1
|
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.
Collapse
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
| |
Collapse
|
2
|
Sarumi OA, Hahn M, Heider D. NeuralBeds: Neural embeddings for efficient DNA data compression and optimized similarity search. Comput Struct Biotechnol J 2024; 23:732-741. [PMID: 38298179 PMCID: PMC10828564 DOI: 10.1016/j.csbj.2023.12.046] [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: 10/27/2023] [Revised: 12/28/2023] [Accepted: 12/28/2023] [Indexed: 02/02/2024] Open
Abstract
The availability of high throughput sequencing tools coupled with the declining costs in the production of DNA sequences has led to the generation of enormous amounts of omics data curated in several databases such as NCBI and EMBL. Identification of similar DNA sequences from these databases is one of the fundamental tasks in bioinformatics. It is essential for discovering homologous sequences in organisms, phylogenetic studies of evolutionary relationships among several biological entities, or detection of pathogens. Improving DNA similarity search is of outmost importance because of the increased complexity of the evergrowing repositories of sequences. Therefore, instead of using the conventional approach of comparing raw sequences, e.g., in fasta format, a numerical representation of the sequences can be used to calculate their similarities and optimize the search process. In this study, we analyzed different approaches for numerical embeddings, including Chaos Game Representation, hashing, and neural networks, and compared them with classical approaches such as principal component analysis. It turned out that neural networks generate embeddings that are able to capture the similarity between DNA sequences as a distance measure and outperform the other approaches on DNA similarity search, significantly.
Collapse
Affiliation(s)
- Oluwafemi A. Sarumi
- Department of Mathematics and Computer Science, University of Marburg, Hans-Meerwein-Str. 6, Marburg, D-35043, Germany
- Institute of Computer Science, Heinrich-Heine-University Duesseldorf, Graf-Adolf-Str. 63, Duesseldorf, D-40215, Germany
| | - Maximilian Hahn
- Department of Mathematics and Computer Science, University of Marburg, Hans-Meerwein-Str. 6, Marburg, D-35043, Germany
| | - Dominik Heider
- Department of Mathematics and Computer Science, University of Marburg, Hans-Meerwein-Str. 6, Marburg, D-35043, Germany
- Institute of Computer Science, Heinrich-Heine-University Duesseldorf, Graf-Adolf-Str. 63, Duesseldorf, D-40215, Germany
| |
Collapse
|
3
|
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.
Collapse
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.
| |
Collapse
|
4
|
Tan C, xiao Y, Liu T, Chen S, Zhou J, Zhang S, Hu Y, Wu A, Li C. Development of multi-epitope mRNA vaccine against Clostridioides difficile using reverse vaccinology and immunoinformatics approaches. Synth Syst Biotechnol 2024; 9:667-683. [PMID: 38817826 PMCID: PMC11137598 DOI: 10.1016/j.synbio.2024.05.008] [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: 01/08/2024] [Revised: 04/28/2024] [Accepted: 05/15/2024] [Indexed: 06/01/2024] Open
Abstract
Clostridioides difficile (C. difficile), as the major pathogen of diarrhea in healthcare settings, has become increasingly prevalent within community populations, resulting in significant morbidity and mortality. However, the therapeutic options for Clostridioides difficile infection (CDI) remain limited, and as of now, no authorized vaccine is available to combat this disease. Therefore, the development of a novel vaccine against C. difficile is of paramount importance. In our study, the complete proteome sequences of 118 strains of C. difficile were downloaded and analyzed. We found four antigenic proteins that were highly conserved and can be used for epitope identification. We designed two vaccines, WLcd1 and WLcd2, that contain the ideal T-cell and B-cell epitopes, adjuvants, and the pan HLA DR-binding epitope (PADRE) sequences. The biophysical and chemical assessments of these vaccine candidates indicated that they were suitable for immunogenic applications. Molecular docking analyses revealed that WLcd1 bonded with higher affinity to Toll-like receptors (TLRs) than WLcd2. Furthermore, molecular dynamics (MD) simulations, performed using Gmx_MMPBSA v1.56, confirmed the binding stability of WLcd1 with TLR2 and TLR4. The preliminary findings suggested that this multi-epitope vaccine could be a promising candidate for protection against CDI; however, experimental studies are necessary to confirm these predictions.
Collapse
Affiliation(s)
- Caixia Tan
- Infection Control Center, Xiangya Hospital, Central South University, Changsha, Hunan Province, 410008, China
- National Clinical Research Center for Geriatric Disorders (XiangYa Hospital), Changsha, Hunan Province, 410008, China
| | - Yuanyuan xiao
- Infection Control Center, Xiangya Hospital, Central South University, Changsha, Hunan Province, 410008, China
- National Clinical Research Center for Geriatric Disorders (XiangYa Hospital), Changsha, Hunan Province, 410008, China
| | - Ting Liu
- Infection Control Center, Xiangya Hospital, Central South University, Changsha, Hunan Province, 410008, China
- National Clinical Research Center for Geriatric Disorders (XiangYa Hospital), Changsha, Hunan Province, 410008, China
| | - Siyao Chen
- Infection Control Center, Xiangya Hospital, Central South University, Changsha, Hunan Province, 410008, China
- National Clinical Research Center for Geriatric Disorders (XiangYa Hospital), Changsha, Hunan Province, 410008, China
| | - Juan Zhou
- Infection Control Center, Xiangya Hospital, Central South University, Changsha, Hunan Province, 410008, China
- National Clinical Research Center for Geriatric Disorders (XiangYa Hospital), Changsha, Hunan Province, 410008, China
| | - Sisi Zhang
- Infection Control Center, Xiangya Hospital, Central South University, Changsha, Hunan Province, 410008, China
- National Clinical Research Center for Geriatric Disorders (XiangYa Hospital), Changsha, Hunan Province, 410008, China
| | - Yiran Hu
- Infection Control Center, Xiangya Hospital, Central South University, Changsha, Hunan Province, 410008, China
- National Clinical Research Center for Geriatric Disorders (XiangYa Hospital), Changsha, Hunan Province, 410008, China
| | - Anhua Wu
- Infection Control Center, Xiangya Hospital, Central South University, Changsha, Hunan Province, 410008, China
- National Clinical Research Center for Geriatric Disorders (XiangYa Hospital), Changsha, Hunan Province, 410008, China
| | - Chunhui Li
- Infection Control Center, Xiangya Hospital, Central South University, Changsha, Hunan Province, 410008, China
- National Clinical Research Center for Geriatric Disorders (XiangYa Hospital), Changsha, Hunan Province, 410008, China
| |
Collapse
|
5
|
Ai C, Cui P, Liu C, Wu J, Xu Y, Liang X, Yang QE, Tang X, Zhou S, Liao H, Friman VP. Viral and thermal lysis facilitates transmission of antibiotic resistance genes during composting. Appl Environ Microbiol 2024:e0069524. [PMID: 39078126 DOI: 10.1128/aem.00695-24] [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: 04/11/2024] [Accepted: 06/06/2024] [Indexed: 07/31/2024] Open
Abstract
While the distribution of extracellular ARGs (eARGs) in the environment has been widely reported, the factors governing their release remain poorly understood. Here, we combined multi-omics and direct experimentation to test whether the release and transmission of eARGs are associated with viral lysis and heat during cow manure composting. Our results reveal that the proportion of eARGs increased 2.7-fold during composting, despite a significant and concomitant reduction in intracellular ARG abundances. This relative increase of eARGs was driven by composting temperature and viral lysis of ARG-carrying bacteria based on metagenome-assembled genome (MAG) analysis. Notably, thermal lysis of mesophilic bacteria carrying ARGs was a key factor in releasing eARGs at the thermophilic phase, while viral lysis played a relatively stronger role during the non-thermal phase of composting. Furthermore, MAG-based tracking of ARGs in combination with direct transformation experiments demonstrated that eARGs released during composting pose a potential transmission risk. Our study provides bioinformatic and experimental evidence of the undiscovered role of temperature and viral lysis in co-driving the spread of ARGs in compost microbiomes via the horizontal transfer of environmentally released DNA. IMPORTANCE The spread of antibiotic resistance genes (ARGs) is a critical global health concern. Understanding the factors influencing the release of extracellular ARGs (eARGs) is essential for developing effective strategies. In this study, we investigated the association between viral lysis, heat, and eARG release during composting. Our findings revealed a substantial increase in eARGs despite reduced intracellular ARG abundance. Composting temperature and viral lysis were identified as key drivers, with thermal lysis predominant during the thermophilic phase and viral lysis during non-thermal phases. Moreover, eARGs released during composting posed a transmission risk through horizontal gene transfer. This study highlights the significance of temperature and phage lysis in ARG spread, providing valuable insights for mitigating antibiotic resistance threats.
Collapse
Affiliation(s)
- Chaofan Ai
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Peng Cui
- Guangdong Provincial Engineering and Technology Research Center for Agricultural Land Pollution Prevention and Control, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Chen Liu
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jiawei Wu
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yuan Xu
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xiaolong Liang
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, Liaoning, China
| | - Qiu-E Yang
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xiang Tang
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Shungui Zhou
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Hanpeng Liao
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | | |
Collapse
|
6
|
Sykes EME, Mateo-Estrada V, Muzaleva A, Zhanel G, Dettman J, Chapados J, Gerdis S, Akineden Ö, Castillo-Ramírez S, Khan IUH, Kumar A. Characterization of a colistin resistant, hypervirulent hospital isolate of Acinetobacter courvalinii from Canada. Eur J Clin Microbiol Infect Dis 2024:10.1007/s10096-024-04873-0. [PMID: 39073669 DOI: 10.1007/s10096-024-04873-0] [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: 02/27/2024] [Accepted: 06/14/2024] [Indexed: 07/30/2024]
Abstract
Non-baumannii Acinetobacter spp. are becoming more prevalent in clinical settings including those that present resistance to last-resort antibiotics such as colistin. AB222-IK40 is an Acinetobacter courvalinii strain isolated from the Ottawa Hospital Research Institute located in Ottawa, Canada. To our knowledge, it is the first report of clinical A. courvalinii in Canada. Based on the susceptibility profile, AB222-IK40 is resistant to colistin and non-susceptible to ertapenem. Whole-genome sequencing allowed for genomic investigation into colistin resistance mechanisms. No previously identified mechanism(s) were observed, but a mobile colistin resistance (mcr)-like gene and a UDP-glucose dehydrogenase gene were identified. Based on phylogenomic analyses, the mcr-like gene is an intrinsic phosphoethanolamine transferase. This gene family is implicated in one of the many mechanisms responsible for colistin resistance in Acinetobacter baumannii as well as Acinetobacter modestus. UDP-glucose dehydrogenase is involved in colistin resistance in Enterobacterales and has been shown to be involved in capsule formation in A. baumannii. Global lipidomics revealed greater abundance of phosphatidyl-myo-inositol and lyso-phosphatidyl ethanolamine moieties in the membrane of A. courvalinii than in A. baumannii. Lipidomic profiles showed differences that were probably responsible for the colistin resistance phenotype in AB222-IK40. This isolate was also hypervirulent based on survival assays in Galleria mellonella. As this is the first report of A. courvalinii from a hospital in Canada, this species may be an emerging clinical pathogen, and therefore, it is important to understand this mechanism of its colistin resistance and hypervirulence.
Collapse
Affiliation(s)
- Ellen M E Sykes
- Department of Microbiology, University of Manitoba Winnipeg, Winnipeg, MB, R3T 2N2, Canada
| | - Valeria Mateo-Estrada
- Programa de Genómica Evolutiva, Centro de Ciencias Génomicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Anna Muzaleva
- Department of Microbiology, University of Manitoba Winnipeg, Winnipeg, MB, R3T 2N2, Canada
| | - George Zhanel
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Canada
| | - Jeremy Dettman
- Ottawa Research and Development Centre (ORDC), Agriculture and Agri-Food Canada, Ottawa, Canada
| | - Julie Chapados
- Ottawa Research and Development Centre (ORDC), Agriculture and Agri-Food Canada, Ottawa, Canada
| | - Suzanne Gerdis
- Ottawa Research and Development Centre (ORDC), Agriculture and Agri-Food Canada, Ottawa, Canada
| | - Ömer Akineden
- Dairy Sciences, Institute of Veterinary Food Science, Justus-Liebig-University of Giessen, Giessen, Germany
| | - Santiago Castillo-Ramírez
- Programa de Genómica Evolutiva, Centro de Ciencias Génomicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Izhar U H Khan
- Ottawa Research and Development Centre (ORDC), Agriculture and Agri-Food Canada, Ottawa, Canada
| | - Ayush Kumar
- Department of Microbiology, University of Manitoba Winnipeg, Winnipeg, MB, R3T 2N2, Canada.
| |
Collapse
|
7
|
Mudhluli TE, Kujawska M, Mueller J, Felsl A, Truppel BA, Hall LJ, Chitsike I, Gomo E, Zhou DT. Exploring the genomic traits of infant-associated microbiota members from a Zimbabwean cohort. BMC Genomics 2024; 25:718. [PMID: 39054474 PMCID: PMC11271062 DOI: 10.1186/s12864-024-10618-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Accepted: 07/15/2024] [Indexed: 07/27/2024] Open
Abstract
INTRODUCTION Our understanding of particular gut microbiota members such as Bifidobacterium and Enterococcus in low-middle-income countries remains very limited, particularly early life strain-level beneficial traits. This study addresses this gap by exploring a collection of bacterial strains isolated from the gut of Zimbabwean infants; comparing their genomic characteristics with strains isolated from infants across North America, Europe, and other regions of Africa. MATERIALS AND METHOD From 110 infant stool samples collected in Harare, Zimbabwe, 20 randomly selected samples were used to isolate dominant early-life gut microbiota members Bifidobacterium and Enterococcus. Isolated strains were subjected to whole genome sequencing and bioinformatics analysis including functional annotation of carbohydrates, human milk oligosaccharide (HMO) and protein degradation genes and clusters, and the presence of antibiotic resistance genes (ARGs). RESULTS The study observed some location-based clustering within the main five identified taxonomic groups. Furthermore, there were varying and overall species-specific numbers of genes belonging to different GH families encoded within the analysed dataset. Additionally, distinct strain- and species-specific variances were identified in the potential of Bifidobacterium for metabolizing HMOs. Analysis of putative protease activity indicated a consistent presence of gamma-glutamyl hydrolases in Bifidobacterium, while Enterococcus genomes exhibited a high abundance of aspartyl peptidases. Both genera harboured resistance genes against multiple classes of antimicrobial drugs, with Enterococcus genomes containing a higher number of ARGs compared to Bifidobacterium, on average. CONCLUSION This study identified promising probiotic strains within Zimbabwean isolates, offering the potential for early-life diet and microbial therapies. However, the presence of antibiotic resistance genes in infant-associated microbes raises concerns for infection risk and next-stage probiotic development. Further investigation in larger cohorts, particularly in regions with limited existing data on antibiotic and probiotic use, is crucial to validate these initial insights. IMPACT STATEMENT This research represents the first investigation of its kind in the Zimbabwean context, focusing on potential probiotic strains within the early-life gut microbiota. By identifying local probiotic strains, this research can contribute to the development of probiotic interventions that are tailored to the Zimbabwean population, which can help address local health challenges and promote better health outcomes for infants. Another essential aspect of the study is the investigation of antimicrobial resistance genes present in Zimbabwean bacterial strains. Antimicrobial resistance is a significant global health concern, and understanding the prevalence and distribution of resistance genes in different regions can help inform public health policies and interventions.
Collapse
Affiliation(s)
- Taona Emmah Mudhluli
- Faculty of Medicine and Health Sciences, Department of Laboratory Diagnostic and Investigative Sciences, Medical Laboratory Sciences Unit, University of Zimbabwe, Box A 178, Avondale, Harare, Zimbabwe.
- Faculty of Medicine and Health Science, Department of Biochemistry, Midlands State University, P. Bag 9055, Senga Road, Gweru, Zimbabwe.
| | - Magdalena Kujawska
- Intestinal Microbiome, ZIEL - Institute for Food & Health, Technical University of Munich, Weihenstephaner Berg 3, 85354, Freising, Germany
| | - Julia Mueller
- Intestinal Microbiome, ZIEL - Institute for Food & Health, Technical University of Munich, Weihenstephaner Berg 3, 85354, Freising, Germany
| | - Angela Felsl
- Intestinal Microbiome, ZIEL - Institute for Food & Health, Technical University of Munich, Weihenstephaner Berg 3, 85354, Freising, Germany
| | - Bastian-Alexander Truppel
- Intestinal Microbiome, ZIEL - Institute for Food & Health, Technical University of Munich, Weihenstephaner Berg 3, 85354, Freising, Germany
- BioSciences Building, APC Microbiome Ireland, University College Cork, Cork, T12 YT20, Ireland
| | - Lindsay J Hall
- Intestinal Microbiome, ZIEL - Institute for Food & Health, Technical University of Munich, Weihenstephaner Berg 3, 85354, Freising, Germany
- Microbiome & Health, Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK
- Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, B15 42TT, UK
| | - Inam Chitsike
- Faculty of Medicine and Health Sciences, Department of Family Health, Paediatrics Unit, University of Zimbabwe, Box A 178, Avondale, Harare, Zimbabwe
| | - Exnevia Gomo
- Faculty of Medicine and Health Sciences, Department of Laboratory Diagnostic and Investigative Sciences, Medical Laboratory Sciences Unit, University of Zimbabwe, Box A 178, Avondale, Harare, Zimbabwe
| | - Danai Tavonga Zhou
- Faculty of Medicine and Health Sciences, Department of Laboratory Diagnostic and Investigative Sciences, Medical Laboratory Sciences Unit, University of Zimbabwe, Box A 178, Avondale, Harare, Zimbabwe
| |
Collapse
|
8
|
Deschner D, Voordouw MJ, Fernando C, Campbell J, Waldner CL, Hill JE. Identification of genetic markers of resistance to macrolide class antibiotics in Mannheimia haemolytica isolates from a Saskatchewan feedlot. Appl Environ Microbiol 2024; 90:e0050224. [PMID: 38864630 PMCID: PMC11267883 DOI: 10.1128/aem.00502-24] [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: 03/17/2024] [Accepted: 05/13/2024] [Indexed: 06/13/2024] Open
Abstract
Mannheimia haemolytica is a major contributor to bovine respiratory disease (BRD), which causes substantial economic losses to the beef industry, and there is an urgent need for rapid and accurate diagnostic tests to provide evidence for treatment decisions and support antimicrobial stewardship. Diagnostic sequencing can provide information about antimicrobial resistance genes in M. haemolytica more rapidly than conventional diagnostics. Realizing the full potential of diagnostic sequencing requires a comprehensive understanding of the genetic markers of antimicrobial resistance. We identified genetic markers of resistance in M. haemolytica to macrolide class antibiotics commonly used for control of BRD. Genome sequences were determined for 99 M. haemolytica isolates with six different susceptibility phenotypes collected over 2 years from a feedlot in Saskatchewan, Canada. Known macrolide resistance genes estT, msr(E), and mph(E) were identified in most resistant isolates within predicted integrative and conjugative elements (ICEs). ICE sequences lacking antibiotic resistance genes were detected in 10 of 47 susceptible isolates. No resistance-associated polymorphisms were detected in ribosomal RNA genes, although previously unreported mutations in the L22 and L23 ribosomal proteins were identified in 12 and 27 resistant isolates, respectively. Pangenome analysis led to the identification of 79 genes associated with resistance to gamithromycin, of which 95% (75 of 79) had no functional annotation. Most of the observed phenotypic resistance was explained by previously identified antibiotic resistance genes, although resistance to the macrolides gamithromycin and tulathromycin was not explained in 39 of 47 isolates, demonstrating the need for continued surveillance for novel determinants of macrolide resistance.IMPORTANCEBovine respiratory disease is the costliest disease of beef cattle in North America and the most common reason for injectable antibiotic use in beef cattle. Metagenomic sequencing offers the potential to make economically significant reductions in turnaround time for diagnostic information for evidence-based selection of antibiotics for use in the feedlot. The success of diagnostic sequencing depends on a comprehensive catalog of antimicrobial resistance genes and other genome features associated with reduced susceptibility. We analyzed the genome sequences of isolates of Mannheimia haemolytica, a major bovine respiratory disease pathogen, and identified both previously known and novel genes associated with reduced susceptibility to macrolide class antimicrobials. These findings reinforce the need for ongoing surveillance for markers of antimicrobial resistance to support improved diagnostics and antimicrobial stewardship.
Collapse
Affiliation(s)
- Darien Deschner
- Department of Veterinary Microbiology, University of Saskatchewan, Saskatoon, Canada
| | - Maarten J. Voordouw
- Department of Veterinary Microbiology, University of Saskatchewan, Saskatoon, Canada
| | - Champika Fernando
- Department of Veterinary Microbiology, University of Saskatchewan, Saskatoon, Canada
| | - John Campbell
- Department of Large Animal Clinical Sciences, University of Saskatchewan, Saskatoon, Canada
| | - Cheryl L. Waldner
- Department of Large Animal Clinical Sciences, University of Saskatchewan, Saskatoon, Canada
| | - Janet E. Hill
- Department of Veterinary Microbiology, University of Saskatchewan, Saskatoon, Canada
| |
Collapse
|
9
|
Glendinning L, Jia X, Kebede A, Oyola SO, Park JE, Park W, Assiri A, Holm JB, Kristiansen K, Han J, Hanotte O. Altitude-dependent agro-ecologies impact the microbiome diversity of scavenging indigenous chicken in Ethiopia. MICROBIOME 2024; 12:138. [PMID: 39044244 PMCID: PMC11267795 DOI: 10.1186/s40168-024-01847-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 05/28/2024] [Indexed: 07/25/2024]
Abstract
BACKGROUND Scavenging indigenous village chickens play a vital role in sub-Saharan Africa, sustaining the livelihood of millions of farmers. These chickens are exposed to vastly different environments and feeds compared to commercial chickens. In this study, we analysed the caecal microbiota of 243 Ethiopian village chickens living in different altitude-dependent agro-ecologies. RESULTS Differences in bacterial diversity were significantly correlated with differences in specific climate factors, topsoil characteristics, and supplemental diets provided by farmers. Microbiota clustered into three enterotypes, with one particularly enriched at high altitudes. We assembled 9977 taxonomically and functionally diverse metagenome-assembled genomes. The vast majority of these were not found in a dataset of previously published chicken microbes or in the Genome Taxonomy Database. CONCLUSIONS The wide functional and taxonomic diversity of these microbes highlights their importance in the local adaptation of indigenous poultry, and the significant impacts of environmental factors on the microbiota argue for further discoveries in other agro-ecologies. Video Abstract.
Collapse
Affiliation(s)
- Laura Glendinning
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, UK.
| | - Xinzheng Jia
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Sciences and Engineering, Foshan University, Foshan, People's Republic of China.
| | - Adebabay Kebede
- CTLGH - LiveGene, International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia
- Amhara Regional Agricultural Research Institute, Bahir Dar, Ethiopia
| | - Samuel O Oyola
- International Livestock Research Institute (ILRI), Nairobi, Kenya
| | - Jong-Eun Park
- Department of Animal Biotechnology, Faculty of Biotechnology, College of Applied Life Sciences, Jeju National University, 63243, Jeju, Republic of Korea
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, 55365, Wanju, Republic of Korea
| | - Woncheoul Park
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, 55365, Wanju, Republic of Korea
| | - Abdulwahab Assiri
- School of Life Sciences, the University of Nottingham, University Park, Nottingham, UK
- Department of Animal and Fisheries Production, King Faisal University, Al-Hofuf, Saudi Arabia
| | - Jacob Bak Holm
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark
- Clinical Microbiomics, Copenhagen, Denmark
| | - Karsten Kristiansen
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark
- Qingdao-Europe Advanced Institute for Life Sciences, BGI-Shenzhen, Qingdao, People's Republic of China
| | - Jianlin Han
- CAAS-ILRI Joint Laboratory On Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, People's Republic of China
| | - Olivier Hanotte
- CTLGH - LiveGene, International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia.
- School of Life Sciences, the University of Nottingham, University Park, Nottingham, UK.
| |
Collapse
|
10
|
Zhang W, Zheng L, Xie J, Su X, Zhang M, Huang H, Schmitz-Esser S, Du S, Yang Y, Xie J, Zhang Q, Yu S, Guo Q, Wang H, Zhang L, Yang K, Hou R. The giant panda gut harbors a high diversity of lactic acid bacteria revealed by a novel culturomics pipeline. mSystems 2024; 9:e0052024. [PMID: 38920380 PMCID: PMC11265448 DOI: 10.1128/msystems.00520-24] [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: 04/10/2024] [Accepted: 05/21/2024] [Indexed: 06/27/2024] Open
Abstract
Some lactic acid bacteria (LAB) can provide significant health benefits, which are critically important for the conservation of endangered animals, such as giant pandas. However, little is known about the diversity and culturability of LAB in the giant panda gut microbiota. To understand the roles of LAB in giant panda conservation, it is critical to culture bacterial strains of interest. In this study, we established a pipeline to culture bacterial strains using enrichment of target bacteria with different liquid media and growth conditions. Then, the strains were isolated in solid media to study their functions. Using 210 samples from the culture enrichment method and 138 culture-independent samples, we obtained 1120 amplicon sequencing variants (ASVs) belonging to Lactobacillales. Out of the 1120 ASVs, 812 ASVs from the culture enrichment approach were twofold more diverse than 336 ASVs from the culture-independent approach. Many ASVs of interest were not detected in the culture-independent approach. Using this pipeline, we isolated many relevant bacterial strains and established a giant panda gut bacteria strain collection that included strains with low-abundance in culture-independent samples and included most of the giant panda LAB described by other researchers. The strain collection consisted of 60 strains representing 35 species of 12 genera. Thus, our pipeline is powerful and provides guidance in culturing gut microbiota of interest in hosts such as the giant panda.IMPORTANCECultivation is necessary to screen strains to experimentally investigate microbial traits, and to confirm the activities of novel genes through functional characterization studies. In the long-term, such work can aid in the identification of potential health benefits conferred by bacteria and this could aid in the identification of bacterial candidate strains that can be applied as probiotics. In this study, we developed a pipeline with low-cost and user-friendly culture enrichment to reveal the diversity of LAB in giant pandas. We compared the difference between culture-independent and culture enrichment methods, screened strains of interest that produced high concentrations of short-chain fatty acids (SCFAs), and we investigated the catalog of virulence factors, antibiotic resistance, butyrate and lactate synthesis genes of the strains at a genomic level. This study will provide guidance for microbiota cultivation and a foundation for future research aiming to understand the functions of specific strains.
Collapse
Affiliation(s)
- Wenping Zhang
- Key Laboratory of Monitoring Biological Diversity in Minshan Mountain of National Park of Giant Pandas at Mianyang Teachers' College of Sichuan Province, College of Life Science and Biotechnology, Mianyang Normal University, Mianyang, Sichuan, China
| | - Lijun Zheng
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan, China
| | - Junjin Xie
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan, China
| | - Xiaoyan Su
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan, China
| | - Mingchun Zhang
- China Conservation and Research Center for the Giant Panda, Chengdu, Sichuan, China
| | - He Huang
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan, China
| | | | - Shizhang Du
- Key Laboratory of Monitoring Biological Diversity in Minshan Mountain of National Park of Giant Pandas at Mianyang Teachers' College of Sichuan Province, College of Life Science and Biotechnology, Mianyang Normal University, Mianyang, Sichuan, China
| | - Yu Yang
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan, China
| | - Jiqin Xie
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan, China
| | - Qinrong Zhang
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan, China
| | - Shuran Yu
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan, China
| | - Qiang Guo
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan, China
| | - Hairui Wang
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan, China
| | - Liang Zhang
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan, China
| | - Kong Yang
- Institute of Qinghai-Tibetan Plateau, Southwest Minzu University, Chengdu, Sichuan, China
| | - Rong Hou
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan, China
| |
Collapse
|
11
|
Ramanan V, Sarkar IN. Augmenting bacterial similarity measures using a graph-based genome representation. mSystems 2024; 9:e0049724. [PMID: 38940518 PMCID: PMC11265277 DOI: 10.1128/msystems.00497-24] [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: 04/16/2024] [Accepted: 06/05/2024] [Indexed: 06/29/2024] Open
Abstract
Relationships between bacterial taxa are traditionally defined using 16S rRNA nucleotide similarity or average nucleotide identity. Improvements in sequencing technology provide additional pairwise information on genome sequences, which may provide valuable information on genomic relationships. Mapping orthologous gene locations between genome pairs, known as synteny, is typically implemented in the discovery of new species and has not been systematically applied to bacterial genomes. Using a data set of 378 bacterial genomes, we developed and tested a new measure of synteny similarity between a pair of genomes, which was scaled onto 16S rRNA distance using covariance matrices. Based on the input gene functions used (i.e., core, antibiotic resistance, and virulence), we observed varying topological arrangements of bacterial relationship networks by applying (i) complete linkage hierarchical clustering and (ii) K-nearest neighbor graph structures to synteny-scaled 16S data. Our metric improved clustering quality comparatively to state-of-the-art average nucleotide identity metrics while preserving clustering assignments for the highest similarity relationships. Our findings indicate that syntenic relationships provide more granular and interpretable relationships for within-genera taxa compared to pairwise similarity measures, particularly in functional contexts. IMPORTANCE Given the prevalence and necessity of the 16S rRNA measure in bacterial identification and analysis, this additional analysis adds a functional and synteny-based layer to the identification of relatives and clustering of bacteria genomes. It is also of computational interest to model the bacterial genome as a graph structure, which presents new avenues of genomic analysis for bacteria and their closely related strains and species.
Collapse
Affiliation(s)
- Vivek Ramanan
- Center of Computational Molecular Biology, Brown University, Providence, Rhode Island, USA
- Center for Biomedical Informatics, Brown University, Providence, Rhode Island, USA
| | - Indra Neil Sarkar
- Center of Computational Molecular Biology, Brown University, Providence, Rhode Island, USA
- Center for Biomedical Informatics, Brown University, Providence, Rhode Island, USA
- Rhode Island Quality Institute, Providence, Rhode Island, USA
| |
Collapse
|
12
|
Romance M, Polash MAUZ, Zahan N, Raihan J, Ali MS, Khan MU, Sarker S, Haque MH. Draft genome sequence of multidrug-resistant Kurthia gibsonii strain Hakim RU_BHWE isolated from sewage water in Bangladesh. Microbiol Resour Announc 2024:e0054624. [PMID: 39037309 DOI: 10.1128/mra.00546-24] [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: 05/22/2024] [Accepted: 06/26/2024] [Indexed: 07/23/2024] Open
Abstract
We have sequenced the genome of Kurthia gibsonii strain Hakim RU_BHWE, isolated from sewage water. The assembled genome consists of 2.891 Mb with 58.6883× coverage, presenting an average GC content of 36.60%. This genome includes 8 CRISPR arrays, 3 prophages, 3 antibiotic resistance genes, and 12 virulence factor genes.
Collapse
Affiliation(s)
- M Romance
- Department of Veterinary and Animal Sciences, University of Rajshahi, Rajshahi, Bangladesh
| | | | - Nusrat Zahan
- Department of Veterinary and Animal Sciences, University of Rajshahi, Rajshahi, Bangladesh
| | - Jafor Raihan
- Department of Veterinary and Animal Sciences, University of Rajshahi, Rajshahi, Bangladesh
| | - Md Sumon Ali
- Department of Veterinary and Animal Sciences, University of Rajshahi, Rajshahi, Bangladesh
| | - Muhib Ullah Khan
- Department of Veterinary and Animal Sciences, University of Rajshahi, Rajshahi, Bangladesh
| | - Subir Sarker
- Biomedical Sciences and Molecular Biology, College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, Australia
| | - Md Hakimul Haque
- Department of Veterinary and Animal Sciences, University of Rajshahi, Rajshahi, Bangladesh
- Biomedical Sciences and Molecular Biology, College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, Australia
| |
Collapse
|
13
|
Ballah FM, Hoque MN, Islam MS, Faisal GM, Rahman AMMT, Khatun MM, Rahman M, Hassan J, Rahman MT. Genomic Insights of a Methicillin-Resistant Biofilm-Producing Staphylococcus aureus Strain Isolated From Food Handlers. BIOMED RESEARCH INTERNATIONAL 2024; 2024:5516117. [PMID: 39071244 PMCID: PMC11283335 DOI: 10.1155/2024/5516117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Revised: 05/27/2024] [Accepted: 06/24/2024] [Indexed: 07/30/2024]
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) is an important zoonotic pathogen associated with a wide range of infections in humans and animals. Thus, the emergence of MRSA clones poses an important threat to human and animal health. This study is aimed at elucidating the genomics insights of a strong biofilm-producing and multidrug-resistant (MDR) S. aureus MTR_BAU_H1 strain through whole-genome sequencing (WGS). The S. aureus MTR_BAU_H1 strain was isolated from food handlers' hand swabs in Bangladesh and phenotypically assessed for antimicrobial susceptibility and biofilm production assays. The isolate was further undergone to high throughput WGS and analysed using different bioinformatics tools to elucidate the genetic diversity, molecular epidemiology, sequence type (ST), antimicrobial resistance, and virulence gene distribution. Phenotypic analyses revealed that the S. aureus MTR_BAU_H1 strain is a strong biofilm-former and carries both antimicrobial resistance (e.g., methicillin resistance; mecA, beta-lactam resistance; blaZ and tetracycline resistance; tetC) and virulence (e.g., sea, tsst, and PVL) genes. The genome of the S. aureus MTR_BAU_H1 belonged to ST1930 that possessed three plasmid replicons (e.g., rep16, rep7c, and rep19), seven prophages, and two clustered regularly interspaced short palindromic repeat (CRISPR) arrays of varying sizes. Phylogenetic analysis showed a close evolutionary relationship between the MTR_BAU_H1 genome and other MRSA clones of diverse hosts and demographics. The MTR_BAU_H1 genome harbours 42 antimicrobial resistance genes (ARGs), 128 virulence genes, and 273 SEED subsystems coding for the metabolism of amino acids, carbohydrates, proteins, cofactors, vitamins, minerals, and lipids. This is the first-ever WGS-based study of a strong biofilm-producing and MDR S. aureus strain isolated from human hand swabs in Bangladesh that unveils new information on the resistomes (ARGs and correlated mechanisms) and virulence potentials that might be linked to staphylococcal pathogenesis in both humans and animals.
Collapse
Affiliation(s)
- Fatimah Muhammad Ballah
- Department of Microbiology and HygieneFaculty of Veterinary ScienceBangladesh Agricultural University, Mymensingh 2202, Bangladesh
| | - M. Nazmul Hoque
- Molecular Biology and Bioinformatics LaboratoryDepartment of GynaecologyObstetrics and Reproductive HealthBangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur 1706, Bangladesh
| | - Md. Saiful Islam
- Department of Microbiology and HygieneFaculty of Veterinary ScienceBangladesh Agricultural University, Mymensingh 2202, Bangladesh
- Department of Animal SciencesUniversity of California-Davis, Davis, California CA 95616, USA
| | - Golam Mahbub Faisal
- Molecular Biology and Bioinformatics LaboratoryDepartment of GynaecologyObstetrics and Reproductive HealthBangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur 1706, Bangladesh
| | | | - Mst. Minara Khatun
- Department of Microbiology and HygieneFaculty of Veterinary ScienceBangladesh Agricultural University, Mymensingh 2202, Bangladesh
| | - Marzia Rahman
- Department of Microbiology and HygieneFaculty of Veterinary ScienceBangladesh Agricultural University, Mymensingh 2202, Bangladesh
| | - Jayedul Hassan
- Department of Microbiology and HygieneFaculty of Veterinary ScienceBangladesh Agricultural University, Mymensingh 2202, Bangladesh
| | - Md. Tanvir Rahman
- Department of Microbiology and HygieneFaculty of Veterinary ScienceBangladesh Agricultural University, Mymensingh 2202, Bangladesh
| |
Collapse
|
14
|
Li R, Zhang N, Deng X, Tao C, Pei X, Yue Y, Xu X, Wang J, Shen Z, Shen Q, Li R. Tomato bacterial wilt disease outbreaks are accompanied by an increase in soil antibiotic resistance. ENVIRONMENT INTERNATIONAL 2024; 190:108896. [PMID: 39068748 DOI: 10.1016/j.envint.2024.108896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 06/18/2024] [Accepted: 07/17/2024] [Indexed: 07/30/2024]
Abstract
The presence of soil-borne disease obstacles and antibiotic resistance genes (ARGs) in soil leads to serious economic losses and health risks to humans. One area in need of attention is the evolution of ARGs as pathogenic soil gradually develops, which introduces uncertainty to the dynamic ability of conventional farming models to predict ARGs. Here, we investigated variations in tomato bacterial wilt disease accompanied by the resistome by metagenomic analysis in soils over 13 seasons of monoculture. The results showed that the abundance and diversity of ARGs and mobile genetic elements (MGEs) exhibited a significant and positive correlation with R. solanacearum. Furthermore, the binning approach indicated that fluoroquinolone (qepA), tetracycline (tetA), multidrug resistance genes (MDR, mdtA, acrB, mexB, mexE), and β-lactamases (ampC, blaGOB) carried by the pathogen itself were responsible for the increase in overall soil ARGs. The relationships between pathogens and related ARGs that might underlie the breakdown of soil ARGs were further studied in R. solanacearum invasion pot experiments. This study revealed the dynamics of soil ARGs as soil-borne diseases develop, indicating that these ecological trends can be anticipated. Overall, this study enhances our understanding of the factors driving ARGs in disease-causing soils.
Collapse
Affiliation(s)
- Ruochen Li
- The Sanya Institute of the Nanjing Agricultural University, Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, Jiangsu, PR China
| | - Na Zhang
- The Sanya Institute of the Nanjing Agricultural University, Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, Jiangsu, PR China
| | - Xuhui Deng
- The Sanya Institute of the Nanjing Agricultural University, Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, Jiangsu, PR China
| | - Chengyuan Tao
- The Sanya Institute of the Nanjing Agricultural University, Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, Jiangsu, PR China
| | - Xin Pei
- The Sanya Institute of the Nanjing Agricultural University, Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, Jiangsu, PR China
| | - Yang Yue
- The Sanya Institute of the Nanjing Agricultural University, Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, Jiangsu, PR China
| | - Xu Xu
- The Sanya Institute of the Nanjing Agricultural University, Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, Jiangsu, PR China
| | - Jiabao Wang
- The Sanya Institute of the Nanjing Agricultural University, Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, Jiangsu, PR China
| | - Zongzhuan Shen
- The Sanya Institute of the Nanjing Agricultural University, Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, Jiangsu, PR China.
| | - Qirong Shen
- The Sanya Institute of the Nanjing Agricultural University, Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, Jiangsu, PR China
| | - Rong Li
- The Sanya Institute of the Nanjing Agricultural University, Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, Jiangsu, PR China.
| |
Collapse
|
15
|
Trinh P, Teichman S, Roberts MC, Rabinowitz PM, Willis AD. A cross-sectional comparison of gut metagenomes between dairy workers and community controls. BMC Genomics 2024; 25:708. [PMID: 39033279 DOI: 10.1186/s12864-024-10562-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 06/25/2024] [Indexed: 07/23/2024] Open
Abstract
BACKGROUND As a nexus of routine antibiotic use and zoonotic pathogen presence, the livestock farming environment is a potential hotspot for the emergence of zoonotic diseases and antibiotic resistant bacteria. Livestock can further facilitate disease transmission by serving as intermediary hosts for pathogens before a spillover event. In light of this, we aimed to characterize the microbiomes and resistomes of dairy workers, whose exposure to the livestock farming environment places them at risk for facilitating community transmission of antibiotic resistant genes and emerging zoonotic diseases. RESULTS Using shotgun sequencing, we investigated differences in the taxonomy, diversity and gene presence of 10 dairy farm workers and 6 community controls' gut metagenomes, contextualizing these samples with additional publicly available gut metagenomes. We found no significant differences in the prevalence of resistance genes, virulence factors, or taxonomic composition between the two groups. The lack of statistical significance may be attributed, in part, to the limited sample size of our study or the potential similarities in exposures between the dairy workers and community controls. We did, however, observe patterns warranting further investigation including greater abundance of tetracycline resistance genes and prevalence of cephamycin resistance genes as well as lower average gene diversity (even after accounting for differential sequencing depth) in dairy workers' metagenomes. We also found evidence of commensal organism association with tetracycline resistance genes in both groups (including Faecalibacterium prausnitzii, Ligilactobacillus animalis, and Simiaoa sunii). CONCLUSIONS This study highlights the utility of shotgun metagenomics in examining the microbiomes and resistomes of livestock workers, focusing on a cohort of dairy workers in the United States. While our study revealed no statistically significant differences between groups in taxonomy, diversity and gene presence, we observed patterns in antibiotic resistance gene abundance and prevalence that align with findings from previous studies of livestock workers in China and Europe. Our results lay the groundwork for future research involving larger cohorts of dairy and non-dairy workers to better understand the impact of occupational exposure to livestock farming on the microbiomes and resistomes of workers.
Collapse
Affiliation(s)
- Pauline Trinh
- Department of Biostatistics, University of Washington, Seattle, USA
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, USA
| | - Sarah Teichman
- Department of Statistics, University of Washington, Seattle, USA
| | - Marilyn C Roberts
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, USA
| | - Peter M Rabinowitz
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, USA
| | - Amy D Willis
- Department of Biostatistics, University of Washington, Seattle, USA.
- Department of Statistics, University of Washington, Seattle, USA.
| |
Collapse
|
16
|
Khan MU, Romance M, Polash MAUZ, Zahan N, Ali MS, Raihan J, Sarker S, Haque MH. Draft genome sequence of carbapenems-resistant Acinetobacter baumannii Hakim RU_CBWP strain isolated from a pond surface water in Bangladesh. Microbiol Resour Announc 2024; 13:e0044024. [PMID: 38864657 PMCID: PMC11256773 DOI: 10.1128/mra.00440-24] [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: 04/28/2024] [Accepted: 05/10/2024] [Indexed: 06/13/2024] Open
Abstract
We have revealed the genomic sequence of Acinetobacter baumannii strain Hakim RU_CBWP isolated from pond surface water. Our assembled genome covers 3.787 Mb with 45.5629× coverage, showcasing an average GC content of 38.60%. This genome contains two CRISPR arrays, 17 prophages, 22 antibiotic resistance genes, and 20 virulence factor genes.
Collapse
Affiliation(s)
- Muhib Ullah Khan
- Department of Veterinary and Animal Sciences, University of Rajshahi, Rajshahi, Bangladesh
| | - M. Romance
- Department of Veterinary and Animal Sciences, University of Rajshahi, Rajshahi, Bangladesh
| | | | - Nusrat Zahan
- Department of Veterinary and Animal Sciences, University of Rajshahi, Rajshahi, Bangladesh
| | - Md. Sumon Ali
- Department of Veterinary and Animal Sciences, University of Rajshahi, Rajshahi, Bangladesh
| | - Jafor Raihan
- Department of Veterinary and Animal Sciences, University of Rajshahi, Rajshahi, Bangladesh
| | - Subir Sarker
- Biomedical Sciences & Molecular Biology, College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, Queensland, Australia
| | - Md. Hakimul Haque
- Department of Veterinary and Animal Sciences, University of Rajshahi, Rajshahi, Bangladesh
- Biomedical Sciences & Molecular Biology, College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, Queensland, Australia
| |
Collapse
|
17
|
Han KI, Shin HD, Lee Y, Baek S, Moon E, Park YB, Cho J, Lee JH, Manoharan RK. Complete genome sequence of strain Lactiplantibacillus plantarum beLP1 a potential probiotic strain with antimicrobial properties isolated from kimchi. Microbiol Resour Announc 2024; 13:e0033924. [PMID: 38860807 PMCID: PMC11256779 DOI: 10.1128/mra.00339-24] [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: 04/02/2024] [Accepted: 05/24/2024] [Indexed: 06/12/2024] Open
Abstract
The complete genome of the potential probiotic Lactiplantibacillus plantarum strain beLP1, isolated from kimchi in South Korea, was sequenced using Illumina and PacBio technologies. The genome comprises one circular chromosome and one plasmid without antimicrobial resistance genes.
Collapse
Affiliation(s)
- Kwon Il Han
- Research and Development Center, Bereum Co., Ltd., Wonju, South Korea
| | - Hyun-Dong Shin
- Research and Development Center, Bereum Co., Ltd., Wonju, South Korea
| | - Yura Lee
- Research and Development Center, Bereum Co., Ltd., Wonju, South Korea
| | - Sunhwa Baek
- Research and Development Center, Bereum Co., Ltd., Wonju, South Korea
| | - Eunjung Moon
- Research and Development Center, Bereum Co., Ltd., Wonju, South Korea
| | - Youn Bum Park
- Research and Development Center, Bereum Co., Ltd., Wonju, South Korea
| | - Junhui Cho
- Research and Development Center, Bereum Co., Ltd., Wonju, South Korea
| | - Jin-Ho Lee
- Division of Biological Science and Technology, Yonsei University, Wonju, South Korea
| | | |
Collapse
|
18
|
Dhariwal A, Rajar P, Salvadori G, Åmdal HA, Berild D, Saugstad OD, Fugelseth D, Greisen G, Dahle U, Haaland K, Petersen FC. Prolonged hospitalization signature and early antibiotic effects on the nasopharyngeal resistome in preterm infants. Nat Commun 2024; 15:6024. [PMID: 39019886 PMCID: PMC11255206 DOI: 10.1038/s41467-024-50433-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 07/10/2024] [Indexed: 07/19/2024] Open
Abstract
Respiratory pathogens, commonly colonizing nasopharynx, are among the leading causes of death due to antimicrobial resistance. Yet, antibiotic resistance determinants within nasopharyngeal microbial communities remain poorly understood. In this prospective cohort study, we investigate the nasopharynx resistome development in preterm infants, assess early antibiotic impact on its trajectory, and explore its association with clinical covariates using shotgun metagenomics. Our findings reveal widespread nasopharyngeal carriage of antibiotic resistance genes (ARGs) with resistomes undergoing transient changes, including increased ARG diversity, abundance, and composition alterations due to early antibiotic exposure. ARGs associated with the critical nosocomial pathogen Serratia marcescens persist up to 8-10 months of age, representing a long-lasting hospitalization signature. The nasopharyngeal resistome strongly correlates with microbiome composition, with inter-individual differences and postnatal age explaining most of the variation. Our report on the collateral effects of antibiotics and prolonged hospitalization underscores the urgency of further studies focused on this relatively unexplored reservoir of pathogens and ARGs.
Collapse
Affiliation(s)
- Achal Dhariwal
- Institute of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway
| | - Polona Rajar
- Institute of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway
- Department of Neonatal Intensive Care, Division of Pediatric and Adolescent Medicine, Oslo University Hospital, Oslo, Norway
| | - Gabriela Salvadori
- Institute of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway
| | - Heidi Aarø Åmdal
- Institute of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway
| | - Dag Berild
- Department of Infectious Diseases, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | | | - Drude Fugelseth
- Department of Neonatal Intensive Care, Division of Pediatric and Adolescent Medicine, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Gorm Greisen
- Department of Neonatology, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Ulf Dahle
- Centre for Antimicrobial Resistance, Norwegian Institute of Public Health, Oslo, Norway
| | - Kirsti Haaland
- Department of Neonatal Intensive Care, Division of Pediatric and Adolescent Medicine, Oslo University Hospital, Oslo, Norway
| | | |
Collapse
|
19
|
Chand Y, Jain T, Singh S. Unveiling a Comprehensive Multi-epitope Subunit Vaccine Strategy Against Salmonella subsp. enterica: Bridging Core, Subtractive Proteomics, and Immunoinformatics. Cell Biochem Biophys 2024:10.1007/s12013-024-01407-5. [PMID: 39018007 DOI: 10.1007/s12013-024-01407-5] [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: 07/04/2024] [Indexed: 07/18/2024]
Abstract
Salmonella subsp. enterica (SE) presents a significant global health challenge in both developed and developing countries. Current SE vaccines have limitations, targeting specific strains and demonstrating moderate efficacy in adults, while also being unsuitable for young children and often unaffordable in regions with lower income levels where the disease is prevalent. To address these challenges, this study employed a computational approach integrating core proteomics, subtractive proteomics, and immunoinformatics to develop a universal SE vaccine and identify potential drug targets. Analysis of the core proteome of 185 SE strains revealed 1964 conserved proteins. Subtractive proteomics identified 9 proteins as potential vaccine candidates and 41 as novel drug targets. Using reverse vaccinology-based immunoinformatics, four multi-epitope-based subunit vaccine constructs (MESVCs) were designed, aiming to stimulate cytotoxic T lymphocyte, helper T lymphocyte, and linear B lymphocyte responses. These constructs underwent comprehensive evaluations for antigenicity, immunogenicity, toxicity, hydropathicity, and physicochemical properties. Predictive modeling, refinement, and validation were conducted to determine the secondary and tertiary structures of the SE-MESVCs, followed by docking studies with MHC-I, MHC-II, and TLR4 receptors. Molecular docking assessments showed favorable binding with all three receptors, with SE-MESVC-4 exhibiting the most promising binding energy. Molecular dynamics simulations confirmed the binding affinity and stability of SE-MESVC-4 with the TLR4/MD2 complex. Additionally, codon optimization and in silico cloning verified the efficient translation and successful expression of SE-MESVC-4 in Escherichia coli (E. coli) str. K12. Subsequent in silico immune simulation evaluated the efficacy of SE-MESVC-4 in triggering an effective immune response. These results suggest that SE-MESVC-4 may induce both humoral and cellular immune responses, making it a potential candidate for an effective SE vaccine. However, further experimental investigations are necessary to validate the immunogenicity and efficacy of SE-MESVC-4, bringing us closer to effectively combating SE infections.
Collapse
Affiliation(s)
- Yamini Chand
- Faculty of Biotechnology, Institute of Biosciences and Technology, Shri Ramswaroop Memorial University, Lucknow-Deva Road, Barabanki, 225003, Uttar Pradesh, India
| | - Tanvi Jain
- Faculty of Biotechnology, Institute of Biosciences and Technology, Shri Ramswaroop Memorial University, Lucknow-Deva Road, Barabanki, 225003, Uttar Pradesh, India
| | - Sachidanand Singh
- Department of Biotechnology, School of Energy and Technology, Pandit Deendayal Energy University, Gandhinagar, 382426, Gujarat, India.
| |
Collapse
|
20
|
Zalewska M, Błażejewska A, Gawor J, Adamska D, Goryca K, Szeląg M, Kalinowski P, Popowska M. A newly identified IncY plasmid from multi-drug-resistant Escherichia coli isolated from dairy cattle feces in Poland. Microbiol Spectr 2024:e0087724. [PMID: 39012117 DOI: 10.1128/spectrum.00877-24] [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: 04/09/2024] [Accepted: 06/27/2024] [Indexed: 07/17/2024] Open
Abstract
Comprehensive whole-genome sequencing was performed on two multi-drug-resistant Escherichia coli strains isolated from cattle manure from a typical dairy farm in Poland in 2020. The identified strains are resistant to beta-lactams, aminoglycosides, tetracyclines, trimethoprim/sulfamethoxazole, and fluoroquinolones. The complete sequences of the harbored plasmids revealed antibiotic-resistance genes located within many mobile genetic elements (e.g., insertional sequences or transposons) and genes facilitating conjugal transfer or promoting horizontal gene transfer. These plasmids are hitherto undescribed. Similar plasmids have been identified, but not in Poland. The identified plasmids carried resistance genes, including the tetracycline resistance gene tet(A), aph family aminoglycoside resistance genes aph(3″)-lb and aph (6)-ld, beta-lactam resistance genes blaTEM-1 and blaCTX-M-15, sulfonamide resistance gene sul2, fluoroquinolone resistance gene qnrS1, and the trimethoprim resistance gene dfrA14. The characterized resistance plasmids were categorized into the IncY incompatibility group, indicating a high possibility for dissemination among the Enterobacteriaceae. While similar plasmids (99% identity) have been found in environmental and clinical samples, none have been identified in farm animals. These findings are significant within the One Health framework, as they underline the potential for antimicrobial-resistant E. coli from livestock and food sources to be transmitted to humans and vice versa. It highlights the need for careful monitoring and strategies to limit the spread of antibiotic resistance in the One Health approach. IMPORTANCE This study reveals the identification of new strains of antibiotic-resistant Escherichia coli in cattle manure from a dairy farm in Poland, offering critical insights into the spread of drug resistance. Through whole-genome sequencing, researchers discovered novel plasmids within these bacteria, which carry genes resistant to multiple antibiotics. These findings are particularly alarming, as these plasmids can transfer between different bacterial species, potentially escalating the spread of antibiotic resistance. This research underscores the vital connection between the health of humans, animals, and the environment, emphasizing the concept of One Health. It points to the critical need for global vigilance and strategies to curb the proliferation of antibiotic resistance. By showcasing the presence of these strains and their advanced resistance mechanisms, the study calls for enhanced surveillance and preventive actions in both agricultural practices and healthcare settings to address the imminent challenge of antibiotic-resistant bacteria.
Collapse
Affiliation(s)
- Magdalena Zalewska
- Department of Bacterial Physiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Aleksandra Błażejewska
- Department of Bacterial Physiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Jan Gawor
- DNA Sequencing and Synthesis Facility, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Dorota Adamska
- Genomics Core Facility, Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | - Krzysztof Goryca
- Genomics Core Facility, Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | - Michał Szeląg
- Genomics Core Facility, Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | - Patryk Kalinowski
- Department of Bacterial Physiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Magdalena Popowska
- Department of Bacterial Physiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| |
Collapse
|
21
|
Olatunji I, Bardaji DKR, Miranda RR, Savka MA, Hudson AO. Artificial intelligence tools for the identification of antibiotic resistance genes. Front Microbiol 2024; 15:1437602. [PMID: 39070267 PMCID: PMC11272472 DOI: 10.3389/fmicb.2024.1437602] [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: 05/24/2024] [Accepted: 06/28/2024] [Indexed: 07/30/2024] Open
Abstract
The fight against bacterial antibiotic resistance must be given critical attention to avert the current and emerging crisis of treating bacterial infections due to the inefficacy of clinically relevant antibiotics. Intrinsic genetic mutations and transferrable antibiotic resistance genes (ARGs) are at the core of the development of antibiotic resistance. However, traditional alignment methods for detecting ARGs have limitations. Artificial intelligence (AI) methods and approaches can potentially augment the detection of ARGs and identify antibiotic targets and antagonistic bactericidal and bacteriostatic molecules that are or can be developed as antibiotics. This review delves into the literature regarding the various AI methods and approaches for identifying and annotating ARGs, highlighting their potential and limitations. Specifically, we discuss methods for (1) direct identification and classification of ARGs from genome DNA sequences, (2) direct identification and classification from plasmid sequences, and (3) identification of putative ARGs from feature selection.
Collapse
Affiliation(s)
- Isaac Olatunji
- Thomas H. Gosnell School of Life Sciences, College of Science, Rochester Institute of Technology, Rochester, NY, United States
| | - Danae Kala Rodriguez Bardaji
- Thomas H. Gosnell School of Life Sciences, College of Science, Rochester Institute of Technology, Rochester, NY, United States
| | - Renata Rezende Miranda
- School of Chemistry and Materials Science, College of Science, Rochester Institute of Technology, Rochester, NY, United States
| | - Michael A. Savka
- Thomas H. Gosnell School of Life Sciences, College of Science, Rochester Institute of Technology, Rochester, NY, United States
| | - André O. Hudson
- Thomas H. Gosnell School of Life Sciences, College of Science, Rochester Institute of Technology, Rochester, NY, United States
| |
Collapse
|
22
|
Barcia-Cruz R, Balboa S, Lema A, Romalde JL. Comparative genomics of Vibrio toranzoniae strains. Int Microbiol 2024:10.1007/s10123-024-00557-z. [PMID: 38995500 DOI: 10.1007/s10123-024-00557-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Revised: 06/25/2024] [Accepted: 07/02/2024] [Indexed: 07/13/2024]
Abstract
Vibrio toranzoniae is a marine bacterium belonging to the Splendidus clade that was originally isolated from healthy clams in Galicia (NW Spain). Its isolation from different hosts and seawater indicated two lifestyles and wide geographical distribution. The aim of the present study was to determine the differences at the genomic level among six strains (4 isolated from clam and 2 from seawater) and to determine their phylogeny. For this purpose, whole genomes of the six strains were sequenced by different technologies including Illumina and PacBio, and the resulting sequences were corrected. Genomes were annotated and compared using different online tools. Furthermore, the study of core- and pan-genomes were examined, and the phylogeny was inferred. The content of the core genome ranged from 2953 to 2766 genes and that of the pangenome ranged from 6278 to 6132, depending on the tool used. Although the strains shared certain homology, with DDH values ranging from 77.10 to 82.30 and values of OrthoANI values higher than 97%, some differences were found related to motility, capsule synthesis, iron acquisition systems or mobile genetic elements. Phylogenetic analysis of the core genome did not reveal a differentiation of the strains according to their lifestyle (commensal or free-living), but that of the pangenome indicated certain geographical isolation in the same growing area. This study led to the reclassification of some isolates formerly described as V. toranzoniae and demonstrated the importance of cured deposited sequences to proper phylogenetic assignment.
Collapse
Affiliation(s)
- Rubén Barcia-Cruz
- Departamento de Microbiología y Parasitología, CIBUS-Facultad de Biología, Universidade de Santiago de Compostela, Campus Vida S/N, 15782, Santiago de Compostela, Spain
- French Agency for Food, Environmental and Occupational Health and Safety (Anses), 94701, Maisons-Alfort Cedex, France
| | - Sabela Balboa
- Departamento de Microbiología y Parasitología, CIBUS-Facultad de Biología, Universidade de Santiago de Compostela, Campus Vida S/N, 15782, Santiago de Compostela, Spain
- Centro de Investigación Interdisciplinar en Tecnología Ambientales (CRETUS), Universidade de Santiago de Compostela, 15782, Santiago de Compostela, Spain
| | - Alberto Lema
- Departamento de Microbiología y Parasitología, CIBUS-Facultad de Biología, Universidade de Santiago de Compostela, Campus Vida S/N, 15782, Santiago de Compostela, Spain
- AllGenetics & Biology SL, Oleiros, 15172, Perillo, A Coruña, Spain
| | - Jesús L Romalde
- Departamento de Microbiología y Parasitología, CIBUS-Facultad de Biología, Universidade de Santiago de Compostela, Campus Vida S/N, 15782, Santiago de Compostela, Spain.
- Centro de Investigación Interdisciplinar en Tecnología Ambientales (CRETUS), Universidade de Santiago de Compostela, 15782, Santiago de Compostela, Spain.
| |
Collapse
|
23
|
Lyytinen OL, Dapuliga C, Wallinger D, Patpatia S, Audu BJ, Kiljunen SJ. Three novel Enterobacter cloacae bacteriophages for therapeutic use from Ghanaian natural waters. Arch Virol 2024; 169:156. [PMID: 38967872 PMCID: PMC11226500 DOI: 10.1007/s00705-024-06081-9] [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: 11/24/2023] [Accepted: 05/15/2024] [Indexed: 07/06/2024]
Abstract
Infections caused by multidrug-resistant (MDR) bacteria are a growing global concern. Enterobacter cloacae complex (ECC) species are particularly adept at developing antibiotic resistance. Phage therapy is proposed as an alternative treatment for pathogens that no longer respond to antibiotics. Unfortunately, ECC phages are understudied when compared to phages of many other bacterial species. In this Ghanaian-Finnish study, we isolated two ECC strains from ready-to-eat food samples and three novel phages from natural waters against these strains. We sequenced the genomic DNA of the novel Enterobacter phages, fGh-Ecl01, fGh-Ecl02, and fGh-Ecl04, and assessed their therapeutic potential. All of the phages were found to be lytic, easy to propagate, and lacking any toxic, integrase, or antibiotic resistance genes and were thus considered suitable for therapy purposes. They all were found to be related to T4-type viruses: fGh-Ecl01 and fGh-Ecl04 to karamviruses and fGh-Ecl02 to agtreviruses. Testing of Finnish clinical ECC strains showed promising susceptibility to these novel phages. As many as 61.1% of the strains were susceptible to fGh-Ecl01 and fGh-Ecl04, and 7.4% were susceptible to fGh-Ecl02. Finally, we investigated the susceptibility of the newly isolated ECC strains to three antibiotics - meropenem, ciprofloxacin, and cefepime - in combination with the novel phages. The use of phages and antibiotics together had synergistic effects. When using an antibiotic-phage combination, even low concentrations of antibiotics fully inhibited the growth of bacteria.
Collapse
Affiliation(s)
- O L Lyytinen
- Human Microbiome Research Program (HUMI), Faculty of Medicine, University of Helsinki, Helsinki, Finland.
| | - C Dapuliga
- Kwame Nkrumah University of Science and Technology (KNUST), Kumasi, Ghana
| | - D Wallinger
- Human Microbiome Research Program (HUMI), Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - S Patpatia
- Human Microbiome Research Program (HUMI), Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - B J Audu
- National Veterinary Research Institute, Vom, Nigeria
| | - S J Kiljunen
- Human Microbiome Research Program (HUMI), Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Division of Clinical Microbiology, HUSLAB, Helsinki University Hospital, Helsinki, Finland
| |
Collapse
|
24
|
Kang HM, Kim KR, Kim G, Lee DG, Kim YJ, Choi EH, Lee J, Yun KW. Antimicrobial resistance genes harbored in invasive Acinetobacter calcoaceticus-baumannii complex isolated from Korean children during the pre-COVID-19 pandemic periods, 2015-2020. Front Cell Infect Microbiol 2024; 14:1410997. [PMID: 39027135 PMCID: PMC11254764 DOI: 10.3389/fcimb.2024.1410997] [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: 04/02/2024] [Accepted: 05/15/2024] [Indexed: 07/20/2024] Open
Abstract
Background Acinetobacter baumannii (AB) has emerged as one of the most challenging pathogens worldwide, causing invasive infections in the critically ill patients due to their ability to rapidly acquire resistance to antibiotics. This study aimed to analyze antibiotic resistance genes harbored in AB and non-baumannii Acinetobacter calcoaceticus-baumannii (NB-ACB) complex causing invasive diseases in Korean children. Methods ACB complexes isolated from sterile body fluid of children in three referral hospitals were prospectively collected. Colistin susceptibility was additionally tested via broth microdilution. Whole genome sequencing was performed and antibiotic resistance genes were analyzed. Results During January 2015 to December 2020, a total of 67 ACB complexes were isolated from sterile body fluid of children in three referral hospitals. The median age of the patients was 0.6 (interquartile range, 0.1-7.2) years old. Among all the isolates, 73.1% (n=49) were confirmed as AB and others as NB-ACB complex by whole genome sequencing. Among the AB isolates, only 22.4% susceptible to carbapenem. In particular, all clonal complex (CC) 92 AB (n=33) showed multi-drug resistance, whereas 31.3% in non-CC92 AB (n=16) (P<0.001). NB-ACB showed 100% susceptibility to all classes of antibiotics except 3rd generation cephalosporin (72.2%). The main mechanism of carbapenem resistance in AB was the bla oxa23 gene with ISAba1 insertion sequence upstream. Presence of pmr gene and/or mutation of lpxA/C gene were not correlated with the phenotype of colistin resistance of ACB. All AB and NB-ACB isolates carried the abe and ade multidrug efflux pumps. Conclusions In conclusion, monitoring and research for resistome in ACB complex is needed to identify and manage drug-resistant AB, particularly CC92 AB carrying the bla oxa23 gene.
Collapse
Affiliation(s)
- Hyun Mi Kang
- Department of Pediatrics, College of Medicine, Seoul National University, Seoul, Republic of Korea
- Department of Pediatrics, 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
| | - Kyung Ran Kim
- Department of Pediatrics, Sungkyunkwan University School of Medicine, Samsung Medical Center, Seoul, Republic of Korea
| | - Gahee Kim
- Department of Pediatrics, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Dong-gun Lee
- Vaccine Bio Research Institute, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
- Department of Internal Medicine, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Yae Jean Kim
- Department of Pediatrics, Sungkyunkwan University School of Medicine, Samsung Medical Center, Seoul, Republic of Korea
| | - Eun Hwa Choi
- Department of Pediatrics, College of Medicine, Seoul National University, Seoul, Republic of Korea
- Department of Pediatrics, Seoul National University Children’s Hospital, Seoul, Republic of Korea
| | - Jina Lee
- Department of Pediatrics, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Ki Wook Yun
- Department of Pediatrics, College of Medicine, Seoul National University, Seoul, Republic of Korea
- Department of Pediatrics, Seoul National University Children’s Hospital, Seoul, Republic of Korea
| |
Collapse
|
25
|
Khan MAS, Islam Z, Barua C, Sarkar MMH, Ahmed MF, Rahman SR. Phenotypic characterization and genomic analysis of a Salmonella phage L223 for biocontrol of Salmonella spp. in poultry. Sci Rep 2024; 14:15347. [PMID: 38961138 PMCID: PMC11222505 DOI: 10.1038/s41598-024-64999-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2024] [Accepted: 06/14/2024] [Indexed: 07/05/2024] Open
Abstract
The escalating incidence of foodborne salmonellosis poses a significant global threat to food safety and public health. As antibiotic resistance in Salmonella continues to rise, there is growing interest in bacteriophages as potential alternatives. In this study, we isolated, characterized, and evaluated the biocontrol efficacy of lytic phage L223 in chicken meat. Phage L223 demonstrated robust stability across a broad range of temperatures (20-70 °C) and pH levels (2-11) and exhibited a restricted host range targeting Salmonella spp., notably Salmonella Typhimurium and Salmonella Enteritidis. Characterization of L223 revealed a short latent period of 30 min and a substantial burst size of 515 PFU/cell. Genomic analysis classified L223 within the Caudoviricetes class, Guernseyvirinae subfamily and Jerseyvirus genus, with a dsDNA genome size of 44,321 bp and 47.9% GC content, featuring 72 coding sequences devoid of antimicrobial resistance, virulence factors, toxins, and tRNA genes. Application of L223 significantly (p < 0.005) reduced Salmonella Typhimurium ATCC 14,028 counts by 1.24, 2.17, and 1.55 log CFU/piece after 2, 4, and 6 h of incubation, respectively, in experimentally contaminated chicken breast samples. These findings highlight the potential of Salmonella phage L223 as a promising biocontrol agent for mitigating Salmonella contamination in food products, emphasizing its relevance for enhancing food safety protocols.
Collapse
Affiliation(s)
| | - Zahidul Islam
- Department of Microbiology, University of Dhaka, Dhaka, Bangladesh
| | - Chayan Barua
- Department of Microbiology, University of Dhaka, Dhaka, Bangladesh
| | - Md Murshed Hasan Sarkar
- Genomics Research Laboratory, Bangladesh Council of Scientific and Industrial Research, BCSIR, Dhaka, 1205, Bangladesh
| | - Md Firoz Ahmed
- Department of Microbiology, Jahangirnagar University, Savar, Dhaka, Bangladesh
| | | |
Collapse
|
26
|
Jakaria Al-Mujahidy SM, Kryukov K, Ikeo K, Saito K, Uddin ME, Ibn Sina AA. Functional genomic analysis of the isolated potential probiotic Lactobacillus delbrueckii subsp. indicus TY-11 and its comparison with other Lactobacillus delbrueckii strains. Microbiol Spectr 2024; 12:e0347023. [PMID: 38771133 PMCID: PMC11218508 DOI: 10.1128/spectrum.03470-23] [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: 11/01/2023] [Accepted: 04/10/2024] [Indexed: 05/22/2024] Open
Abstract
Probiotics refer to living microorganisms that exert a variety of beneficial effects on human health. On the contrary, they also can cause infection, produce toxins within the body, and transfer antibiotic-resistant genes to the other microorganisms in the digestive tract necessitating a comprehensive safety assessment. This study aimed to conduct functional genomic analysis and some relevant biochemical tests to uncover the probiotic potentials of Lactobacillus delbrueckii subsp. indicus TY-11 isolated from native yogurt in Bangladesh. We also performed transmission electron microscopic (TEM) analysis, comparative genomic study as well as phylogenetic tree construction with 332 core genes from 262 genomes. The strain TY-11 was identified as Lactobacillus delbrueckii subsp. indicus, whose genome (1,916,674 bp) contained 1911 CDS, and no gene was identified for either antibiotic resistance or toxic metabolites. It carried genes for the degradation of toxic metabolites, treatment of lactose intolerance, toll-like receptor 2-dependent innate immune response, heat and cold shock, bile salts tolerance, and acidic pH tolerance. Genes were annotated for inhibiting pathogenic bacteria by inhibitory substances [bacteriocin: Helveticin-J (331 bp) and Enterolysin-A (275 bp), hydrogen peroxide, and acid]; blockage of adhesion sites; and competition for nutrients. The genes involved in its metabolic pathway were detected as suitable for digesting indigestible nutrients in the human gut. The TY-11 genome possessed an additional 37 core genes of subspecies indicus which were deficient in the core genome of the most popular subsp. bulgaricus. During the phenotypic testing, the isolate TY-11 demonstrated high antagonistic activity (inhibition zone of 21.33 ± 1.53 mm) against Escherichia coli ATCC 8739 and was not sensitive to any of the 10 tested antibiotics. This study was the first study to explore the molecular insights into probiotic roles, including antimicrobial activities and antibiotic sensitivity, of a representative strain (TY-11) of Lactobacillus delbrueckii subsp. indicus. IMPORTANCE This study aimed to conduct functional genomic analysis to uncover the probiotic potential of Lactobacillus delbrueckii subsp. indicus TY-11 isolated from native yogurt in Bangladesh. We also performed transmission electron microscopic (TEM) analysis, comparative genomic study as well as phylogenetic tree construction with 332 core genes from 262 genomes. In our current investigation, we revealed a number of common and unique excellences of the probiotic Lactobacillus delbrueckii subsp. indicus TY-11 that are likely to be important to illustrate its intestinal residence and probiotic roles. This is the first study to explore the molecular insights into intestinal residence and probiotic roles, including antimicrobial activities and antibiotic sensitivity, of a representative strain (TY-11) of Lactobacillus delbrueckii subsp. indicus.
Collapse
Affiliation(s)
- Sk. Md. Jakaria Al-Mujahidy
- DNA Data Analysis Laboratory, Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Kirill Kryukov
- Center for Genome Informatics, Joint Support-Center for Data Science Research, Research Organization of Information and Systems, Mishima, Shizuoka, Japan
- Bioinformation and DDBJ Center, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Kazuho Ikeo
- DNA Data Analysis Laboratory, Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Kei Saito
- Laboratory of Physics and Cell Biology, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Md. Ekhlas Uddin
- Department of Biochemistry and Molecular Biology, Gono Bishwabidyalay, Savar, Dhaka, Bangladesh
| | - Abu Ali Ibn Sina
- Australian Institute for Bioengineering & Nanotechnology (AIBN), The University of Queensland, Brisbane, Queensland, Australia
- Department of Systems Biology, Columbia University Irving Medical Center, New York, New York, USA
| |
Collapse
|
27
|
Lu X, Ji L, Wang H, Zhang Q, Wang X, Liu Y, Shen Q, Yang S, Ma X, Zhang W, Shan T. Highly diverse RNA viruses and phage sequences concealed within birds. Microbiol Spectr 2024; 12:e0080224. [PMID: 38860816 PMCID: PMC11218532 DOI: 10.1128/spectrum.00802-24] [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: 03/28/2024] [Accepted: 04/30/2024] [Indexed: 06/12/2024] Open
Abstract
The diversity of birds in most parts of the world is very high, and thus, they may carry different types of highly differentiated and unknown viruses. Thanks to advanced sequencing technologies, studies on the diversity of bird-associated viruses have increased over the past few years. In this study, a large-scale viral metagenomics survey was performed on cloacal swabs of 2,990 birds from nine provinces of the Chinese mainland. To detect undescribed RNA viruses in birds, more than 1,800 sequences sharing relatively low (<60%) amino acid sequence identity with the best match in the GenBank database were screened. Potentially novel viruses related to vertebrates have been identified, and several potential recombination signals were found. Additionally, hundreds of RNA viral sequences related to plants, fungi, and insects were detected, including previously unknown viruses. Furthermore, we investigated the novelty, functionality, and classification of the phages examined in this study. These viruses occupied topological positions on the evolutionary trees to a certain extent and might form novel putative families, genera, or species, thus providing information to fill the phylogenetic gaps of related viruses. These findings provided new insights into bird-associated viruses, but the interactions among these viruses remain unknown and require further investigation.IMPORTANCEStudying the diversity of RNA viruses in birds and mammals is crucial due to their potential impact on human health and the global ecosystem. Many RNA viruses, such as influenza and coronaviruses, have been shown to cross the species barrier and cause zoonotic diseases. In this metagenomics study involving 2,990 birds from at least 82 species, we identified over 1,800 RNA sequences with distant relationships to known viruses, some of which are rare in birds. The study highlights the scope and diversity of RNA viruses in birds, providing data to predict disease risks and monitor potential viral threats to wildlife, livestock, and human health. This information can aid in the development of strategies for disease prevention and control.
Collapse
Affiliation(s)
- Xiang Lu
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Likai Ji
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Haoning Wang
- School of Geography and Tourism, Harbin University, Harbin, Heilongjiang, China
| | - Qing Zhang
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
- Qinghai Institute of Endemic Disease Prevention and Control, Xining, Qinghai, China
| | - Xiaochun Wang
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Yuwei Liu
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Quan Shen
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Shixing Yang
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Xiao Ma
- Qinghai Institute of Endemic Disease Prevention and Control, Xining, Qinghai, China
| | - Wen Zhang
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Tongling Shan
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| |
Collapse
|
28
|
Yamaguchi M, Uchihashi T, Kawabata S. Hybrid sequence-based analysis reveals the distribution of bacterial species and genes in the oral microbiome at a high resolution. Biochem Biophys Rep 2024; 38:101717. [PMID: 38708423 PMCID: PMC11066573 DOI: 10.1016/j.bbrep.2024.101717] [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: 03/05/2024] [Revised: 04/14/2024] [Accepted: 04/19/2024] [Indexed: 05/07/2024] Open
Abstract
Bacteria in the oral microbiome are poorly identified owing to the lack of established culture methods for them. Thus, this study aimed to use culture-free analysis techniques, including bacterial single-cell genome sequencing, to identify bacterial species and investigate gene distribution in saliva. Saliva samples from the same individual were classified as inactivated or viable and then analyzed using 16S rRNA sequencing, metagenomic shotgun sequencing, and bacterial single-cell sequencing. The results of 16S rRNA sequencing revealed similar microbiota structures in both samples, with Streptococcus being the predominant genus. Metagenomic shotgun sequencing showed that approximately 80 % of the DNA in the samples was of non-bacterial origin, whereas single-cell sequencing showed an average contamination rate of 10.4 % per genome. Single-cell sequencing also yielded genome sequences for 43 out of 48 wells for the inactivated samples and 45 out of 48 wells for the viable samples. With respect to resistance genes, four out of 88 isolates carried cfxA, which encodes a β-lactamase, and four isolates carried erythromycin resistance genes. Tetracycline resistance genes were found in nine bacteria. Metagenomic shotgun sequencing provided complete sequences of cfxA, ermF, and ermX, whereas other resistance genes, such as tetQ and tetM, were detected as fragments. In addition, virulence factors from Streptococcus pneumoniae were the most common, with 13 genes detected. Our average nucleotide identity analysis also suggested five single-cell-isolated bacteria as potential novel species. These data would contribute to expanding the oral microbiome data resource.
Collapse
Affiliation(s)
- Masaya Yamaguchi
- Bioinformatics Research Unit, Osaka University Graduate School of Dentistry, Suita, Osaka, Japan
- Department of Microbiology, Osaka University Graduate School of Dentistry, Suita, Osaka, Japan
- Bioinformatics Center, Research Institute for Microbial Diseases, Osaka University, Japan
- Center for Infectious Diseases Education and Research, Osaka University, Japan
| | - Toshihiro Uchihashi
- Department of Oral and Maxillofacial Surgery, Osaka University Graduate School of Dentistry, Suita, Osaka, Japan
| | - Shigetada Kawabata
- Department of Microbiology, Osaka University Graduate School of Dentistry, Suita, Osaka, Japan
- Center for Infectious Diseases Education and Research, Osaka University, Japan
| |
Collapse
|
29
|
Boutroux M, Favre-Rochex S, Gorgette O, Touak G, Mühle E, Bouchier C, Chesneau O, Veyrier FJ, Clermont D, Rahi P. Neisseria leonii sp. nov., isolated from the nose, lung, and liver of rabbits. Int J Syst Evol Microbiol 2024; 74. [PMID: 39023135 DOI: 10.1099/ijsem.0.006460] [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: 07/20/2024] Open
Abstract
A taxogenomic study of three strains (3986T, 51.81, and JF 2415) isolated from rabbits between 1972 and 2000 led to the description of a new Neisseria species. The highest sequence similarity of the 16S rRNA gene was found to Neisseria animalis NCTC 10212T (96.7 %). The 16S rRNA gene similarity above 99 % and average nucleotide identity (ANI) values above 96 % among the strains, indicated that they belong to the same species. At the same time, the strains shared ANI values below 81 % and dDDH values below 24 % with all described Neisseria species. In the bac120 gene phylogenetic tree, the three strains clustered near Neisseria elongata and Neisseria bacilliformis in the Neisseria clade. However, the Neisseria clade is not monophyletic, and includes the type strains of Morococcus cerebrosus, Bergeriella denitrificans, Kingella potus, Uruburuella suis, and Uruburuella testudinis. Neisseria shayeganii clustered outside the clade with members of the genus Eikenella. Amino acid identity (AAI) values were calculated, and a threshold of 71 % was used to circumscribe the genus Neisseria. According to this proposed AAI threshold, strains 3986T, 51.81, and JF 2415 were placed within the genus Neisseria. The cells of the three strains were Gram-stain-negative diplococcobacilli and non-motile. Optimal growth on trypticase soy agar occurred at 37 °C and pH 8.5 in aerobic conditions. Notably, all strains exhibited indole production in the API-NH test, which is atypical for Neisseria and the family Neisseriaceae. The strains exhibited a common set of 68 peaks in their MALDI-TOF MS profiles, facilitating the swift and accurate identification of this species. Based on genotypic and phenotypic data, it is proposed that strains 3986T, 51.81, and JF 2415 represent a novel species within the genus Neisseria, for which the name Neisseria leonii sp. nov. is proposed (type strain 3986T=R726T=CIP 109994T=LMG 32907T).
Collapse
Affiliation(s)
- Martin Boutroux
- Institut Pasteur, Université Paris Cité, Center of Biological Resources of Institut Pasteur (CRBIP), 75015 Paris, France
- Present address: River Ecosystems Laboratory, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Sandrine Favre-Rochex
- Institut Pasteur, Université Paris Cité, Collection of Institut Pasteur (CIP), 75015 Paris, France
| | - Olivier Gorgette
- Institut Pasteur, Université Paris Cité, Ultrastructural BioImaging Unit, 75015 Paris, France
| | - Gérald Touak
- Institut Pasteur, Université Paris Cité, Collection of Institut Pasteur (CIP), 75015 Paris, France
| | - Estelle Mühle
- Institut Pasteur, Université Paris Cité, Collection of Institut Pasteur (CIP), 75015 Paris, France
| | - Christiane Bouchier
- Institut Pasteur, Université Paris Cité, Collection of Institut Pasteur (CIP), 75015 Paris, France
| | - Olivier Chesneau
- Institut Pasteur, Université Paris Cité, Collection of Institut Pasteur (CIP), 75015 Paris, France
| | - Frédéric J Veyrier
- INRS-Centre Armand-Frappier Santé Biotechnologie, Bacterial Symbionts Evolution, Laval, Quebec H7V 1B7, Canada
| | - Dominique Clermont
- Institut Pasteur, Université Paris Cité, Collection of Institut Pasteur (CIP), 75015 Paris, France
| | - Praveen Rahi
- Institut Pasteur, Université Paris Cité, Collection of Institut Pasteur (CIP), 75015 Paris, France
| |
Collapse
|
30
|
Mac Aogáin M, Xaverius Ivan F, Jaggi TK, Richardson H, Shoemark A, Narayana JK, Dicker AJ, Koh MS, Lee KCH, Thun How O, Poh ME, Chin KK, Hou ALY, Ser Hon P, Low TB, Abisheganaden JA, Dimakou K, Digalaki A, Kosti C, Gkousiou A, Hansbro PM, Blasi F, Aliberti S, Chalmers JD, Chotirmall SH. Airway "Resistotypes" and Clinical Outcomes in Bronchiectasis. Am J Respir Crit Care Med 2024; 210:47-62. [PMID: 38271608 PMCID: PMC11197066 DOI: 10.1164/rccm.202306-1059oc] [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: 06/19/2023] [Accepted: 01/16/2024] [Indexed: 01/27/2024] Open
Abstract
Rationale: Chronic infection and inflammation shapes the airway microbiome in bronchiectasis. Utilizing whole-genome shotgun metagenomics to analyze the airway resistome provides insight into interplay between microbes, resistance genes, and clinical outcomes. Objectives: To apply whole-genome shotgun metagenomics to the airway microbiome in bronchiectasis to highlight a diverse pool of antimicrobial resistance genes: the "resistome," the clinical significance of which remains unclear. Methods: Individuals with bronchiectasis were prospectively recruited into cross-sectional and longitudinal cohorts (n = 280), including the international multicenter cross-sectional Cohort of Asian and Matched European Bronchiectasis 2 (CAMEB 2) study (n = 251) and two independent cohorts, one describing patients experiencing acute exacerbation and a further cohort of patients undergoing Pseudomonas aeruginosa eradication treatment. Sputum was subjected to metagenomic sequencing, and the bronchiectasis resistome was evaluated in association with clinical outcomes and underlying host microbiomes. Measurements and Main Results: The bronchiectasis resistome features a unique resistance gene profile and increased counts of aminoglycoside, bicyclomycin, phenicol, triclosan, and multidrug resistance genes. Longitudinally, it exhibits within-patient stability over time and during exacerbations despite between-patient heterogeneity. Proportional differences in baseline resistome profiles, including increased macrolide and multidrug resistance genes, associate with shorter intervals to the next exacerbation, whereas distinct resistome archetypes associate with frequent exacerbations, poorer lung function, geographic origin, and the host microbiome. Unsupervised analysis of resistome profiles identified two clinically relevant "resistotypes," RT1 and RT2, the latter characterized by poor clinical outcomes, increased multidrug resistance, and P. aeruginosa. Successful targeted eradication in P. aeruginosa-colonized individuals mediated reversion from RT2 to RT1, a more clinically favorable resistome profile demonstrating reduced resistance gene diversity. Conclusions: The bronchiectasis resistome associates with clinical outcomes, geographic origin, and the underlying host microbiome. Bronchiectasis resistotypes link to clinical disease and are modifiable through targeted antimicrobial therapy.
Collapse
Affiliation(s)
- Micheál Mac Aogáin
- Biochemical Genetics Laboratory, Department of Biochemistry, St. James’s Hospital, Dublin, Ireland
- Clinical Biochemistry Unit, School of Medicine, Trinity College Dublin, Dublin, Ireland
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | | | - Tavleen Kaur Jaggi
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | - Hollian Richardson
- University of Dundee, Ninewells Hospital and Medical School, Dundee, United Kingdom
| | - Amelia Shoemark
- University of Dundee, Ninewells Hospital and Medical School, Dundee, United Kingdom
| | | | - Alison J. Dicker
- University of Dundee, Ninewells Hospital and Medical School, Dundee, United Kingdom
| | - Mariko Siyue Koh
- Department of Respiratory and Critical Care Medicine, Singapore General Hospital, Singapore
| | - Ken Cheah Hooi Lee
- Department of Respiratory and Critical Care Medicine, Singapore General Hospital, Singapore
| | - Ong Thun How
- Department of Respiratory and Critical Care Medicine, Singapore General Hospital, Singapore
| | - Mau Ern Poh
- Department of Medicine, Faculty of Medicine, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Ka Kiat Chin
- Department of Medicine, Faculty of Medicine, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Albert Lim Yick Hou
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
- Department of Respiratory and Critical Care Medicine, Tan Tock Seng Hospital, Singapore
| | - Puah Ser Hon
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
- Department of Respiratory and Critical Care Medicine, Tan Tock Seng Hospital, Singapore
| | - Teck Boon Low
- Department of Respiratory and Critical Care Medicine, Changi General Hospital, Singapore
| | - John Arputhan Abisheganaden
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
- Department of Respiratory and Critical Care Medicine, Tan Tock Seng Hospital, Singapore
| | - Katerina Dimakou
- 5th Respiratory Medicine Department, General Hospital for Chest Diseases of Athens “Sotiria”, Athens, Greece
| | - Antonia Digalaki
- 5th Respiratory Medicine Department, General Hospital for Chest Diseases of Athens “Sotiria”, Athens, Greece
| | - Chrysavgi Kosti
- 5th Respiratory Medicine Department, General Hospital for Chest Diseases of Athens “Sotiria”, Athens, Greece
| | - Anna Gkousiou
- 5th Respiratory Medicine Department, General Hospital for Chest Diseases of Athens “Sotiria”, Athens, Greece
| | - Philip M. Hansbro
- Centre for Inflammation, Centenary Institute and University of Technology Sydney, Faculty of Science, School of Life Sciences, Sydney, Australia
| | - Francesco Blasi
- Respiratory Unit and Cystic Fibrosis Center, Foundation IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
- Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy
| | - Stefano Aliberti
- Department of Biomedical Sciences, Humanitas University, Milan, Italy; and
- IRCCS Humanitas Research Hospital, Respiratory Unit, Rozzano, Milan, Italy
| | - James D. Chalmers
- University of Dundee, Ninewells Hospital and Medical School, Dundee, United Kingdom
| | - Sanjay H. Chotirmall
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
- Department of Respiratory and Critical Care Medicine, Tan Tock Seng Hospital, Singapore
| |
Collapse
|
31
|
Zhao W, Wu J, Luo S, Jiang X, He T, Hu X. Subtask-Aware Representation Learning for Predicting Antibiotic Resistance Gene Properties via Gating-Controlled Mechanism. IEEE J Biomed Health Inform 2024; 28:4348-4360. [PMID: 38640044 DOI: 10.1109/jbhi.2024.3390246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/21/2024]
Abstract
The crisis of antibiotic resistance has become a significant global threat to human health. Understanding properties of antibiotic resistance genes (ARGs) is the first step to mitigate this issue. Although many methods have been proposed for predicting properties of ARGs, most of these methods focus only on predicting antibiotic classes, while ignoring other properties of ARGs, such as resistance mechanisms and transferability. However, acquiring all of these properties of ARGs can help researchers gain a more comprehensive understanding of the essence of antibiotic resistance, which will facilitate the development of antibiotics. In this paper, the task of predicting properties of ARGs is modeled as a multi-task learning problem, and an effective subtask-aware representation learning-based framework is proposed accordingly. More specifically, property-specific expert networks and shared expert networks are utilized respectively to learn subtask-specific features for each subtask and shared features among different subtasks. In addition, a gating-controlled mechanism is employed to dynamically allocate weights to subtask-specific semantics and shared semantics obtained respectively from property-specific expert networks and shared expert networks, thus adjusting distinctive contributions of subtask-specific features and shared features to achieve optimal performance for each subtask simultaneously. Extensive experiments are conducted on publicly available data, and experimental results demonstrate the effectiveness of the proposed framework on the task of ARGs properties prediction.
Collapse
|
32
|
Katahira K, Gotoh Y, Kasama K, Yoshimura D, Itoh T, Shimauchi C, Tajiri A, Hayashi T. Mobile genetic element-driven genomic changes in a community-associated methicillin-resistant Staphylococcus aureus clone during its transmission in a regional community outbreak in Japan. Microb Genom 2024; 10. [PMID: 39017043 DOI: 10.1099/mgen.0.001272] [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: 07/18/2024] Open
Abstract
Community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) infections are now a public health concern in both community and healthcare settings worldwide. We previously identified a suspected case of a maternity clinic-centred outbreak of CA-MRSA skin infection in a regional community in Japan by PFGE-based analysis. In this study, we performed genome sequence-based analyses of 151 CA-MRSA isolates, which included not only outbreak-related isolates that we previously defined based on identical or similar PFGE patterns but also other isolates obtained during the same period in the same region. Our analysis accurately defined 133 isolates as outbreak-related isolates, collectively called the TDC clone. They belonged to a CA-MRSA lineage in clonal complex (CC) 30, known as the South West Pacific (SWP) clone. A high-resolution phylogenetic analysis of these isolates combined with their epidemiological data revealed that the TDC clone was already present and circulating in the region before the outbreak was recognized, and only the isolates belonging to two sublineages (named SL4 and SL5) were directly involved in the outbreak. Long persistence in patients/carriers and frequent intrahousehold transmission of the TDC clone were also revealed by this analysis. Moreover, by systematic analyses of the genome changes that occurred in this CA-MRSA clone during transmission in the community, we revealed that most variations were associated with mobile genetic elements (MGEs). Variant PFGE types were generated by alterations of prophages and genomic islands or insertion sequence (IS)-mediated insertion of a plasmid or a sequence of unknown origin. Dynamic changes in plasmid content, which were linked to changes in antimicrobial resistance profiles in specific isolates, were generated by frequent gain and loss of plasmids, most of which were self-transmissible or mobilizable. The introduction of IS256 by a plasmid (named pTDC02) into sublineage SL5 led to SL5-specific amplification of IS256, and amplified IS256 copies were involved in some of the structural changes of chromosomes and plasmids and generated variations in the repertoire of virulence-related genes in limited isolates. These data revealed how CA-MRSA genomes change during transmission in the community and how MGEs are involved in this process.
Collapse
Affiliation(s)
- Katsuyuki Katahira
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Higashi-ku, Fukuoka 812-8582, Japan
- Department of Respiratory Medicine, Graduate School of Medical Sciences, Kyushu University, Higashi-ku, Fukuoka 812-8582, Japan
- Department of Respiratory Medicine, NHO Omuta Hospital, Tachibana, Omuta City 837-0911, Japan
| | - Yasuhiro Gotoh
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Higashi-ku, Fukuoka 812-8582, Japan
| | - Kentaro Kasama
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Higashi-ku, Fukuoka 812-8582, Japan
| | - Dai Yoshimura
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8550, Japan
| | - Takehiko Itoh
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8550, Japan
| | - Chieko Shimauchi
- Department of Nursing Humanics I, Miyazaki Prefectural Nursing University, Manabino, Miyazaki 880-0929, Japan
| | - Akihiko Tajiri
- Tajiri Dermatology Clinic, Kiyotake, Miyazaki 889-1067, Japan
| | - Tetsuya Hayashi
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Higashi-ku, Fukuoka 812-8582, Japan
| |
Collapse
|
33
|
Nguyen HV, Trinh ATV, Bui LNH, Hoang ATL, Tran QTL, Trinh TT. Streptococcus raffinosi sp. nov., isolated from human breast milk samples. Int J Syst Evol Microbiol 2024; 74. [PMID: 38958657 DOI: 10.1099/ijsem.0.006442] [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: 07/04/2024] Open
Abstract
Novel Gram-positive, catalase-negative, α-haemolytic cocci were isolated from breast milk samples of healthy mothers living in Hanoi, Vietnam. The 16S rRNA gene sequences of these strains varied by 0-2 nucleotide polymorphisms. The 16S rRNA gene sequence of one strain, designated as BME SL 6.1T, showed the highest similarity to those of Streptococcus salivarius NCTC 8618T (99.4 %), Streptococcus vestibularis ATCC 49124T (99.4 %), and Streptococcus thermophilus ATCC 19258T (99.3 %) in the salivarius group. Whole genome sequencing was performed on three selected strains. Phylogeny based on 631 core genes clustered the three strains into the salivarius group, and the strains were clearly distinct from the other species in this group. The average nucleotide identity (ANI) value of strain BME SL 6.1T exhibited the highest identity with S. salivarius NCTC 8618T (88.4 %), followed by S. vestibularis ATCC 49124T (88.3 %) and S. thermophilus ATCC 19258T (87.4 %). The ANI and digital DNA-DNA hybridization values between strain BME SL 6.1T and other species were below the cut-off value (95 and 70 %, respectively), indicating that it represents a novel species of the genus Streptococcus. The strains were able to produce α-galactosidase and acid from raffinose and melibiose. Therefore, we propose to assign the strains to a new species of the genus Streptococcus as Streptococcus raffinosi sp. nov. The type strain is BME SL 6.1T (=VTCC 12812T=NBRC 116368T).
Collapse
Affiliation(s)
- Ha Viet Nguyen
- VNU-Institute of Microbiology and Biotechnology, Vietnam National University, Hanoi, Vietnam
| | - Anh Thi Van Trinh
- VNU-Institute of Microbiology and Biotechnology, Vietnam National University, Hanoi, Vietnam
| | - Linh Nguyen Hai Bui
- VNU-Institute of Microbiology and Biotechnology, Vietnam National University, Hanoi, Vietnam
| | - Anh Thi Lan Hoang
- VNU-Institute of Microbiology and Biotechnology, Vietnam National University, Hanoi, Vietnam
| | - Quyen Thi Le Tran
- VNU-Institute of Microbiology and Biotechnology, Vietnam National University, Hanoi, Vietnam
| | - Trung Thanh Trinh
- VNU-Institute of Microbiology and Biotechnology, Vietnam National University, Hanoi, Vietnam
| |
Collapse
|
34
|
Mogoi NN, Sifuna AW, Okoth PK, Reva O, Malaba R, Negesa R, Nyongesa KP, Osoro KE, Welch M. Staphylococcus aureus associated with surgical site infections in Western Kenya reveals genomic hotspots for pathogen evolution. Access Microbiol 2024; 6:000734.v4. [PMID: 39045253 PMCID: PMC11261728 DOI: 10.1099/acmi.0.000734.v4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 06/03/2024] [Indexed: 07/25/2024] Open
Abstract
Objectives. Staphylococcus aureus is one of the most common pathogens attributed to hospital infections. Although S. aureus infections have been well studied in developed countries, far less is known about the biology of the pathogen in sub-Saharan Africa. Methods. Here, we report on the isolation, antibiotic resistance profiling, whole genome sequencing, and genome comparison of six multi-drug resistant isolates of S. aureus obtained from a referral hospital in Kakamega, Western Kenya. Results. Five of the six isolates contained a 20.7 kb circular plasmid carrying blaZ (associated with resistance to β-lactam antibiotics). These five strains all belonged to the same sequence type, ST152. Despite the similarity of the plasmid in these isolates, whole genome sequencing revealed that the strains differed, depending on whether they were associated with hospital-acquired or community-acquired infections. Conclusion. The intriguing finding is that the hospital-acquired and the community-acquired isolates of S. aureus belonging to the same genotype, ST152, formed two separate sub-clusters in the phylogenetic tree and differed by the repertoire of accessory virulence genes. These data suggest ongoing adaptive evolution and significant genomic plasticity.
Collapse
Affiliation(s)
- Nyabera Nicholas Mogoi
- Department of Biological sciences, Masinde Muliro University of Science and Technology, Kakamega, Kenya
| | - Anthony Wawire Sifuna
- Department of Medical Biochemistry, Masinde Muliro University of Science and Technology, Kakamega, Kenya
| | - Patrick Kirsteen Okoth
- Department of Biological sciences, Masinde Muliro University of Science and Technology, Kakamega, Kenya
| | - Oleg Reva
- Department of Biochemistry, Genetics and Microbiology, Centre For Bioinformatics And Computational Biology, University of Pretoria, Pretoria, South Africa
| | - Rose Malaba
- Kakamega County General Teaching and Referral Hospital, Kakamega, Kenya
| | - Ruth Negesa
- Kakamega County General Teaching and Referral Hospital, Kakamega, Kenya
| | - Kuloba Peter Nyongesa
- Department of Medical Microbiology and Parasitology, Masinde Muliro University of Science and Technology, Kakamega, Kenya
| | - Kombo Ezra Osoro
- Department of Medical Biochemistry, Masinde Muliro University of Science and Technology, Kakamega, Kenya
| | - Martin Welch
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| |
Collapse
|
35
|
Brown CL, Maile-Moskowitz A, Lopatkin AJ, Xia K, Logan LK, Davis BC, Zhang L, Vikesland PJ, Pruden A. Selection and horizontal gene transfer underlie microdiversity-level heterogeneity in resistance gene fate during wastewater treatment. Nat Commun 2024; 15:5412. [PMID: 38926391 PMCID: PMC11208604 DOI: 10.1038/s41467-024-49742-8] [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: 11/03/2023] [Accepted: 06/14/2024] [Indexed: 06/28/2024] Open
Abstract
Activated sludge is the centerpiece of biological wastewater treatment, as it facilitates removal of sewage-associated pollutants, fecal bacteria, and pathogens from wastewater through semi-controlled microbial ecology. It has been hypothesized that horizontal gene transfer facilitates the spread of antibiotic resistance genes within the wastewater treatment plant, in part because of the presence of residual antibiotics in sewage. However, there has been surprisingly little evidence to suggest that sewage-associated antibiotics select for resistance at wastewater treatment plants via horizontal gene transfer or otherwise. We addressed the role of sewage-associated antibiotics in promoting antibiotic resistance using lab-scale sequencing batch reactors fed field-collected wastewater, metagenomic sequencing, and our recently developed bioinformatic tool Kairos. Here, we found confirmatory evidence that fluctuating levels of antibiotics in sewage are associated with horizontal gene transfer of antibiotic resistance genes, microbial ecology, and microdiversity-level differences in resistance gene fate in activated sludge.
Collapse
Affiliation(s)
- Connor L Brown
- Dept. of Civil and Environmental Engineering, Virginia Tech, Blacksburg, USA
| | | | | | - Kang Xia
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, USA
| | | | - Benjamin C Davis
- Office of Research and Development, U.S. Environmental Protection Agency, Cincinnati, USA
| | - Liqing Zhang
- Dept. of Computer Science, Virginia Tech, Blacksburg, USA
| | - Peter J Vikesland
- Dept. of Civil and Environmental Engineering, Virginia Tech, Blacksburg, USA.
| | - Amy Pruden
- Dept. of Civil and Environmental Engineering, Virginia Tech, Blacksburg, USA.
| |
Collapse
|
36
|
Bello-López E, Escobedo-Muñoz AS, Guerrero G, Cruz-Córdova A, Garza-González E, Hernández-Castro R, Zarain PL, Morfín-Otero R, Volkow P, Xicohtencatl-Cortes J, Cevallos MA. Acinetobacter pittii: the emergence of a hospital-acquired pathogen analyzed from the genomic perspective. Front Microbiol 2024; 15:1412775. [PMID: 38989032 PMCID: PMC11233732 DOI: 10.3389/fmicb.2024.1412775] [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: 04/08/2024] [Accepted: 05/22/2024] [Indexed: 07/12/2024] Open
Abstract
Acinetobacter pittii has increasingly been associated with several types of hospital-acquired severe infections. Genes implicated in carbapenem resistance, tigecycline resistance, or genes encoding extended spectrum cephalosporinases, such as blaADC, are commonly found in isolates implicated in these infections. A. pittii strains that are pandrug resistant have occasionally been identified. Food for human consumption, animals and plants are environmental sources of this pathogen. An alarming situation is that A. pitti has been identified as responsible for outbreaks in different regions worldwide. In this study, 384 genomes of A. pittii were analyzed, comprising sequences from clinical and non-clinical origins from 32 countries. The objective was to investigate if clinical strains possess genetic traits facilitating hospital adaptation. Results indicate significant genomic variability in terms of size and gene content among A. pittii isolates. The core genome represents a small portion (25-36%) of each isolate's genome, while genes associated with antibiotic resistance and virulence predominantly belong to the accessory genome. Notably, antibiotic resistance genes are encoded by a diverse array of plasmids. As the core genome between environmental and hospital isolates is the same, we can assume that hospital isolates acquired ARGs due to a high selective pressure in these settings. The strain's phylogeographic distribution indicates that there is no geographical bias in the isolate distribution; isolates from different geographic regions are dispersed throughout a core genome phylogenetic tree. A single clade may include isolates from extremely distant geographical areas. Furthermore, strains isolated from the environment or animal, or plant sources frequently share the same clade as hospital isolates. Our analysis showed that the clinical isolates do not already possess specific genes, other than antibiotic-resistant genes, to thrive in the hospital setting.
Collapse
Affiliation(s)
- Elena Bello-López
- Universidad Nacional Autónoma de México, Centro de Ciencias Genómicas, Programa de Genómica Evolutiva, Cuernavaca, Mexico
| | - Ana Sofía Escobedo-Muñoz
- Universidad Nacional Autónoma de México, Centro de Ciencias Genómicas, Programa de Genómica Evolutiva, Cuernavaca, Mexico
| | - Gabriela Guerrero
- Universidad Nacional Autónoma de México, Centro de Ciencias Genómicas, Unidad de Análisis Bioinformáticos, Cuernavaca, Mexico
| | - Ariadnna Cruz-Córdova
- Unidad de Enfermedades Infecciosas, Laboratorio de Investigación en Bacteriología Intestinal, Hospital Infantil de México Federico Gómez, Ciudad de México, Mexico
| | - Elvira Garza-González
- Universidad Autónoma de Nuevo León, Facultad de Medicina/Hospital Universitario Dr. José Eleuterio González, Departamento de Bioquímica y Medicina Molecular, Monterrey, Mexico
| | - Rigoberto Hernández-Castro
- Departamento de Ecología de Agentes Patógenos, Hospital General Dr. Manuel Gea González, Ciudad de México, Mexico
| | - Patricia Lozano Zarain
- Benemérita Universidad Autónoma de Puebla, Instituto de Ciencias, Centro de Investigaciones en Ciencias Microbiológicas, Laboratorio de Microbiología Hospitalaria y de la Comunidad, Puebla, Mexico
| | - Rayo Morfín-Otero
- Instituto de Patología Infecciosa y Experimental, Universidad de Guadalajara, Guadalajara, Mexico
| | - Patricia Volkow
- Instituto Nacional de Cancerología, Departamento de Enfermedades Infecciosas, Ciudad de México, Mexico
| | - Juan Xicohtencatl-Cortes
- Unidad de Enfermedades Infecciosas, Laboratorio de Investigación en Bacteriología Intestinal, Hospital Infantil de México Federico Gómez, Ciudad de México, Mexico
| | - Miguel A Cevallos
- Universidad Nacional Autónoma de México, Centro de Ciencias Genómicas, Programa de Genómica Evolutiva, Cuernavaca, Mexico
| |
Collapse
|
37
|
Grodner B, Shi H, Farchione O, Vill AC, Ntekas I, Diebold PJ, Wu DT, Chen CY, Kim DM, Zipfel WR, Brito IL, De Vlaminck I. Spatial mapping of mobile genetic elements and their bacterial hosts in complex microbiomes. Nat Microbiol 2024:10.1038/s41564-024-01735-5. [PMID: 38918467 DOI: 10.1038/s41564-024-01735-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 05/17/2024] [Indexed: 06/27/2024]
Abstract
The exchange of mobile genetic elements (MGEs) facilitates the spread of functional traits including antimicrobial resistance within bacterial communities. Tools to spatially map MGEs and identify their bacterial hosts in complex microbial communities are currently lacking, limiting our understanding of this process. Here we combined single-molecule DNA fluorescence in situ hybridization (FISH) with multiplexed ribosomal RNA-FISH to enable simultaneous visualization of both MGEs and bacterial taxa. We spatially mapped bacteriophage and antimicrobial resistance (AMR) plasmids and identified their host taxa in human oral biofilms. This revealed distinct clusters of AMR plasmids and prophage, coinciding with densely packed regions of host bacteria. Our data suggest spatial heterogeneity in bacterial taxa results in heterogeneous MGE distribution within the community, with MGE clusters resulting from horizontal gene transfer hotspots or expansion of MGE-carrying strains. Our approach can help advance the study of AMR and phage ecology in biofilms.
Collapse
Affiliation(s)
- Benjamin Grodner
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - Hao Shi
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
- Kanvas Biosciences, Inc, Monmouth Junction, NJ, USA
| | - Owen Farchione
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - Albert C Vill
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - Ioannis Ntekas
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - Peter J Diebold
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - David T Wu
- Division of Periodontology, Department of Oral Medicine, Infection, and Immunity, Harvard School of Dental Medicine, Boston, MA, USA
| | - Chia-Yu Chen
- Division of Periodontology, Department of Oral Medicine, Infection, and Immunity, Harvard School of Dental Medicine, Boston, MA, USA
| | - David M Kim
- Division of Periodontology, Department of Oral Medicine, Infection, and Immunity, Harvard School of Dental Medicine, Boston, MA, USA
| | - Warren R Zipfel
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - Ilana L Brito
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - Iwijn De Vlaminck
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA.
| |
Collapse
|
38
|
Sankaranarayanan G, Kodiveri Muthukaliannan G. Exploring antimicrobial resistance determinants in the Neanderthal microbiome. Microbiol Spectr 2024:e0266223. [PMID: 38916350 DOI: 10.1128/spectrum.02662-23] [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: 01/23/2024] [Accepted: 05/24/2024] [Indexed: 06/26/2024] Open
Abstract
This study aimed to investigate the presence of antimicrobial resistance determinants (ARDs) in the Neanderthal microbiome through meticulous analysis of metagenomic data derived directly from dental calculus and fecal sediments across diverse Neanderthal sites in Europe. Employing a targeted locus mapping approach followed by a consensus strategy instead of an assembly-first approach, we aimed to identify and characterize ARDs within these ancient microbial communities. A comprehensive and redundant ARD database was constructed by amalgamating data from various antibiotic resistance gene repositories. Our results highlighted the efficacy of the KMA tool in providing a robust alignment of ancient metagenomic reads to the antibiotic resistance gene database. Notably, the KMA tool identified a limited number of ARDs, with only the 23S ribosomal gene from the dental calculus sample of Neanderthal remains at Goyet Troisieme Caverne exhibiting ancient DNA (aDNA) characteristics. Despite not identifying ARDs with typical ancient DNA damage patterns or negative distance proportions, our findings suggest a nuanced identification of putative antimicrobial resistance determinants in the Neanderthal microbiome's genetic repertoire based on the taxonomy-habitat correlation. Nevertheless, our findings are limited by factors such as environmental DNA contamination, DNA fragmentation, and cytosine deamination of aDNA. The study underscores the necessity for refined methodologies to unlock the genomic assets of prehistoric populations, fostering a comprehensive understanding of the intricate dynamics shaping the microbial landscape across history. IMPORTANCE The results of our analysis demonstrate the challenges in identifying determinants of antibiotic resistance within the endogenous microbiome of Neanderthals. Despite the comprehensive investigation of multiple studies and the utilization of advanced analytical techniques, the detection of antibiotic resistance determinants in the ancient microbial communities proved to be particularly difficult. However, our analysis did reveal the presence of some authentic ancient conservative genes, indicating the preservation of certain genetic elements over time. These findings raise intriguing questions about the factors influencing the presence or absence of antibiotic resistance in ancient microbial communities. It could be speculated that the spread of current antibiotic resistance, which has reached alarming levels in modern times, is primarily driven by anthropogenic factors such as the widespread use and misuse of antibiotics in medical and agricultural practices.
Collapse
|
39
|
Machado RAR, Malan AP, Boss A, Claasen NJ, Bhat AH, Abolafia J. Photorhabdus africana sp. nov. isolated from Heterorhabditis entomopathogenic nematodes. Curr Microbiol 2024; 81:240. [PMID: 38910178 PMCID: PMC11194217 DOI: 10.1007/s00284-024-03744-3] [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: 11/29/2023] [Accepted: 05/20/2024] [Indexed: 06/25/2024]
Abstract
One Gram-negative, rod-shaped bacterial strain, isolated from an undescribed Heterorhabditis entomopathogenic nematode species was characterized to determine its taxonomic position. The 16S rRNA gene sequences indicate that it belongs to the class Gammaproteobacteria, to the family Morganellaceae, to the genus Photorhabdus, and likely represents a novel bacterial species. This strain, designated here as CRI-LCT, was therefore molecularly, biochemically, and morphologically characterized to describe the novel bacterial species. Phylogenetic reconstructions using 16S rRNA gene sequences show that CRI-LCT is closely related to P. laumondii subsp. laumondii TT01T and to P. laumondii subsp. clarkei BOJ-47T. The 16rRNA gene sequences between CRI-LCT and P. laumondii subsp. laumondii TT01T are 99.1% identical, and between CRI-LCT and P. laumondii subsp. clarkei BOJ-47T are 99.2% identical. Phylogenetic reconstructions using whole genome sequences show that CRI-LCT is closely related to P. laumondii subsp. laumondii TT01T and to P. laumondii subsp. clarkei BOJ-47T. Moreover, digital DNA-DNA hybridization (dDDH) values between CRI-LCT and its two relative species P. laumondii subsp. laumondii TT01T and P. laumondii subsp. clarkei BOJ-47T are 65% and 63%, respectively. In addition, we observed that average nucleotide identity (ANI) values between CRI-LCT and its two relative species P. laumondii subsp. laumondii TT01T and P. laumondii subsp. clarkei BOJ-47T are 95.8% and 95.5%, respectively. These values are below the 70% dDDH and the 95-96% ANI divergence thresholds that delimits prokaryotic species. Based on these genomic divergence values, and the phylogenomic separation, we conclude that CRI-LCT represents a novel bacterial species, for which we propose the name Photorhabdus africana sp. nov. with CRI-LCT (= CCM 9390T = CCOS 2112T) as the type strain. The following biochemical tests allow to differentiate P. africana sp. nov. CRI-LCT from other species of the genus, including its more closely related taxa: β-Galactosidase, citrate utilization, urease and tryptophan deaminase activities, indole and acetoin production, and glucose and inositol oxidation. Our study contributes to a better understanding of the taxonomy and biodiversity of this important bacterial group with great biotechnological and agricultural potential.
Collapse
Affiliation(s)
- Ricardo A R Machado
- Experimental Biology Research Group, Institute of Biology, University of Neuchâtel, Rue Emile-Argand 11, 2000, Neuchâtel, Switzerland.
| | - Antoinette P Malan
- Department of Conservation Ecology and Entomology, Stellenbosch University, Private Bag X1, Matieland, 7602, South Africa
| | - Anja Boss
- Experimental Biology Research Group, Institute of Biology, University of Neuchâtel, Rue Emile-Argand 11, 2000, Neuchâtel, Switzerland
| | - Nicholle J Claasen
- Department of Conservation Ecology and Entomology, Stellenbosch University, Private Bag X1, Matieland, 7602, South Africa
| | - Aashaq Hussain Bhat
- Department of Biosciences and University Center for Research and Development, Chandigarh University, Gharuan, Mohali, Punjab, 140413, India
- Department of Biomaterials, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences (SIMATS), Saveetha University, Chennai, 600077, India
| | - Joaquín Abolafia
- Departamento de Biología Animal, Biología Vegetal y Ecología, Universidad de Jaén, Campus 'Las Lagunillas', Jaén, Spain
| |
Collapse
|
40
|
Jiang Y, Kang H, Dou H, Guo D, Yuan Q, Dong L, Du Z, Zhao W, Xin D. Comparative genomic sequencing to characterize Mycoplasma pneumoniae genome, typing, and drug resistance. Microbiol Spectr 2024:e0361523. [PMID: 38904371 DOI: 10.1128/spectrum.03615-23] [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: 11/09/2023] [Accepted: 04/13/2024] [Indexed: 06/22/2024] Open
Abstract
To analyze the characteristics of Mycoplasma pneumoniae as well as macrolide antibiotic resistance through whole-genome sequencing and comparative genomics. Thirteen clinical strains isolated from 2003 to 2019 were selected, 10 of which were resistant to erythromycin (MIC >64 µg/mL), including 8 P1-type I and 2 P1-type II. Three were sensitive (<1 µg/mL) and P1-type II. One resistant strain had an A→G point mutation at position 2064 in region V of the 23S rRNA, the others had it at position 2063, while the three sensitive strains had no mutation here. Genome assembly and comparative genome analysis revealed a high level of genome consistency within the P1 type, and the primary differences in genome sequences concentrated in the region encoding the P1 protein. In P1-type II strains, three specific gene mutations were identified: C162A and A430G in L4 gene and T1112G mutation in the CARDS gene. Clinical information showed seven cases were diagnosed with severe pneumonia, all of which were infected with drug-resistant strains. Notably, BS610A4 and CYM219A1 exhibited a gene multi-copy phenomenon and shared a conserved functional domain with the DUF31 protein family. Clinically, the patients had severe refractory pneumonia, with pleural effusion, necessitating treatment with glucocorticoids and bronchoalveolar lavage. The primary variations between strains occur among different P1-types, while there is a high level of genomic consistency within P1-types. Three mutation loci associated with specific types were identified, and no specific genetic alterations directly related to clinical presentation were observed.IMPORTANCEMycoplasma pneumoniae is an important pathogen of community-acquired pneumonia, and macrolide resistance brings difficulties to clinical treatment. We analyzed the characteristics of M. pneumoniae as well as macrolide antibiotic resistance through whole-genome sequencing and comparative genomics. The work addressed primary variations between strains that occur among different P1-types, while there is a high level of genomic consistency within P1-types. In P1-type II strains, three specific gene mutations were identified: C162A and A430G in L4 gene and T1112G mutation in the CARDS gene. All the strains isolated from severe pneumonia cases were drug-resistant, two of which exhibited a gene multi-copy phenomenon, sharing a conserved functional domain with the DUF31 protein family. Three mutation loci associated with specific types were identified, and no specific genetic alterations directly related to clinical presentation were observed.
Collapse
Affiliation(s)
- Yue Jiang
- Pediatric Department, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
| | - Hailong Kang
- National Genomics Data Center and CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Haiwei Dou
- Tropical Medicine Research Institute, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Dongxing Guo
- Tropical Medicine Research Institute, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Qing Yuan
- Tropical Medicine Research Institute, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Lili Dong
- National Genomics Data Center and CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China
| | - Zhenglin Du
- National Genomics Data Center and CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China
| | - Wenming Zhao
- National Genomics Data Center and CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China
- School of Future Technology, University of Chinese Academy of Sciences, Beijing, China
| | - Deli Xin
- Tropical Medicine Research Institute, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| |
Collapse
|
41
|
Xue M, Huang R, Liu W, Cheng J, Liu Y, Zhang J, Wang L, Liu D, Jiang H. Identification and characterization of a potential strain for the production of polyhydroxyalkanoate from glycerol. Front Microbiol 2024; 15:1413120. [PMID: 38966388 PMCID: PMC11223650 DOI: 10.3389/fmicb.2024.1413120] [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: 04/06/2024] [Accepted: 05/20/2024] [Indexed: 07/06/2024] Open
Abstract
While poly (3-hydroxybutyrate) (PHB) holds promise as a bioplastic, its commercial utilization has been hampered by the high cost of raw materials. However, glycerol emerges as a viable feedstock for PHB production, offering a sustainable production approach and substantial cost reduction potential. Glycerol stands out as a promising feedstock for PHB production, offering a pathway toward sustainable manufacturing and considerable cost savings. The identification and characterization of strains capable of converting glycerol into PHB represent a pivotal strategy in advancing PHB production research. In this study, we isolated a strain, Ralstonia sp. RRA (RRA). The strain exhibits remarkable proficiency in synthesizing PHB from glycerol. With glycerol as the carbon source, RRA achieved a specific growth rate of 0.19 h-1, attaining a PHB content of approximately 50% within 30 h. Through third-generation genome and transcriptome sequencing, we elucidated the genome composition and identified a total of eight genes (glpR, glpD, glpS, glpT, glpP, glpQ, glpV, and glpK) involved in the glycerol metabolism pathway. Leveraging these findings, the strain RRA demonstrates significant promise in producing PHB from low-cost renewable carbon sources.
Collapse
Affiliation(s)
- Mengheng Xue
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan, China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin, China
| | - Rong Huang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin, China
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Wei Liu
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan, China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin, China
| | - Jian Cheng
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin, China
| | - Yuwan Liu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin, China
| | - Jie Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin, China
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Limei Wang
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan, China
| | - Dingyu Liu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin, China
| | - Huifeng Jiang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin, China
| |
Collapse
|
42
|
Vences-Guzmán MÁ, Jiménez-Rodríguez M, Lozano L, Rojas-Juárez S, Ramírez-Estudillo JA, Hernández-Vázquez ÁY, Pita-Ortiz IY, Ramírez-Ceballos KG, Medina-Medina S, Sohlenkamp C. A clinical metagenomic study of biopsies from Mexican endophthalmitis patients reveals the presence of complex bacterial communities and a diversity of resistance genes. Access Microbiol 2024; 6:000639.v3. [PMID: 39045243 PMCID: PMC11261729 DOI: 10.1099/acmi.0.000639.v3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 05/13/2024] [Indexed: 07/25/2024] Open
Abstract
Infectious endophthalmitis is a severe ophthalmic emergency. This infection can be caused by bacteria and fungi. For efficient treatment, the administration of antimicrobial drugs to which the microbes are susceptible is essential. The aim of this study was to identify micro-organisms in biopsies of Mexican endophthalmitis patients using metagenomic next-generation sequencing and determine which antibiotic resistance genes were present in the biopsy samples. In this prospective case study, 19 endophthalmitis patients were recruited. Samples of vitreous or aqueous humour were extracted for DNA extraction for metagenomic next-generation sequencing. Analysis of the sequencing results revealed the presence of a wide variety of bacteria in the biopsies. Resistome analysis showed that homologues of antibiotic resistance genes were present in several biopsy samples. Genes possibly conferring resistance to ceftazidime and vancomycin were detected in addition to various genes encoding efflux pumps. Our findings contrast with the widespread opinion that only one or a few bacterial strains are present in the infected tissues of endophthalmitis patients. These diverse communities might host many of the resistance genes that were detected, which can further complicate the infections.
Collapse
Affiliation(s)
| | | | - Luis Lozano
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Sergio Rojas-Juárez
- Departamento de Retina, Fundación Hospital Nuestra Señora de la Luz IAP, Mexico City, Mexico
| | | | | | | | | | - Silvia Medina-Medina
- Departamento de Retina, Fundación Hospital Nuestra Señora de la Luz IAP, Mexico City, Mexico
| | - Christian Sohlenkamp
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| |
Collapse
|
43
|
Cataldo PG, Urquiza Martínez MP, Villena J, Kitazawa H, Saavedra L, Hebert EM. Comprehensive characterization of γ-aminobutyric acid (GABA) production by Levilactobacillus brevis CRL 2013: insights from physiology, genomics, and proteomics. Front Microbiol 2024; 15:1408624. [PMID: 38962125 PMCID: PMC11219586 DOI: 10.3389/fmicb.2024.1408624] [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: 03/28/2024] [Accepted: 06/10/2024] [Indexed: 07/05/2024] Open
Abstract
Introduction Levilactobacillus brevis CRL 2013, a plant-derived lactic acid bacterium (LAB) with immunomodulatory properties, has emerged as an efficient producer of γ-aminobutyric acid (GABA). Notably, not all LAB possess the ability to produce GABA, highlighting the importance of specific genetic and environmental conditions for GABA synthesis. This study aimed to elucidate the intriguing GABA-producing machinery of L. brevis CRL 2013 and support its potential for safe application through comprehensive genome analysis. Methods A comprehensive genome analysis of L. brevis CRL 2013 was performed to identify the presence of antibiotic resistance genes, virulence markers, and genes associated with the glutamate decarboxylase system, which is essential for GABA biosynthesis. Then, an optimized chemically defined culture medium (CDM) was supplemented with monosodium glutamate (MSG) and yeast extract (YE) to analyze their influence on GABA production. Proteomic and transcriptional analyses were conducted to assess changes in protein and gene expression related to GABA production. Results The absence of antibiotic resistance genes and virulence markers in the genome of L. brevis CRL 2013 supports its safety for potential probiotic applications. Genes encoding the glutamate decarboxylase system, including two gad genes (gadA and gadB) and the glutamate antiporter gene (gadC), were identified. The gadB gene is located adjacent to gadC, while gadA resides separately on the chromosome. The transcriptional regulator gadR was found upstream of gadC, with transcriptional analyses demonstrating cotranscription of gadR with gadC. Although MSG supplementation alone did not activate GABA synthesis, the addition of YE significantly enhanced GABA production in the optimized CDM containing glutamate. Proteomic analysis revealed minimal differences between MSG-supplemented and non-supplemented CDM cultures, whereas YE supplementation resulted in significant proteomic changes, including upregulation of GadB. Transcriptional analysis confirmed increased expression of gadB and gadR upon YE supplementation, supporting its role in activating GABA production. Conclusion These findings provide valuable insights into the influence of nutrient composition on GABA production. Furthermore, they unveil the potential of L. brevis CRL 2013 as a safe, nonpathogenic strain with valuable biotechnological traits which can be further leveraged for its probiotic potential in the food industry.
Collapse
Affiliation(s)
- Pablo G. Cataldo
- Centro de Referencia para Lactobacilos (CERELA-CONICET), San Miguel de Tucumán, Argentina
| | | | - Julio Villena
- Centro de Referencia para Lactobacilos (CERELA-CONICET), San Miguel de Tucumán, Argentina
| | - Haruki Kitazawa
- Food and Feed Immunology Group, Laboratory of Animal Food Function, Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
- Livestock Immunology Unit, International Education and Research Centre for Food and Agricultural Immunology (CFAI), Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
| | - Lucila Saavedra
- Centro de Referencia para Lactobacilos (CERELA-CONICET), San Miguel de Tucumán, Argentina
| | - Elvira M. Hebert
- Centro de Referencia para Lactobacilos (CERELA-CONICET), San Miguel de Tucumán, Argentina
| |
Collapse
|
44
|
Lee DH, Lee K, Kim YS, Cha CJ. Comprehensive genomic landscape of antibiotic resistance in Staphylococcus epidermidis. mSystems 2024; 9:e0022624. [PMID: 38727238 PMCID: PMC11237394 DOI: 10.1128/msystems.00226-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Accepted: 04/04/2024] [Indexed: 06/19/2024] Open
Abstract
Staphylococcus epidermidis, a common commensal bacterium found on human skin, can cause infections in clinical settings, and the presence of antibiotic resistance genes (ARGs) impedes the treatment of S. epidermidis infections. However, studies characterizing the ARGs in S. epidermidis with regard to genomic and ecological diversities are limited. Thus, we performed a comprehensive and comparative analysis of 405 high-quality S. epidermidis genomes, including those of 35 environmental isolates from the Han River, to investigate the genomic diversity of antibiotic resistance in this pathogen. Comparative genomic analysis revealed the prevalence of ARGs in S. epidermidis genomes associated with multi-locus sequence types. The genes encoding dihydrofolate reductase (dfrC) and multidrug efflux pump (norA) were genome-wide core ARGs. β-Lactam class ARGs were also highly prevalent in the S. epidermidis genomes, which was consistent with the resistance phenotype observed in river isolates. Furthermore, we identified chloramphenicol acetyltransferase genes (cat) in the plasmid-like sequences of the six river isolates, which have not been reported previously in S. epidermidis genomes. These genes were identical to those harbored by the Enterococcus faecium plasmids and associated with the insertion sequence 6 family transposases, homologous to those found in Staphylococcus aureus plasmids, suggesting the possibility of horizontal gene transfer between these Gram-positive pathogens. Comparison of the ARG and virulence factor profiles between S. epidermidis and S. aureus genomes revealed that these two species were clearly distinguished, suggesting genomic demarcation despite ecological overlap. Our findings provide a comprehensive understanding of the genomic diversity of antibiotic resistance in S. epidermidis. IMPORTANCE A comprehensive understanding of the antibiotic resistance gene (ARG) profiles of the skin commensal bacterium and opportunistic pathogen Staphylococcus epidermidis needs to be documented from a genomic point of view. Our study encompasses a comparative analysis of entire S. epidermidis genomes from various habitats, including those of 35 environmental isolates from the Han River sequenced in this study. Our results shed light on the distribution and diversity of ARGs within different S. epidermidis multi-locus sequence types, providing valuable insights into the ecological and genetic factors associated with antibiotic resistance. A comparison between S. epidermidis and Staphylococcus aureus revealed marked differences in ARG and virulence factor profiles, despite their overlapping ecological niches.
Collapse
Affiliation(s)
- Do-Hoon Lee
- Department of Systems Biotechnology and Center for Antibiotic Resistome, Chung-Ang University, Anseong, South Korea
| | - Kihyun Lee
- Department of Systems Biotechnology and Center for Antibiotic Resistome, Chung-Ang University, Anseong, South Korea
| | - Yong-Seok Kim
- Department of Systems Biotechnology and Center for Antibiotic Resistome, Chung-Ang University, Anseong, South Korea
| | - Chang-Jun Cha
- Department of Systems Biotechnology and Center for Antibiotic Resistome, Chung-Ang University, Anseong, South Korea
| |
Collapse
|
45
|
Fu Z, Gong X, Hu Z, Wei B, Zhang H. Unveiling biosynthetic potential of an Arctic marine-derived strain Aspergillus sydowii MNP-2. BMC Genomics 2024; 25:603. [PMID: 38886660 PMCID: PMC11181645 DOI: 10.1186/s12864-024-10501-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2024] [Accepted: 06/05/2024] [Indexed: 06/20/2024] Open
Abstract
BACKGROUND A growing number of studies have demonstrated that the polar regions have the potential to be a significant repository of microbial resources and a potential source of active ingredients. Genome mining strategy plays a key role in the discovery of bioactive secondary metabolites (SMs) from microorganisms. This work highlighted deciphering the biosynthetic potential of an Arctic marine-derived strain Aspergillus sydowii MNP-2 by a combination of whole genome analysis and antiSMASH as well as feature-based molecular networking (MN) in the Global Natural Products Social Molecular Networking (GNPS). RESULTS In this study, a high-quality whole genome sequence of an Arctic marine strain MNP-2, with a size of 34.9 Mb was successfully obtained. Its total number of genes predicted by BRAKER software was 13,218, and that of non-coding RNAs (rRNA, sRNA, snRNA, and tRNA) predicted by using INFERNAL software was 204. AntiSMASH results indicated that strain MNP-2 harbors 56 biosynthetic gene clusters (BGCs), including 18 NRPS/NRPS-like gene clusters, 10 PKS/PKS-like gene clusters, 8 terpene synthse gene clusters, 5 indole synthase gene clusters, 10 hybrid gene clusters, and 5 fungal-RiPP gene clusters. Metabolic analyses of strain MNP-2 grown on various media using GNPS networking revealed its great potential for the biosynthesis of bioactive SMs containing a variety of heterocyclic and bridge-ring structures. For example, compound G-8 exhibited a potent anti-HIV effect with an IC50 value of 7.2 nM and an EC50 value of 0.9 nM. Compound G-6 had excellent in vitro cytotoxicities against the K562, MCF-7, Hela, DU145, U1975, SGC-7901, A549, MOLT-4, and HL60 cell lines, with IC50 values ranging from 0.10 to 3.3 µM, and showed significant anti-viral (H1N1 and H3N2) activities with IC50 values of 15.9 and 30.0 µM, respectively. CONCLUSIONS These findings definitely improve our knowledge about the molecular biology of genus A. sydowii and would effectively unveil the biosynthetic potential of strain MNP-2 using genomics and metabolomics techniques.
Collapse
Affiliation(s)
- Zhiyang Fu
- School of Pharmaceutical Sciences, Zhejiang University of Technology, 310014, Hangzhou, China
| | - Xiangzhou Gong
- School of Pharmaceutical Sciences, Zhejiang University of Technology, 310014, Hangzhou, China
| | - Zhe Hu
- School of Pharmaceutical Sciences, Zhejiang University of Technology, 310014, Hangzhou, China
| | - Bin Wei
- School of Pharmaceutical Sciences, Zhejiang University of Technology, 310014, Hangzhou, China
| | - Huawei Zhang
- School of Pharmaceutical Sciences, Zhejiang University of Technology, 310014, Hangzhou, China.
| |
Collapse
|
46
|
Tran TA, Sridhar S, Reece ST, Lunguya O, Jacobs J, Van Puyvelde S, Marks F, Dougan G, Thomson NR, Nguyen BT, Bao PT, Baker S. Combining machine learning with high-content imaging to infer ciprofloxacin susceptibility in isolates of Salmonella Typhimurium. Nat Commun 2024; 15:5074. [PMID: 38871710 PMCID: PMC11176356 DOI: 10.1038/s41467-024-49433-4] [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: 10/04/2023] [Accepted: 06/05/2024] [Indexed: 06/15/2024] Open
Abstract
Antimicrobial resistance (AMR) is a growing public health crisis that requires innovative solutions. Current susceptibility testing approaches limit our ability to rapidly distinguish between antimicrobial-susceptible and -resistant organisms. Salmonella Typhimurium (S. Typhimurium) is an enteric pathogen responsible for severe gastrointestinal illness and invasive disease. Despite widespread resistance, ciprofloxacin remains a common treatment for Salmonella infections, particularly in lower-resource settings, where the drug is given empirically. Here, we exploit high-content imaging to generate deep phenotyping of S. Typhimurium isolates longitudinally exposed to increasing concentrations of ciprofloxacin. We apply machine learning algorithms to the imaging data and demonstrate that individual isolates display distinct growth and morphological characteristics that cluster by time point and susceptibility to ciprofloxacin, which occur independently of ciprofloxacin exposure. Using a further set of S. Typhimurium clinical isolates, we find that machine learning classifiers can accurately predict ciprofloxacin susceptibility without exposure to it or any prior knowledge of resistance phenotype. These results demonstrate the principle of using high-content imaging with machine learning algorithms to predict drug susceptibility of clinical bacterial isolates. This technique may be an important tool in understanding the morphological impact of antimicrobials on the bacterial cell to identify drugs with new modes of action.
Collapse
Affiliation(s)
- Tuan-Anh Tran
- The Department of Medicine, University of Cambridge, Cambridge, UK
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Sushmita Sridhar
- The Department of Medicine, University of Cambridge, Cambridge, UK
- The Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - Stephen T Reece
- The Department of Medicine, University of Cambridge, Cambridge, UK
- Sanofi, Kymab, Babraham Research Campus, Cambridge, UK
| | - Octavie Lunguya
- Department of Microbiology, Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of Congo
- Service de Microbiologie, Cliniques Universitaires de Kinshasa, Kinshasa, Democratic Republic of Congo
| | - Jan Jacobs
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Sandra Van Puyvelde
- The Department of Medicine, University of Cambridge, Cambridge, UK
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Florian Marks
- The Department of Medicine, University of Cambridge, Cambridge, UK
- International Vaccine Institute, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
- Heidelberg Institute of Global Health, University of Heidelberg, Heidelberg, Germany
- Madagascar Institute for Vaccine Research, University of Antananarivo, Antananarivo, Madagascar
| | - Gordon Dougan
- The Department of Medicine, University of Cambridge, Cambridge, UK
| | - Nicholas R Thomson
- The Wellcome Sanger Institute, Hinxton, Cambridge, UK
- London School of Hygiene and Tropical Medicine, London, UK
| | - Binh T Nguyen
- Faculty of Mathematics and Computer Science, University of Science, Vietnam National University Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Pham The Bao
- Information Science Faculty, Saigon University, Ho Chi Minh City, Vietnam
| | - Stephen Baker
- The Department of Medicine, University of Cambridge, Cambridge, UK.
- IAVI, Chelsea and Westminster Hospital, London, UK.
| |
Collapse
|
47
|
Islam MS, Pramanik PK, Rana ML, Ullah MA, Neloy FH, Ramasamy S, Schreinemachers P, Oliva R, Rahman MT. Draft genome sequence of Escherichia coli MTR_GS_S1457 strain isolated from a soil sample of a vegetable garden in Gazipur, Bangladesh. Microbiol Resour Announc 2024; 13:e0002124. [PMID: 38757962 PMCID: PMC11237423 DOI: 10.1128/mra.00021-24] [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: 01/28/2024] [Accepted: 04/29/2024] [Indexed: 05/18/2024] Open
Abstract
We announce the sequence of the Escherichia coli MTR_GS_S1457 strain isolated from a soil sample of a vegetable gardening system for the first time in Bangladesh. With a length of 4,918,647 bp, this strain contained one plasmid, two CRISPR arrays, 54 predicted antibiotic resistance genes, and 81 predicted virulence factor genes.
Collapse
Affiliation(s)
- Md. Saiful Islam
- Department of Microbiology and Hygiene, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh, Bangladesh
- Department of Animal Sciences, University of California—Davis, Davis, California, USA
| | - Pritom Kumar Pramanik
- Department of Microbiology and Hygiene, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Md. Liton Rana
- Department of Microbiology and Hygiene, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Md. Ashek Ullah
- Department of Microbiology and Hygiene, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Fahim Haque Neloy
- Department of Microbiology and Hygiene, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Srinivasan Ramasamy
- Safe and Sustainable Value Chains Flagship Program, World Vegetable Center, Shanhua, Tainan, Taiwan
| | - Pepijn Schreinemachers
- Healthy Diets and Enabling Impact Flagship Programs, World Vegetable Center–East and Southeast Asia, Bangkok, Thailand
| | - Ricardo Oliva
- Safe and Sustainable Value Chains Flagship Program, World Vegetable Center, Shanhua, Tainan, Taiwan
| | - Md. Tanvir Rahman
- Department of Microbiology and Hygiene, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh, Bangladesh
| |
Collapse
|
48
|
Lukovic B, Kabic J, Dragicevic M, Kuljanin S, Dimkic I, Jovcic B, Gajic I. Genetic basis of antimicrobial resistance, virulence features and phylogenomics of carbapenem-resistant Acinetobacter baumannii clinical isolates. Infection 2024:10.1007/s15010-024-02316-8. [PMID: 38856809 DOI: 10.1007/s15010-024-02316-8] [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: 03/06/2024] [Accepted: 06/03/2024] [Indexed: 06/11/2024]
Abstract
PURPOSE The worldwide emergence and clonal spread of carbapenem-resistant Acinetobacter baumannii (CRAB) is of great concern. In the present study, we determined the mechanisms of antimicrobial resistance, virulence gene repertoire and genomic relatedness of CRAB isolates circulating in Serbian hospitals. METHODS CRAB isolates were analyzed using whole-genome sequencing (WGS) for the presence of antimicrobial resistance-encoding genes, virulence factors-encoding genes, mobile genetic elements and genomic relatedness. Antimicrobial susceptibility testing was done by disk diffusion and broth microdilution methods. RESULTS Eleven isolates exhibited an MDR resistance phenotype, while four of them were XDR. MIC90 for meropenem and imipenem were > 64 µg/mL and 32 µg/mL, respectively. While all CRABs harbored blaOXA-66 variant of blaOXA-51 gene, those assigned to STPas2, STPas636 and STPas492 had blaADC-73,blaADC-74 and blaADC-30 variants, respectively. The following acquired carbapenemases-encoding genes were found: blaOXA-72 (n = 12), blaOXA-23 (n = 3), and blaNDM-1(n = 5), and were mapped to defined mobile genetic elements. MLST analysis assigned the analyzed CRAB isolates to three Pasteur sequence types (STs): STPas2, STPas492, and STPas636. The Majority of strains belonged to International Clone II (ICII) and carried tested virulence-related genes liable for adherence, biofilm formation, iron uptake, heme biosynthesis, zinc utilization, serum resistance, stress adaptation, intracellular survival and toxin activity. CONCLUSION WGS elucidated the resistance and virulence profiles of CRABs isolated from clinical samples in Serbian hospitals and genomic relatedness of CRAB isolates from Serbia and globally distributed CRABs.
Collapse
Affiliation(s)
- Bojana Lukovic
- College of Health Sciences, Academy of Applied Studies Belgrade, Cara Dusana 254, Belgrade, 11080, Serbia.
| | - Jovana Kabic
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - Milan Dragicevic
- Institute for Biological Research "Siniša Stanković", National Institute of the Republic of Serbia, University of Belgrade, Belgrade, Serbia
| | | | - Ivica Dimkic
- Faculty of Biology, University of Belgrade, Belgrade, Serbia
| | - Branko Jovcic
- Faculty of Biology, University of Belgrade, Belgrade, Serbia
- Laboratory for Molecular Microbiology, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Ina Gajic
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| |
Collapse
|
49
|
Rubio Garcia E, Casadellà M, Parera M, Vila J, Paredes R, Noguera-Julian M. Gut resistome linked to sexual preference and HIV infection. BMC Microbiol 2024; 24:201. [PMID: 38851693 PMCID: PMC11162057 DOI: 10.1186/s12866-024-03335-z] [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: 08/07/2023] [Accepted: 05/16/2024] [Indexed: 06/10/2024] Open
Abstract
BACKGROUND People living with HIV (PLWH) are at increased risk of acquisition of multidrug resistant organisms due to higher rates of predisposing factors. The gut microbiome is the main reservoir of the collection of antimicrobial resistance determinants known as the gut resistome. In PLWH, changes in gut microbiome have been linked to immune activation and HIV-1 associated complications. Specifically, gut dysbiosis defined by low microbial gene richness has been linked to low Nadir CD4 + T-cell counts. Additionally, sexual preference has been shown to strongly influence gut microbiome composition in PLWH resulting in different Prevotella or Bacteroides enriched enterotypes, in MSM (men-who-have-sex-with-men) or no-MSM, respectively. To date, little is known about gut resistome composition in PLWH due to the scarcity of studies using shotgun metagenomics. The present study aimed to detect associations between different microbiome features linked to HIV-1 infection and gut resistome composition. RESULTS Using shotgun metagenomics we characterized the gut resistome composition of 129 HIV-1 infected subjects showing different HIV clinical profiles and 27 HIV-1 negative controls from a cross-sectional observational study conducted in Barcelona, Spain. Most no-MSM showed a Bacteroides-enriched enterotype and low microbial gene richness microbiomes. We did not identify differences in resistome diversity and composition according to HIV-1 infection or immune status. However, gut resistome was more diverse in MSM group, Prevotella-enriched enterotype and gut micorbiomes with high microbial gene richness compared to no-MSM group, Bacteroides-enriched enterotype and gut microbiomes with low microbial gene richness. Additionally, gut resistome beta-diversity was different according to the defined groups and we identified a set of differentially abundant antimicrobial resistance determinants based on the established categories. CONCLUSIONS Our findings reveal a significant correlation between gut resistome composition and various host variables commonly associated with gut microbiome, including microbiome enterotype, microbial gene richness, and sexual preference. These host variables have been previously linked to immune activation and lower Nadir CD4 + T-Cell counts, which are prognostic factors of HIV-related comorbidities. This study provides new insights into the relationship between antibiotic resistance and clinical characteristics of PLWH.
Collapse
Affiliation(s)
- Elisa Rubio Garcia
- Department of Microbiology, CDB, Hospital Clinic, University of Barcelona, Barcelona, Spain.
- Molecuar Core Facilty, Hospital Clínic de Barcelona, Barcelona, Spain.
- ISGlobal Barcelona Institute for Global Health, Barcelona, Spain.
| | | | | | - Jordi Vila
- Department of Microbiology, CDB, Hospital Clinic, University of Barcelona, Barcelona, Spain
- ISGlobal Barcelona Institute for Global Health, Barcelona, Spain
- Infectious Disease Networking Biomedical Research Center (CIBERINFEC), Carlos III Health Institute, Madrid, Spain
| | - Roger Paredes
- IrsiCaixa, Ctra de Canyet S/N, 08916, Badalona, Spain
- Universitat de Vic-Universitat Central de Catalunya, Vic, Spain
- Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
- Department of Infectious Diseasest &, Lluita Contra La SIDA Foundation, Hospital Universitari Germans Trias I Pujol, Badalona, Spain
- Infectious Disease Networking Biomedical Research Center (CIBERINFEC), Carlos III Health Institute, Madrid, Spain
| | - Marc Noguera-Julian
- IrsiCaixa, Ctra de Canyet S/N, 08916, Badalona, Spain
- Universitat de Vic-Universitat Central de Catalunya, Vic, Spain
- Infectious Disease Networking Biomedical Research Center (CIBERINFEC), Carlos III Health Institute, Madrid, Spain
| |
Collapse
|
50
|
Vukovic D, Gostimirovic S, Cvetanovic J, Gavric D, Aleksic Sabo V, Todorovic D, Medic D, Knezevic P. Antibacterial Potential of Non-Tailed Icosahedral Phages Alone and in Combination with Antibiotics. Curr Microbiol 2024; 81:215. [PMID: 38849666 DOI: 10.1007/s00284-024-03705-w] [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: 01/29/2024] [Accepted: 04/13/2024] [Indexed: 06/09/2024]
Abstract
Non-tailed icosahedral phages belonging to families Fiersviridae (phages MS2 and Qbeta), Tectiviridae (PRD1) and Microviridae (phiX174) have not been considered in detail so far as potential antibacterial agents. The aim of the study was to examine various aspects of the applicability of these phages as antibacterial agents. Antibacterial potential of four phages was investigated via bacterial growth and biofilm formation inhibition, lytic spectra determination, and phage safety examination. The phage phiX174 was combined with different classes of antibiotics to evaluate potential synergistic interactions. In addition, the incidence of phiX174-insensitive mutants was analyzed. The results showed that only phiX174 out of four phages tested against their corresponding hosts inhibited bacterial growth for > 90% at different multiplicity of infection and that only this phage considerably prevented biofilm formation. Although all phages show the absence of potentially undesirable genes, they also have extremely narrow lytic spectra. The synergism was determined between phage phiX174 and ceftazidime, ceftriaxone, ciprofloxacin, macrolides, and chloramphenicol. It was shown that the simultaneous application of agents is more effective than successive treatment, where one agent is applied first. The analysis of the appearance of phiX174 bacteriophage-insensitive mutants showed that mutations occur with a frequency of 10-3. The examined non-tailed phages have a limited potential for use as antibacterial agents, primarily due to a very narrow lytic spectrum and the high frequency of resistant mutants appearance, but Microviridae can be considered in the future as biocontrol agents against susceptible strains of E. coli in combinations with conventional antimicrobial agents.
Collapse
Affiliation(s)
- Darija Vukovic
- Department of Biology and Ecology, Faculty of Sciences, University of Novi Sad, Novi Sad, Serbia
| | - Sonja Gostimirovic
- Department of Biology and Ecology, Faculty of Sciences, University of Novi Sad, Novi Sad, Serbia
| | - Jelena Cvetanovic
- Department of Biology and Ecology, Faculty of Sciences, University of Novi Sad, Novi Sad, Serbia
| | - Damir Gavric
- Department of Biology and Ecology, Faculty of Sciences, University of Novi Sad, Novi Sad, Serbia
| | - Verica Aleksic Sabo
- Department of Biology and Ecology, Faculty of Sciences, University of Novi Sad, Novi Sad, Serbia
| | | | - Deana Medic
- Faculty of Medicine, University of Novi Sad, Novi Sad, Serbia
| | - Petar Knezevic
- Department of Biology and Ecology, Faculty of Sciences, University of Novi Sad, Novi Sad, Serbia.
| |
Collapse
|