
| | - Sophie Miller
- Microbiome and Host Health Program, South Australian Health and Medical Research Institute, Adelaide, SA, Australia; Infection and Immunity, Flinders Health and Medical Research Institute, College of Medicine and Public Health, Flinders University, Bedford Park, SA, Australia
| | - Erin Flynn
- Microbiome and Host Health Program, South Australian Health and Medical Research Institute, Adelaide, SA, Australia; SA Pathology, SA Health, Adelaide, SA, Australia
| | - Jocelyn M Choo
- Microbiome and Host Health Program, South Australian Health and Medical Research Institute, Adelaide, SA, Australia; Infection and Immunity, Flinders Health and Medical Research Institute, College of Medicine and Public Health, Flinders University, Bedford Park, SA, Australia
| | - Josephine Collins
- Microbiome and Host Health Program, South Australian Health and Medical Research Institute, Adelaide, SA, Australia
| | - Andrew P Shoubridge
- Microbiome and Host Health Program, South Australian Health and Medical Research Institute, Adelaide, SA, Australia; Infection and Immunity, Flinders Health and Medical Research Institute, College of Medicine and Public Health, Flinders University, Bedford Park, SA, Australia
| | - David Gordon
- SA Pathology, SA Health, Adelaide, SA, Australia; Department of Microbiology and Infectious Diseases, Flinders Medical Centre, Bedford Park, SA, Australia
| | - David J Lynn
- Infection and Immunity, Flinders Health and Medical Research Institute, College of Medicine and Public Health, Flinders University, Bedford Park, SA, Australia; Computational & Systems Biology Program, South Australian Health and Medical Research Institute, Adelaide, SA, Australia
| | - Craig Whitehead
- Department of Rehabilitation, Aged and Palliative Care, Flinders Medical Centre, Flinders University, Bedford Park, SA, Australia; Registry of Senior Australians, South Australian Health and Medical Research Institute, Adelaide, SA, Australia
| | | | - Kerry L Ivey
- Division of Aging, Department of Medicine, Brigham and Women's Hospital, Boston, MA, United States; Department of Medicine, Harvard Medical School, Boston, MA, United States
| | - Steve L Wesselingh
- Microbiome and Host Health Program, South Australian Health and Medical Research Institute, Adelaide, SA, Australia; Infection and Immunity, Flinders Health and Medical Research Institute, College of Medicine and Public Health, Flinders University, Bedford Park, SA, Australia; Registry of Senior Australians, South Australian Health and Medical Research Institute, Adelaide, SA, Australia
| | - Maria C Inacio
- Registry of Senior Australians, South Australian Health and Medical Research Institute, Adelaide, SA, Australia; Allied Health and Human Performance, University of South Australia, Adelaide, SA, Australia
| | - Maria Crotty
- Department of Rehabilitation, Aged and Palliative Care, Flinders Medical Centre, Flinders University, Bedford Park, SA, Australia; Registry of Senior Australians, South Australian Health and Medical Research Institute, Adelaide, SA, Australia
| | - Lito E Papanicolas
- Microbiome and Host Health Program, South Australian Health and Medical Research Institute, Adelaide, SA, Australia; Infection and Immunity, Flinders Health and Medical Research Institute, College of Medicine and Public Health, Flinders University, Bedford Park, SA, Australia; SA Pathology, SA Health, Adelaide, SA, Australia
| | - Steven L Taylor
- Microbiome and Host Health Program, South Australian Health and Medical Research Institute, Adelaide, SA, Australia; Infection and Immunity, Flinders Health and Medical Research Institute, College of Medicine and Public Health, Flinders University, Bedford Park, SA, Australia
| | - Geraint B Rogers
- Microbiome and Host Health Program, South Australian Health and Medical Research Institute, Adelaide, SA, Australia; Infection and Immunity, Flinders Health and Medical Research Institute, College of Medicine and Public Health, Flinders University, Bedford Park, SA, Australia.
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26
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Li M, Sun X, Zhao L, Du W, Shang D. The antibacterial activity and mechanisms of Trp-containing peptides against multidrug-resistant Pseudomonas aeruginosa persisters. Biochimie 2024; 225:133-145. [PMID: 38815647 DOI: 10.1016/j.biochi.2024.05.019] [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: 03/03/2024] [Revised: 04/27/2024] [Accepted: 05/22/2024] [Indexed: 06/01/2024]
Abstract
Bacterial persisters avoid antibiotic-mediated death by entering a dormant state and are considered a major cause of antibiotic treatment failure. Antimicrobial peptides (AMPs) with membrane-disrupting activity are promising drugs to eradicate persister cells. In this study, carbonyl cyanide m-chlorophenylhydrazone (CCCP), ciprofloxacin (CIP), and rifampicin (RFP) were applied to induce the formation of multidrug-resistant Pseudomonas aeruginosa (MRPA0108) persisters, and the antibacterial activity and mechanisms of I1W and L12W (two Trp-containing peptides designed in our lab) against MRPA0108 persisters were investigated. The results showed that I1W and L12W displayed potent antibacterial activity against MRPA0108 persisters. Both Trp-containing peptides disturbed the inner and outer membrane of MRPA0108 persisters. In addition, I1W and L12W revealed novel antibacterial mechanisms by decreasing the enzymatic activities of superoxide dismutase (SOD) and catalase (CAT), increasing reactive oxygen species (ROS) and malondialdehyde (MDA) levels, consequently leading to oxidative stress. The transcriptome profile of I1W-treated MRPA0108 persisters revealed that the genes involved in carbon metabolism, biosynthesis of amino acids, and the TCA cycle were downregulated, indicating that I1W interfered with metabolism and energy synthesis processes. Furthermore, both Trp-containing peptides displayed synergistic activities with antibiotic tobramycin and showed additive activities with cefepime or ciprofloxacin, which revealed a potential therapeutic strategy for the eradication of MRPA0108 persisters.
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Affiliation(s)
- Mengmiao Li
- School of Life Sciences, Liaoning Normal University, Dalian, China; Liaoning Provincial Key Laboratory of Biotechnology and Drug Discovery, Liaoning Normal University, Dalian, China
| | - Xiaomi Sun
- School of Life Sciences, Liaoning Normal University, Dalian, China
| | - Lei Zhao
- School of Life Sciences, Liaoning Normal University, Dalian, China
| | - Wanying Du
- School of Life Sciences, Liaoning Normal University, Dalian, China
| | - Dejing Shang
- School of Life Sciences, Liaoning Normal University, Dalian, China; Liaoning Provincial Key Laboratory of Biotechnology and Drug Discovery, Liaoning Normal University, Dalian, China.
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Zhou X, Yang M, Chen F, Wang L, Han P, Jiang Z, Shen S, Rao G, Yang F. Prediction of antimicrobial resistance in Klebsiella pneumoniae using genomic and metagenomic next-generation sequencing data. J Antimicrob Chemother 2024; 79:2509-2517. [PMID: 39028665 DOI: 10.1093/jac/dkae248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 07/04/2024] [Indexed: 07/21/2024] Open
Abstract
OBJECTIVES Klebsiella pneumoniae is a significant pathogen with increasing resistance and high mortality rates. Conventional antibiotic susceptibility testing methods are time-consuming. Next-generation sequencing has shown promise for predicting antimicrobial resistance (AMR). This study aims to develop prediction models using whole-genome sequencing data and assess their feasibility with metagenomic next-generation sequencing data from clinical samples. METHODS On the basis of 4170 K. pneumoniae genomes, the main genetic characteristics associated with AMR were identified using a LASSO regression model. Consequently, the prediction model was established, validated and optimized using clinical isolate read simulation sequences. To evaluate the efficacy of the model, clinical specimens were collected. RESULTS Four predictive models for amikacin, ciprofloxacin, levofloxacin, and piperacillin/tazobactam, initially had positive predictive values (PPVs) of 92%, 98%, 99%, 94%, respectively, when they were originally constructed. When applied to clinical specimens, their PPVs were 96%, 96%, 95%, and 100%, respectively. Meanwhile, there were negative predictive values (NPVs) of 100% for ciprofloxacin and levofloxacin, and 'not applicable' (NA) for amikacin and piperacillin/tazobactam. Our method achieved antibacterial phenotype classification accuracy rates of 95.92% for amikacin, 96.15% for ciprofloxacin, 95.31% for levofloxacin and 100% for piperacillin/tazobactam. The sequence-based prediction antibiotic susceptibility testing (AST) reported results in an average time of 19.5 h, compared with the 67.9 h needed for culture-based AST, resulting in a significant reduction of 48.4 h. CONCLUSIONS These preliminary results demonstrated that the performance of prediction model for a clinically significant antimicrobial-species pair was comparable to that of phenotypic methods, thereby encouraging the expansion of sequence-based susceptibility prediction and its clinical validation and application.
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Affiliation(s)
- Xun Zhou
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China
- Key Laboratory of Clinical Pharmacology of Antibiotics, Ministry of Health, Shanghai, China
| | - Ming Yang
- The Second Affiliated Hospital of Air Force Military Medical University, Xi'an, China
| | | | - Leilei Wang
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China
- Key Laboratory of Clinical Pharmacology of Antibiotics, Ministry of Health, Shanghai, China
| | - Peng Han
- Genskey Medical Technology Co. Ltd., Beijing, China
| | - Zhi Jiang
- Genskey Medical Technology Co. Ltd., Beijing, China
| | - Siquan Shen
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China
- Key Laboratory of Clinical Pharmacology of Antibiotics, Ministry of Health, Shanghai, China
| | - Guanhua Rao
- Genskey Medical Technology Co. Ltd., Beijing, China
| | - Fan Yang
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China
- Key Laboratory of Clinical Pharmacology of Antibiotics, Ministry of Health, Shanghai, China
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Ling X, Gu X, Shen Y, Fu C, Zhou Y, Yin Y, Gao Y, Zhu Y, Lou Y, Zheng M. Comparative genomic analysis of Acanthamoeba from different sources and horizontal transfer events of antimicrobial resistance genes. mSphere 2024:e0054824. [PMID: 39352766 DOI: 10.1128/msphere.00548-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2024] [Accepted: 09/10/2024] [Indexed: 10/04/2024] Open
Abstract
Acanthamoeba species are among the most common free-living amoeba and ubiquitous protozoa, mainly distributed in water and soil, and cause Acanthamoeba keratitis (AK) and severe visual impairment in patients. Although several studies have reported genomic characteristics of Acanthamoeba, limited sample sizes and sources have resulted in an incomplete understanding of the genetic diversity of Acanthamoeba from different sources. While endosymbionts exert a significant influence on the phenotypes of Acanthamoeba, including pathogenicity, virulence, and drug resistance, the species diversity and functional characterization remain largely unexplored. Herein, our study sequenced and analyzed the whole genomes of 19 Acanthamoeba pathogenic strains that cause AK, and by integrating publicly available genomes, we sampled 29 Acanthamoeba strains from ocular, environmental, and other sources. Combined pan-genomic and comparative functional analyses revealed genetic differences and evolutionary relationships among the different sources of Acanthamoeba, as well as classification into multiple functional groups, with ocular isolates in particular showing significant differences that may account for differences in pathogenicity. Phylogenetic and rhizome gene mosaic analyses of ocular Acanthamoeba strains suggested that genomic exchanges between Acanthamoeba and endosymbionts, particularly potential antimicrobial resistance genes trafficking including the adeF, amrA, and amrB genes exchange events, potentially contribute to Acanthamoeba drug resistance. In conclusion, this study elucidated the adaptation of Acanthamoeba to different ecological niches and the influence of gene exchange on the evolution of ocular Acanthamoeba genome, guiding the clinical diagnosis and treatment of AK and laying a theoretical groundwork for developing novel therapeutic approaches. IMPORTANCE Acanthamoeba causes a serious blinding keratopathy, Acanthamoeba keratitis, which is currently under-recognized by clinicians. In this study, we analyzed 48 strains of Acanthamoeba using a whole-genome approach, revealing differences in pathogenicity and function between strains of different origins. Horizontal transfer events of antimicrobial resistance genes can help provide guidance as potential biomarkers for the treatment of specific Acanthamoeba keratitis cases.
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Affiliation(s)
- Xinyi Ling
- Wenzhou Key Laboratory of Sanitary Microbiology, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Xiaobin Gu
- Wenzhou Key Laboratory of Sanitary Microbiology, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Yue Shen
- National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, China
- Eye Hospital, School of Ophthalmology and Optometry, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Chunyan Fu
- National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, China
- Eye Hospital, School of Ophthalmology and Optometry, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Yumei Zhou
- National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, China
- Eye Hospital, School of Ophthalmology and Optometry, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Yiling Yin
- National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, China
- Eye Hospital, School of Ophthalmology and Optometry, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Yanqiu Gao
- Wenzhou Key Laboratory of Sanitary Microbiology, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Yiwei Zhu
- National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, China
- Eye Hospital, School of Ophthalmology and Optometry, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Yongliang Lou
- Wenzhou Key Laboratory of Sanitary Microbiology, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Meiqin Zheng
- Wenzhou Key Laboratory of Sanitary Microbiology, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, Zhejiang, China
- National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, China
- Eye Hospital, School of Ophthalmology and Optometry, Wenzhou Medical University, Wenzhou, Zhejiang, China
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Furlan JPR, Sellera FP, Gonzalez IHL, Ramos PL, Stehling EG. The curious case of the rare Citrobacter pasteurii isolated from an endangered primate in Brazil. Comp Immunol Microbiol Infect Dis 2024; 113:102234. [PMID: 39276760 DOI: 10.1016/j.cimid.2024.102234] [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: 08/08/2024] [Accepted: 09/02/2024] [Indexed: 09/17/2024]
Abstract
The genus Citrobacter comprises clinically important human pathogens but has been less frequently associated with wildlife infections. Citrobacter pasteurii was first identified as causing human diarrhea and remains rarely documented. In this study, a Gram-negative bacterial strain, named A318, was identified as causing diarrhea in a black lion tamarin. This strain was biochemically identified as Trabulsiella guamensis, a species of unusual nature, and was submitted to whole-genome characterization. Curiously, phylogenomic analysis showed that A318 strain belonged to the genus Citrobacter, with confirmation of the species C. pasteurii by average nucleotide identity (99.02 %) and digital DNA-DNA hybridization (93.80 %) analyzes. Cases of misidentification of C. pasteurii as Citrobacter youngae were detected and corrected in this study. In addition to the genome sequence of the type strain of C. pasteurii, only two others from the Australian cockle and Portuguese silver gull are publicly available. Single nucleotide polymorphism differences among all C. pasteurii indicated a highly diverse population. No acquired antimicrobial resistance genes and plasmid replicons were found. Therefore, our findings emphasize the importance of gold-standard methods for accurate identification and underscores the importance of continued surveillance and research to mitigate the risks posed by zoonotic and zooanthroponotic pathogens.
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Affiliation(s)
- João Pedro Rueda Furlan
- Department of Clinical Analyses, Toxicology and Food Science, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Brazil
| | - Fábio Parra Sellera
- Department of Internal Medicine, School of Veterinary Medicine and Animal Science, University of São Paulo, São Paulo, Brazil; School of Veterinary Medicine, Metropolitan University of Santos, Santos, Brazil
| | - Irys Hany Lima Gonzalez
- Wildlife Coordination, Secretary of Environment, Infrastructure and Logistics, São Paulo, Brazil
| | - Patrícia Locosque Ramos
- Wildlife Coordination, Secretary of Environment, Infrastructure and Logistics, São Paulo, Brazil
| | - Eliana Guedes Stehling
- Department of Clinical Analyses, Toxicology and Food Science, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Brazil.
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Bote L, Taylor-Brown A, Maes M, Ingle DJ, Valcanis M, Howden BP, Thomson NR. Surveillance of travel-associated isolates elucidates the diversity of non-pandemic Vibrio cholerae. Microb Genom 2024; 10. [PMID: 39412871 DOI: 10.1099/mgen.0.001307] [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] [Indexed: 10/18/2024] Open
Abstract
Vibrio cholerae is a Gram-negative bacterium found in aquatic environments and is the aetiological agent of cholera, characterized by acute watery diarrhoea and severe dehydration. Cholera presents a significant global health burden of an estimated 1.3-5 million annual cases, with the current pandemic caused by a toxigenic lineage of the O1 El Tor biotype called seventh pandemic El Tor (7PET) that is still ongoing. Whilst it is known that non-7PET lineages can cause sporadic disease, little is known about the transmission of these non-epidemic lineages. Thirty-four V. cholerae isolates were obtained from travellers returning from Indonesia to Australia between 2005 and 2017. These were whole genome sequenced, placed into a global phylogenetic context with 883 isolates, and screened for known genes associated with antimicrobial resistance and virulence. This analysis revealed that 30 isolates fell within non-7PET lineages and four within the 7PET lineage. Both 7PET and non-7PET isolates carried genes for resistance to antibiotics that are commonly used in cholera treatment such as tetracyclines and fluoroquinolones. Diverse virulence factors were also present in non-7PET isolates, with two isolates notably carrying toxin-coregulated pilus genes, which are primarily responsible for intestinal colonization in 7PET V. cholerae. This study demonstrates the role of travel in long-range carriage of epidemic and non-epidemic lineages of V. cholerae, and how sentinel travel surveillance can enrich our knowledge of V. cholerae diversity, reveal new biology about the spread of diverse lineages with differing disease potential and illuminate disease presence in endemic regions with limited surveillance data.
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Affiliation(s)
- Lia Bote
- Wellcome Sanger Institute, Hinxton, UK
| | | | | | - Danielle J Ingle
- The Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Mary Valcanis
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Benjamin P Howden
- The Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
- Centre for Pathogen Genomics, The University of Melbourne, Melbourne, Australia
- Department of Infectious Diseases and Immunology, Austin Health, Heidelberg, Australia
| | - Nicholas R Thomson
- Wellcome Sanger Institute, Hinxton, UK
- London School of Hygiene and Tropical Medicine, London, UK
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31
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Wang H, Wang X, Cao Y, Chen Y, Zou Z, Lu X, Shan F, Tu J, Liu J, Liu J, Sa J, Zhou N, Peng SM, Zou JJ, Shen X, Zhai J, Chen Z, Holmes EC, Chen W, Shen Y. Identification of Corynebacterium ulcerans and Erysipelothrix sp. in Malayan pangolins-a potential threat to public health? mSphere 2024:e0055124. [PMID: 39345123 DOI: 10.1128/msphere.00551-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2024] [Accepted: 09/11/2024] [Indexed: 10/01/2024] Open
Abstract
The discovery of severe acute respiratory syndrome-coronavirus-2-like and Middle East respiratory syndrome-coronavirus-like viruses in Malayan pangolins has raised concerns about their potential role in the spread of zoonotic diseases. Herein, we describe the isolation and whole-genome sequencing of potentially zoonotic two bacterial pathogens from diseased Malaysian pangolins (Manis javanica)-Corynebacterium ulcerans and Erysipelothrix sp. The newly identified species were designated as C. ulcerans P69 and Erysipelothrix sp. P66. C. ulcerans P69 exhibited 99.2% whole-genome nucleotide identity to human bacterial isolate 4940, suggesting that it might have zoonotic potential. Notably, C. ulcerans P69 lacked the diphtheria toxin (tox) gene that is widely used in vaccines to protect humans from corynebacterial infection, which suggests that the current vaccine may be of limited efficacy against this pangolin strain. C. ulcerans P69 also contains other known virulence-associated genes such as pld and exhibits resistance to several antibiotics (erythromycin, clindamycin, penicillin G, gentamicin, tetracycline), which may affect its effective control. Erysipelothrix sp. P66 was closely related to Erysipelothrix sp. strain 2-related strains, exhibiting 98.8% whole-genome nucleotide identity. This bacterium is lethal in mice, and two commercial vaccines failed to protect its challenge, such that it could potentially pose a threat to the swine industry. Overall, this study highlights that, in addition to viruses, pangolins harbor bacteria that may pose a potential threat to humans and domestic animals, and which merit attention. IMPORTANCE This study firstly reports the presence of two potentially zoonotic bacteria, Corynebacterium ulcerans and Erysipelothrix sp., in diseased Malaysian pangolins collected in 2019. The pangolin C. ulcerans is lethal in mice and resists many antibiotics. It clustered with a lethal human strain but lacked the diphtheria toxin gene. Diphtheria toxin is widely used as a vaccine around the world to protect humans from the infection of corynebacteria. The lack of the tox gene suggests that the current vaccine may be of limited efficacy against this pangolin strain. The pangolin Erysipelothrix sp. is the sister clade of Erysipelothrix rhusiopathiae. It is lethal in mice, and two commercial vaccines failed to protect the mice against challenge with the pangolin Erysipelothrix sp., such that this strain could potentially pose a threat to the swine industry. These findings emphasize the potential threat of pangolin bacteria.
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Affiliation(s)
- Hai Wang
- State Key Laboratory for Animal Disease Control and Prevention, Guangdong Laboratory for Lingnan Modern Agriculture, Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Xiao Wang
- State Key Laboratory for Animal Disease Control and Prevention, Guangdong Laboratory for Lingnan Modern Agriculture, Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Yilin Cao
- State Key Laboratory for Animal Disease Control and Prevention, Guangdong Laboratory for Lingnan Modern Agriculture, Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Yiting Chen
- State Key Laboratory for Animal Disease Control and Prevention, Guangdong Laboratory for Lingnan Modern Agriculture, Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Zanjian Zou
- State Key Laboratory for Animal Disease Control and Prevention, Guangdong Laboratory for Lingnan Modern Agriculture, Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Xingbang Lu
- State Key Laboratory for Animal Disease Control and Prevention, Guangdong Laboratory for Lingnan Modern Agriculture, Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Fen Shan
- Guangzhou Zoo, Guangzhou Wildlife Research Center, Guangzhou, China
| | - Jieying Tu
- College of Veterinary Medicine, National Risk Assessment Laboratory for Antimicrobial Resistant of Microorganisms in Animals, Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, Key Laboratory of Zoonosis of Ministry of Agricultural and Rural Affairs, Center for Emerging and Zoonotic Diseases, South China Agricultural University, Guangzhou, China
| | - Jianhua Liu
- College of Veterinary Medicine, National Risk Assessment Laboratory for Antimicrobial Resistant of Microorganisms in Animals, Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, Key Laboratory of Zoonosis of Ministry of Agricultural and Rural Affairs, Center for Emerging and Zoonotic Diseases, South China Agricultural University, Guangzhou, China
| | - Jiameng Liu
- State Key Laboratory for Animal Disease Control and Prevention, Guangdong Laboratory for Lingnan Modern Agriculture, Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Jiaqi Sa
- Guangzhou Zoo, Guangzhou Wildlife Research Center, Guangzhou, China
| | - Niu Zhou
- Guangzhou Zoo, Guangzhou Wildlife Research Center, Guangzhou, China
| | - Shi-Ming Peng
- Guangzhou Zoo, Guangzhou Wildlife Research Center, Guangzhou, China
| | - Jie-Jian Zou
- Guangdong Provincial Wildlife Monitoring and Rescue Center, Guangzhou, China
| | - Xuejuan Shen
- State Key Laboratory for Animal Disease Control and Prevention, Guangdong Laboratory for Lingnan Modern Agriculture, Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Junqiong Zhai
- Guangzhou Zoo, Guangzhou Wildlife Research Center, Guangzhou, China
| | - Zujin Chen
- Guangzhou Zoo, Guangzhou Wildlife Research Center, Guangzhou, China
| | - Edward C Holmes
- School of Medical Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Wu Chen
- Guangzhou Zoo, Guangzhou Wildlife Research Center, Guangzhou, China
| | - Yongyi Shen
- State Key Laboratory for Animal Disease Control and Prevention, Guangdong Laboratory for Lingnan Modern Agriculture, Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, Guangzhou, Guangdong, China
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Afolayan JS, Varney AM, Thomas JC, McLean S, Perry CC. A rapid microwave approach for 'one-pot' synthesis of antibiotic conjugated silver nanoparticles with antimicrobial activity against multi-drug resistant bacterial pathogens. Colloids Surf B Biointerfaces 2024; 245:114280. [PMID: 39362073 DOI: 10.1016/j.colsurfb.2024.114280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 09/26/2024] [Accepted: 09/27/2024] [Indexed: 10/05/2024]
Abstract
Deaths directly attributable to drug-resistant infections reached 1.27 million in 2019 and continue to rise. This escalating resistance to antibiotics has driven a resurgence in the exploration of ancient antimicrobials to develop efficacious alternatives. The modern field of nanomaterials is a promising area of research with silver nanoparticles performing well as antimicrobial agents due to their large surface area and multiple bacterial targets. In the current study antibiotic conjugated silver nanoparticles (3-35 nm) were synthesized using β-lactam antibiotic, ampicillin. The method of heating during synthesis either microwave (4 min) or convection (4 h) influenced the physical characteristics of the ampicillin coated silver nanoparticles, however both approaches produced nanomaterials with antimicrobial activity against a variety of multi-drug resistant (MDR) clinical isolates in physiologically relevant media (when present at <0.2-2.28 mg L-1 in defined media). Critically, the microwave method is five times faster than the traditional water bath method, allowing rapid synthesis of ampicillin-conjugated nanoparticles, which supports scale up processes for industry. We suggest that the combination of antibiotic and silver in these nanoparticles produces a synergistic effect that circumvents resistance mechanisms and has the potential to provide a new line of combinatorial agents able to treat multi-drug resistant infections.
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Affiliation(s)
- Juwon S Afolayan
- School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham NG11 8NS, UK
| | - Adam M Varney
- School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham NG11 8NS, UK
| | - Jonathan C Thomas
- School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham NG11 8NS, UK
| | - Samantha McLean
- School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham NG11 8NS, UK.
| | - Carole C Perry
- School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham NG11 8NS, UK.
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Tierney BT, Foox J, Ryon KA, Butler D, Damle N, Young BG, Mozsary C, Babler KM, Yin X, Carattini Y, Andrews D, Lucaci AG, Solle NS, Kumar N, Shukla B, Vidović D, Currall B, Williams SL, Schürer SC, Stevenson M, Amirali A, Beaver CC, Kobetz E, Boone MM, Reding B, Laine J, Comerford S, Lamar WE, Tallon JJ, Wain Hirschberg J, Proszynski J, Al Ghalith G, Can Kurt K, Sharkey ME, Church GM, Grills GS, Solo-Gabriele HM, Mason CE. Towards geospatially-resolved public-health surveillance via wastewater sequencing. Nat Commun 2024; 15:8386. [PMID: 39333485 PMCID: PMC11436780 DOI: 10.1038/s41467-024-52427-x] [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: 06/23/2024] [Accepted: 09/05/2024] [Indexed: 09/29/2024] Open
Abstract
Wastewater is a geospatially- and temporally-linked microbial fingerprint of a given population, making it a potentially valuable tool for tracking public health across locales and time. Here, we integrate targeted and bulk RNA sequencing (N = 2238 samples) to track the viral, bacterial, and functional content over geospatially distinct areas within Miami Dade County, USA, from 2020-2022. We used targeted amplicon sequencing to track diverse SARS-CoV-2 variants across space and time, and we found a tight correspondence with positive PCR tests from University students and Miami-Dade hospital patients. Additionally, in bulk metatranscriptomic data, we demonstrate that the bacterial content of different wastewater sampling locations serving small population sizes can be used to detect putative, host-derived microorganisms that themselves have known associations with human health and diet. We also detect multiple enteric pathogens (e.g., Norovirus) and characterize viral diversity across sites. Moreover, we observed an enrichment of antimicrobial resistance genes (ARGs) in hospital wastewater; antibiotic-specific ARGs correlated to total prescriptions of those same antibiotics (e.g Ampicillin, Gentamicin). Overall, this effort lays the groundwork for systematic characterization of wastewater that can potentially influence public health decision-making.
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Affiliation(s)
- Braden T Tierney
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA.
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA.
| | - Jonathan Foox
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Krista A Ryon
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Daniel Butler
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Namita Damle
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Benjamin G Young
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Christopher Mozsary
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Kristina M Babler
- Department of Human Genetics, University of Utah, Salt Lake City, UT, USA
- Department of Chemical, Environmental, and Materials Engineering, University of Miami, Coral Gables, FL, USA
| | - Xue Yin
- Department of Chemical, Environmental, and Materials Engineering, University of Miami, Coral Gables, FL, USA
| | - Yamina Carattini
- Department of Pathology and Laboratory Medicine, University of Miami Miller School of Medicine, Miami, FL, USA
| | - David Andrews
- Department of Pathology and Laboratory Medicine, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Alexander G Lucaci
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | | | - Naresh Kumar
- Department of Public Health Sciences, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Bhavarth Shukla
- Department of Medicine, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Dušica Vidović
- Department of Molecular & Cellular Pharmacology, University of Miami Miller School of Medicine, Miami, FL, USA
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Benjamin Currall
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Sion L Williams
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Stephan C Schürer
- Department of Molecular & Cellular Pharmacology, University of Miami Miller School of Medicine, Miami, FL, USA
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, USA
- Institute for Data Science & Computing, University of Miami, Coral Gables, FL, USA
| | - Mario Stevenson
- Department of Medicine, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Ayaaz Amirali
- Department of Chemical, Environmental, and Materials Engineering, University of Miami, Coral Gables, FL, USA
| | - Cynthia Campos Beaver
- Department of Medicine, University of Miami Miller School of Medicine, Miami, FL, USA
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Erin Kobetz
- Department of Medicine, University of Miami Miller School of Medicine, Miami, FL, USA
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Melinda M Boone
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Brian Reding
- Environmental Health and Safety, University of Miami, Miami, FL, USA
| | - Jennifer Laine
- Environmental Health and Safety, University of Miami, Miami, FL, USA
| | - Samuel Comerford
- Environmental Health and Safety, University of Miami, Miami, FL, USA
| | - Walter E Lamar
- Division of Occupational Health, Safety & Compliance, University of Miami Health System, Miami, FL, USA
| | - John J Tallon
- Facilities and Operations, University of Miami, Coral Gables, FL, USA
| | | | | | | | - Kübra Can Kurt
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Mark E Sharkey
- Department of Pathology and Laboratory Medicine, University of Miami Miller School of Medicine, Miami, FL, USA
| | - George M Church
- Harvard Medical School and the Wyss Institute, Boston, MA, USA
| | - George S Grills
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Helena M Solo-Gabriele
- Department of Chemical, Environmental, and Materials Engineering, University of Miami, Coral Gables, FL, USA.
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA.
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA.
- The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA.
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Zelasko S, Swaney MH, Suh WS, Sandstrom S, Carlson C, Cagnazzo J, Golfinos A, Fossen J, Andes D, Kalan LR, Safdar N, Currie CR. Altered oral microbiota of drug-resistant organism carriers exhibit impaired gram-negative pathogen inhibition. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.24.614756. [PMID: 39386697 PMCID: PMC11463450 DOI: 10.1101/2024.09.24.614756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/12/2024]
Abstract
The oral microbiome has been understudied as a reservoir for clinical pathogens, including drug-resistant strains. Understanding how alterations in microbiome functioning render this site vulnerable to colonization is essential, as multidrug-resistant organisms (MDRO) carriage is a major risk factor for developing serious infections. To advance our knowledge of oral MDRO carriage and protection against pathogen colonization conferred by native microbiota, we examined microbiomes from individuals colonized by MDROs (n=33) and non-colonized age-matched controls (n=30). Shotgun metagenomic analyses of oral swabs from study participants revealed significant differences in microbial communities with depletion of Streptococcus spp. among those colonized by multidrug-resistant gram-negative bacilli (RGNB), compared to non-carriers. We utilized metagenomic sequencing to characterize the oral resistome and find antimicrobial resistance genes are present in higher abundance among RNGB carriers versus non-carriers. High-throughput co-culture screening revealed oral bacteria isolated from MDRO non-carriers demonstrate greater inhibition of gram-negative pathogens, compared to isolates from carriers. Moreover, biosynthetic gene clusters from streptococci are found in higher abundance from non-carrier microbiomes, compared to RGNB carrier microbiomes. Bioactivity-guided fractionation of extracts from Streptococcus isolate SID2657 demonstrated evidence of strong E. coli and A. baumannii inhibition in a murine model of infection. Together, this provides evidence that oral microbiota shape this dynamic microbial community and may serve as an untapped source for much-needed antimicrobial small-molecules.
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Chen L, Zhang L, Li Y, Qiao L, Kumar S. Screening of promising molecules against potential drug targets in Yersinia pestis by integrative pan and subtractive genomics, docking and simulation approach. Arch Microbiol 2024; 206:415. [PMID: 39320535 DOI: 10.1007/s00203-024-04140-y] [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: 07/19/2024] [Revised: 09/02/2024] [Accepted: 09/10/2024] [Indexed: 09/26/2024]
Abstract
This study focuses on Yersinia pestis, the bacterium responsible for plague, which posed a severe threat to public health in history. Despite the availability of antibiotics treatment, the emergence of antibiotic resistance in this pathogen has increased challenges of controlling the infections and plague outbreaks. The development of new drug targets and therapies is urgently needed. This research aims to identify novel protein targets from 28 Y. pestis strains by the integrative pan-genomic and subtractive genomics approach. Additionally, it seeks to screen out potential safe and effective alternative therapies against these targets via high-throughput virtual screening. Targets should lack homology to human, gut microbiota, and known human 'anti-targets', while should exhibit essentiality for pathogen's survival and virulence, druggability, antibiotic resistance, and broad spectrum across multiple pathogenic bacteria. We identified two promising targets: the aminotransferase class I/class II domain-containing protein and 3-oxoacyl-[acyl-carrier-protein] synthase 2. These proteins were modeled using AlphaFold2, validated through several structural analyses, and were subjected to molecular docking and ADMET analysis. Molecular dynamics simulations determined the stability of the ligand-target complexes, providing potential therapeutic options against Y. pestis.
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Affiliation(s)
- Lei Chen
- Jiangsu Vocational College of Medicine, Yancheng, China
- School of Graduate Studies, Management and Science University, Shah Alam, Malaysia
| | - Lihu Zhang
- Jiangsu Vocational College of Medicine, Yancheng, China
| | - Yanping Li
- Jiangsu Vocational College of Medicine, Yancheng, China
| | - Liang Qiao
- School of Environmental Science and Engineering, Yancheng Institute of Technology, Yancheng, China
| | - Suresh Kumar
- Faculty of Health and Life Sciences, Management and Science University, University Drive, Off Persiaran Olahraga, 40100, Shah Alam, Selangor, Malaysia.
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Hoque MN, Hossain A, Faisal GM, Bukharid MZ, Hossain MA, Sultana M. Draft genome sequence of an arsenotrophic Achromobacter aegrifaciens strain isolated from soil in Bangladesh. Microbiol Resour Announc 2024:e0013724. [PMID: 39315834 DOI: 10.1128/mra.00137-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Accepted: 09/06/2024] [Indexed: 09/25/2024] Open
Abstract
We report the draft genome of an arsenotrophic Achromobacter aegrifaciens BAS32 isolated from arsenic (As)-contaminated soil in Bangladesh. This genome contains several predicted gene clusters for As-conversion, namely, As resistance (arsHCsO), arsenite-oxidizing (aioBA), and arsenate-reducing (arsRCDAB) gene clusters along with antibiotic resistance genes (ARGs).
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Affiliation(s)
- M Nazmul Hoque
- Department of Microbiology, University of Dhaka, Dhaka, Bangladesh
- Molecular Biology and Bioinformatics Laboratory, Department of Gynaecology, Obstetrics and Reproductive Health, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, Bangladesh
| | - Anamica Hossain
- Department of Microbiology, University of Dhaka, Dhaka, Bangladesh
| | - Golam Mahbub Faisal
- Molecular Biology and Bioinformatics Laboratory, Department of Gynaecology, Obstetrics and Reproductive Health, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, Bangladesh
| | - Momtaz Zamila Bukharid
- Department of Microbiology, University of Dhaka, Dhaka, Bangladesh
- Research Fellow, One Health Laboratory, icddr,b, Dhaka, Bangladesh
| | - M Anwar Hossain
- Department of Microbiology, University of Dhaka, Dhaka, Bangladesh
- Jashore University of Science and Technology, Jashore, Bangladesh
| | - Munawar Sultana
- Department of Microbiology, University of Dhaka, Dhaka, Bangladesh
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Lévesque S, Rouleau S, Bergeron D, Brown N, Bekal S, Lalancette C, Alarie I. Xenophilus aerolatus isolate misidentified as Brucella spp. by MALDI-TOF MS (VITEK-MS) system. Diagn Microbiol Infect Dis 2024; 110:116543. [PMID: 39316926 DOI: 10.1016/j.diagmicrobio.2024.116543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2024] [Revised: 09/17/2024] [Accepted: 09/19/2024] [Indexed: 09/26/2024]
Abstract
We report the characterization of Xenophilus aerolatus strain identified from a screening rectal swab specimen in human, initially misidentified as Brucella spp. by MALDI-TOF MS (VITEK-MS system). The strain is able to growth on ColorexTM mSuperCARBA plate, suggesting carbapenem resistance. Whole genome sequencing identified several potential antimicrobial resistance mechanisms.
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Affiliation(s)
- Simon Lévesque
- Service de microbiologie, CIUSSS de l'Estrie - Centre Hospitalier Universitaire de Sherbrooke, Sherbrooke, Québec, Canada; Département de microbiologie et infectiologie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec, Canada.
| | - Samuel Rouleau
- Plateforme de RNomique, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Danny Bergeron
- Plateforme de RNomique, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Nathalie Brown
- Service de microbiologie, CIUSSS de l'Estrie - Centre Hospitalier Universitaire de Sherbrooke, Sherbrooke, Québec, Canada
| | - Sadjia Bekal
- Laboratoire de santé publique du Québec, Institut national de santé publique du Québec, Sainte-Anne-de-Bellevue, Québec, Canada
| | - Cindy Lalancette
- Laboratoire de santé publique du Québec, Institut national de santé publique du Québec, Sainte-Anne-de-Bellevue, Québec, Canada
| | - Isabelle Alarie
- Service de microbiologie, CIUSSS de l'Estrie - Centre Hospitalier Universitaire de Sherbrooke, Sherbrooke, Québec, Canada; Département de microbiologie et infectiologie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec, Canada
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Stanley S, Silva-Costa C, Gomes-Silva J, Melo-Cristino J, Malley R, Ramirez M. CC180 clade dynamics do not universally explain Streptococcus pneumoniae serotype 3 persistence post-vaccine: a global comparative population genomics study. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.08.29.24312665. [PMID: 39252931 PMCID: PMC11383505 DOI: 10.1101/2024.08.29.24312665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/11/2024]
Abstract
Background Clonal complex 180 (CC180) is currently the major clone of serotype 3 Streptococcus pneumoniae (Spn). The 13-valent pneumococcal conjugate vaccine (PCV13) does not have significant efficacy against serotype 3 despite polysaccharide inclusion in the vaccine. It was hypothesized that PCV13 may effectively control Clade I of CC180 but that Clades III and IV are resistant, provoking a population shift that enables serotype 3 persistence. This has been observed in the United States, England, and Wales but not Spain. We tested this hypothesis further utilizing a dataset from Portugal. Methods We whole-genome sequenced (WGS) 501 serotype 3 strains from Portugal isolated from patients with pneumococcal infections between 1999-2020. The draft genomes underwent phylogenetic analyses, pangenome profiling, and a genome-wide association study (GWAS). We also completed antibiotic susceptibility testing and compiled over 2,600 serotype 3 multilocus sequence type 180 (MLST180) WGSs to perform global comparative genomics. Findings CC180 Clades I, II, III, IV, and VI distributions were similar when comparing non-invasive pneumonia isolates and invasive disease isolates (Fisher's exact test, P=0.29), and adult and pediatric cases (Fisher's exact test, P=0.074). The serotype 3 CCs shifted post-PCV13 (Fisher's exact test, P<0.0001) and Clade I became dominant. Clade I is largely antibiotic-sensitive and carries the phiOXC141 prophage but the pangenome is heterogenous. Strains from Portugal and Spain, where Clade I remains dominant post-PCV13, have larger pangenomes and are associated with the presence of two genes encoding hypothetical proteins. Interpretation Clade I became dominant in Portugal post-PCV13, despite the burden of the prophage and antibiotic sensitivity. The accessory genome content may mitigate these fitness costs. Regional differences in Clade I prevalence and pangenome heterogeneity suggest that clade dynamics is not a generalizable approach to understanding serotype 3 vaccine escape. Funding National Institute of Child Health and Human Development, Pfizer, and Merck Sharp & Dohme.
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Lee YQ, Sri La Sri Ponnampalavanar S, Wong JH, Kong ZX, Ngoi ST, Karunakaran R, Lau MY, Abdul Jabar K, Teh CSJ. Investigation on the mechanisms of carbapenem resistance among the non-carbapenemase-producing carbapenem-resistant Klebsiella pneumoniae. Front Cell Infect Microbiol 2024; 14:1464816. [PMID: 39359938 PMCID: PMC11445613 DOI: 10.3389/fcimb.2024.1464816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2024] [Accepted: 08/26/2024] [Indexed: 10/04/2024] Open
Abstract
Background In Malaysia, an increase in non-carbapenemase-producing carbapenem-resistant Klebsiella pneumoniae (NC-CRKP) has been observed over the years. Previously, four NC-CRKP with increased susceptibility to ciprofloxacin in the presence of phenylalanine-arginine β-naphthylamide (PAβN) were identified. However, no contribution of the PAβN-inhibited efflux pump to carbapenem resistance was observed. All four NC-CRKP harboured non-carbapenemase β-lactamase, with two also exhibiting porin loss. In this study, we further investigated the genomic features and resistance mechanisms of these four isolates. Methods All four NC-CRKP were subjected to whole-genome sequencing, followed by comparative genomic and phylogenetic analyses. Results Multi-locus sequence typing (MLST) analysis divided the four NC-CRKP into different sequence types: ST392, ST45, ST14, and ST5947. Neither major nor rare carbapenemase genes were detected. Given the presence of non-carbapenemase β-lactamase in all isolates, we further investigated the potential mechanisms of resistance by identifying related chromosomal mutations. Deletion mutation was detected in the cation efflux system protein CusF. Insertion mutation was identified in the nickel/cobalt efflux protein RcnA. Missense mutation of ompK36 porin was detected in two isolates, while the loss of ompK36 porin was observed in another two isolates. Conclusions This study revealed that NC-CRKP may confer carbapenem resistance through a combination of non-carbapenemase β-lactamase and potential chromosomal mutations including missense mutation or loss of ompK36 porin and/or a frameshift missense mutation in efflux pump systems, such as cation efflux system protein CusF and nickel/cobalt efflux protein RcnA. Our findings highlighted the significance of implementing whole-genome sequencing into clinical practice to promote the surveillance of carbapenem resistance mechanisms among NC-CRKP.
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Affiliation(s)
- Yee Qing Lee
- Department of Medical Microbiology, Faculty of Medicine, Universiti Malaya, Kuala Lumpur, Malaysia
| | | | - Jia Haw Wong
- Department of Medical Microbiology, Faculty of Medicine, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Zhi Xian Kong
- Department of Medical Microbiology, Faculty of Medicine, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Soo Tein Ngoi
- Department of Anaesthesiology, Faculty of Medicine, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Rina Karunakaran
- Department of Medical Microbiology, Faculty of Medicine, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Min Yi Lau
- Department of Medical Microbiology, Faculty of Medicine, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Kartini Abdul Jabar
- Department of Medical Microbiology, Faculty of Medicine, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Cindy Shuan Ju Teh
- Department of Medical Microbiology, Faculty of Medicine, Universiti Malaya, Kuala Lumpur, Malaysia
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Garner E, Maile-Moskowitz A, Angeles LF, Flach CF, Aga DS, Nambi I, Larsson DGJ, Bürgmann H, Zhang T, Vikesland PJ, Pruden A. Metagenomic Profiling of Internationally Sourced Sewage Influents and Effluents Yields Insight into Selecting Targets for Antibiotic Resistance Monitoring. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:16547-16559. [PMID: 39229966 PMCID: PMC11411718 DOI: 10.1021/acs.est.4c03726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2024]
Abstract
It has been debated whether wastewater treatment plants (WWTPs) primarily act to attenuate or amplify antibiotic resistance genes (ARGs). However, ARGs are highly diverse with respect to their resistance mechanisms, mobilities, and taxonomic hosts and therefore their behavior in WWTPs should not be expected to be universally conserved. We applied metagenomic sequencing to wastewater influent and effluent samples from 12 international WWTPs to classify the behavior of specific ARGs entering and exiting WWTPs. In total, 1079 different ARGs originating from a variety of bacteria were detected. This included ARGs that could be mapped to assembled scaffolds corresponding to nine human pathogens. While the relative abundance (per 16S rRNA gene) of ARGs decreased during treatment at 11 of the 12 WWTPs sampled and absolute abundance (per mL) decreased at all 12 WWTPs, increases in relative abundance were observed for 40% of the ARGs detected at the 12th WWTP. Also, the relative abundance of mobile genetic elements (MGE) increased during treatment, but the fraction of ARGs known to be transmissible between species decreased, thus demonstrating that increased MGE prevalence may not be generally indicative of an increase in ARGs. A distinct conserved resistome was documented in both influent and effluent across samples, suggesting that well-functioning WWTPs generally attenuate influent antibiotic resistance loads. This work helps inform strategies for wastewater surveillance of antibiotic resistance, highlighting the utility of tracking ARGs as indicators of treatment performance and relative risk reduction.
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Affiliation(s)
- Emily Garner
- Wadsworth Department of Civil and Environmental Engineering, West Virginia University, Morgantown, West Virginia 26505, United States
| | - Ayella Maile-Moskowitz
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Luisa F Angeles
- Department of Chemistry, University at Buffalo, Buffalo, New York 14260, United States
| | - Carl-Fredrik Flach
- Institute of Biomedicine, Department of Infectious Diseases, Centre for Antibiotic Resistance Research in Gothenburg (CARe), University of Gothenburg, Västra Götaland, SE-405 30 Gothenburg, Sweden
| | - Diana S Aga
- Department of Chemistry, University at Buffalo, Buffalo, New York 14260, United States
| | - Indumathi Nambi
- Department of Civil Engineering, Indian Institute of Technology, Madras, Chennai 600036, India
| | - D G Joakim Larsson
- Institute of Biomedicine, Department of Infectious Diseases, Centre for Antibiotic Resistance Research in Gothenburg (CARe), University of Gothenburg, Västra Götaland, SE-405 30 Gothenburg, Sweden
| | - Helmut Bürgmann
- Eawag: Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum CH-6047, Switzerland
| | - Tong Zhang
- Department of Civil Engineering, The University of Hong Kong, Pokfulam 999077, Hong Kong
| | - Peter J Vikesland
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Amy Pruden
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, Virginia 24061, United States
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Wang X, Qian Y, Wang Y, Wang S, Bi J, Shi C, Han Q, Wan-Yan R, Yu Q, Li H. Metagenomics reveals the potential transmission risk of resistomes from urban park environment to human. JOURNAL OF HAZARDOUS MATERIALS 2024; 477:135387. [PMID: 39094311 DOI: 10.1016/j.jhazmat.2024.135387] [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: 06/11/2024] [Revised: 07/20/2024] [Accepted: 07/29/2024] [Indexed: 08/04/2024]
Abstract
Urban parks play a significant role in urban ecosystems and are strongly associated with human health. Nevertheless, the biological contamination of urban parks - opportunistic pathogens and antibiotic resistance genes (ARGs) - has been poorly reported. Here, metagenomic and 16 S rRNA sequencing methods were used to study the distribution and assembly of opportunistic pathogens and ARGs in soil and water from nine parks in Lanzhou city, and further compared them with local human gut microbiomes to investigate the potential transmission risk. Our results revealed that the most important type of drug resistance in urban parks was multidrug resistance, with various resistance mechanisms. Approximately half of ARGs were shared between human gut and park environment, and it was noteworthy that cross-species transmission might exist among some high-risk ARGs, such as mepA and mdtE, with a significant enrichment in human gut. Metagenomic binning uncovered several bacterial genomes carrying adjacent ARGs, MGEs, and virulence genes, indicating a possibility that these genes may jointly transfer among different environments, particularly from park environment to human. Our results provided a reference point for the management of environmental pollutants in urban parks.
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Affiliation(s)
- Xiaochen Wang
- School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Yuan Qian
- School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Yu Wang
- School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Sijie Wang
- School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Jie Bi
- School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Chenwei Shi
- School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Qian Han
- School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Ruijun Wan-Yan
- School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Qiaoling Yu
- State Key Laboratory of Grassland Agro-ecosystems, Center for Grassland microbiome, Lanzhou University, Lanzhou 730000, China
| | - Huan Li
- School of Public Health, Lanzhou University, Lanzhou 730000, China; State Key Laboratory of Grassland Agro-ecosystems, Center for Grassland microbiome, Lanzhou University, Lanzhou 730000, China.
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Berwa A, Caspar Y. Easy analysis of bacterial whole-genome sequencing data for clinical microbiologists using open-source Galaxy platform: Characterization of ESBL-producing Enterobacterales from bloodstream infections. J Glob Antimicrob Resist 2024; 39:153-158. [PMID: 39278463 DOI: 10.1016/j.jgar.2024.08.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2024] [Revised: 07/30/2024] [Accepted: 08/21/2024] [Indexed: 09/18/2024] Open
Abstract
OBJECTIVES Clinical microbiologists require easy-to-use open access tools with graphical interfaces to perform bacterial whole-genome sequencing (WGS) in routine practice. This study aimed to build a bioinformatics pipeline on the open-source Galaxy platform, facilitating comprehensive and reproducible analysis of bacterial WGS data in a few steps. We then used it to characterize our local epidemiology of ESBL-producing Enterobacterales isolated from patients with bacteremia. METHODS We built a bioinformatics pipeline consisting of the following sequential tools: Fastp (input data trimming); FastQC (read quality control); SPAdes (genome assembly); Quast (quality control of genome assembly); Prokka (gene annotation); Staramr (ResFinder database) and ABRicate (CARD database) for antimicrobial resistance (AMR) gene screening and molecular strain typing. Paired-end short read WGS data from all ESBL-producing Enterobacterales strains isolated from patients with bacteremia over one year were analysed. RESULTS The Galaxy platform does not require command line tools. The bioinformatics pipeline was constructed within one hour. It only required uploading fastq files and facilitated systematization of de novo assembly of genomes, MLST typing, and AMR gene screening in one step. Among the 66 ESBL-producing strains analysed, the two most frequent ESBL genes were blaCTX-M-15 (62.1%) and blaCTX-M-27 (13.6%). CONCLUSIONS The open-access Galaxy platform provides a graphical interface and easy-to-use tools suitable for routine use in clinical microbiology laboratories without bioinformatics specialists. We believe that this platform will facilitate fast and low-cost analysis of bacterial WGS data, especially in resource-limited settings.
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Affiliation(s)
- Aimé Berwa
- Laboratoire de Bactériologie-Hygiène Hospitalière, CHU Grenoble Alpes, Grenoble, France; Univ. Grenoble Alpes, CNRS, CHU Grenoble Alpes, CEA, IBS, Grenoble, France
| | - Yvan Caspar
- Laboratoire de Bactériologie-Hygiène Hospitalière, CHU Grenoble Alpes, Grenoble, France; Univ. Grenoble Alpes, CNRS, CHU Grenoble Alpes, CEA, IBS, Grenoble, France.
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Varney AM, Smitten KL, Southam HM, Fairbanks SD, Robertson CC, Thomas JA, McLean S. In Vitro and In Vivo Studies on a Mononuclear Ruthenium Complex Reveals It is a Highly Effective, Fast-Acting, Broad-Spectrum Antimicrobial in Physiologically Relevant Conditions. ACS Infect Dis 2024; 10:3346-3357. [PMID: 39106475 PMCID: PMC11406528 DOI: 10.1021/acsinfecdis.4c00447] [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] [Indexed: 08/09/2024]
Abstract
The crystal structure of a previously reported antimicrobial RuII complex that targets bacterial DNA is presented. Studies utilizing clinical isolates of Gram-negative bacteria that cause catheter-associated urinary tract infection, (CA)UTI, in media that model urine and plasma reveal that good antimicrobial activity is maintained in all conditions tested. Experiments with a series of Staphylococcus aureus clinical isolates show that, unlike the majority of previously reported RuII-based antimicrobial leads, the compound retains its potent activity even in MRSA strains. Furthermore, experiments using bacteria in early exponential growth and at different pHs reveal that the compound also retains its activity across a range of conditions that are relevant to those encountered in clinical settings. Combinatorial studies involving cotreatment with conventional antibiotics or a previously reported analogous dinuclear RuII complex showed no antagonistic effects. In fact, although all combinations show distinct additive antibacterial activity, in one case, this effect approaches synergy. It was found that the Galleria Mellonella model organism infected with a multidrug resistant strain of the ESKAPE pathogen Acinetobacter baumannii could be successfully treated and totally cleared within 48 h after a single dose of the lead complex with no detectable deleterious effect to the host.
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Affiliation(s)
- Adam M Varney
- School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham NG11 8NS, U.K
- Medical Technologies Innovation Facility (MTIF), Clifton Lane, Nottingham NG11 8NS, U.K
| | - Kirsty L Smitten
- Department of Chemistry, University of Sheffield, Brook Hill, Sheffield S3 7HF, U.K
- School of Bioscience, The University of Sheffield, Western Bank, Sheffield S10 2TN, U.K
| | - Hannah M Southam
- School of Bioscience, The University of Sheffield, Western Bank, Sheffield S10 2TN, U.K
| | - Simon D Fairbanks
- Department of Chemistry, University of Sheffield, Brook Hill, Sheffield S3 7HF, U.K
| | - Craig C Robertson
- Department of Chemistry, University of Sheffield, Brook Hill, Sheffield S3 7HF, U.K
| | - Jim A Thomas
- Department of Chemistry, University of Sheffield, Brook Hill, Sheffield S3 7HF, U.K
| | - Samantha McLean
- School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham NG11 8NS, U.K
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Salamzade R, Tran PQ, Martin C, Manson AL, Gilmore MS, Earl AM, Anantharaman K, Kalan LR. zol & fai: large-scale targeted detection and evolutionary investigation of gene clusters. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.06.07.544063. [PMID: 37333121 PMCID: PMC10274777 DOI: 10.1101/2023.06.07.544063] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Many universally and conditionally important genes are genomically aggregated within clusters. Here, we introduce fai and zol, which together enable large-scale comparative analysis of different types of gene clusters and mobile-genetic elements (MGEs), such as biosynthetic gene clusters (BGCs) or viruses. Fundamentally, they overcome a current bottleneck to reliably perform comprehensive orthology inference at large scale across broad taxonomic contexts and thousands of genomes. First, fai allows the identification of orthologous instances of a query gene cluster of interest amongst a database of target genomes. Subsequently, zol enables reliable, context-specific inference of ortholog groups for individual protein-encoding genes across gene cluster instances. In addition, zol performs functional annotation and computes a variety of evolutionary statistics for each inferred ortholog group. Importantly, in comparison to tools for visual exploration of homologous relationships between gene clusters, zol can scale to thousands of gene cluster instances and produce detailed reports that are easy to digest. To showcase fai and zol, we apply them for: (i) longitudinal tracking of a virus in metagenomes, (ii) discovering novel population-level genetic insights of two common BGCs in the fungal species Aspergillus flavus, and (iii) uncovering large-scale evolutionary trends of a virulence-associated gene cluster across thousands of genomes from a diverse bacterial genus.
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Affiliation(s)
- Rauf Salamzade
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI, USA
| | - Patricia Q. Tran
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
- Freshwater and Marine Science Doctoral Program, University of Wisconsin-Madison, WI, USA
| | - Cody Martin
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI, USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
| | - Abigail L. Manson
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Michael S. Gilmore
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Ophthalmology, Harvard Medical School and Mass Eye and Ear, Boston, Massachusetts, USA
- Department of Microbiology, Harvard Medical School and Mass Eye and Ear, Boston, Massachusetts, USA
| | - Ashlee M. Earl
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | | | - Lindsay R. Kalan
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
- Department of Medicine, Division of Infectious Disease, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
- M.G. DeGroote Institute for Infectious Disease Research, David Braley Centre for Antibiotic Discovery, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
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Li C, Zhang Y, Shi W, Peng Y, Han Y, Jiang S, Dong X, Zhang R. Viral diversity within marine biofilms and interactions with corrosive microbes. ENVIRONMENTAL RESEARCH 2024; 263:119991. [PMID: 39276831 DOI: 10.1016/j.envres.2024.119991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2024] [Revised: 08/25/2024] [Accepted: 09/11/2024] [Indexed: 09/17/2024]
Abstract
In marine environments, a wide variety of microbes like bacteria, and archaea influence on the corrosion of materials. Viruses are widely distributed in biofilms among these microbes and may affect the corrosion process through interactions with key corrosive prokaryotes. However, understanding of the viral communities within biofilms and their interactions with corrosive microbes remains is limited. To improve this knowledge gap, 53 metagenomes were utilized to investigate the diversity of viruses within biofilms on 8 different materials and their interactions with corrosive microbes. Notably, the viruses within biofilms predominantly belonged to Caudoviricetes, and phylogenetic analysis of Caudoviricetes and protein-sharing networks with other environments revealed the presence of numerous novel viral clades in biofilms. The virus‒host linkages revealed a close association between viruses and corrosive microbes in biofilms. This means that viruses may modulate host corrosion-related metabolism through auxiliary metabolic genes. It was observed that the virus could enhance host resistance to metals and antibiotics via horizontal gene transfer. Interestingly, viruses could protect themselves from host antiviral systems through anti-defense systems. This study illustrates the diversity of viruses within biofilms formed on materials and the intricate interactions between viruses and corrosive microbes, showing the potential roles of viruses in corrosive biofilms.
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Affiliation(s)
- Chengpeng Li
- Key Laboratory of Advanced Marine Materials, Key Laboratory of Marine Environmental Corrosion and Bio-fouling, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yimeng Zhang
- Key Laboratory of Advanced Marine Materials, Key Laboratory of Marine Environmental Corrosion and Bio-fouling, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Wenqing Shi
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Xiamen University, Xiamen, 361102, China
| | - Yongyi Peng
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005, China; School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519082, China
| | - Yingchun Han
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005, China
| | - Shuqing Jiang
- Key Laboratory of Advanced Marine Materials, Key Laboratory of Marine Environmental Corrosion and Bio-fouling, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiyang Dong
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005, China.
| | - Ruiyong Zhang
- Key Laboratory of Advanced Marine Materials, Key Laboratory of Marine Environmental Corrosion and Bio-fouling, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Institute of Marine Corrosion Protection, Guangxi Key Laboratory of Marine Environmental Science, Guangxi Academy of Sciences, Nanning, China.
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46
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Howe S, Wei X, Kovac J, Zhao J. Draft genome sequence of Ruoffia tabacinasalis isolated from a bovine nasal swab: a novel member of the bovine nasal microbiota. Microbiol Resour Announc 2024; 13:e0008724. [PMID: 39082814 PMCID: PMC11385104 DOI: 10.1128/mra.00087-24] [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: 02/25/2024] [Accepted: 06/08/2024] [Indexed: 09/11/2024] Open
Abstract
We report the isolation and draft genome sequence of Ruoffia tabacinasalis, a novel member of the bovine nasal microbiota. The genome, which is estimated to be 90.5% complete, is composed of one contig comprising 2,363,349 bp with a GC content of 36.66%.
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Affiliation(s)
- Samantha Howe
- Department of Animal Science, University of Arkansas, Fayetteville, Arkansas, USA
| | - Xiaoyuan Wei
- Department of Food Science, Pennsylvania State University, State College, Pennsylvania, USA
| | - Jasna Kovac
- Department of Food Science, Pennsylvania State University, State College, Pennsylvania, USA
| | - Jiangchao Zhao
- Department of Animal Science, University of Arkansas, Fayetteville, Arkansas, USA
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Yoon KN, Yang J, Yeom SJ, Kim SS, Park JH, Song BS, Eun JB, Park SH, Lee JH, Kim HB, Lee JH, Kim JK. Lactiplantibacillus argentoratensis AGMB00912 protects weaning mice from ETEC infection and enhances gut health. Front Microbiol 2024; 15:1440134. [PMID: 39318427 PMCID: PMC11420142 DOI: 10.3389/fmicb.2024.1440134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2024] [Accepted: 08/30/2024] [Indexed: 09/26/2024] Open
Abstract
Maintaining a healthy intestinal environment, optimal epithelial barrier integrity, and balanced gut microbiota composition are essential for the growth performance of weaning pigs. We identified Lactiplantibacillus argentoratensis AGMB00912 (LA) in healthy porcine feces as having antimicrobial activity against pathogens and enhanced short-chain fatty acid (SCFA) production. Herein, we assess the protective role of LA using a weaning mouse model with enterotoxigenic Escherichia coli (ETEC) infection. LA treatment improves feed intake and weight gain and alleviates colon shortening. Furthermore, LA inhibits intestinal damage, increases the small intestine villus height compared with the ETEC group, and enhances SCFA production. Using the Kyoto Encyclopedia of Genes and Genomes and other bioinformatic tools, including InterProScan and COGNIZER, we validated the presence of SCFA-producing pathways of LA and Lactiplantibacillus after whole genome sequencing. LA mitigates ETEC-induced shifts in the gut microbiota, decreasing the proportion of Escherichia and Enterococcus and increasing SCFA-producing bacteria, including Kineothrix, Lachnoclostridium, Roseuburia, Lacrimispora, Jutongia, and Blautia. Metabolic functional prediction analysis revealed enhanced functions linked to carbohydrate, amino acid, and vitamin biosynthesis, along with decreased functions associated with infectious bacterial diseases compared to the ETEC group. LA mitigates the adverse effects of ETEC infection in weaning mice, enhances growth performance and intestinal integrity, rebalances gut microbiota, and promotes beneficial metabolic functions. These findings validate the functionality of LA in a small animal model, supporting its potential application in improving the health and growth performance of weaning pigs.
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Affiliation(s)
- Ki-Nam Yoon
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup-si, Republic of Korea
- Department of Food Science and Technology, Graduate School of Chonnam National University, Gwangju, Republic of Korea
| | - Jihye Yang
- Departments of Food and Animal Biotechnology and Agricultural Biotechnology, Research Institute of Agriculture and Life Sciences, Center for Food and Bioconvergence, Seoul National University, Seoul, Republic of Korea
| | - Seo-Joon Yeom
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup-si, Republic of Korea
| | - Sang-Su Kim
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup-si, Republic of Korea
| | - Jong-Heum Park
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup-si, Republic of Korea
| | - Beom-Seok Song
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup-si, Republic of Korea
| | - Jong-Bang Eun
- Department of Food Science and Technology, Graduate School of Chonnam National University, Gwangju, Republic of Korea
| | - Seung-Hwan Park
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, Jeongeup-si, Republic of Korea
| | - Ju Huck Lee
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, Jeongeup-si, Republic of Korea
| | - Hyeun Bum Kim
- Department of Animal Resources Science, Dankook University, Cheonan, Republic of Korea
| | - Ju-Hoon Lee
- Departments of Food and Animal Biotechnology and Agricultural Biotechnology, Research Institute of Agriculture and Life Sciences, Center for Food and Bioconvergence, Seoul National University, Seoul, Republic of Korea
| | - Jae-Kyung Kim
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup-si, Republic of Korea
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Hamza M, Sivaraman GK, Mothadaka MP. Genomic portraits of methicillin-resistant staphylococci (MRS) from food fish unveiled the genes associated with staphylococcal food poisoning (SFP), virulence and antimicrobial resistance. BMC Microbiol 2024; 24:334. [PMID: 39251908 PMCID: PMC11386389 DOI: 10.1186/s12866-024-03469-0] [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: 12/06/2023] [Accepted: 08/19/2024] [Indexed: 09/11/2024] Open
Abstract
BACKGROUND Characteristics of non-clinical strains of methicillin-resistant Staphylococcus aureus (MRSA) especially from fishery environment are poorly understood. This research, in addition to comprehensive characterisation, sought to delineate the genetic relatedness between the MRSA strains originating from clinical as well as non-clinical settings. Out of 39 methicillin-resistant staphylococcal isolates from 197 fish samples, 6 (Three each of methicillin-resistant S. haemolyticus (MRSH) and MRSA) with distinct resistance profiles were selected for whole-genome sequencing. Using respective bioinformatics tools, MRSA genomes were comprehensively characterized for resistome, virulomes, molecular epidemiology and phylogenetic analysis. Simultaneously, MRSH genomes were specifically examined to characterize antimicrobial resistance genes (ARGs), owing to the fact that MRSH is often recognized as a reservoir for resistance determinants. RESULTS Three MRSA clones identified in this study include ST672-IVd/t13599 (sequence type-SCCmec type/spa type), ST88-V/t2526, and ST672-IVa/t1309. Though, the isolates were phenotypically vancomycin-sensitive, five of the six genomes carried vancomycin resistance genes including the VanT (VanG cluster) or VanY (VanM cluster). Among the three MRSA, only one harbored the gene encoding Panton-Valentine Leukocidin (PVL) toxin, while staphylococcal enterotoxin (SEs) genes such as sea and seb, associated with staphylococcal food poisoning were identified in two other MRSA. Genomes of MRSH carried a composite of type V staphylococcal cassette chromosome mec (SCCmec) elements (5C2 & 5). This finding may be explained by the inversion and recombination events that may facilitate the integration of type V elements to the SCC elements of S. aureus with a methicillin-susceptible phenotype. Phylogenetically, MRSA from a non-clinical setting displayed a considerable relatedness to that from clinical settings. CONCLUSION This study highlights the genetic diversity and resistance profiles of MRSA and MRSH, with non-clinical MRSA showing notable relatedness to clinical strains. Future research should explore resistance gene transfer mechanisms and environmental reservoirs to better manage MRSA spread.
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Affiliation(s)
- Muneeb Hamza
- Faculty of Science, Cochin University of Science and Technology, Cochin-682022, India
- Microbiology Fermentation and Biotechnology (MFB) Division, ICAR- Central Institute of Fisheries Technology (ICAR-CIFT), Matsyapuri P.O., Willingdon, Cochin 682029, India
| | - Gopalan Krishnan Sivaraman
- Microbiology Fermentation and Biotechnology (MFB) Division, ICAR- Central Institute of Fisheries Technology (ICAR-CIFT), Matsyapuri P.O., Willingdon, Cochin 682029, India.
| | - Mukteswar Prasad Mothadaka
- Visakhapatnam Research Centre of ICAR-CIFT, Andhra University P.O., Ocean View Layout, Pandurangapuram, Visakhapatnam, Andhra Pradesh, 530 003, India.
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49
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Rastegar S, Skurnik M, Niaz H, Tadjrobehkar O, Samareh A, Hosseini-Nave H, Sabouri S. Isolation, characterization, and potential application of Acinetobacter baumannii phages against extensively drug-resistant strains. Virus Genes 2024:10.1007/s11262-024-02103-5. [PMID: 39256307 DOI: 10.1007/s11262-024-02103-5] [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: 04/28/2024] [Accepted: 08/15/2024] [Indexed: 09/12/2024]
Abstract
One of the significant issues in treating bacterial infections is the increasing prevalence of extensively drug-resistant (XDR) strains of Acinetobacter baumannii. In the face of limited or no viable treatment options for extensively drug-resistant (XDR) bacteria, there is a renewed interest in utilizing bacteriophages as a treatment option. Three Acinetobacter phages (vB_AbaS_Ftm, vB_AbaS_Eva, and vB_AbaS_Gln) were identified from hospital sewage and analyzed for their morphology, host ranges, and their genome sequences were determined and annotated. These phages and vB_AbaS_SA1 were combined to form a phage cocktail. The antibacterial effects of this cocktail and its combinations with selected antimicrobial agents were evaluated against the XDR A. baumannii strains. The phages exhibited siphovirus morphology. Out of a total of 30 XDR A. baumannii isolates, 33% were sensitive to vB_AbaS_Ftm, 30% to vB_AbaS_Gln, and 16.66% to vB_AbaS_Eva. When these phages were combined with antibiotics, they demonstrated a synergistic effect. The genome sizes of vB_AbaS_Ftm, vB_AbaS_Eva, and vB_AbaS_Gln were 48487, 50174, and 50043 base pairs (bp), respectively, and showed high similarity. Phage cocktail, when combined with antibiotics, showed synergistic effects on extensively drug-resistant (XDR) strains of A. baumannii. However, the need for further study to fully understand the mechanisms of action and potential limitations of using these phages is highlighted.
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Affiliation(s)
- Sanaz Rastegar
- Medical Mycology and Bacteriology Research Center, Kerman University of Medical Sciences, Kerman, Iran
- Department of Medical Microbiology (Bacteriology and Virology), Afzalipour School of Medicine, Kerman, Iran
| | - Mikael Skurnik
- Department of Bacteriology and Immunology, Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Hira Niaz
- Department of Bacteriology and Immunology, Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Omid Tadjrobehkar
- Medical Mycology and Bacteriology Research Center, Kerman University of Medical Sciences, Kerman, Iran
- Department of Medical Microbiology (Bacteriology and Virology), Afzalipour School of Medicine, Kerman, Iran
| | - Ali Samareh
- Department of Biochemistry, School of Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | - Hossein Hosseini-Nave
- Medical Mycology and Bacteriology Research Center, Kerman University of Medical Sciences, Kerman, Iran.
- Department of Medical Microbiology (Bacteriology and Virology), Afzalipour School of Medicine, Kerman, Iran.
- Department of Microbiology and Virology, School of Medicine, Kerman University of Medical Sciences, Kerman, 7616913439, Iran.
| | - Salehe Sabouri
- Extremophile and Productive Microorganisms Research Center, Kerman University of Medical Sciences, Kerman, Iran.
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran.
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50
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Celona K, Williamson CHD, Dholakia R, Sahl JW, Monroy FP, Settles EW. Whole-genome sequencing of Helicobacter pylori isolates from Native American gastric biopsy specimens. Microbiol Resour Announc 2024; 13:e0016024. [PMID: 39140765 PMCID: PMC11385945 DOI: 10.1128/mra.00160-24] [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: 02/16/2024] [Accepted: 07/05/2024] [Indexed: 08/15/2024] Open
Abstract
Helicobacter pylori infection has been linked to gastrointestinal diseases including gastric cancer. High rates of H. pylori infection and gastric cancer have been reported in indigenous populations within the United States. We report whole-genome sequencing of three H. pylori isolates originating from Native American patients presenting with gastric disease.
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Affiliation(s)
- Kimberly Celona
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
| | - Charles H D Williamson
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
| | - Rishi Dholakia
- Winslow Indian Health Care Center, Winslow, Arizona, USA
| | - Jason W Sahl
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA
| | - Fernando P Monroy
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA
| | - Erik W Settles
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA
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