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Wang H, Gu Y, Ju C, Li Y, Chen X, Zhou G, Zhang X, Liu C, Chen J, Han Y, Zhang J, Shao Z, Zhang M. Genetic characteristics and potential pathogenic agents in Campylobacter upsaliensis based on genomic analysis. Emerg Microbes Infect 2024; 13:2294857. [PMID: 38085548 PMCID: PMC10810667 DOI: 10.1080/22221751.2023.2294857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Accepted: 12/11/2023] [Indexed: 01/26/2024]
Abstract
Campylobacter upsaliensis was the most common Campylobacter species in pets' gastrointestinal tracts and has been isolated from patients with bacteremia, hemolytic-uremic syndrome, spontaneous abortion, and Guillain-Barré syndrome. However, the genetic characteristics and the full extent of its significance as a human pathogen remain to be fully understood. This study involved an investigation for genomic analysis of 154 strains from different sources and additional antimicrobial resistance profiles of 26 strains for this species. The genomes contained 1,558-1,971 CDS and the genome sizes were estimated to vary from 1.53 Mb to 1.86 Mb, with an average GC content of 34.71%. The entire analyzed genomes could be divided into three clades (A, B, and C) based on ANI and phylogenomic analysis. Significantly, nearly all strains in Clade B were isolated from patient samples, and the virulence-related sequences FlgD, GmhA, and CdtC might serve as determining factors for the classification of Clade B. Half of the tested isolates had MIC values over 64 μg mL-1 for nalidixic acid, gentamicin, and streptomycin. Isolates from pets in China carried more resistant elements in the genomes. This study both provided a comprehensive profile of C. upsaliensis for its genomic features and suggested some pathogenic agents for human infection with this species.
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Affiliation(s)
- Hairui Wang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
| | - Yixin Gu
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
| | - Changyan Ju
- Nanshan Center for Disease Control and Prevention, Shenzhen, People’s Republic of China
| | - Ying Li
- Shunyi District Center for Disease Control and Prevention, Beijing, People’s Republic of China
| | - Xiaoli Chen
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
| | - Guilan Zhou
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
| | - Xin Zhang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
| | - Chang Liu
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
| | - Jing Chen
- Meilianzhonghe Veterinary Hospital Companion Branch, Beijing, People’s Republic of China
| | - Yue Han
- Meilianzhonghe Veterinary Hospital Jingxi Branch, Beijing, People’s Republic of China
| | - Jianzhong Zhang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
| | - Zhujun Shao
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
| | - Maojun Zhang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
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Parzygnat JL, Crespo R, Koci MD, Dunn RR, Harden L, Fosnaught M, Thakur S. Widespread prevalence of plasmid-mediated blaCTX-M type extended-spectrum beta-lactamase Escherichia coli in backyard broiler production systems in the United States. PLoS One 2024; 19:e0304599. [PMID: 38829840 PMCID: PMC11146730 DOI: 10.1371/journal.pone.0304599] [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: 01/18/2024] [Accepted: 05/14/2024] [Indexed: 06/05/2024] Open
Abstract
Extended-spectrum beta-lactamase (ESBL) Escherichia coli (E. coli) is an emerging pathogen of high concern given its resistance to extended-spectrum cephalosporins. Broiler chicken, which is the number one consumed meat in the United States and worldwide, can be a reservoir of ESBL E. coli. Backyard poultry ownership is on the rise in the United States, yet there is little research investigating prevalence of ESBL E. coli in this setting. This study aims to identify the prevalence and antimicrobial resistance profiles (phenotypically and genotypically) of ESBL E. coli in some backyard and commercial broiler farms in the U.S. For this study ten backyard and ten commercial farms were visited at three time-points across flock production. Fecal (n = 10), litter/compost (n = 5), soil (n = 5), and swabs of feeders and waterers (n = 6) were collected at each visit and processed for E. coli. Assessment of ESBL phenotype was determined through using disk diffusion with 3rd generation cephalosporins, cefotaxime and ceftazidime, and that with clavulanic acid. Broth microdilution and whole genome sequencing were used to investigate both phenotypic and genotypic resistance profiles, respectively. ESBL E. coli was more prevalent in backyard farms with 12.95% of samples testing positive whereas 0.77% of commercial farm samples were positive. All isolates contained a blaCTX-M gene, the dominant variant being blaCTX-M-1, and its presence was entirely due to plasmids. Our study confirms concerns of growing resistance to fourth generation cephalosporin, cefepime, as roughly half (51.4%) of all isolates were found to be susceptible dose-dependent and few were resistant. Resistance to non-beta lactams, gentamicin and ciprofloxacin, was also detected in our samples. Our study identifies prevalence of blaCTX-M type ESBL E. coli in U.S. backyard broiler farms, emphasizing the need for interventions for food and production safety.
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Affiliation(s)
- Jessica L. Parzygnat
- Department of Population Health and Pathobiology, North Carolina State University College of Veterinary Medicine, Raleigh, NC, United States of America
| | - Rocio Crespo
- Department of Population Health and Pathobiology, North Carolina State University College of Veterinary Medicine, Raleigh, NC, United States of America
| | - Matthew D. Koci
- Prestage Department of Poultry Science, North Carolina State University, Raleigh, NC, United States of America
| | - Robert R. Dunn
- Department of Applied Ecology, North Carolina State University, Raleigh, NC, United States of America
| | - Lyndy Harden
- Department of Population Health and Pathobiology, North Carolina State University College of Veterinary Medicine, Raleigh, NC, United States of America
| | - Mary Fosnaught
- Prestage Department of Poultry Science, North Carolina State University, Raleigh, NC, United States of America
| | - Siddhartha Thakur
- Department of Population Health and Pathobiology, North Carolina State University College of Veterinary Medicine, Raleigh, NC, United States of America
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Choudhary BK, Choudhary M, Barbuddhe SB, Shanker A. Partial genomic characterization of Chromobacterium piscinae from India reveals multi drug resistance. Braz J Microbiol 2024; 55:1557-1567. [PMID: 38374322 PMCID: PMC11153472 DOI: 10.1007/s42770-024-01288-z] [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: 11/25/2022] [Accepted: 02/10/2024] [Indexed: 02/21/2024] Open
Abstract
Species of genus Chromobacterium have been isolated from diverse geographical settings, which exhibits significant metabolic flexibility as well as biotechnological and pathogenic properties. This study describes the isolation, characterization, draft assembly, and detailed sequence analysis of Chromobacterium piscinae strain W1B-CG-NIBSM isolated from water samples from multi use community pond. The organism was characterized by biochemical tests, Matrix Assisted Laser Desorption/Ionization Time of Flight Mass Spectrometry (MALDI TOF-MS) and partial genome sequencing. The partial genomic data of Chromobacterium pisciane isolate W1B NIBSM strain was submitted to GenBank with Bio project number PRJNA803347 and accession no CP092474. An integrated genome analysis of Chromobacterium piscinae has been accomplished with PATRIC which indicates good quality genome. DNA sequencing using the illumina HiSeq 4000 system generated total length of 4,155,481 bp with 63 contig with G + C content is 62.69%. This partial genome contains 4,126 protein-coding sequences (CDS), 27 repeats region and 78 transfer RNA (tRNA) genes as well as 3 ribosomal RNA (rRNA) genes. The genomic annotation of Chromobacterium W1B depicts 2,925 proteins with functional assignments and 1201 hypothetical proteins. A repertoire of specialty genes implicated in antibiotic resistance (45 genes), drug target (6 genes), Transporter (3 genes) and virulence factor (10 genes). The genomic analysis reveals the adaptability, displays metabolic varied pathways and shows specific structural complex and various virulence factors which makes this strain multi drug resistant. The isolate was found to be highly resistant to β-lactam antibiotics whereas it showed sensitivity towards aminoglycosides and fluoroquinolone antibiotics. Hence, the recovery of Chromobacterium piscinae from community pond evidenced for uncertain hidden source of public health hazard. To the best of authors knowledge this is first report of isolation and genomic description of C. piscinae from India.
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Affiliation(s)
- Binod Kumar Choudhary
- Indian Council of Agricultural Research-National Institute of Biotic Stress Management, Baronda, Raipur, 493 225, Chhattisgarh, India.
| | - Mamta Choudhary
- Indian Council of Agricultural Research-National Institute of Biotic Stress Management, Baronda, Raipur, 493 225, Chhattisgarh, India
| | | | - Asheesh Shanker
- Department of Bioinformatics, Central University of South Bihar, Gaya, Bihar, 824236, India
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Irby I, Broddrick JT. Microbial adaptation to spaceflight is correlated with bacteriophage-encoded functions. Nat Commun 2024; 15:3474. [PMID: 38750067 PMCID: PMC11096397 DOI: 10.1038/s41467-023-42104-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: 02/25/2023] [Accepted: 09/27/2023] [Indexed: 05/18/2024] Open
Abstract
Evidence from the International Space Station suggests microbial populations are rapidly adapting to the spacecraft environment; however, the mechanism of this adaptation is not understood. Bacteriophages are prolific mediators of bacterial adaptation on Earth. Here we survey 245 genomes sequenced from bacterial strains isolated on the International Space Station for dormant (lysogenic) bacteriophages. Our analysis indicates phage-associated genes are significantly different between spaceflight strains and their terrestrial counterparts. In addition, we identify 283 complete prophages, those that could initiate bacterial lysis and infect additional hosts, of which 21% are novel. These prophage regions encode functions that correlate with increased persistence in extreme environments, such as spaceflight, to include antimicrobial resistance and virulence, DNA damage repair, and dormancy. Our results correlate microbial adaptation in spaceflight to bacteriophage-encoded functions that may impact human health in spaceflight.
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Affiliation(s)
- Iris Irby
- Space Biosciences Research Branch, NASA Ames Research Center, Moffett Field, CA, USA
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Jared T Broddrick
- Space Biosciences Research Branch, NASA Ames Research Center, Moffett Field, CA, USA.
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Pei Y, Shum MHH, Liao Y, Leung VW, Gong YN, Smith DK, Yin X, Guan Y, Luo R, Zhang T, Lam TTY. ARGNet: using deep neural networks for robust identification and classification of antibiotic resistance genes from sequences. MICROBIOME 2024; 12:84. [PMID: 38725076 PMCID: PMC11080312 DOI: 10.1186/s40168-024-01805-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 04/02/2024] [Indexed: 05/12/2024]
Abstract
BACKGROUND Emergence of antibiotic resistance in bacteria is an important threat to global health. Antibiotic resistance genes (ARGs) are some of the key components to define bacterial resistance and their spread in different environments. Identification of ARGs, particularly from high-throughput sequencing data of the specimens, is the state-of-the-art method for comprehensively monitoring their spread and evolution. Current computational methods to identify ARGs mainly rely on alignment-based sequence similarities with known ARGs. Such approaches are limited by choice of reference databases and may potentially miss novel ARGs. The similarity thresholds are usually simple and could not accommodate variations across different gene families and regions. It is also difficult to scale up when sequence data are increasing. RESULTS In this study, we developed ARGNet, a deep neural network that incorporates an unsupervised learning autoencoder model to identify ARGs and a multiclass classification convolutional neural network to classify ARGs that do not depend on sequence alignment. This approach enables a more efficient discovery of both known and novel ARGs. ARGNet accepts both amino acid and nucleotide sequences of variable lengths, from partial (30-50 aa; 100-150 nt) sequences to full-length protein or genes, allowing its application in both target sequencing and metagenomic sequencing. Our performance evaluation showed that ARGNet outperformed other deep learning models including DeepARG and HMD-ARG in most of the application scenarios especially quasi-negative test and the analysis of prediction consistency with phylogenetic tree. ARGNet has a reduced inference runtime by up to 57% relative to DeepARG. CONCLUSIONS ARGNet is flexible, efficient, and accurate at predicting a broad range of ARGs from the sequencing data. ARGNet is freely available at https://github.com/id-bioinfo/ARGNet , with an online service provided at https://ARGNet.hku.hk . Video Abstract.
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Grants
- T21-705/20-N Hong Kong Research Grants Council's Theme-based Research Scheme
- T21-705/20-N Hong Kong Research Grants Council's Theme-based Research Scheme
- T21-705/20-N Hong Kong Research Grants Council's Theme-based Research Scheme
- T21-705/20-N Hong Kong Research Grants Council's Theme-based Research Scheme
- T21-705/20-N Hong Kong Research Grants Council's Theme-based Research Scheme
- T21-705/20-N Hong Kong Research Grants Council's Theme-based Research Scheme
- 2019B121205009, HZQB-KCZYZ-2021014, 200109155890863, 190830095586328 and 190824215544727 Innovation and Technology Commission's InnoHK funding (D24H), and the Government of Guangdong Province
- 2019B121205009, HZQB-KCZYZ-2021014, 200109155890863, 190830095586328 and 190824215544727 Innovation and Technology Commission's InnoHK funding (D24H), and the Government of Guangdong Province
- 2019B121205009, HZQB-KCZYZ-2021014, 200109155890863, 190830095586328 and 190824215544727 Innovation and Technology Commission's InnoHK funding (D24H), and the Government of Guangdong Province
- 2019B121205009, HZQB-KCZYZ-2021014, 200109155890863, 190830095586328 and 190824215544727 Innovation and Technology Commission's InnoHK funding (D24H), and the Government of Guangdong Province
- 2019B121205009, HZQB-KCZYZ-2021014, 200109155890863, 190830095586328 and 190824215544727 Innovation and Technology Commission's InnoHK funding (D24H), and the Government of Guangdong Province
- 2019B121205009, HZQB-KCZYZ-2021014, 200109155890863, 190830095586328 and 190824215544727 Innovation and Technology Commission's InnoHK funding (D24H), and the Government of Guangdong Province
- 2019B121205009, HZQB-KCZYZ-2021014, 200109155890863, 190830095586328 and 190824215544727 Innovation and Technology Commission's InnoHK funding (D24H), and the Government of Guangdong Province
- 2019B121205009, HZQB-KCZYZ-2021014, 200109155890863, 190830095586328 and 190824215544727 Innovation and Technology Commission's InnoHK funding (D24H), and the Government of Guangdong Province
- 31922087 National Natural Science Foundation of China's Excellent Young Scientists Fund (Hong Kong and Macau)
- Hong Kong Research Grants Council’s Theme-based Research Scheme
- Innovation and Technology Commission’s InnoHK funding (D24H), and the Government of Guangdong Province
- National Natural Science Foundation of China’s Excellent Young Scientists Fund (Hong Kong and Macau)
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Affiliation(s)
- Yao Pei
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
- Joint Institute of Virology (Shantou University and The University of Hong Kong), Guangdong-Hongkong Joint Laboratory of Emerging Infectious Diseases, Shantou University, Shantou, Guangdong, 515063, China
- Laboratory of Data Discovery for Health (D²4H), Hong Kong Science Park, Pak Shek Kok, Hong Kong SAR, China
- Advanced Pathogen Research Institute, Futian District, Shenzhen City, Guangdong, 518045, China
| | - Marcus Ho-Hin Shum
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
- Joint Institute of Virology (Shantou University and The University of Hong Kong), Guangdong-Hongkong Joint Laboratory of Emerging Infectious Diseases, Shantou University, Shantou, Guangdong, 515063, China
- Laboratory of Data Discovery for Health (D²4H), Hong Kong Science Park, Pak Shek Kok, Hong Kong SAR, China
- Advanced Pathogen Research Institute, Futian District, Shenzhen City, Guangdong, 518045, China
| | - Yunshi Liao
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
- Joint Institute of Virology (Shantou University and The University of Hong Kong), Guangdong-Hongkong Joint Laboratory of Emerging Infectious Diseases, Shantou University, Shantou, Guangdong, 515063, China
- Advanced Pathogen Research Institute, Futian District, Shenzhen City, Guangdong, 518045, China
- Centre for Immunology & Infection (C2i), Hong Kong Science Park, Pak Shek Kok, Hong Kong SAR, China
| | - Vivian W Leung
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
- Joint Institute of Virology (Shantou University and The University of Hong Kong), Guangdong-Hongkong Joint Laboratory of Emerging Infectious Diseases, Shantou University, Shantou, Guangdong, 515063, China
- Laboratory of Data Discovery for Health (D²4H), Hong Kong Science Park, Pak Shek Kok, Hong Kong SAR, China
- Advanced Pathogen Research Institute, Futian District, Shenzhen City, Guangdong, 518045, China
| | - Yu-Nong Gong
- Division of Biotechnology, Research Center of Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- International Master Degree Program for Molecular Medicine in Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Taiwan
| | - David K Smith
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
- Laboratory of Data Discovery for Health (D²4H), Hong Kong Science Park, Pak Shek Kok, Hong Kong SAR, China
| | - Xiaole Yin
- Department of Civil Engineering, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Yi Guan
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
- Joint Institute of Virology (Shantou University and The University of Hong Kong), Guangdong-Hongkong Joint Laboratory of Emerging Infectious Diseases, Shantou University, Shantou, Guangdong, 515063, China
- Laboratory of Data Discovery for Health (D²4H), Hong Kong Science Park, Pak Shek Kok, Hong Kong SAR, China
- Advanced Pathogen Research Institute, Futian District, Shenzhen City, Guangdong, 518045, China
| | - Ruibang Luo
- Department of Computer Science, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Tong Zhang
- Department of Civil Engineering, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Tommy Tsan-Yuk Lam
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Pokfulam, Hong Kong SAR, China.
- Joint Institute of Virology (Shantou University and The University of Hong Kong), Guangdong-Hongkong Joint Laboratory of Emerging Infectious Diseases, Shantou University, Shantou, Guangdong, 515063, China.
- Laboratory of Data Discovery for Health (D²4H), Hong Kong Science Park, Pak Shek Kok, Hong Kong SAR, China.
- Advanced Pathogen Research Institute, Futian District, Shenzhen City, Guangdong, 518045, China.
- Centre for Immunology & Infection (C2i), Hong Kong Science Park, Pak Shek Kok, Hong Kong SAR, China.
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Herman EK, Lacoste SR, Freeman CN, Otto SJG, McCarthy EL, Links MG, Stothard P, Waldner CL. Bacterial enrichment prior to third-generation metagenomic sequencing improves detection of BRD pathogens and genetic determinants of antimicrobial resistance in feedlot cattle. Front Microbiol 2024; 15:1386319. [PMID: 38779502 PMCID: PMC11110911 DOI: 10.3389/fmicb.2024.1386319] [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: 02/15/2024] [Accepted: 04/08/2024] [Indexed: 05/25/2024] Open
Abstract
Introduction Bovine respiratory disease (BRD) is one of the most important animal health problems in the beef industry. While bacterial culture and antimicrobial susceptibility testing have been used for diagnostic testing, the common practice of examining one isolate per species does not fully reflect the bacterial population in the sample. In contrast, a recent study with metagenomic sequencing of nasal swabs from feedlot cattle is promising in terms of bacterial pathogen identification and detection of antimicrobial resistance genes (ARGs). However, the sensitivity of metagenomic sequencing was impeded by the high proportion of host biomass in the nasal swab samples. Methods This pilot study employed a non-selective bacterial enrichment step before nucleic acid extraction to increase the relative proportion of bacterial DNA for sequencing. Results Non-selective bacterial enrichment increased the proportion of bacteria relative to host sequence data, allowing increased detection of BRD pathogens compared with unenriched samples. This process also allowed for enhanced detection of ARGs with species-level resolution, including detection of ARGs for bacterial species of interest that were not targeted for culture and susceptibility testing. The long-read sequencing approach enabled ARG detection on individual bacterial reads without the need for assembly. Metagenomics following non-selective bacterial enrichment resulted in substantial agreement for four of six comparisons with culture for respiratory bacteria and substantial or better correlation with qPCR. Comparison between isolate susceptibility results and detection of ARGs was best for macrolide ARGs in Mannheimia haemolytica reads but was also substantial for sulfonamide ARGs within M. haemolytica and Pasteurella multocida reads and tetracycline ARGs in Histophilus somni reads. Discussion By increasing the proportion of bacterial DNA relative to host DNA through non-selective enrichment, we demonstrated a corresponding increase in the proportion of sequencing data identifying BRD-associated pathogens and ARGs in deep nasopharyngeal swabs from feedlot cattle using long-read metagenomic sequencing. This method shows promise as a detection strategy for BRD pathogens and ARGs and strikes a balance between processing time, input costs, and generation of on-target data. This approach could serve as a valuable tool to inform antimicrobial management for BRD and support antimicrobial stewardship.
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Affiliation(s)
- Emily K. Herman
- Department of Agricultural, Food, and Nutritional Science, Faculty of Agricultural, Life, and Environmental Sciences, University of Alberta, Edmonton, AB, Canada
| | - Stacey R. Lacoste
- Department of Large Animal Clinical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - Claire N. Freeman
- Department of Large Animal Clinical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - Simon J. G. Otto
- HEAT-AMR (Human-Environment-Animal Transdisciplinary AMR) Research Group, School of Public Health, University of Alberta, Edmonton, AB, Canada
- Healthy Environments Thematic Area Lead, Centre for Healthy Communities, School of Public Health, University of Alberta, Edmonton, AB, Canada
| | - E. Luke McCarthy
- Department of Animal and Poultry Science, College of Agriculture and Bioresources, University of Saskatchewan, Saskatoon, SK, Canada
| | - Matthew G. Links
- Department of Animal and Poultry Science, College of Agriculture and Bioresources, University of Saskatchewan, Saskatoon, SK, Canada
- Department of Computer Science, College of Arts and Science, University of Saskatchewan, Saskatoon, SK, Canada
| | - Paul Stothard
- Department of Agricultural, Food, and Nutritional Science, Faculty of Agricultural, Life, and Environmental Sciences, University of Alberta, Edmonton, AB, Canada
| | - Cheryl L. Waldner
- Department of Large Animal Clinical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, Canada
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Zimmermann J, Piecyk A, Sieber M, Petersen C, Johnke J, Moitinho-Silva L, Künzel S, Bluhm L, Traulsen A, Kaleta C, Schulenburg H. Gut-associated functions are favored during microbiome assembly across a major part of C. elegans life. mBio 2024; 15:e0001224. [PMID: 38634692 PMCID: PMC11077962 DOI: 10.1128/mbio.00012-24] [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: 01/02/2024] [Accepted: 03/22/2024] [Indexed: 04/19/2024] Open
Abstract
The microbiome expresses a variety of functions that influence host biology. The range of functions depends on the microbiome's composition, which can change during the host's lifetime due to neutral assembly processes, host-mediated selection, and environmental conditions. To date, the exact dynamics of microbiome assembly, the underlying determinants, and the effects on host-associated functions remain poorly understood. Here, we used the nematode Caenorhabditis elegans and a defined community of fully sequenced, naturally associated bacteria to study microbiome dynamics and functions across a major part of the worm's lifetime of hosts under controlled experimental conditions. Bacterial community composition initially shows strongly declining levels of stochasticity, which increases during later time points, suggesting selective effects in younger animals as opposed to more random processes in older animals. The adult microbiome is enriched in genera Ochrobactrum and Enterobacter compared to the direct substrate and a host-free control environment. Using pathway analysis, metabolic, and ecological modeling, we further find that the lifetime assembly dynamics increase competitive strategies and gut-associated functions in the host-associated microbiome, indicating that the colonizing bacteria benefit the worm. Overall, our study introduces a framework for studying microbiome assembly dynamics based on stochastic, ecological, and metabolic models, yielding new insights into the processes that determine host-associated microbiome composition and function. IMPORTANCE The microbiome plays a crucial role in host biology. Its functions depend on the microbiome composition that can change during a host's lifetime. To date, the dynamics of microbiome assembly and the resulting functions still need to be better understood. This study introduces a new approach to characterize the functional consequences of microbiome assembly by modeling both the relevance of stochastic processes and metabolic characteristics of microbial community changes. The approach was applied to experimental time-series data obtained for the microbiome of the nematode Caenorhabditis elegans across the major part of its lifetime. Stochastic processes played a minor role, whereas beneficial bacteria as well as gut-associated functions enriched in hosts. This indicates that the host might actively shape the composition of its microbiome. Overall, this study provides a framework for studying microbiome assembly dynamics and yields new insights into C. elegans microbiome functions.
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Affiliation(s)
- Johannes Zimmermann
- Research Group Evolutionary Ecology and Genetics, Zoological Institute, Kiel University, Kiel, Germany
- Max Planck Fellow Group Antibiotic Resistance Evolution, Max Planck Institute for Evolutionary Biology, Ploen, Germany
- Research Group Medical Systems Biology, Institute of Experimental Medicine, Kiel University, Kiel, Germany
| | - Agnes Piecyk
- Research Group Evolutionary Ecology and Genetics, Zoological Institute, Kiel University, Kiel, Germany
| | - Michael Sieber
- Department for Evolutionary Theory, Max Planck Institute for Evolutionary Biology, Ploen, Germany
| | - Carola Petersen
- Research Group Evolutionary Ecology and Genetics, Zoological Institute, Kiel University, Kiel, Germany
| | - Julia Johnke
- Research Group Evolutionary Ecology and Genetics, Zoological Institute, Kiel University, Kiel, Germany
| | - Lucas Moitinho-Silva
- />Institute of Clinical Molecular Biology, Christian-Albrechts University, Kiel, Germany
| | - Sven Künzel
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Ploen, Germany
| | - Lena Bluhm
- Research Group Evolutionary Ecology and Genetics, Zoological Institute, Kiel University, Kiel, Germany
| | - Arne Traulsen
- Department for Evolutionary Theory, Max Planck Institute for Evolutionary Biology, Ploen, Germany
| | - Christoph Kaleta
- Research Group Medical Systems Biology, Institute of Experimental Medicine, Kiel University, Kiel, Germany
| | - Hinrich Schulenburg
- Research Group Evolutionary Ecology and Genetics, Zoological Institute, Kiel University, Kiel, Germany
- Max Planck Fellow Group Antibiotic Resistance Evolution, Max Planck Institute for Evolutionary Biology, Ploen, Germany
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Veschetti L, Paiella S, Carelli M, Zotti F, Secchettin E, Malleo G, Signoretto C, Zulianello G, Nocini R, Crovetto A, Salvia R, Bassi C, Malerba G. Dental plaque microbiota sequence counts for microbial profiling and resistance genes detection. Appl Microbiol Biotechnol 2024; 108:319. [PMID: 38709303 DOI: 10.1007/s00253-024-13152-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 01/03/2024] [Accepted: 04/16/2024] [Indexed: 05/07/2024]
Abstract
Shotgun metagenomics sequencing experiments are finding a wide range of applications. Nonetheless, there are still limited guidelines regarding the number of sequences needed to acquire meaningful information for taxonomic profiling and antimicrobial resistance gene (ARG) identification. In this study, we explored this issue in the context of oral microbiota by sequencing with a very high number of sequences (~ 100 million), four human plaque samples, and one microbial community standard and by evaluating the performance of microbial identification and ARGs detection through a downsampling procedure. When investigating the impact of a decreasing number of sequences on quantitative taxonomic profiling in the microbial community standard datasets, we found some discrepancies in the identified microbial species and their abundances when compared to the expected ones. Such differences were consistent throughout downsampling, suggesting their link to taxonomic profiling methods limitations. Overall, results showed that the number of sequences has a great impact on metagenomic samples at the qualitative (i.e., presence/absence) level in terms of loss of information, especially in experiments having less than 40 million reads, whereas abundance estimation was minimally affected, with only slight variations observed in low-abundance species. The presence of ARGs was also assessed: a total of 133 ARGs were identified. Notably, 23% of them inconsistently resulted as present or absent across downsampling datasets of the same sample. Moreover, over half of ARGs were lost in datasets having less than 20 million reads. This study highlights the importance of carefully considering sequencing aspects and suggests some guidelines for designing shotgun metagenomics experiments with the final goal of maximizing oral microbiome analyses. Our findings suggest varying optimized sequence numbers according to different study aims: 40 million for microbiota profiling, 50 million for low-abundance species detection, and 20 million for ARG identification. KEY POINTS: • Forty million sequences are a cost-efficient solution for microbiota profiling • Fifty million sequences allow low-abundance species detection • Twenty million sequences are recommended for ARG identification.
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Affiliation(s)
- Laura Veschetti
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Verona, Italy
| | - Salvatore Paiella
- General and Pancreatic Surgery Unit, Pancreas Institute, University of Verona, Verona, Italy
| | - Maria Carelli
- Department of Diagnostics and Public Health, University of Verona, Verona, Italy
| | - Francesca Zotti
- Department of Surgical Sciences, Dentistry, Gynaecology and Paediatrics, University of Verona, Verona, Italy
| | - Erica Secchettin
- General and Pancreatic Surgery Unit, Pancreas Institute, University of Verona, Verona, Italy
| | - Giuseppe Malleo
- General and Pancreatic Surgery Unit, Pancreas Institute, University of Verona, Verona, Italy
| | - Caterina Signoretto
- Department of Diagnostics and Public Health, University of Verona, Verona, Italy
| | - Giorgia Zulianello
- General and Pancreatic Surgery Unit, Pancreas Institute, University of Verona, Verona, Italy
| | - Riccardo Nocini
- Department of Surgical Sciences, Dentistry, Gynaecology and Paediatrics, University of Verona, Verona, Italy
| | - Anna Crovetto
- General and Pancreatic Surgery Unit, Pancreas Institute, University of Verona, Verona, Italy
| | - Roberto Salvia
- General and Pancreatic Surgery Unit, Pancreas Institute, University of Verona, Verona, Italy
| | - Claudio Bassi
- General and Pancreatic Surgery Unit, Pancreas Institute, University of Verona, Verona, Italy
| | - Giovanni Malerba
- Department of Surgical Sciences, Dentistry, Gynaecology and Paediatrics, University of Verona, Verona, Italy.
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Arzika AM, Abdou A, Maliki R, Beido N, Kadri B, Harouna AN, Galo AN, Alio MK, Lebas E, Oldenburg CE, O’Brien KS, Chen C, Zhong L, Zhou Z, Yan D, Hinterwirth A, Keenan JD, Porco TC, Lietman TM, Doan T. Prolonged mass azithromycin distributions and macrolide resistance determinants among preschool children in Niger: A sub-study of a cluster-randomized trial (MORDOR). PLoS Med 2024; 21:e1004386. [PMID: 38709718 PMCID: PMC11073710 DOI: 10.1371/journal.pmed.1004386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 03/26/2024] [Indexed: 05/08/2024] Open
Abstract
BACKGROUND Randomized controlled trials found that twice-yearly mass azithromycin administration (MDA) reduces childhood mortality, presumably by reducing infection burden. World Health Organization (WHO) issued conditional guidelines for mass azithromycin administration in high-mortality settings in sub-Saharan Africa given concerns for antibiotic resistance. While prolonged twice-yearly MDA has been shown to increase antibiotic resistance in small randomized controlled trials, the objective of this study was to determine if macrolide and non-macrolide resistance in the gut increases with the duration of azithromycin MDA in a larger setting. METHODS AND FINDINGS The Macrolide Oraux pour Réduire les Décès avec un Oeil sur la Résistance (MORDOR) study was conducted in Niger from December 2014 to June 2020. It was a cluster-randomized trial of azithromycin (A) versus placebo (P) aimed at evaluating childhood mortality. This is a sub-study in the MORDOR trial to track changes in antibiotic resistance after prolonged azithromycin MDA. A total of 594 communities were eligible. Children 1 to 59 months in 163 randomly chosen communities were eligible to receive treatment and included in resistance monitoring. Participants, staff, and investigators were masked to treatment allocation. At the conclusion of MORDOR Phase I, by design, all communities received an additional year of twice-yearly azithromycin treatments (Phase II). Thus, at the conclusion of Phase II, the treatment history (1 letter per 6-month period) for the participating communities was either (PP-PP-AA) or (AA-AA-AA). In Phase III, participating communities were then re-randomized to receive either another 3 rounds of azithromycin or placebo, thus resulting in 4 treatment histories: Group 1 (AA-AA-AA-AA-A, N = 51), Group 2 (PP-PP-AA-AA-A, N = 40), Group 3 (AA-AA-AA-PP-P, N = 27), and Group 4 (PP-PP-AA-PP-P, N = 32). Rectal swabs from each child (N = 5,340) were obtained 6 months after the last treatment. Each child contributed 1 rectal swab and these were pooled at the community level, processed for DNA-seq, and analyzed for genetic resistance determinants. The primary prespecified outcome was macrolide resistance determinants in the gut. Secondary outcomes were resistance to beta-lactams and other antibiotic classes. Communities recently randomized to azithromycin (groups 1 and 2) had significantly more macrolide resistance determinants than those recently randomized to placebo (groups 3 and 4) (fold change 2.18, 95% CI 1.5 to 3.51, Punadj < 0.001). However, there was no significant increase in macrolide resistance in communities treated 4.5 years (group 1) compared to just the most recent 2.5 years (group 2) (fold change 0.80, 95% CI 0.50 to 1.00, Padj = 0.010), or between communities that had been treated for 3 years in the past (group 3) versus just 1 year in the past (group 4) (fold change 1.00, 95% CI 0.78 to 2.35, Padj = 0.52). We also found no significant differences for beta-lactams or other antibiotic classes. The main limitations of our study were the absence of phenotypic characterization of resistance, no complete placebo arm, and no monitoring outside of Niger limiting generalizability. CONCLUSIONS In this study, we observed that mass azithromycin distribution for childhood mortality among preschool children in Niger increased macrolide resistance determinants in the gut but that resistance may plateau after 2 to 3 years of treatment. Co-selection to other classes needs to be monitored. TRIAL REGISTRATION NCT02047981 https://classic.clinicaltrials.gov/ct2/show/NCT02047981.
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Affiliation(s)
| | - Amza Abdou
- Programme National de Santé Oculaire, Niamey, Niger
| | | | | | | | | | | | | | - Elodie Lebas
- Francis I Proctor Foundation, University of California, San Francisco, California, United States of America
| | - Catherine E. Oldenburg
- Francis I Proctor Foundation, University of California, San Francisco, California, United States of America
- Department of Ophthalmology, University of California, San Francisco, California, United States of America
- Department of Epidemiology & Biostatistics, University of California, San Francisco, California, United States of America
| | - Kieran S. O’Brien
- Francis I Proctor Foundation, University of California, San Francisco, California, United States of America
- Department of Ophthalmology, University of California, San Francisco, California, United States of America
- Department of Epidemiology & Biostatistics, University of California, San Francisco, California, United States of America
| | - Cindi Chen
- Francis I Proctor Foundation, University of California, San Francisco, California, United States of America
| | - Lina Zhong
- Francis I Proctor Foundation, University of California, San Francisco, California, United States of America
| | - Zhaoxia Zhou
- Francis I Proctor Foundation, University of California, San Francisco, California, United States of America
| | - Daisy Yan
- Francis I Proctor Foundation, University of California, San Francisco, California, United States of America
| | - Armin Hinterwirth
- Francis I Proctor Foundation, University of California, San Francisco, California, United States of America
| | - Jeremy D. Keenan
- Francis I Proctor Foundation, University of California, San Francisco, California, United States of America
- Department of Ophthalmology, University of California, San Francisco, California, United States of America
| | - Travis C. Porco
- Francis I Proctor Foundation, University of California, San Francisco, California, United States of America
- Department of Ophthalmology, University of California, San Francisco, California, United States of America
- Department of Epidemiology & Biostatistics, University of California, San Francisco, California, United States of America
| | - Thomas M. Lietman
- Francis I Proctor Foundation, University of California, San Francisco, California, United States of America
- Department of Ophthalmology, University of California, San Francisco, California, United States of America
- Department of Epidemiology & Biostatistics, University of California, San Francisco, California, United States of America
| | - Thuy Doan
- Francis I Proctor Foundation, University of California, San Francisco, California, United States of America
- Department of Ophthalmology, University of California, San Francisco, California, United States of America
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10
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Markova J, Langova D, Babak V, Kostovova I. Ovine and Caprine Strains of Corynebacterium pseudotuberculosis on Czech Farms-A Comparative Study. Microorganisms 2024; 12:875. [PMID: 38792705 PMCID: PMC11123211 DOI: 10.3390/microorganisms12050875] [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: 04/01/2024] [Revised: 04/19/2024] [Accepted: 04/23/2024] [Indexed: 05/26/2024] Open
Abstract
Caseous lymphadenitis (CLA) is a worldwide disease of small ruminants caused by Corynebacterium pseudotuberculosis, a facultative intracellular pathogen that is able to survive and multiply in certain white blood cells of the host. In this study, 33 strains of C. pseudotuberculosis were isolated from sheep and goats suffering from CLA on nine farms in the Czech Republic. All these strains were tested for their antibiotic susceptibility, ability to form a biofilm and resistance to the effects of commonly used disinfectant agents. To better understand the virulence of C. pseudotuberculosis, the genomes of strains were sequenced and comparative genomic analysis was performed with another 123 genomes of the same species, including ovis and equi biovars, downloaded from the NCBI. The genetic determinants for the virulence factors responsible for adherence and virulence factors specialized for iron uptake and exotoxin phospholipase D were revealed in every analyzed genome. Carbohydrate-Active Enzymes were compared, revealing the presence of genetic determinants encoding exo-α-sialidase (GH33) and the CP40 protein in most of the analyzed genomes. Thirty-three Czech strains of C. pseudotuberculosis were identified as the biovar ovis on the basis of comparative genome analysis. All the compared genomes of the biovar ovis strains were highly similar regardless of their country of origin or host, reflecting their clonal behavior.
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Affiliation(s)
- Jirina Markova
- Department of Microbiology and Antimicrobial Resistance, Veterinary Research Institute, 62100 Brno, Czech Republic; (D.L.); (V.B.); (I.K.)
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11
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Kavanova K, Kostovova I, Moravkova M, Kubasova T, Babak V, Crhanova M. Comparative Genome Analysis and Characterization of the Probiotic Properties of Lactic Acid Bacteria Isolated from the Gastrointestinal Tract of Wild Boars in the Czech Republic. Probiotics Antimicrob Proteins 2024:10.1007/s12602-024-10259-7. [PMID: 38652229 DOI: 10.1007/s12602-024-10259-7] [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] [Accepted: 04/09/2024] [Indexed: 04/25/2024]
Abstract
Probiotics are crucial components for maintaining a healthy gut microbiota in pigs, especially during the weaning period. Lactic acid bacteria (LAB) derived from the gastrointestinal tract of wild boars can serve as an abundant source of beneficial probiotic strains with suitable properties for use in pig husbandry. In this study, we analyzed and characterized 15 strains of Limosilactobacillus mucosae obtained from the gut contents of wild boars to assess their safety and suitability as probiotic candidates. The strains were compared using pan-genomic analysis with 49 L. mucosae strains obtained from the NCBI database. All isolated strains demonstrated their safety by showing an absence of transferrable antimicrobial resistance genes and hemolysin activity. Based on the presence of beneficial genes, five candidates with probiotic properties were selected and subjected to phenotypic profiling. These five selected isolates exhibited the ability to survive conditions mimicking passage through the host's digestive tract, such as low pH and the presence of bile salts. Furthermore, five selected strains demonstrated the presence of corresponding carbohydrate-active enzymes and the ability to utilize various carbohydrate substrates. These strains can enhance the digestibility of oligosaccharide or polysaccharide substrates found in food or feed, specifically resistant starch, α-galactosides, cellobiose, gentiobiose, and arabinoxylans. Based on the results obtained, the L. mucosae isolates tested in this study appear to be promising candidates for use as probiotics in pigs.
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Affiliation(s)
- Katerina Kavanova
- Department of Microbiology and Antimicrobial Resistance, Veterinary Research Institute, Hudcova 296/70, 621 00, Brno, Czech Republic.
- Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 753/5, 625 00, Brno, Czech Republic.
| | - Iveta Kostovova
- Department of Microbiology and Antimicrobial Resistance, Veterinary Research Institute, Hudcova 296/70, 621 00, Brno, Czech Republic
| | - Monika Moravkova
- Department of Microbiology and Antimicrobial Resistance, Veterinary Research Institute, Hudcova 296/70, 621 00, Brno, Czech Republic
| | - Tereza Kubasova
- Department of Microbiology and Antimicrobial Resistance, Veterinary Research Institute, Hudcova 296/70, 621 00, Brno, Czech Republic
| | - Vladimir Babak
- Department of Microbiology and Antimicrobial Resistance, Veterinary Research Institute, Hudcova 296/70, 621 00, Brno, Czech Republic
| | - Magdalena Crhanova
- Department of Microbiology and Antimicrobial Resistance, Veterinary Research Institute, Hudcova 296/70, 621 00, Brno, Czech Republic
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12
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Rao RSP, Ghate SD, Pinto L, Suravajhala P, Patil P, Shetty P, Ahsan N. Extent of Virulence and Antibiotic Resistance Genes in Helicobacter pylori and Campylobacteria. Curr Microbiol 2024; 81:154. [PMID: 38652129 DOI: 10.1007/s00284-024-03653-5] [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: 12/11/2023] [Accepted: 02/26/2024] [Indexed: 04/25/2024]
Abstract
Helicobacter pylori, a member of the clade campylobacteria, is the leading cause of chronic gastritis and gastric cancer. Virulence and antibiotic resistance of H. pylori are of great concern to public health. However, the relationship between virulence and antibiotic resistance genes in H. pylori in relation to other campylobacteria remains unclear. Using the virulence and comprehensive antibiotic resistance databases, we explored all available 354 complete genomes of H. pylori and compared it with 90 species of campylobacteria for virulence and antibiotic resistance genes/proteins. On average, H. pylori had 129 virulence genes, highest among Helicobacter spp. and 71 antibiotic resistance genes, one of the lowest among campylobacteria. Just 2.6% of virulence genes were shared by all campylobacterial members, whereas 9.4% were unique to H. pylori. The cytotoxin-associated genes (cags) seemed to be exclusive to H. pylori. Majority of the isolates from Asia and South America were cag2-negative and many antibiotic resistance genes showed isolate-specific patterns of occurrence. Just 15 (8.8%) antibiotic resistance genes, but 103 (66%) virulence genes including 25 cags were proteomically identified in H. pylori. Arcobacterial members showed large variation in the number of antibiotic resistance genes and there was a positive relation with the genome size. Large repository of antibiotic resistance genes in campylobacteria and a unique set of virulence genes might have important implications in shaping the course of virulence and antibiotic resistance in H. pylori.
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Affiliation(s)
- R Shyama Prasad Rao
- Center for Bioinformatics, NITTE Deemed to be University, Mangaluru, 575018, India.
| | - Sudeep D Ghate
- Center for Bioinformatics, NITTE Deemed to be University, Mangaluru, 575018, India.
| | - Larina Pinto
- Center for Bioinformatics, NITTE Deemed to be University, Mangaluru, 575018, India
- School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Prashanth Suravajhala
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Clappana, Kerala, 690525, India
| | - Prakash Patil
- Central Research Laboratory, KS Hegde Medical Academy (KSHEMA), NITTE Deemed to be University, Mangaluru, 575018, India
| | - Praveenkumar Shetty
- Central Research Laboratory, KS Hegde Medical Academy (KSHEMA), NITTE Deemed to be University, Mangaluru, 575018, India
- Department of Biochemistry, KS Hegde Medical Academy (KSHEMA), NITTE Deemed to be University, Mangaluru, 575018, India
| | - Nagib Ahsan
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, USA
- Mass Spectrometry, Proteomics and Metabolomics Core Facility, Stephenson Life Sciences Research Center, The University of Oklahoma, Norman, OK, USA
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13
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Parzygnat JL, Crespo R, Fosnaught M, Muyyarrikkandy M, Hull D, Harden L, Thakur S. Megaplasmid Dissemination in Multidrug-Resistant Salmonella Serotypes from Backyard and Commercial Broiler Production Systems in the Southeastern United States. Foodborne Pathog Dis 2024. [PMID: 38635963 DOI: 10.1089/fpd.2023.0181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2024] Open
Abstract
Over the past decade, there has been a rise in U.S. backyard poultry ownership, raising concern for residential area antimicrobial-resistant (AMR) Salmonella contamination. This study aims to lay the groundwork to better understand the persistence of AMR Salmonella in residential broiler production systems and make comparisons with commercial systems. Ten backyard and 10 commercial farms were sampled at three time points across bird production. Both fecal (n = 10) and environmental (soil, n = 5, litter/compost, n = 5, feeder, and waterer swabs, n = 6) samples were collected at each visit on days 10, 31, and 52 of production for backyard farms and days 10, 24, and 38 of production for commercial farms. AMR Salmonella was characterized phenotypically by broth microdilution and genotypically by whole-genome sequencing. Overall, Salmonella was more prevalent in commercial farm samples (52.31%) over backyard farms (19.10%). Kentucky (sequence type (ST) 152) was the most common serotype found in both backyard and commercial farms. Multidrug-resistant (MDR, resistance to ≥3 or more antimicrobial classes) isolates were found in both production systems, while ciprofloxacin- and nalidixic acid-resistant and intermediate isolates were more prevalent in commercial (33%) than backyard samples (1%). Plasmids that have been associated with MDR were found in Kentucky and Infantis isolates, particularly IncFIB(K)_1_Kpn3 megaplasmid (Infantis). Our study emphasizes the need to understand the selection pressures in disseminating megaplasmids in MDR Salmonella in distinct broiler production systems.
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Affiliation(s)
- Jessica L Parzygnat
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, USA
| | - Rocio Crespo
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, USA
| | - Mary Fosnaught
- Prestage Department of Poultry Science, North Carolina State University, Raleigh, North Carolina, USA
| | - Muhammed Muyyarrikkandy
- Department of Veterinary and Biomedical Sciences, South Dakota State University, Brooking, South Dakota, USA
| | - Dawn Hull
- Bacterial Diseases Branch, Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Lyndy Harden
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, USA
| | - Siddhartha Thakur
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, USA
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14
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Ramnarine SDBJ, Jayaraman J, Ramsubhag A. Crucifer Lesion-Associated Xanthomonas Strains Show Multi-Resistance to Heavy Metals and Antibiotics. Curr Microbiol 2024; 81:136. [PMID: 38598029 DOI: 10.1007/s00284-024-03646-4] [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: 11/20/2023] [Accepted: 02/20/2024] [Indexed: 04/11/2024]
Abstract
Copper resistance in phytopathogens is a major challenge to crop production globally and is known to be driven by excessive use of copper-based pesticides. However, recent studies have shown co-selection of multiple heavy metal and antibiotic resistance genes in bacteria exposed to heavy metal and xenobiotics, which may impact the epidemiology of plant, animal, and human diseases. In this study, multi-resistance to heavy metals and antibiotics were evaluated in local Xanthomonas campestris pv. campestris (Xcc) and co-isolated Xanthomonas melonis (Xmel) strains from infected crucifer plants in Trinidad. Resistance to cobalt, cadmium, zinc, copper, and arsenic (V) was observed in both Xanthomonas species up to 25 mM. Heavy metal resistance (HMR) genes were found on a small plasmid-derived locus with ~ 90% similarity to a Stenotrophomonas spp. chromosomal locus and a X. perforans pLH3.1 plasmid. The co-occurrence of mobile elements in these regions implies their organization on a composite transposon-like structure. HMR genes in Xcc strains showed the lowest similarity to references, and the cus and ars operons appear to be unique among Xanthomonads. Overall, the similarity of HMR genes to Stenotrophomonas sp. chromosomal genomes suggest their origin in this genus or a related organism and subsequent spread through lateral gene transfer events. Further resistome characterization revealed the presence of small multidrug resistance (SMR), multidrug resistance (MDR) efflux pumps, and bla (Xcc) genes for broad biocide resistance in both species. Concurrently, resistance to antibiotics (streptomycin, kanamycin, tetracycline, chloramphenicol, and ampicillin) up to 1000 µg/mL was confirmed.
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Affiliation(s)
- Stephen D B Jr Ramnarine
- Department of Life Sciences, Faculty of Science and Technology, The University of The West Indies, St. Augustine, Trinidad and Tobago
| | - Jayaraj Jayaraman
- Department of Life Sciences, Faculty of Science and Technology, The University of The West Indies, St. Augustine, Trinidad and Tobago
| | - Adesh Ramsubhag
- Department of Life Sciences, Faculty of Science and Technology, The University of The West Indies, St. Augustine, Trinidad and Tobago.
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15
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Pell ME, Blankenship HM, Gaddy JA, Davies HD, Manning SD. Intrapartum antibiotic prophylaxis selects for mutators in group B streptococci among persistently colonized patients. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.01.587590. [PMID: 38617326 PMCID: PMC11014637 DOI: 10.1101/2024.04.01.587590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Through vaginal colonization, GBS causes severe pregnancy outcomes including neonatal sepsis and meningitis. Although intrapartum antibiotic prophylaxis (IAP) has reduced early-onset disease rates, persistent GBS colonization has been observed in patients following prophylaxis. To determine whether IAP selects for genomic signatures that enhance GBS survival and persistence in the vaginal tract, whole-genome sequencing was performed on 97 isolates from 58 patients before (prenatal) and after (postpartum) IAP/childbirth. Core-gene mutation analysis identified 7,025 mutations between the paired isolates. Three postpartum isolates accounted for 98% of mutations and were classified as "mutators" because of point mutations within DNA repair systems. In vitro assays revealed stronger biofilms in two mutators. These findings suggest that antibiotics select for mutations that promote survival in vivo, which increases the likelihood of transmission to neonates. They also demonstrate how mutators can provide a reservoir of beneficial mutations that enhance fitness and genetic diversity in the GBS population.
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Affiliation(s)
- Macy E Pell
- Michigan State University, Department of Microbiology, Genetics, and Immunology (MGI), E. Lansing, MI
| | - Heather M Blankenship
- Michigan Department of Health and Human Services, Bureau of Laboratories, Division of Infectious Diseases, Lansing, MI
| | - Jennifer A Gaddy
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN
- Tennessee Valley Healthcare Systems, Department of Veterans Affairs, Nashville, TN
| | | | - Shannon D Manning
- Michigan State University, Department of Microbiology, Genetics, and Immunology (MGI), E. Lansing, MI
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16
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Liu J, Hao D, Ding X, Shi M, Wang Q, He H, Cheng B, Wang M, Wang Q, Xiang Y, Chen L. Epidemiological investigation and β-lactam antibiotic resistance of Riemerella anatipestifer isolates with waterfowl origination in Anhui Province, China. Poult Sci 2024; 103:103490. [PMID: 38387287 PMCID: PMC10899037 DOI: 10.1016/j.psj.2024.103490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 01/16/2024] [Accepted: 01/19/2024] [Indexed: 02/24/2024] Open
Abstract
Riemerella anatipestifer (R. anatipestifer) is a highly pathogenic and complex serotypes waterfowl pathogen with inherent resistance to multiple antibiotics. This study was aimed to investigate the antibiotic resistance characteristics and genomic features of R. anatipestifer isolates in Anhui Province, China in 2023. A total of 287 cases were analysed from duck farms and goose farms, and the R. anatipestifer isolates were subjected to drug resistance tests for 30 antimicrobials. Whole genome sequencing (WGS) and bioinformatics analysis were performed on the bacterial genomes, targeting the β-lactam resistance genes. The results showed that a total of 74 isolates of R. anatipestifer were isolated from 287 cases, with a prevalence of 25.8%. The antimicrobial susceptibility testing (AST) revealed that all the 74 isolates were resistant to multiple drugs, ranging from 13 to 26 kinds of drugs. Notably, these isolates showed significant resistance to aminoglycosides and macrolides, which are also commonly used in clinical practices. Data revealed the presence of several β-lactamase-related genes among the isolates, including a novel blaRASA-1 variant (16.2%), the class A extended-spectrum β-lactamase blaRAA-1 (12.2%), and a blaOXA-209 variant (98.6%). Functional analysis of the variants blaRASA-1 and blaOXA-209 showed that the blaRASA-1 variant exhibited activity against various β-lactam antibiotics while their occurrence in R. anatipestifer were not common. The blaOXA-209 variant, on the other hand, did not perform any β-lactam antibiotic resistance. Furthermore, we observed that blaRAA-1 could undergo horizontal transmission among different bacteria via the insertion sequence IS982. In conclusion, this study delves into the high prevalence of R. anatipestifer infection in waterfowl in Anhui, China. The isolated strains exhibit severe drug resistance issues, closely associated with the prevalence of antibiotic resistance genes (ARG). Additionally, our research investigates the β-lactam antibiotic resistance mechanism in R. anatipestifer.
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Affiliation(s)
- Junfeng Liu
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou City 450000, Henan Province, China; Ministry of Education Key Laboratory for Animal Pathogens and Biosafety, Zhengzhou City 450000, China; Anhui Qiangying Food Group, Suzhou City 234000, Anhui Province, China
| | - Dongmin Hao
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou City 450000, Henan Province, China; Henan Key Laboratory of Animal Food Safety Zhengzhou City 450000, Henan Province, China; Anhui Qiangying Food Group, Suzhou City 234000, Anhui Province, China
| | - Xueyan Ding
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou City 450000, Henan Province, China; Ministry of Education Key Laboratory for Animal Pathogens and Biosafety, Zhengzhou City 450000, China
| | - Mingzhen Shi
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou City 450000, Henan Province, China; Ministry of Education Key Laboratory for Animal Pathogens and Biosafety, Zhengzhou City 450000, China
| | - Qiaojun Wang
- College of Veterinary Medicine, Yangzhou University, Yangzhou City 225000, Jiangsu Province, China
| | - Hengxu He
- College of Veterinary Medicine, Yangzhou University, Yangzhou City 225000, Jiangsu Province, China
| | - Binghua Cheng
- Anhui Qiangying Food Group, Suzhou City 234000, Anhui Province, China
| | - Mengping Wang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou City 450000, Henan Province, China
| | - Qingxiu Wang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou City 450000, Henan Province, China
| | - Yuqiang Xiang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou City 450000, Henan Province, China; Ministry of Education Key Laboratory for Animal Pathogens and Biosafety, Zhengzhou City 450000, China
| | - Liying Chen
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou City 450000, Henan Province, China; Ministry of Education Key Laboratory for Animal Pathogens and Biosafety, Zhengzhou City 450000, China; Henan Key Laboratory of Animal Food Safety Zhengzhou City 450000, Henan Province, China.
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17
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Dillon L, Dimonaco NJ, Creevey CJ. Accessory genes define species-specific routes to antibiotic resistance. Life Sci Alliance 2024; 7:e202302420. [PMID: 38228374 DOI: 10.26508/lsa.202302420] [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: 10/06/2023] [Revised: 12/29/2023] [Accepted: 01/03/2024] [Indexed: 01/18/2024] Open
Abstract
A deeper understanding of the relationship between the antimicrobial resistance (AMR) gene carriage and phenotype is necessary to develop effective response strategies against this global burden. AMR phenotype is often a result of multi-gene interactions; therefore, we need approaches that go beyond current simple AMR gene identification tools. Machine-learning (ML) methods may meet this challenge and allow the development of rapid computational approaches for AMR phenotype classification. To examine this, we applied multiple ML techniques to 16,950 bacterial genomes across 28 genera, with corresponding MICs for 23 antibiotics with the aim of training models to accurately determine the AMR phenotype from sequenced genomes. This resulted in a >1.5-fold increase in AMR phenotype prediction accuracy over AMR gene identification alone. Furthermore, we revealed 528 unique (often species-specific) genomic routes to antibiotic resistance, including genes not previously linked to the AMR phenotype. Our study demonstrates the utility of ML in predicting AMR phenotypes across diverse clinically relevant organisms and antibiotics. This research proposes a rapid computational method to support laboratory-based identification of the AMR phenotype in pathogens.
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Affiliation(s)
- Lucy Dillon
- School of Biological Sciences, Queen's University Belfast, Belfast, UK
| | - Nicholas J Dimonaco
- School of Biological Sciences, Queen's University Belfast, Belfast, UK
- https://ror.org/02fa3aq29 Department of Medicine, McMaster University, Hamilton, Ontario, Canada
- https://ror.org/02fa3aq29 Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, Canada
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Chakrawarti A, Eckstrom K, Laaguiby P, Barlow JW. Hybrid Illumina-Nanopore assembly improves identification of multilocus sequence types and antimicrobial resistance genes of Staphylococcus aureus isolated from Vermont dairy farms: comparison to Illumina-only and R9.4.1 nanopore-only assemblies. Access Microbiol 2024; 6:000766.v3. [PMID: 38725589 PMCID: PMC11077346 DOI: 10.1099/acmi.0.000766.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: 01/10/2024] [Accepted: 02/23/2024] [Indexed: 05/12/2024] Open
Abstract
Antimicrobial resistance (AMR) in Staphylococcus aureus is a pressing public health challenge with significant implications for the dairy industry, encompassing bovine mastitis concerns and potential zoonotic threats. To delve deeper into the resistance mechanisms of S. aureus, this study employed a hybrid whole genome assembly approach that synergized the precision of Illumina with the continuity of Oxford Nanopore. A total of 62 isolates, collected from multiple sources from Vermont dairy farms, were sequenced using the GridION Oxford Nanopore R9.4.1 platform and the Illumina platform, and subsequently processed through our long-read first bioinformatics pipeline. Our analyses showcased the hybrid-assembled genome's superior completeness compared to Oxford Nanopore (R9.4.1)-only or Illumina-only assembled genomes. Furthermore, the hybrid assembly accurately determined multilocus sequence typing (MLST) strain types across all isolates. The comprehensive probe for antibiotic resistance genes (ARGs) using databases like CARD, Resfinder, and MEGARES 2.0 characterized AMR in S. aureus isolates from Vermont dairy farms, and revealed the presence of notable resistance genes, including beta-lactam genes blaZ, blaI, and blaR. In conclusion, the hybrid assembly approach emerged as a tool for uncovering the genomic nuances of S. aureus isolates collected from multiple sources on dairy farms. Our findings offer a pathway for detecting AMR gene prevalence and shaping AMR management strategies crucial for safeguarding human and animal health.
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Affiliation(s)
- Ashma Chakrawarti
- Department of Animal and Veterinary Sciences, University of Vermont, Burlington, VT, USA
| | - Korin Eckstrom
- Department of Microbiology and Molecular Genetics, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington, VT, USA
| | - Pheobe Laaguiby
- Advanced Genome Technologies Core, Vermont Integrative Genomics Resource, The Robert Larner, M.D. College of Medicine, University of Vermont, Burlington, VT, USA
| | - John W. Barlow
- Department of Animal and Veterinary Sciences, University of Vermont, Burlington, VT, USA
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19
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Hossain MA, Al Amin M, Khan MA, Refat MRR, Sohel M, Rahman MH, Islam A, Hoque MN. Genome-Wide Investigation Reveals Potential Therapeutic Targets in Shigella spp. BIOMED RESEARCH INTERNATIONAL 2024; 2024:5554208. [PMID: 38595330 PMCID: PMC11003385 DOI: 10.1155/2024/5554208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Revised: 02/21/2024] [Accepted: 03/01/2024] [Indexed: 04/11/2024]
Abstract
Shigella stands as a major contributor to bacterial dysentery worldwide scale, particularly in developing countries with inadequate sanitation and hygiene. The emergence of multidrug-resistant strains exacerbates the challenge of treating Shigella infections, particularly in regions where access to healthcare and alternative antibiotics is limited. Therefore, investigations on how bacteria evade antibiotics and eventually develop resistance could open new avenues for research to develop novel therapeutics. The aim of this study was to analyze whole genome sequence (WGS) of human pathogenic Shigella spp. to elucidate the antibiotic resistance genes (ARGs) and their mechanism of resistance, gene-drug interactions, protein-protein interactions, and functional pathways to screen potential therapeutic candidate(s). We comprehensively analyzed 45 WGS of Shigella, including S. flexneri (n = 17), S. dysenteriae (n = 14), S. boydii (n = 11), and S. sonnei (n = 13), through different bioinformatics tools. Evolutionary phylogenetic analysis showed three distinct clades among the circulating strains of Shigella worldwide, with less genomic diversity. In this study, 2,146 ARGs were predicted in 45 genomes (average 47.69 ARGs/genome), of which only 91 ARGs were found to be shared across the genomes. Majority of these ARGs conferred their resistance through antibiotic efflux pump (51.0%) followed by antibiotic target alteration (23%) and antibiotic target replacement (18%). We identified 13 hub proteins, of which four proteins (e.g., tolC, acrR, mdtA, and gyrA) were detected as potential hub proteins to be associated with antibiotic efflux pump and target alteration mechanisms. These hub proteins were significantly (p < 0.05) enriched in biological process, molecular function, and cellular components. Therefore, the finding of this study suggests that human pathogenic Shigella strains harbored a wide range of ARGs that confer resistance through antibiotic efflux pumps and antibiotic target modification mechanisms, which must be taken into account to devise and formulate treatment strategy against this pathogen. Moreover, the identified hub proteins could be exploited to design and develop novel therapeutics against MDR pathogens like Shigella.
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Affiliation(s)
- Md. Arju Hossain
- Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Tangail 1902, Bangladesh
- Department of Microbiology, Primeasia University, Dhaka 1213, Bangladesh
| | - Md. Al Amin
- Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Tangail 1902, Bangladesh
| | - Md. Arif Khan
- Institute of Epidemiology, Disease Control and Research (IEDCR), Dhaka 1212, Bangladesh
- EcoHealth Alliance, New York, NY 10018, USA
| | - Md. Rashedur Rahman Refat
- Department of Information and Communication Technology, Mawlana Bhashani Science and Technology University, Tangail 1902, Bangladesh
| | - Md Sohel
- Department of Biochemistry and Molecular Biology, Primeasia University, Banani, Dhaka 1213, Bangladesh
- Department of Biochemistry and Molecular Biology, Mawlana Bhashani Science and Technology University, Santosh, Tangail 1902, Bangladesh
| | - Md Habibur Rahman
- Department of Computer Science and Engineering, Islamic University, Kushtia 7003, Bangladesh
- Center for Advanced Bioinformatics and Artificial Intelligence Research, Islamic University, Kushtia 7003, Bangladesh
| | - Ariful Islam
- Institute of Epidemiology, Disease Control and Research (IEDCR), Dhaka 1212, Bangladesh
- EcoHealth Alliance, New York, NY 10018, USA
| | - M. Nazmul Hoque
- Department of Gynecology, Obstetrics and Reproductive Health, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur 1706, Bangladesh
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20
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Hoque MN, Faisal GM, Jerin S, Moyna Z, Islam MA, Talukder AK, Alam MS, Das ZC, Isalm T, Hossain MA, Rahman ANMA. Unveiling distinct genetic features in multidrug-resistant Escherichia coli isolated from mammary tissue and gut of mastitis induced mice. Heliyon 2024; 10:e26723. [PMID: 38434354 PMCID: PMC10904246 DOI: 10.1016/j.heliyon.2024.e26723] [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: 10/26/2023] [Revised: 02/08/2024] [Accepted: 02/19/2024] [Indexed: 03/05/2024] Open
Abstract
Escherichia coli is one of the major pathogens causing mastitis in lactating mammals. We hypothesized that E. coli from the gut and mammary glands may have similar genomic characteristics in the causation of mastitis. To test this hypothesis, we used whole genome sequencing to analyze two multidrug resistant E. coli strains isolated from mammary tissue (G2M6U) and fecal sample (G6M1F) of experimentally induced mastitis mice. Both strains showed resistance to multiple (>7) antibiotics such as oxacillin, aztreonam, nalidixic acid, streptomycin, gentamicin, cefoxitin, ampicillin, tetracycline, azithromycin and nitrofurantoin. The genome of E. coli G2M6U had 59 antimicrobial resistance genes (ARGs) and 159 virulence factor genes (VFGs), while the E. coli G6M1F genome possessed 77 ARGs and 178 VFGs. Both strains were found to be genetically related to many E. coli strains causing mastitis and enteric diseases originating from different hosts and regions. The G6M1F had several unique ARGs (e.g., QnrS1, sul2, tetA, tetR, emrK, blaTEM-1/105, and aph(6)-Id, aph(3″)-Ib) conferring resistance to certain antibiotics, whereas G2M6U had a unique heat-stable enterotoxin gene (astA) and 7192 single nucleotide polymorphisms. Furthermore, there were 43 and 111 unique genes identified in G2M6U and G6M1F genomes, respectively. These results indicate distinct differences in the genomic characteristics of E. coli strain G2M6U and G6M1F that might have important implications in the pathophysiology of mammalian mastitis, and treatment strategies for mastitis in dairy animals.
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Affiliation(s)
- M. Nazmul Hoque
- Molecular Biology and Bioinformatics Laboratory, Department of Gynecology, Obstetrics and Reproductive Health, Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur, 1706, Bangladesh
| | - Golam Mahbub Faisal
- Molecular Biology and Bioinformatics Laboratory, Department of Gynecology, Obstetrics and Reproductive Health, Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur, 1706, Bangladesh
| | - Shobnom Jerin
- Molecular Biology and Bioinformatics Laboratory, Department of Gynecology, Obstetrics and Reproductive Health, Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur, 1706, Bangladesh
| | - Zannatara Moyna
- Molecular Biology and Bioinformatics Laboratory, Department of Gynecology, Obstetrics and Reproductive Health, Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur, 1706, Bangladesh
| | - Md Aminul Islam
- Advanced Molecular Lab, Department of Microbiology, President Abdul Hamid Medical College, Karimganj, 2310, Bangladesh
| | - Anup Kumar Talukder
- Molecular Biology and Bioinformatics Laboratory, Department of Gynecology, Obstetrics and Reproductive Health, Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur, 1706, Bangladesh
| | | | - Ziban Chandra Das
- Molecular Biology and Bioinformatics Laboratory, Department of Gynecology, Obstetrics and Reproductive Health, Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur, 1706, Bangladesh
| | - Tofazzal Isalm
- Institute of Biotechnology and Genetic Engineering (IBGE), BSMRAU, Gazipur, 1706, Bangladesh
| | - M. Anwar Hossain
- Jashore University of Science and Technology, Jashore, 7408, Bangladesh
| | - Abu Nasar Md Aminoor Rahman
- Molecular Biology and Bioinformatics Laboratory, Department of Gynecology, Obstetrics and Reproductive Health, Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur, 1706, Bangladesh
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21
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Baev V, Iliev I, Stefanov Y, Tsankova M, Marhova M, Apostolova E, Gozmanova M, Yahubyan G, Kostadinova S. Exploring the Genomic Landscape of Bacillus paranthracis PUMB_17 as a Proficient Phosphatidylcholine-Specific Phospholipase C Producer. Curr Issues Mol Biol 2024; 46:2497-2513. [PMID: 38534774 DOI: 10.3390/cimb46030158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 03/08/2024] [Accepted: 03/12/2024] [Indexed: 03/28/2024] Open
Abstract
Phospholipases find versatile applications across industries, including detergent production, food modification, pharmaceuticals (especially in drug delivery systems), and cell signaling research. In this study, we present a strain of Bacillus paranthracis for the first time, demonstrating significant potential in the production of phosphatidylcholine-specific phospholipase C (PC-PLC). The investigation thoroughly examines the B. paranthracis PUMB_17 strain, focusing on the activity of PC-PLC and its purification process. Notably, the PUMB_17 strain displays extracellular PC-PLC production with high specific activity during the late exponential growth phase. To unravel the genetic makeup of PUMB_17, we employed nanopore-based whole-genome sequencing and subsequently conducted a detailed genome annotation. The genome comprises a solitary circular chromosome spanning 5,250,970 bp, featuring a guanine-cytosine ratio of 35.49. Additionally, two plasmids of sizes 64,250 bp and 5845 bp were identified. The annotation analysis reveals the presence of 5328 genes, encompassing 5186 protein-coding sequences, and 142 RNA genes, including 39 rRNAs, 103 tRNAs, and 5 ncRNAs. The aim of this study was to make a comprehensive genomic exploration that promises to enhance our understanding of the previously understudied and recently documented capabilities of Bacillus paranthracis and to shed light on a potential use of the strain in the industrial production of PC-PLC.
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Affiliation(s)
- Vesselin Baev
- Department of Molecular Biology, Faculty of Biology, University of Plovdiv, Tzar Assen 24, 4000 Plovdiv, Bulgaria
| | - Ivan Iliev
- Department of Biochemistry and Microbiology, Faculty of Biology, University of Plovdiv, Tzar Assen 24, 4000 Plovdiv, Bulgaria
| | | | - Marinela Tsankova
- Department of Biochemistry and Microbiology, Faculty of Biology, University of Plovdiv, Tzar Assen 24, 4000 Plovdiv, Bulgaria
| | - Mariana Marhova
- Department of Biochemistry and Microbiology, Faculty of Biology, University of Plovdiv, Tzar Assen 24, 4000 Plovdiv, Bulgaria
| | - Elena Apostolova
- Department of Molecular Biology, Faculty of Biology, University of Plovdiv, Tzar Assen 24, 4000 Plovdiv, Bulgaria
| | - Mariyana Gozmanova
- Department of Molecular Biology, Faculty of Biology, University of Plovdiv, Tzar Assen 24, 4000 Plovdiv, Bulgaria
| | - Galina Yahubyan
- Department of Molecular Biology, Faculty of Biology, University of Plovdiv, Tzar Assen 24, 4000 Plovdiv, Bulgaria
| | - Sonya Kostadinova
- Department of Biochemistry and Microbiology, Faculty of Biology, University of Plovdiv, Tzar Assen 24, 4000 Plovdiv, Bulgaria
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22
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Hoque MN, Faisal GM, Das ZC, Sakif TI, Al Mahtab M, Hossain MA, Islam T. Genomic features and pathophysiological impact of a multidrug-resistant Staphylococcus warneri variant in murine mastitis. Microbes Infect 2024; 26:105285. [PMID: 38154518 DOI: 10.1016/j.micinf.2023.105285] [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: 11/04/2023] [Revised: 12/05/2023] [Accepted: 12/22/2023] [Indexed: 12/30/2023]
Abstract
Non-aureus staphylococci (NAS) represent a major etiological agent in dairy animal mastitis, yet their role and impact remain insufficiently studied. This study aimed to elucidate the genomic characteristics of a newly identified multidrug-resistant NAS strain, specifically Staphylococcus warneri G1M1F, isolated from murine feces in an experimental mastitis model. Surprisingly, NAS species accounted for 54.35 % of murine mastitis cases, with S. warneri being the most prevalent at 40.0 %. S. warneri G1M1F exhibited resistance to 10 major antibiotics. Whole-genome sequencing established a genetic connection between G1M1F and S. warneri strains isolated previously from various sources including mastitis milk in dairy animals, human feces and blood across diverse geographical regions. Genomic analysis of S. warneri G1M1F unveiled 34 antimicrobial resistance genes (ARGs), 30 virulence factor genes (VFGs), and 278 metabolic features. A significant portion of identified ARGs (64 %) conferred resistance through antibiotic efflux pumps, while VFGs primarily related to bacterial adherence and biofilm formation. Inoculation with G1M1F in mice resulted in pronounced inflammatory lesions in mammary and colon tissues, indicating pathogenic potential. Our findings highlight distinctive genomic traits in S. warneri G1M1F, signifying the emergence of a novel multidrug-resistant NAS variant. These insights contribute to understanding NAS-related mastitis pathophysiology and inform strategies for effective treatment in dairy animals.
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Affiliation(s)
- M Nazmul Hoque
- Molecular Biology and Bioinformatics Laboratory, Department of Gynecology, Obstetrics and Reproductive Health, Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur 1706, Bangladesh.
| | - Golam Mahbub Faisal
- Molecular Biology and Bioinformatics Laboratory, Department of Gynecology, Obstetrics and Reproductive Health, Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur 1706, Bangladesh
| | - Ziban Chandra Das
- Molecular Biology and Bioinformatics Laboratory, Department of Gynecology, Obstetrics and Reproductive Health, Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur 1706, Bangladesh
| | | | - Mamun Al Mahtab
- Interventional Hepatology Division, Bangabandhu Sheikh Mujib Medical University, Dhaka 1000, Bangladesh
| | - M Anwar Hossain
- Jashore University of Science and Technology, Jashore 7408, Bangladesh
| | - Tofazzal Islam
- Institute of Biotechnology and Genetic Engineering (IBGE), BSMRAU, Gazipur 1706, Bangladesh
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23
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Vanbaelen T, Laumen J, Van Dijck C, De Block T, Manoharan-Basil SS, Kenyon C. Lack of Association between Antimicrobial Consumption and Antimicrobial Resistance in a HIV Preexposure Prophylaxis Population: A Cross-Sectional Study. Antibiotics (Basel) 2024; 13:188. [PMID: 38391574 PMCID: PMC10886153 DOI: 10.3390/antibiotics13020188] [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: 01/10/2024] [Revised: 02/01/2024] [Accepted: 02/13/2024] [Indexed: 02/24/2024] Open
Abstract
BACKGROUND In antibiotic naïve populations, there is a strong association between the use of an antimicrobial and resistance to this antimicrobial. Less evidence is available as to whether this relationship is weakened in populations highly exposed to antimicrobials. Individuals taking HIV preexposure prophylaxis (PrEP) have a high intake of antimicrobials. We previously found that there was no difference in the prevalence of pheno- and genotypic antimicrobial resistance between two groups of PrEP clients who had, and had not, taken antimicrobials in the prior 6 months. Both groups did, however, have a higher prevalence of resistance than a sample of the general population. METHODS In the current study, we used zero-inflated negative binomial regression models to evaluate if there was an individual level association between the consumption of antimicrobials and 1. the minimum inhibitory susceptibilities of oral Neisseria subflava and 2. the abundance of antimicrobial resistance genes in the oropharynges of these individuals. RESULTS We found no evidence of an association between the consumption of antimicrobials and the minimum inhibitory susceptibilities of oral Neisseria subflava or the abundance of antimicrobial resistance genes in these individuals. CONCLUSIONS We conclude that in high-antimicrobial-consumption populations, the association between antimicrobial consumption and resistance may be attenuated. This conclusion would not apply to lower-consumption populations.
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Affiliation(s)
- Thibaut Vanbaelen
- STI Unit, Department of Clinical Sciences, Institute of Tropical Medicine, 2000 Antwerp, Belgium
| | - Jolein Laumen
- STI Unit, Department of Clinical Sciences, Institute of Tropical Medicine, 2000 Antwerp, Belgium
| | - Christophe Van Dijck
- STI Unit, Department of Clinical Sciences, Institute of Tropical Medicine, 2000 Antwerp, Belgium
| | - Tessa De Block
- Clinical Reference Laboratory, Department of Clinical Sciences, Institute of Tropical Medicine, 2000 Antwerp, Belgium
| | | | - Chris Kenyon
- STI Unit, Department of Clinical Sciences, Institute of Tropical Medicine, 2000 Antwerp, Belgium
- Division of Infectious Diseases and HIV Medicine, University of Cape Town, Cape Town 7700, South Africa
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24
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Ferraris L, Delannoy J, Mazuet C, Diancourt L, Mesa-Schein V, Barbut F, Aires J. Clostridium neonatale antimicrobial susceptibility, genetic resistance determinants, and genotyping: a multicentre spatiotemporal retrospective analysis. J Antimicrob Chemother 2024; 79:271-279. [PMID: 38084883 PMCID: PMC10832599 DOI: 10.1093/jac/dkad369] [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: 07/04/2023] [Accepted: 11/21/2023] [Indexed: 02/02/2024] Open
Abstract
BACKGROUND Clostridium neonatale was isolated during an outbreak of neonatal necrotizing enterocolitis (NEC) in 2002. C. neonatale was validated as a new species within the genus Clostridium sensu stricto in 2018. In the present study, we evaluated the antimicrobial susceptibility, genetic determinants of resistance, and phylogenetic relationships of a collection of clinical isolates of C. neonatale. METHODS C. neonatale strains (n = 68) were isolated from the stools of preterm neonates who either developed NEC or were asymptomatic carriers of C. neonatale in different periods and in different hospitals. Antimicrobial susceptibility was determined by the disc diffusion method. The MICs of clindamycin, cefotaxime and tetracycline were determined. Genetic determinants of resistance were screened by PCR (n = 68) and WGS (n = 35). Genotyping of the isolates was performed by MLST. RESULTS Antimicrobial resistance was found to clindamycin (n = 24; 35%), cefotaxime (n = 7; 10%) and tetracycline (n = 1; 1%). One clindamycin-resistant isolate carried erm(B) by PCR. In addition, one isolate carrying tet(M) was tetracycline resistant (MIC = 16 mg/L) and 44 isolates carrying either tet(O), tet(32) or tet(M) were tetracycline susceptible (MICs < 16 mg/L). MLST showed that ST2 and ST15 were significantly associated with tet(32) (P < 0.0001) and tet(O) (P < 0.0001), respectively. From WGS, we identified aph(3')-IIa and blaTEM-116 genes and a blaCBP-1-like gene. CONCLUSIONS C. neonatale is susceptible to anti-anaerobic molecules but resistant to clindamycin, cefotaxime and tetracycline. Genes encoding tetracycline ribosomal protection, macrolide-lincosamide-streptogramin B rRNA methyltransferase, aminoglycoside 3'-phosphotransferase and β-lactamases have been identified in genomic regions flanked by mobile genetic elements.
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Affiliation(s)
- Laurent Ferraris
- Faculté de Pharmacie de Paris, Université Paris Cité, INSERM, UMR-S 1139 (3PHM), Paris F-75006, France
| | - Johanne Delannoy
- Faculté de Pharmacie de Paris, Université Paris Cité, INSERM, UMR-S 1139 (3PHM), Paris F-75006, France
| | - Christelle Mazuet
- Institut Pasteur, Université Paris Cité, Centre National de Référence des Bactéries anaérobies et Botulisme, Paris F-75015, France
| | - Laure Diancourt
- Institut Pasteur, Université Paris Cité, Centre National de Référence des Bactéries anaérobies et Botulisme, Paris F-75015, France
| | - Victoria Mesa-Schein
- Faculté de Pharmacie de Paris, Université Paris Cité, INSERM, UMR-S 1139 (3PHM), Paris F-75006, France
| | - Frédéric Barbut
- Faculté de Pharmacie de Paris, Université Paris Cité, INSERM, UMR-S 1139 (3PHM), Paris F-75006, France
| | - Julio Aires
- Faculté de Pharmacie de Paris, Université Paris Cité, INSERM, UMR-S 1139 (3PHM), Paris F-75006, France
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25
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Ko S, Kim J, Lim J, Lee SM, Park JY, Woo J, Scott-Nevros ZK, Kim JR, Yoon H, Kim D. Blanket antimicrobial resistance gene database with structural information, BOARDS, provides insights on historical landscape of resistance prevalence and effects of mutations in enzyme structure. mSystems 2024; 9:e0094323. [PMID: 38085058 PMCID: PMC10871167 DOI: 10.1128/msystems.00943-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 11/02/2023] [Indexed: 01/24/2024] Open
Abstract
Antimicrobial resistance (AMR) in pathogenic bacteria poses a significant threat to public health, yet there is still a need for development in the tools to deeply understand AMR genes based on genetic or structural information. In this study, we present an interactive web database named Blanket Overarching Antimicrobial-Resistance gene Database with Structural information (BOARDS, sbml.unist.ac.kr), a database that comprehensively includes 3,943 reported AMR gene information for 1,997 extended spectrum beta-lactamase (ESBL) and 1,946 other genes as well as a total of 27,395 predicted protein structures. These structures, which include both wild-type AMR genes and their mutants, were derived from 80,094 publicly available whole-genome sequences. In addition, we developed the rapid analysis and detection tool of antimicrobial-resistance (RADAR), a one-stop analysis pipeline to detect AMR genes across whole-genome sequencing (WGSs). By integrating BOARDS and RADAR, the AMR prevalence landscape for eight multi-drug resistant pathogens was reconstructed, leading to unexpected findings such as the pre-existence of the MCR genes before their official reports. Enzymatic structure prediction-based analysis revealed that the occurrence of mutations found in some ESBL genes was found to be closely related to the binding affinities with their antibiotic substrates. Overall, BOARDS can play a significant role in performing in-depth analysis on AMR.IMPORTANCEWhile the increasing antibiotic resistance (AMR) in pathogen has been a burden on public health, effective tools for deep understanding of AMR based on genetic or structural information remain limited. In this study, a blanket overarching antimicrobial-resistance gene database with structure information (BOARDS)-a web-based database that comprehensively collected AMR gene data with predictive protein structural information was constructed. Additionally, we report the development of a RADAR pipeline that can analyze whole-genome sequences as well. BOARDS, which includes sequence and structural information, has shown the historical landscape and prevalence of the AMR genes and can provide insight into single-nucleotide polymorphism effects on antibiotic degrading enzymes within protein structures.
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Affiliation(s)
- Seyoung Ko
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, South Korea
- School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, South Korea
| | - Jaehyung Kim
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, South Korea
| | - Jaewon Lim
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, South Korea
| | - Sang-Mok Lee
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, South Korea
| | - Joon Young Park
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, South Korea
| | - Jihoon Woo
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, South Korea
| | - Zoe K. Scott-Nevros
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, South Korea
| | - Jong R. Kim
- School of Engineering and Digital Sciences, Nazarbayev University, Astan, Kazakhstan
| | - Hyunjin Yoon
- Department of Molecular Science and Technology, Ajou University, Suwon, South Korea
| | - Donghyuk Kim
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, South Korea
- School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, South Korea
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26
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Chai J, Zhuang Y, Cui K, Bi Y, Zhang N. Metagenomics reveals the temporal dynamics of the rumen resistome and microbiome in goat kids. MICROBIOME 2024; 12:14. [PMID: 38254181 PMCID: PMC10801991 DOI: 10.1186/s40168-023-01733-5] [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: 01/23/2022] [Accepted: 11/28/2023] [Indexed: 01/24/2024]
Abstract
BACKGROUND The gut microbiome of domestic animals carries antibiotic resistance genes (ARGs) which can be transmitted to the environment and humans, resulting in challenges of antibiotic resistance. Although it has been reported that the rumen microbiome of ruminants may be a reservoir of ARGs, the factors affecting the temporal dynamics of the rumen resistome are still unclear. Here, we collected rumen content samples of goats at 1, 7, 14, 28, 42, 56, 70, and 84 days of age, analyzed their microbiome and resistome profiles using metagenomics, and assessed the temporal dynamics of the rumen resistome in goats at the early stage of life under a conventional feeding system. RESULTS In our results, the rumen resistome of goat kids contained ARGs to 41 classes, and the richness of ARGs decreased with age. Four antibiotic compound types of ARGs, including drugs, biocides, metals, and multi-compounds, were found during milk feeding, while only drug types of ARGs were observed after supplementation with starter feed. The specific ARGs for each age and their temporal dynamics were characterized, and the network inference model revealed that the interactions among ARGs were related to age. A strong correlation between the profiles of rumen resistome and microbiome was found using Procrustes analysis. Ruminal Escherichia coli within Proteobacteria phylum was the main carrier of ARGs in goats consuming colostrum, while Prevotella ruminicola and Fibrobacter succinogenes associated with cellulose degradation were the carriers of ARGs after starter supplementation. Milk consumption was likely a source of rumen ARGs, and the changes in the rumen resistome with age were correlated with the microbiome modulation by starter supplementation. CONCLUSIONS Our data revealed that the temporal dynamics of the rumen resistome are associated with the microbiome, and the reservoir of ARGs in the rumen during early life is likely related to age and diet. It may be a feasible strategy to reduce the rumen and its downstream dissemination of ARGs in ruminants through early-life dietary intervention. Video Abstract.
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Affiliation(s)
- Jianmin Chai
- Institute of Feed Research of Chinese Academy of Agricultural Sciences, Key Laboratory of Feed Biotechnology of the Ministry of Agriculture and Rural Affairs, Beijing, 100081, China
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, College of Life Science and Engineering, Foshan University, Foshan, 528225, China
- Department of Animal Science, Division of Agriculture, University of Arkansas, Fayetteville, AR, 72701, USA
| | - Yimin Zhuang
- Institute of Feed Research of Chinese Academy of Agricultural Sciences, Key Laboratory of Feed Biotechnology of the Ministry of Agriculture and Rural Affairs, Beijing, 100081, China
| | - Kai Cui
- Institute of Feed Research of Chinese Academy of Agricultural Sciences, Key Laboratory of Feed Biotechnology of the Ministry of Agriculture and Rural Affairs, Beijing, 100081, China
| | - Yanliang Bi
- Institute of Feed Research of Chinese Academy of Agricultural Sciences, Key Laboratory of Feed Biotechnology of the Ministry of Agriculture and Rural Affairs, Beijing, 100081, China.
| | - Naifeng Zhang
- Institute of Feed Research of Chinese Academy of Agricultural Sciences, Key Laboratory of Feed Biotechnology of the Ministry of Agriculture and Rural Affairs, Beijing, 100081, China.
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27
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Ottesen A, Kocurek B, Deaver C, Chiesa O, Cohen R, Reed E, Commichaux S, Mammel M, McDermott P, Strain E, Myers M. Fecal microbiomes of laboratory beagles receiving antiparasitic formulations in an experimental setting. Microbiol Resour Announc 2024; 13:e0086023. [PMID: 38018965 DOI: 10.1128/mra.00860-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 10/10/2023] [Indexed: 11/30/2023] Open
Abstract
Here, we describe the fecal microbiome of laboratory beagles in a non-invasive experiment designed to contrast in vivo versus in vitro bioequivalence in response to antiparasitic drug administration. The experiment provided a unique opportunity to evaluate metagenomic profiles of canine feces before and after anti-parasitic drug exposure.
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Affiliation(s)
- Andrea Ottesen
- Center for Veterinary Medicine, United States Food and Drug Administration , Laurel, Maryland, USA
| | - Brandon Kocurek
- Center for Veterinary Medicine, United States Food and Drug Administration , Laurel, Maryland, USA
| | - Christine Deaver
- Center for Veterinary Medicine, United States Food and Drug Administration , Laurel, Maryland, USA
| | - Oscar Chiesa
- Center for Veterinary Medicine, United States Food and Drug Administration , Laurel, Maryland, USA
| | - Rachael Cohen
- Center for Veterinary Medicine, United States Food and Drug Administration , Laurel, Maryland, USA
| | - Elizabeth Reed
- Center for Food Safety and Applied Nutrition, United States Food and Drug Administration , College Park, Maryland, USA
| | - Seth Commichaux
- Center for Food Safety and Applied Nutrition, United States Food and Drug Administration , Laurel, Maryland, USA
| | - Mark Mammel
- Center for Food Safety and Applied Nutrition, United States Food and Drug Administration , Laurel, Maryland, USA
| | - Patrick McDermott
- Center for Veterinary Medicine, United States Food and Drug Administration , Laurel, Maryland, USA
| | - Errol Strain
- Center for Food Safety and Applied Nutrition, United States Food and Drug Administration , College Park, Maryland, USA
| | - Michael Myers
- Center for Veterinary Medicine, United States Food and Drug Administration , Laurel, Maryland, USA
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28
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Kocurek B, Behling S, Martin G, Ramachandran P, Reed E, Grim C, Mammel M, Zheng J, Franklin A, Garland J, Tadesse DA, Sharma M, Tyson GH, Kabera C, Tate H, McDermott PF, Strain E, Ottesen A. Metagenomic survey of antimicrobial resistance (AMR) in Maryland surface waters differentiated by high and low human impact. Microbiol Resour Announc 2024; 13:e0047723. [PMID: 38032210 DOI: 10.1128/mra.00477-23] [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: 06/09/2023] [Accepted: 10/24/2023] [Indexed: 12/01/2023] Open
Abstract
Here, we examine surface waters as a modality to better understand baseline antimicrobial resistance (AMR) across the environment to supplement existing AMR monitoring in pathogens associated with humans, foods, and animals. Data from metagenomic and quasimetagenomic (shotgun sequenced enrichments) are used to describe AMR in Maryland surface waters from high and low human impact classifications.
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Affiliation(s)
- Brandon Kocurek
- Center for Veterinary Medicine, United States Food and Drug Administration , Laurel, Maryland, USA
| | - Shawn Behling
- Washington Department of Fish and Wildlife , Seattle, Washington, USA
| | - Gordon Martin
- Center for Veterinary Medicine, United States Food and Drug Administration , Laurel, Maryland, USA
| | - Padmini Ramachandran
- Center for Food Safety and Applied Nutrition, United States Food and Drug Administration , College Park, Maryland, USA
| | - Elizabeth Reed
- Center for Food Safety and Applied Nutrition, United States Food and Drug Administration , College Park, Maryland, USA
| | - Christopher Grim
- Center for Food Safety and Applied Nutrition, United States Food and Drug Administration , College Park, Maryland, USA
| | - Mark Mammel
- Center for Food Safety and Applied Nutrition, United States Food and Drug Administration , College Park, Maryland, USA
| | - Jie Zheng
- Center for Food Safety and Applied Nutrition, United States Food and Drug Administration , College Park, Maryland, USA
| | - Alison Franklin
- Center for Environmental Measurement and Modeling, United States Environmental Protection Agency , Cincinnati, Ohio, USA
| | - Jay Garland
- Center for Environmental Measurement and Modeling, United States Environmental Protection Agency , Cincinnati, Ohio, USA
| | - Daniel A Tadesse
- Center for Veterinary Medicine, United States Food and Drug Administration , Laurel, Maryland, USA
| | - Manan Sharma
- Environmental Microbial & Food Safety Lab, United States Department of Agriculture , Beltsville, Maryland, USA
| | - Gregory H Tyson
- Center for Veterinary Medicine, United States Food and Drug Administration , Laurel, Maryland, USA
| | - Claudine Kabera
- Center for Veterinary Medicine, United States Food and Drug Administration , Laurel, Maryland, USA
| | - Heather Tate
- Center for Veterinary Medicine, United States Food and Drug Administration , Laurel, Maryland, USA
| | - Patrick F McDermott
- Center for Veterinary Medicine, United States Food and Drug Administration , Laurel, Maryland, USA
| | - Errol Strain
- Center for Veterinary Medicine, United States Food and Drug Administration , Laurel, Maryland, USA
| | - Andrea Ottesen
- Center for Veterinary Medicine, United States Food and Drug Administration , Laurel, Maryland, USA
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29
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Zhang H, Xu Y, Shen T, Jia X, Xu Y, Shi T, Pan D, Hua R, Wu X. Chicken feedlot revisited: Co-dispersal of antibiotic and metal resistome under banning in-feed veterinary antibiotics. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 341:122932. [PMID: 37979651 DOI: 10.1016/j.envpol.2023.122932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 11/04/2023] [Accepted: 11/11/2023] [Indexed: 11/20/2023]
Abstract
Intensive livestock farming has been implicated as a notorious hotspot for antibiotic resistance genes (ARGs) due to the excessive or inappropriate use of in-feed antibiotics over the past few decades. Since China implemented a ban on the use of antibiotics in animal feed since 2020, the dissemination of ARGs in the vicinity of feedlots has remained unclear. This study presents a case study that aims to investigate the dispersal of antibiotics and ARGs from a chicken feedlot (established in 2020) to the adjacent aquatic and soil environments. Comparing the sample collected from upstream area, the water and sediment samples from midstream and downstream areas showed an increase in total antibiotic residues and metal content (Cu and Zn) by 4.2-5.3 fold and 1.3-22.6 fold, respectively. The downstream water samples exhibited a 2.49-2.93-fold increase in the abundance of ARGs and a 1.48-1.75-fold increase in the abundance of metal resistance genes (MRGs). The results of Pearson correlation and metagenome-assembled genome revealed a tendency for the co-occurrence of ARGs and MRGs. The dissemination of ARGs and MRGs is primarily driven by tetracycline, tylosin, Cu, and, Mn, with mobile genetic elements playing a more significant role than bacterial communities. These findings shed light on the overlooked co-dispersal pattern of ARGs and MRGs in the environment surrounding feedlots, particularly in the context of banning in-feed veterinary antibiotics.
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Affiliation(s)
- Houpu Zhang
- College of Resources and Environment, Anhui Agricultural University, Key Laboratory of Agri-food Safety of Anhui Province, Hefei, 230036, PR China
| | - Yingqian Xu
- College of Resources and Environment, Anhui Agricultural University, Key Laboratory of Agri-food Safety of Anhui Province, Hefei, 230036, PR China
| | - Tiantian Shen
- College of Resources and Environment, Anhui Agricultural University, Key Laboratory of Agri-food Safety of Anhui Province, Hefei, 230036, PR China
| | - Xinyu Jia
- College of Resources and Environment, Anhui Agricultural University, Key Laboratory of Agri-food Safety of Anhui Province, Hefei, 230036, PR China
| | - Yuer Xu
- College of Resources and Environment, Anhui Agricultural University, Key Laboratory of Agri-food Safety of Anhui Province, Hefei, 230036, PR China
| | - Taozhong Shi
- College of Resources and Environment, Anhui Agricultural University, Key Laboratory of Agri-food Safety of Anhui Province, Hefei, 230036, PR China
| | - Dandan Pan
- College of Resources and Environment, Anhui Agricultural University, Key Laboratory of Agri-food Safety of Anhui Province, Hefei, 230036, PR China
| | - Rimao Hua
- College of Resources and Environment, Anhui Agricultural University, Key Laboratory of Agri-food Safety of Anhui Province, Hefei, 230036, PR China
| | - Xiangwei Wu
- College of Resources and Environment, Anhui Agricultural University, Key Laboratory of Agri-food Safety of Anhui Province, Hefei, 230036, PR China.
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30
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Gao Y, Liu J, Fang Y, Xu X, Wang F, Tang Y, Yin D, Cookson AL, Zhu W, Mao S, Zhong R. Straw-based compost cultivation disproportionally contributes to the environmental persistence of antibiotic resistance from raw cattle manure to organic vegetables. Microbiol Res 2024; 278:127540. [PMID: 37976735 DOI: 10.1016/j.micres.2023.127540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 10/19/2023] [Accepted: 10/30/2023] [Indexed: 11/19/2023]
Abstract
Cattle manure, is a reservoir of antimicrobial resistance genes, but the mechanisms by which they migrate from farm to table remain obscure. Here, we chose Agaricus bisporus as a model vegetable to examine such migration and characterized the resistome in 112 metagenomes covering samples from raw manure, composting substrates, rhizosphere, and surfaces of mushrooms. A total of 1864 resistance genes, representing 113 unique mechanisms of resistance, were identified. Monensin treatment on beef specifically enriched fecal resistance genes within Moraxellaceae, but this effect did not persist in downstream mushrooms. Interestingly, we found that resistance genes were significantly more enriched on mushroom surfaces when cultivated with corn-based compost compared to rice and wheat, likely a result of the disproportional propagation of Pseudomonadaceae and varied ability of lateral gene transfer. Importantly, our sequence alignment together with genome-centric analysis observed that 89 resistance genes, mainly conferring resistance to drug and biocide (20.22%) and mercury (19.10%), were shared across all types of samples, indicating an efficient transmission of resistance in food production. Moreover, co-occurrence of genes conferring resistance to different compounds frequently occurred in parallel with microbial migration. Together, we present the influences of antibiotic treatment and straw-based composting on resistome along the mushroom production chain (from manure to straw-based compost, rhizosphere of compost cultivated mushroom and surface of mushroom) and highlighted the risks of resistance genes migration.
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Affiliation(s)
- Yunlong Gao
- Ruminant Nutrition and Feed Engineering Technology Research Center, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Jinxin Liu
- Ruminant Nutrition and Feed Engineering Technology Research Center, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China.
| | - Yi Fang
- State Key Laboratory of Black Soils Conservation and Utilization, Jilin Provincial Key Laboratory of Grassland Farming, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, Jilin 130102, China
| | - Xinming Xu
- State Key Laboratory of Black Soils Conservation and Utilization, Jilin Provincial Key Laboratory of Grassland Farming, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, Jilin 130102, China; Ruminant Nutrition and Feed Engineering Technology Research Center, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; Institutes of Biomedical Sciences, Fudan University, Shanghai 200030, China; Department of Nutrition and Food Hygiene, School of Public Health, Institute of Nutrition, Fudan University, Shanghai 200030, China
| | - Fei Wang
- State Key Laboratory of Black Soils Conservation and Utilization, Jilin Provincial Key Laboratory of Grassland Farming, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, Jilin 130102, China
| | - Yijun Tang
- Ruminant Nutrition and Feed Engineering Technology Research Center, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Di Yin
- Ruminant Nutrition and Feed Engineering Technology Research Center, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Adrian L Cookson
- School of Veterinary Science, Massey University, Palmerston North 4410, New Zealand; AgResearch Ltd, Hopkirk Research Institute, Massey University, Palmerston North 4410, New Zealand
| | - Weiyun Zhu
- Ruminant Nutrition and Feed Engineering Technology Research Center, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Shengyong Mao
- Ruminant Nutrition and Feed Engineering Technology Research Center, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China.
| | - Rongzhen Zhong
- State Key Laboratory of Black Soils Conservation and Utilization, Jilin Provincial Key Laboratory of Grassland Farming, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, Jilin 130102, China.
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31
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Neal K, Amachawadi RG, White BJ, Shippy TD, Theurer ME, Larson RL, Lubbers BV, Kleinhenz M. Nasopharyngeal Bacterial Prevalence and Microbial Diversity at First Treatment for Bovine Respiratory Disease (BRD) and Its Associations with Health and Mortality Outcomes in Feedyard Cattle. Microorganisms 2023; 12:33. [PMID: 38257861 PMCID: PMC10818627 DOI: 10.3390/microorganisms12010033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 12/17/2023] [Accepted: 12/21/2023] [Indexed: 01/24/2024] Open
Abstract
Bovine respiratory disease (BRD) is an economically important disease in feedyards influencing both animal welfare and antimicrobial utilization. Major pathogens associated with BRD have been identified in previous research, but little information is available on the relationship between nasopharyngeal microbiota and health outcomes. The objective of this study was to identify potential associations between nasopharyngeal microbiota and antimicrobial resistance patterns of clinical cases that lived or died compared to non-diseased controls. Enrolled animals were subdivided based on clinical disease status and case outcome (subsequent mortality). Deep nasopharyngeal swabs were collected on enrolled animals and submitted for bacterial isolation, antimicrobial susceptibility determination, and metagenomics analysis. Enrolled cattle were represented in three groups: animals at first treatment for BRD that subsequently died (BRDM, n = 9), animals at first treatment for BRD that subsequently lived (BRDL, n = 15), and animals that were never treated for BRD during the feeding phase (CONT, n = 11). Antimicrobial resistance patterns for Pasteurella multocida illustrated cattle in each outcome category had isolates that were pan-susceptible or only showed resistance to oxytetracycline. The relative abundance of species and genera illustrated few differences among the three outcomes. Higher alpha diversity was identified in BRDL compared to CONT at the species level, and both BRDL and BRDM showed increased alpha diversity compared to CONT at the general level. Overall, this work illustrated nasopharyngeal microbiota showed relatively few differences among BRD cases that lived or died compared to animals without BRD.
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Affiliation(s)
- Kyndall Neal
- Beef Cattle Institute, Department of Clinical Sciences, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA; (K.N.); (B.J.W.); (R.L.L.); (B.V.L.)
| | - Raghavendra G. Amachawadi
- Beef Cattle Institute, Department of Clinical Sciences, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA; (K.N.); (B.J.W.); (R.L.L.); (B.V.L.)
| | - Brad J. White
- Beef Cattle Institute, Department of Clinical Sciences, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA; (K.N.); (B.J.W.); (R.L.L.); (B.V.L.)
| | - Teresa D. Shippy
- Data Science Center, Division of Biology, Kansas State University, Manhattan, KS 66506, USA;
| | - Miles E. Theurer
- Veterinary Research and Consulting Services LLC, Hays, KS 67601, USA;
| | - Robert L. Larson
- Beef Cattle Institute, Department of Clinical Sciences, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA; (K.N.); (B.J.W.); (R.L.L.); (B.V.L.)
| | - Brian V. Lubbers
- Beef Cattle Institute, Department of Clinical Sciences, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA; (K.N.); (B.J.W.); (R.L.L.); (B.V.L.)
| | - Michael Kleinhenz
- Veterinary Education, Research and Outreach, Texas A&M University, Canyon, TX 79015, USA;
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Mejía L, Espinosa-Mata E, Freire AL, Zapata S, González-Candelas F. Listeria monocytogenes, a silent foodborne pathogen in Ecuador. Front Microbiol 2023; 14:1278860. [PMID: 38179446 PMCID: PMC10764610 DOI: 10.3389/fmicb.2023.1278860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 11/23/2023] [Indexed: 01/06/2024] Open
Abstract
Listeria monocytogenes is a foodborne pathogen that can produce serious, even fatal, infections. Among other foods, it can be found in unpasteurized dairy and ready-to-eat products. Surveillance of L. monocytogenes is of great interest since sources of infection are difficult to determine due to the long incubation period, and because the symptoms of listeriosis are similar to other diseases. We performed a genomic study of L. monocytogenes isolated from fresh cheeses and clinical samples from Ecuador. Sixty-five isolates were evaluated and sequenced, 14 isolates from cheese samples and 20 from clinical listeriosis cases from the National Institute of National Institute of Public Health Research, and 31 isolates from artisanal cheese samples from 8 provinces. All isolates exhibited heterogeneous patterns of the presence of pathogenicity islands. All isolates exhibited at least 4 genes from LIPI-1, but all references (26 L. monocytogenes closed genomes available in the NCBI database) showed the complete island, which encompasses 5 genes but is present in only two Ecuadorian isolates. Most isolates lacked gene actA. Genes from LIPI-2 were absent in all isolates. LIPI-3 and LIPI-4 were present in only a few references and isolates. With respect to the stress survival islets, our samples either presented SSI-1 or SSI-F2365, except for one isolate that presented SSI-F2365 and also one gene from SSI-1. None of the samples presented SSI-2. The predominant ST (sequence type) was ST2 (84.62% 55/65), and the only ST found in food (93.33% 42/45) and clinical samples (65% 13/20). Isolates were not grouped according to their sampling origin, date, or place in a phylogenetic tree obtained from the core alignment. The presence of ST2 in food and clinical samples, with high genomic similarity, suggests a foodborne infection risk linked to the consumption of fresh cheeses in Ecuador.
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Affiliation(s)
- Lorena Mejía
- Colegio de Ciencias Biológicas y Ambientales, Instituto de Microbiología, Universidad San Francisco de Quito USFQ, Quito, Ecuador
- Institute for Integrative Systems Biology, University of Valencia, Valencia, Spain
- Joint Research Unit “Infection and Public Health” FISABIO-University of Valencia, Valencia, Spain
| | - Estefanía Espinosa-Mata
- Colegio de Ciencias Biológicas y Ambientales, Instituto de Microbiología, Universidad San Francisco de Quito USFQ, Quito, Ecuador
| | - Ana Lucía Freire
- Colegio de Ciencias Biológicas y Ambientales, Instituto de Microbiología, Universidad San Francisco de Quito USFQ, Quito, Ecuador
| | - Sonia Zapata
- Colegio de Ciencias Biológicas y Ambientales, Instituto de Microbiología, Universidad San Francisco de Quito USFQ, Quito, Ecuador
| | - Fernando González-Candelas
- Institute for Integrative Systems Biology, University of Valencia, Valencia, Spain
- Joint Research Unit “Infection and Public Health” FISABIO-University of Valencia, Valencia, Spain
- CIBER (Centro de Investigación Biomédica en Red) in Epidemiology and Public Health, Valencia, Spain
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Kawamura T, Prah I, Mahazu S, Ablordey A, Saito R. Types A and F Clostridium perfringens in healthcare wastewater from Ghana. Appl Environ Microbiol 2023; 89:e0161923. [PMID: 38051072 PMCID: PMC10734495 DOI: 10.1128/aem.01619-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 10/18/2023] [Indexed: 12/07/2023] Open
Abstract
IMPORTANCE Clostridium perfringens causes gas gangrene and food poisoning in humans, and monitoring this bacterium is important for public health. Although whole-genome sequencing is useful to comprehensively understand the virulence, resistome, and global genetic relatedness of bacteria, limited genomic data from environmental sources and developing countries hamper our understanding of the richness of the intrinsic genomic diversity of this pathogen. Here, we successfully accumulated the genetic data on C. perfringens strains isolated from hospital effluent and provided the first evidence that predicted pathogenic C. perfringens may be disseminated in the clinical environment in Ghana. Our findings suggest the importance of risk assessment in the environment as well as the clinical setting to mitigate the potential outbreak of C. perfringens food poisoning in Ghana.
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Affiliation(s)
- Taira Kawamura
- Department of Molecular Microbiology and Immunology, Graduate School of Medicine and Dental Science, Tokyo Medical and Dental University, Tokyo, Japan
| | - Isaac Prah
- Department of Molecular Microbiology and Immunology, Graduate School of Medicine and Dental Science, Tokyo Medical and Dental University, Tokyo, Japan
| | - Samiratu Mahazu
- Department of Molecular Microbiology and Immunology, Graduate School of Medicine and Dental Science, Tokyo Medical and Dental University, Tokyo, Japan
| | - Anthony Ablordey
- Department of Bacteriology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Ryoichi Saito
- Department of Molecular Microbiology and Immunology, Graduate School of Medicine and Dental Science, Tokyo Medical and Dental University, Tokyo, Japan
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Jdeed G, Morozova V, Kozlova Y, Tikunov A, Ushakova T, Bardasheva A, Manakhov A, Mitina M, Zhirakovskaya E, Tikunova N. StM171, a Stenotrophomonas maltophilia Bacteriophage That Affects Sensitivity to Antibiotics in Host Bacteria and Their Biofilm Formation. Viruses 2023; 15:2455. [PMID: 38140696 PMCID: PMC10747581 DOI: 10.3390/v15122455] [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: 11/14/2023] [Revised: 12/08/2023] [Accepted: 12/16/2023] [Indexed: 12/24/2023] Open
Abstract
Stenotrophomonas maltophilia mainly causes respiratory infections that are associated with a high mortality rate among immunocompromised patients. S. maltophilia exhibits a high level of antibiotic resistance and can form biofilms, which complicates the treatment of patients infected with this bacterium. Phages combined with antibiotics could be a promising treatment option. Currently, ~60 S. maltophilia phages are known, and their effects on biofilm formation and antibiotic sensitivity require further examination. Bacteriophage StM171, which was isolated from hospital wastewater, showed a medium host range, low burst size, and low lytic activity. StM171 has a 44kbp dsDNA genome that encodes 59 open-reading frames. A comparative genomic analysis indicated that StM171, along with the Stenotrophomonas phage Suso (MZ326866) and Xanthomonas phage HXX_Dennis (ON711490), are members of a new putative Nordvirus genus. S. maltophilia strains that developed resistance to StM171 (bacterial-insensitive mutants) showed a changed sensitivity to antibiotics compared to the originally susceptible strains. Some bacterial-insensitive mutants restored sensitivity to cephalosporin and penicillin-like antibiotics and became resistant to erythromycin. StM171 shows strain- and antibiotic-dependent effects on the biofilm formation of S. maltophilia strains.
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Affiliation(s)
- Ghadeer Jdeed
- Laboratory of Molecular Microbiology, Institute of Chemical Biology and Fundamental Medicine Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia; (G.J.); (V.M.); (Y.K.); (A.T.); (T.U.); (A.B.)
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Vera Morozova
- Laboratory of Molecular Microbiology, Institute of Chemical Biology and Fundamental Medicine Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia; (G.J.); (V.M.); (Y.K.); (A.T.); (T.U.); (A.B.)
| | - Yuliya Kozlova
- Laboratory of Molecular Microbiology, Institute of Chemical Biology and Fundamental Medicine Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia; (G.J.); (V.M.); (Y.K.); (A.T.); (T.U.); (A.B.)
| | - Artem Tikunov
- Laboratory of Molecular Microbiology, Institute of Chemical Biology and Fundamental Medicine Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia; (G.J.); (V.M.); (Y.K.); (A.T.); (T.U.); (A.B.)
| | - Tatyana Ushakova
- Laboratory of Molecular Microbiology, Institute of Chemical Biology and Fundamental Medicine Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia; (G.J.); (V.M.); (Y.K.); (A.T.); (T.U.); (A.B.)
| | - Alevtina Bardasheva
- Laboratory of Molecular Microbiology, Institute of Chemical Biology and Fundamental Medicine Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia; (G.J.); (V.M.); (Y.K.); (A.T.); (T.U.); (A.B.)
| | - Andrey Manakhov
- Department of Genetics, Centre for Genetics and Life Science, Sirius University of Science and Technology, Sirius 354340, Russia; (A.M.); (M.M.)
| | - Maria Mitina
- Department of Genetics, Centre for Genetics and Life Science, Sirius University of Science and Technology, Sirius 354340, Russia; (A.M.); (M.M.)
| | - Elena Zhirakovskaya
- Laboratory of Molecular Microbiology, Institute of Chemical Biology and Fundamental Medicine Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia; (G.J.); (V.M.); (Y.K.); (A.T.); (T.U.); (A.B.)
| | - Nina Tikunova
- Laboratory of Molecular Microbiology, Institute of Chemical Biology and Fundamental Medicine Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia; (G.J.); (V.M.); (Y.K.); (A.T.); (T.U.); (A.B.)
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Lee C, Zaheer R, Munns K, Holman DB, Van Domselaar G, Zovoilis A, McAllister TA. Effect of Antimicrobial Use in Conventional Versus Natural Cattle Feedlots on the Microbiome and Resistome. Microorganisms 2023; 11:2982. [PMID: 38138126 PMCID: PMC10745953 DOI: 10.3390/microorganisms11122982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 12/08/2023] [Accepted: 12/12/2023] [Indexed: 12/24/2023] Open
Abstract
Antimicrobial use (AMU) in the livestock industry has been associated with increased levels of antimicrobial resistance. Recently, there has been an increase in the number of "natural" feedlots in the beef cattle sector that raise cattle without antibiotics. Shotgun metagenomics was employed to characterize the impact of AMU in feedlot cattle on the microbiome, resistome, and mobilome. Sequenced fecal samples identified a decline (q < 0.01) in the genera Methanobrevibacter and Treponema in the microbiome of naturally vs. conventionally raised feedlot cattle, but this difference was not (q > 0.05) observed in catch basin samples. No differences (q > 0.05) were found in the class-level resistome between feedlot practices. In fecal samples, decreases from conventional to natural (q < 0.05) were noted in reads for the antimicrobial-resistant genes (ARGs) mefA, tet40, tetO, tetQ, and tetW. Plasmid-associated ARGs were more common in feces from conventional than natural feedlot cattle. Interestingly, more chromosomal- than plasmid-associated macrolide resistance genes were observed in both natural and conventional feedlots, suggesting that they were more stably conserved than the predominately plasmid-associated tetracycline resistance genes. This study suggests that generationally selected resistomes through decades of AMU persist even after AMU ceases in natural production systems.
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Affiliation(s)
- Catrione Lee
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Government of Canada, 5403 1st Avenue South, Lethbridge, AB T1J 4B1, Canada; (C.L.); (R.Z.); (K.M.)
- Southern Alberta Genomic Sciences Centre, Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, AB T1K 3M4, Canada;
| | - Rahat Zaheer
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Government of Canada, 5403 1st Avenue South, Lethbridge, AB T1J 4B1, Canada; (C.L.); (R.Z.); (K.M.)
| | - Krysty Munns
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Government of Canada, 5403 1st Avenue South, Lethbridge, AB T1J 4B1, Canada; (C.L.); (R.Z.); (K.M.)
| | - Devin B. Holman
- Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, Government of Canada, 6000 C and E Trail, Lacombe, AB T4L 1W1, Canada;
| | - Gary Van Domselaar
- National Microbiology Laboratory, Public Health Agency of Canada, Government of Canada, 1015 Arlington Street, Winnipeg, MB R3E 3R2, Canada;
| | - Athanasios Zovoilis
- Southern Alberta Genomic Sciences Centre, Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, AB T1K 3M4, Canada;
| | - Tim A. McAllister
- Southern Alberta Genomic Sciences Centre, Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, AB T1K 3M4, Canada;
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Takeda-Nishikawa K, Palanichamy R, Miyazato N, Suzuki T. What samples are suitable for monitoring antimicrobial-resistant genes? Using NGS technology, a comparison between eDNA and mrDNA analysis from environmental water. Front Microbiol 2023; 14:954783. [PMID: 38179449 PMCID: PMC10765985 DOI: 10.3389/fmicb.2023.954783] [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: 05/27/2022] [Accepted: 08/14/2023] [Indexed: 01/06/2024] Open
Abstract
Introduction The rise in antimicrobial resistance (AMR) that is affecting humans, animals, and the environment, compromises the human immune system and represents a significant threat to public health. Regarding the impact on water sanitation, the risk that antimicrobial-resistant genes (ARGs) and antimicrobial-resistant bacteria in surface water in cities pose to human health remains unclear. To determine the prevalence of AMR in environmental surface water in Japan, we used DNA sequencing techniques on environmental water DNA (eDNA) and the DNA of multidrug-resistant bacteria (mrDNA). Methods The eDNA was extracted from four surface water samples obtained from the Tokyo area and subjected to high- throughput next-generation DNA sequencing using Illumina-derived shotgun metagenome analysis. The sequence data were analyzed using the AmrPlusPlus pipeline and the MEGARes database. Multidrug-resistant bacteria were isolated using a culture-based method from water samples and were screened by antimicrobial susceptibility testing (for tetracycline, ampicillin-sulbactam, amikacin, levofloxacin, imipenem, and clarithromycin). Of the 284 isolates, 22 were identified as multidrug-resistant bacteria. The mrDNA was sequenced using the Oxford nanopore MinION system and analyzed by NanoARG, a web service for detecting and contextualizing ARGs. Results and discussion The results from eDNA and mrDNA revealed that ARGs encoding beta-lactams and multidrug resistance, including multidrug efflux pump genes, were frequently detected in surface water samples. However, mrDNA also revealed many sequence reads from multidrug-resistant bacteria, as well as nonspecific ARGs, whereas eDNA revealed specific ARGs such as pathogenic OXA-type and New Delhi metallo (NDM)-beta-lactamase ARGs. Conclusion To estimate potential AMR pollution, our findings suggested that eDNA is preferable for detecting pathogen ARGs.
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Affiliation(s)
| | - Rajaguru Palanichamy
- Department of Biotechnology, Central University of Tamil Nadu, Thiruvarur, India
| | - Naoki Miyazato
- National Institute of Technology (KOSEN), Gunma College, Maebashi, Japan
| | - Takayoshi Suzuki
- Division of Molecular Target and Gene Therapy Products, National Institute of Health Sciences, Kawasaki, Japan
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Larcombe S, Williams GC, Amy J, Lim SC, Riley TV, Muleta A, Barugahare AA, Powell DR, Johanesen PA, Cheng AC, Peleg AY, Lyras D. A genomic survey of Clostridioides difficile isolates from hospitalized patients in Melbourne, Australia. Microbiol Spectr 2023; 11:e0135223. [PMID: 37815385 PMCID: PMC10715045 DOI: 10.1128/spectrum.01352-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 07/18/2023] [Indexed: 10/11/2023] Open
Abstract
IMPORTANCE There has been a decrease in healthcare-associated Clostridioides difficile infection in Australia, but an increase in the genetic diversity of infecting strains, and an increase in community-associated cases. Here, we studied the genetic relatedness of C. difficile isolated from patients at a major hospital in Melbourne, Australia. Diverse ribotypes were detected, including those associated with community and environmental sources. Some types of isolates were more likely to carry antimicrobial resistance determinants, and many of these were associated with mobile genetic elements. These results correlate with those of other recent investigations, supporting the observed increase in genetic diversity and prevalence of community-associated C. difficile, and consequently the importance of sources of transmission other than symptomatic patients. Thus, they reinforce the importance of surveillance for in both hospital and community settings, including asymptomatic carriage, food, animals, and other environmental sources to identify and circumvent important sources of C. difficile transmission.
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Affiliation(s)
- Sarah Larcombe
- Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Melbourne, Victoria, Australia
| | - Galain C. Williams
- Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Melbourne, Victoria, Australia
| | - Jacob Amy
- Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Melbourne, Victoria, Australia
| | - Su Chen Lim
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, Western Australia, Australia
- School of Biomedical Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Thomas V. Riley
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, Western Australia, Australia
- School of Biomedical Sciences, The University of Western Australia, Perth, Western Australia, Australia
- Medical, Molecular, and Forensic Sciences, Murdoch University, Perth, Western Australia, Australia
| | - Anthony Muleta
- Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Melbourne, Victoria, Australia
| | | | | | - Priscilla A. Johanesen
- Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Melbourne, Victoria, Australia
| | - Allen C. Cheng
- Department of Infectious Diseases, Alfred Hospital, Melbourne, Victoria, Australia
| | - Anton Y. Peleg
- Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Melbourne, Victoria, Australia
- Department of Infectious Diseases, Alfred Hospital, Melbourne, Victoria, Australia
| | - Dena Lyras
- Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Melbourne, Victoria, Australia
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Chen Y, Fu X, Ou Z, Li J, Lin S, Wu Y, Wang X, Deng Y, Sun Y. Environmental determinants and demographic influences on global urban microbiomes, antimicrobial resistance and pathogenicity. NPJ Biofilms Microbiomes 2023; 9:94. [PMID: 38062054 PMCID: PMC10703778 DOI: 10.1038/s41522-023-00459-4] [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: 03/08/2023] [Accepted: 11/20/2023] [Indexed: 12/18/2023] Open
Abstract
Urban microbiome plays crucial roles in human health and are related to various diseases. The MetaSUB Consortium has conducted the most comprehensive global survey of urban microbiomes to date, profiling microbial taxa/functional genes across 60 cities worldwide. However, the influence of environmental/demographic factors on urban microbiome remains to be elucidated. We collected 35 environmental and demographic characteristics to examine their effects on global urban microbiome diversity/composition by PERMANOVA and regression models. PM10 concentration was the primary determinant factor positively associated with microbial α-diversity (observed species: p = 0.004, β = 1.66, R2 = 0.46; Fisher's alpha: p = 0.005, β = 0.68, R2 = 0.43), whereas GDP per capita was negatively associated (observed species: p = 0.046, β = -0.70, R2 = 0.10; Fisher's alpha: p = 0.004, β = -0.34, R2 = 0.22). The β-diversity of urban microbiome was shaped by seven environmental characteristics, including Köppen climate type, vegetation type, greenness fraction, soil type, PM2.5 concentration, annual average precipitation and temperature (PERMANOVA, p < 0.001, R2 = 0.01-0.06), cumulatively accounted for 20.3% of the microbial community variance. Canonical correspondence analysis (CCA) identified microbial species most strongly associated with environmental characteristic variation. Cities in East Asia with higher precipitation showed an increased abundance of Corynebacterium metruchotii, and cities in America with a higher greenness fraction exhibited a higher abundance of Corynebacterium casei. The prevalence of antimicrobial resistance (AMR) genes were negatively associated with GDP per capita and positively associated with solar radiation (p < 0.005). Total pathogens prevalence was positively associated with urban population and negatively associated with average temperature in June (p < 0.05). Our study presents the first comprehensive analysis of the influence of environmental/demographic characteristics on global urban microbiome. Our findings indicate that managing air quality and urban greenness is essential for regulating urban microbial diversity and composition. Meanwhile, socio-economic considerations, particularly reducing antibiotic usage in regions with lower GDP, are paramount in curbing the spread of antimicrobial resistance in urban environments.
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Affiliation(s)
- Yang Chen
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, P. R. China
| | - Xi Fu
- Guangdong Provincial Engineering Research Center of Public Health Detection and Assessment, School of Public Health, Guangdong Pharmaceutical University, 510006, Guangzhou, P. R. China.
| | - Zheyuan Ou
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, P. R. China
| | - Jiang Li
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, P. R. China
| | - Simiao Lin
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, P. R. China
| | - Yaoxuan Wu
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, P. R. China
| | - Xuwei Wang
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, P. R. China
| | - Yiqun Deng
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, P. R. China.
| | - Yu Sun
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, P. R. China.
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Shepherd JA, Parker MD. Repeat-exposure in vitro protocol to assess the risk of antimicrobial resistance (AMR) development from use of personal care products: Case study using an antibacterial liquid handwash. J Microbiol Methods 2023; 215:106851. [PMID: 37907118 DOI: 10.1016/j.mimet.2023.106851] [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: 09/12/2023] [Revised: 10/17/2023] [Accepted: 10/27/2023] [Indexed: 11/02/2023]
Abstract
The global crisis we are facing with regard to antibiotic resistance has been largely attributed to the overuse and misuse of antibiotics in healthcare and agriculture. However, there is also growing global concern about cross-resistance between biocides and antibiotics. This has made clear the need for more research in this area along with easy-to-perform, but realistic, methods to characterise the potential risk associated with cross-resistance to antibiotics due to biocide use. The primary aim of this work was to develop a repeat-exposure method for predicting bacterial resistance to microbicides, including their cross-resistance to antibiotics. Realism is incorporated in the presented protocol through the use of relevant concentrations and contact times, validated neutralisers, appropriate test organisms and repeat-exposures. The protocol can be applied to formulated microbicides, as shown in the liquid handwash case study presented here. Five bacterial strains were included in the study: Staphylococcus aureus ATCC 6538, Pseudomonas aeruginosa ATCC 15442, Staphylococcus epidermidis ATCC 14990, Escherichia coli ATCC 10536 and Enterococcus hirae ATCC 10541. The protocol parameters used in the case study reflected a worst-case exposure scenario (in terms of contact time and concentration). The results demonstrated that repeated exposure to the liquid handwash would not be expected to lead to development of bacterial resistance or cross-resistance to antibiotics. It is envisaged that this protocol could be used by manufacturers of microbicidal formulations to assess whether repeated use of the test products would contribute to bacterial resistance development or cross-resistance to antibiotics.
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Affiliation(s)
- J A Shepherd
- Unilever Safety and Environmental Assurance Centre (SEAC), Colworth Science Park, Sharnbrook, Bedfordshire MK44 1LQ, UK.
| | - M D Parker
- Unilever Safety and Environmental Assurance Centre (SEAC), Colworth Science Park, Sharnbrook, Bedfordshire MK44 1LQ, UK
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40
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Diaz GR, Gaire TN, Ferm P, Case L, Caixeta LS, Goldsmith TJ, Armstrong J, Noyes NR. Effect of castration timing and weaning strategy on the taxonomic and functional profile of ruminal bacteria and archaea of beef calves. Anim Microbiome 2023; 5:61. [PMID: 38041127 PMCID: PMC10691087 DOI: 10.1186/s42523-023-00284-2] [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: 07/20/2023] [Accepted: 11/28/2023] [Indexed: 12/03/2023] Open
Abstract
BACKGROUND Beef cattle experience several management challenges across their lifecycle. Castration and weaning, two major interventions in the early life of beef cattle, can have a substantial impact on animal performance. Despite the key role of the rumen microbiome on productive traits of beef cattle, the effect of castration timing and weaning strategy on this microbial community has not been formally described. We assessed the effect of four castration time windows (at birth, turnout, pre-weaning and weaning) and two weaning strategies (fence-line and truck transportation) on the rumen microbiome in a randomized controlled study with 32 male calves across 3 collection days (i.e., time points). Ruminal fluid samples were submitted to shotgun metagenomic sequencing and changes in the taxonomic (microbiota) and functional profile (metagenome) of the rumen microbiome were described. RESULTS Using a comprehensive yet stringent taxonomic classification approach, we identified 10,238 unique taxa classified under 40 bacterial and 7 archaeal phyla across all samples. Castration timing had a limited long-term impact on the rumen microbiota and was not associated with changes in alpha and beta diversity. The interaction of collection day and weaning strategy was associated with changes in the rumen microbiota, which experienced a significant decrease in alpha diversity and shifts in beta diversity within 48 h post-weaning, especially in calves abruptly weaned by truck transportation. Calves weaned using a fence-line weaning strategy had lower relative abundance of Bacteroides, Lachnospira, Fibrobacter and Ruminococcus genera compared to calves weaned by truck transportation. Some genes involved in the hydrogenotrophic methanogenesis pathway (fwdB and fwdF) had higher relative abundance in fence-line-weaned calves post-weaning. The antimicrobial resistance gene tetW consistently represented more than 50% of the resistome across time, weaning and castration groups, without significant changes in relative abundance. CONCLUSIONS Within the context of this study, castration timing had limited long-term effects on the rumen microbiota, while weaning strategy had short-term effects on the rumen microbiota and methane-associated metagenome, but not on the rumen resistome.
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Affiliation(s)
- Gerardo R Diaz
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, 55108, USA
| | - Tara N Gaire
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, 55108, USA
| | - Peter Ferm
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, 55108, USA
| | - Lacey Case
- North Central Research and Outreach Center, Department of Animal Science, University of Minnesota, St. Paul, MN, 55108, USA
| | - Luciano S Caixeta
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, 55108, USA
| | - Timothy J Goldsmith
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, 55108, USA
| | - Joe Armstrong
- Agricultural and Natural Resource Systems, University of Minnesota Extension, University of Minnesota, St. Paul, MN, 55108, USA
| | - Noelle R Noyes
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, 55108, USA.
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Aziz G, Zaidi A, Sullivan DJO'. Insights from metagenome-assembled genomes on the genetic stability and safety of over-the-counter probiotic products. Curr Genet 2023; 69:213-234. [PMID: 37237157 DOI: 10.1007/s00294-023-01271-5] [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: 01/02/2023] [Revised: 04/04/2023] [Accepted: 05/10/2023] [Indexed: 05/28/2023]
Abstract
The demand for and acceptance of probiotics is determined by their quality and safety. Illumina NGS sequencing and analytics were used to examine eight marketed probiotics. Up to the species level, sequenced DNA was taxonomically identified, and relative abundances were determined using Kaiju. The genomes were constructed using GTDB and validated through PATRICK and TYGS. A FastTree 2 phylogenetic tree was constructed using several type strain sequences from relevant species. Bacteriocin and ribosomally synthesized polypeptide (RiPP) genes were discovered, and a safety check was performed to test for toxins, antibiotic resistance, and genetic drift genes. Except for two products with unclaimed species, the labeling was taxonomically correct. In three product formulations, Lactobacillus acidophilus, Limosilactobacillus reuteri, Lacticaseibacillus paracasei, and Bifidobacterium animalis exhibited two to three genomic alterations, while Streptococcus equinus was found in one. TYGS and GDTB discovered E. faecium and L. paracasei in distinctly different ways. All the bacteria tested had the genetic repertoire to tolerate GIT transit, although some exhibited antibiotic resistance, and one strain had two virulence genes. Except for Bifidobacterium strains, the others revealed a variety of bacteriocins and ribosomally synthesized polypeptides (RiPP), 92% of which were unique and non-homologous to known ones. Plasmids and mobile genetic elements are present in strains of L. reuteri (NPLps01.et_L.r and NPLps02.uf_L.r), Lactobacillus delbrueckii (NPLps01.et_L.d), Streptococcus thermophilus (NPLps06.ab_S.t), and E. faecium (NPLps07.nf_E.f). Our findings support the use of metagenomics to build better and efficient production and post-production practices for probiotic quality and safety assessment.
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Affiliation(s)
- Ghazal Aziz
- National Probiotic Laboratory, National Institute for Biotechnology and Genetic Engineering College (NIBGE-C), Punjab, 38000, Faisalabad, Pakistan
- Pakistan Institute of Engineering and Applied Sciences (PIEAS), Nilore, 45650, Islamabad (ICT), Pakistan
- Department of Food Science and Nutrition, Center for Microbial and Plant Genomics, University of Minnesota, 1500 Gortner Ave, St. Paul, MN, 55108, USA
| | - Arsalan Zaidi
- National Probiotic Laboratory, National Institute for Biotechnology and Genetic Engineering College (NIBGE-C), Punjab, 38000, Faisalabad, Pakistan.
- Pakistan Institute of Engineering and Applied Sciences (PIEAS), Nilore, 45650, Islamabad (ICT), Pakistan.
| | - Daniel J O ' Sullivan
- Department of Food Science and Nutrition, Center for Microbial and Plant Genomics, University of Minnesota, 1500 Gortner Ave, St. Paul, MN, 55108, USA
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Fishbein SRS, Mahmud B, Dantas G. Antibiotic perturbations to the gut microbiome. Nat Rev Microbiol 2023; 21:772-788. [PMID: 37491458 DOI: 10.1038/s41579-023-00933-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/15/2023] [Indexed: 07/27/2023]
Abstract
Antibiotic-mediated perturbation of the gut microbiome is associated with numerous infectious and autoimmune diseases of the gastrointestinal tract. Yet, as the gut microbiome is a complex ecological network of microorganisms, the effects of antibiotics can be highly variable. With the advent of multi-omic approaches for systems-level profiling of microbial communities, we are beginning to identify microbiome-intrinsic and microbiome-extrinsic factors that affect microbiome dynamics during antibiotic exposure and subsequent recovery. In this Review, we discuss factors that influence restructuring of the gut microbiome on antibiotic exposure. We present an overview of the currently complex picture of treatment-induced changes to the microbial community and highlight essential considerations for future investigations of antibiotic-specific outcomes. Finally, we provide a synopsis of available strategies to minimize antibiotic-induced damage or to restore the pretreatment architectures of the gut microbial community.
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Affiliation(s)
- Skye R S Fishbein
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Bejan Mahmud
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Gautam Dantas
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO, USA.
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA.
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Wiradiputra MRD, Thirapanmethee K, Khuntayaporn P, Wanapaisan P, Chomnawang MT. Comparative genotypic characterization related to antibiotic resistance phenotypes of clinical carbapenem-resistant Acinetobacter baumannii MTC1106 (ST2) and MTC0619 (ST25). BMC Genomics 2023; 24:689. [PMID: 37978344 PMCID: PMC10655397 DOI: 10.1186/s12864-023-09734-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 10/11/2023] [Indexed: 11/19/2023] Open
Abstract
BACKGROUND The prevalence of Acinetobacter baumannii in nosocomial infections and its remarkable ability to develop antimicrobial resistance have been a critical issue in hospital settings. Here, we examined the genomic features related to resistance phenotype displayed by carbapenem-resistant A. baumannii (CRAB) MTC1106 (ST2) and MTC0619 (ST25). RESULTS Resistome analysis of both strains revealed that MTC1106 possessed higher numbers of antimicrobial resistance genes compared to MTC0619. Some of those genetic determinants were present in accordance with the susceptibility profile of the isolates. The predicted ISAba1 region upstream of blaOXA-23 gene was related to carbapenem resistance since this IS element was well-characterized to mediate overexpression of carbapenemase genes and eventually provided capability to confer resistance. Unlike MTC0619 strain, which only carried class B and D β-lactamase genes, MTC1106 strain also possessed blaTEM-1D, a class A β-lactamase. Regarding to aminoglycosides resistance, MTC0619 contained 5 related genes in which all of them belonged to three groups of aminoglycosides modifying enzyme (AME), namely, N-acetyltransferase (AAC), O-nucleotidyltransferase (ANT), and O-phosphotransferase (APH). On the other hand, MTC1106 lacked only the AAC of which found in MTC0619, yet it also carried an armA gene encoding for 16S rRNA methyltransferase. Two macrolides resistance genes, mph(E) and msr(E), were identified next to the armA gene of MTC1106 isolate in which they encoded for macrolide 2'-phosphotransferase and ABC-type efflux pump, respectively. Besides acquired resistance genes, some chromosomal genes and SNPs associated with resistance to fluoroquinolones (i.e. gyrA and parC) and colistin (i.e. pmrCAB, eptA, and emrAB) were observed. However, gene expression analysis suggested that the genetic determinants significantly contributing to low-level colistin resistance remained unclear. In addition, similar number of efflux pumps genes were identified in both lineages with only the absence of adeC, a part of adeABC RND-type multidrug efflux pump in MTC0619 strain. CONCLUSIONS We found that MTC1106 strain harbored more antimicrobial resistance genes and showed higher resistance to antibiotics than MTC0619 strain. Regarding genomic characterization, this study was likely the first genome comparative analysis of CARB that specifically included isolates belonging to ST2 and ST25 which were widely spread in Thailand. Taken altogether, this study suggests the importance to monitor the resistance status of circulating A. baumannii clones and identify genes that may contribute to shifting the resistance trend among isolates.
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Affiliation(s)
- Made Rai Dwitya Wiradiputra
- Antimicrobial Resistance Interdisciplinary Group (AmRIG), Faculty of Pharmacy, Mahidol University, Bangkok, Thailand
- Biopharmaceutical Sciences Program, Faculty of Pharmacy, Mahidol University, Bangkok, Thailand
| | - Krit Thirapanmethee
- Antimicrobial Resistance Interdisciplinary Group (AmRIG), Faculty of Pharmacy, Mahidol University, Bangkok, Thailand
- Department of Microbiology, Faculty of Pharmacy, Mahidol University, Bangkok, Thailand
| | - Piyatip Khuntayaporn
- Antimicrobial Resistance Interdisciplinary Group (AmRIG), Faculty of Pharmacy, Mahidol University, Bangkok, Thailand
- Department of Microbiology, Faculty of Pharmacy, Mahidol University, Bangkok, Thailand
| | - Pagakrong Wanapaisan
- Antimicrobial Resistance Interdisciplinary Group (AmRIG), Faculty of Pharmacy, Mahidol University, Bangkok, Thailand
- Department of Microbiology, Faculty of Pharmacy, Mahidol University, Bangkok, Thailand
| | - Mullika Traidej Chomnawang
- Antimicrobial Resistance Interdisciplinary Group (AmRIG), Faculty of Pharmacy, Mahidol University, Bangkok, Thailand.
- Department of Microbiology, Faculty of Pharmacy, Mahidol University, Bangkok, Thailand.
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Brumfield KD, Usmani M, Santiago S, Singh K, Gangwar M, Hasan NA, Netherland M, Deliz K, Angelini C, Beatty NL, Huq A, Jutla AS, Colwell RR. Genomic diversity of Vibrio spp. and metagenomic analysis of pathogens in Florida Gulf coastal waters following Hurricane Ian. mBio 2023; 14:e0147623. [PMID: 37931127 PMCID: PMC10746180 DOI: 10.1128/mbio.01476-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 08/30/2023] [Indexed: 11/08/2023] Open
Abstract
Changing climatic conditions influence parameters associated with the growth of pathogenic Vibrio spp. in the environment and, hence, are linked to increased incidence of vibriosis. Between 1992 and 2022, a long-term increase in Vibrio spp. infections was reported in Florida, USA. Furthermore, a spike in Vibrio spp. infections was reported post Hurricane Ian, a category five storm that made landfall in Florida on 28 September 2022. During October 2022, water and oyster samples were collected from three stations in Lee County in an area significantly impacted by Ian. Vibrio spp. were isolated, and whole-genome sequencing and phylogenetic analysis were done, with a focus on Vibrio parahaemolyticus and Vibrio vulnificus to provide genetic insight into pathogenic strains circulating in the environment. Metagenomic analysis of water samples provided insight with respect to human health-related factors, notably the detection of approximately 12 pathogenic Vibrio spp., virulence and antibiotic resistance genes, and mobile genetic elements, including the SXT/R391 family of integrative conjugative elements. Environmental parameters were monitored as part of a long-term time series analysis done using satellite remote sensing. In addition to anomalous rainfall and storm surge, changes in sea surface temperature and chlorophyll concentration during and after Ian favored the growth of Vibrio spp. In conclusion, genetic analysis coupled with environmental data and remote sensing provides useful public health information and, hence, constitute a valuable tool to proactively detect and characterize environmental pathogens, notably vibrios. These data can aid the development of early warning systems by yielding a larger source of information for public health during climate change. Evidence suggests warming temperatures are associated with the spread of potentially pathogenic Vibrio spp. and the emergence of human disease globally. Following Hurricane Ian, the State of Florida reported a sharp increase in the number of reported Vibrio spp. infections and deaths. Hence, monitoring of pathogens, including vibrios, and environmental parameters influencing their occurrence is critical to public health. Here, DNA sequencing was used to investigate the genomic diversity of Vibrio parahaemolyticus and Vibrio vulnificus, both potential human pathogens, in Florida coastal waters post Hurricane Ian, in October 2022. Additionally, the microbial community of water samples was profiled to detect the presence of Vibrio spp. and other microorganisms (bacteria, fungi, protists, and viruses) present in the samples. Long-term environmental data analysis showed changes in environmental parameters during and after Ian were optimal for the growth of Vibrio spp. and related pathogens. Collectively, results will be used to develop predictive risk models during climate change.
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Affiliation(s)
- Kyle D. Brumfield
- Maryland Pathogen Research Institute, University of Maryland, College Park, Maryland, USA
- University of Maryland Institute for Advanced Computer Studies, University of Maryland, College Park, Maryland, USA
| | - Moiz Usmani
- Department of Environmental Engineering Sciences, Geohealth and Hydrology Laboratory, University of Florida, Gainesville, Florida, USA
| | - Sanneri Santiago
- Department of Environmental Engineering Sciences, Engineering School of Sustainable Infrastructure and Environment, University of Florida, Gainesville, Florida, USA
| | - Komalpreet Singh
- Department of Environmental Engineering Sciences, Geohealth and Hydrology Laboratory, University of Florida, Gainesville, Florida, USA
| | - Mayank Gangwar
- Department of Environmental Engineering Sciences, Geohealth and Hydrology Laboratory, University of Florida, Gainesville, Florida, USA
| | | | | | - Katherine Deliz
- Department of Environmental Engineering Sciences, Engineering School of Sustainable Infrastructure and Environment, University of Florida, Gainesville, Florida, USA
| | - Christine Angelini
- Department of Environmental Engineering Sciences, Engineering School of Sustainable Infrastructure and Environment, University of Florida, Gainesville, Florida, USA
| | - Norman L. Beatty
- Department of Medicine, Division of Infectious Diseases and Global Medicine, University of Florida, Gainesville, Florida, USA
| | - Anwar Huq
- Maryland Pathogen Research Institute, University of Maryland, College Park, Maryland, USA
| | - Antarpreet S. Jutla
- Department of Environmental Engineering Sciences, Geohealth and Hydrology Laboratory, University of Florida, Gainesville, Florida, USA
| | - Rita R. Colwell
- Maryland Pathogen Research Institute, University of Maryland, College Park, Maryland, USA
- University of Maryland Institute for Advanced Computer Studies, University of Maryland, College Park, Maryland, USA
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Wang Q, Peng K, Liu Z, Li Y, Xiao X, Du XD, Li R, Wang Z. Genomic insights into linezolid-resistant Enterococci revealed its evolutionary diversity and poxtA copy number heterogeneity. Int J Antimicrob Agents 2023; 62:106929. [PMID: 37487950 DOI: 10.1016/j.ijantimicag.2023.106929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 07/03/2023] [Accepted: 07/15/2023] [Indexed: 07/26/2023]
Abstract
OBJECTIVES This study aimed to determine the molecular mechanisms of linezolid-resistant enterococci (LRE) in swine slaughterhouses in China and apply the "One Health" perspective to analyse the evolutionary dynamics of poxtA-positive E. faecium in clinical and non-clinical settings worldwide. METHODS The phenotypic and genomic characteristics of multiple LRE isolates were systematically investigated using antimicrobial susceptibility testing, transfer assays, evolutionary experiments, quantitative RT-PCR assays, whole-genome sequencing, and bioinformatics analyses. RESULTS Swine faeces served as a significant reservoir for LRE isolates, and optrA and poxtA were the primary contributors to linezolid resistance. Co-occurrence network analysis revealed a significant interconnection between optrA and several other ARGs. The poxtA copy number heterogeneity and polymorphism were initially observed in E. faecium parental and evolved isolates. The poxtA-carrying tandem repeat region exhibits high mobility and has undergone extensive duplication owing to linezolid pressure. The poxtA copy number varies from four copies on the plasmid of E. faecium IC25 to 11 copies on the plasmid and six copies on the chromosome in the evolved isolate IC25-50_poxtA. Furthermore, phylogenetic analysis of 185 poxtA-positive E. faecium strains worldwide found that one isolate from a French patient in 2018 shared only two SNPs with CC17 E. faecium isolates IC25 and IC7-2 from this study, highlighting the potential global transmission of CC17 poxtA-positive E. faecium between humans and animals. CONCLUSION This study identified amplification of poxtA as a response of E. faecium to linezolid pressure. Phylogenetic analysis shed light on the potential global transmission of hospital-associated CC17 poxtA-positive E. faecium in clinical and non-clinical settings.
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Affiliation(s)
- Qiaojun Wang
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, P.R. China; Institute of Comparative Medicine, Yangzhou University, Yangzhou, Jiangsu, P. R. China
| | - Kai Peng
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, P.R. China; Institute of Comparative Medicine, Yangzhou University, Yangzhou, Jiangsu, P. R. China
| | - Ziyi Liu
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, P.R. China; Institute of Comparative Medicine, Yangzhou University, Yangzhou, Jiangsu, P. R. China
| | - Yan Li
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, P.R. China; Institute of Comparative Medicine, Yangzhou University, Yangzhou, Jiangsu, P. R. China
| | - Xia Xiao
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, P.R. China; Institute of Comparative Medicine, Yangzhou University, Yangzhou, Jiangsu, P. R. China
| | - Xiang-Dang Du
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, P. R. China
| | - Ruichao Li
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, P.R. China; Institute of Comparative Medicine, Yangzhou University, Yangzhou, Jiangsu, P. R. China.
| | - Zhiqiang Wang
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, P.R. China; Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou, Jiangsu, P. R. China.
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46
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Lee C, Polo RO, Zaheer R, Van Domselaar G, Zovoilis A, McAllister TA. Evaluation of metagenomic assembly methods for the detection and characterization of antimicrobial resistance determinants and associated mobilizable elements. J Microbiol Methods 2023; 213:106815. [PMID: 37699502 DOI: 10.1016/j.mimet.2023.106815] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 08/31/2023] [Accepted: 08/31/2023] [Indexed: 09/14/2023]
Abstract
Antimicrobial resistance genes (ARGs) can be transferred between members of a bacterial population by mobile genetic elements (MGE). Understanding the risk of these transfer events is important in monitoring and predicting antimicrobial resistance (AMR), especially in the context of a One Health Continuum. However, there is no universally accepted method for detection of ARGs and MGEs, and especially for determining their linkages. This study used publicly available shotgun metagenomic DNA short-read (Illumina, 100 bp paired-end) sequence data from samples across the One Health Continuum (including beef cattle composite feces from feedlots, catch basin water at feedlots, agricultural soil from feedlot manured surrounding fields, and urban/municipal sewage influent from two municipal wastewater treatment plants) to develop a workflow to identify and associate ARGs and MGEs. ARG- and MGE-based targeted-assemblies with available short-read data were unable to meet this analysis goal. In contrast, de novo assembly of contigs provided enough sequence context to associate ARGs and MGEs, without compromising discovery rate. However, to estimate the relative abundance of these elements, unassembled sequence data must still be used.
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Affiliation(s)
- Catrione Lee
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Government of Canada, 5403 1st Avenue South, Lethbridge, AB T1J 4B1, Canada; Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, AB T3M 2L7, Canada
| | - Rodrigo Ortega Polo
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Government of Canada, 5403 1st Avenue South, Lethbridge, AB T1J 4B1, Canada
| | - Rahat Zaheer
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Government of Canada, 5403 1st Avenue South, Lethbridge, AB T1J 4B1, Canada
| | - Gary Van Domselaar
- National Microbiology Laboratory, Public Health Agency of Canada, Government of Canada, 1015 Arlington Street, Winnipeg, MB R3E 3R2, Canada
| | - Athanasios Zovoilis
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, AB T3M 2L7, Canada
| | - Tim A McAllister
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Government of Canada, 5403 1st Avenue South, Lethbridge, AB T1J 4B1, Canada.
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47
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Zhang Y, Kitazumi A, Liao YT, de los Reyes BG, Wu VCH. Metagenomic investigation reveals bacteriophage-mediated horizontal transfer of antibiotic resistance genes in microbial communities of an organic agricultural ecosystem. Microbiol Spectr 2023; 11:e0022623. [PMID: 37754684 PMCID: PMC10581182 DOI: 10.1128/spectrum.00226-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 07/10/2023] [Indexed: 09/28/2023] Open
Abstract
Agricultural microbiomes are major reservoirs of antibiotic resistance genes (ARGs), posing continuous risks to human health. To understand the role of bacteriophages as vehicles for the horizontal transfer of ARGs in the agricultural microbiome, we investigated the diversity of bacterial and viral microbiota from fecal and environmental samples on an organic farm. The profiles of the microbiome indicated the highest abundance of Bacteroidetes, Firmicutes, and Proteobacteria phyla in animal feces, with varying Actinobacteria and Spirochaetes abundance across farm animals. The most predominant composition in environmental samples was the phylum Proteobacteria. Compared to the microbiome profiles, the trends in virome indicated much broader diversity with more specific signatures between the fecal and environmental samples. Overall, viruses belonging to the order Caudovirales were the most prevalent across the agricultural samples. Additionally, the similarities within and between fecal and environmental components of the agricultural environment based on ARG-associated bacteria alone were much lower than those of total microbiome composition. However, there were significant similarities in the profiles of ARG-associated viruses across the fecal and environmental components. Moreover, the predictive models of phage-bacterial interactions on bipartite ARG transfer networks indicated that phages belonging to the order Caudovirales, particularly in the Siphoviridae family, contained diverse ARG types in different samples. Their interaction with various bacterial hosts further implied the important role of bacteriophages in ARG transmission across bacterial populations. Our findings provided a novel insight into the potential mechanisms of phage-mediated ARG transmission and their correlation with resistome evolution in natural agricultural environments. IMPORTANCE Antibiotic resistance has become a serious health concern worldwide. The potential impact of viruses, bacteriophages in particular, on spreading antibiotic resistance genes is still controversial due to the complexity of bacteriophage-bacterial interactions within diverse environments. In this study, we determined the microbiome profiles and the potential antibiotic resistance gene (ARG) transfer between bacterial and viral populations in different agricultural samples using a high-resolution analysis of the metagenomes. The results of this study provide compelling genetic evidence for ARG transfer through bacteriophage-bacteria interactions, revealing the inherent risks associated with bacteriophage-mediated ARG transfer across the agricultural microbiome.
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Affiliation(s)
- Yujie Zhang
- U.S. Department of Agriculture, Produce Safety and Microbiology Research Unit, Agricultural Research Service, Western Regional Research Center, Albany, California, USA
| | - Ai Kitazumi
- Department of Plant and Soil Science, Texas Tech University, Lubbock, Texas, USA
| | - Yen-Te Liao
- U.S. Department of Agriculture, Produce Safety and Microbiology Research Unit, Agricultural Research Service, Western Regional Research Center, Albany, California, USA
| | | | - Vivian C. H. Wu
- U.S. Department of Agriculture, Produce Safety and Microbiology Research Unit, Agricultural Research Service, Western Regional Research Center, Albany, California, USA
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Akter S, Rahman MS, Ali H, Minch B, Mehzabin K, Siddique MM, Galib SM, Yesmin F, Azmuda N, Adnan N, Hasan NA, Rahman SR, Moniruzzaman M, Ahmed MF. Phylogenetic diversity and functional potential of the microbial communities along the Bay of Bengal coast. Sci Rep 2023; 13:15976. [PMID: 37749192 PMCID: PMC10520010 DOI: 10.1038/s41598-023-43306-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 09/21/2023] [Indexed: 09/27/2023] Open
Abstract
The Bay of Bengal, the world's largest bay, is bordered by populous countries and rich in resources like fisheries, oil, gas, and minerals, while also hosting diverse marine ecosystems such as coral reefs, mangroves, and seagrass beds; regrettably, its microbial diversity and ecological significance have received limited research attention. Here, we present amplicon (16S and 18S) profiling and shotgun metagenomics data regarding microbial communities from BoB's eastern coast, viz., Saint Martin and Cox's Bazar, Bangladesh. From the 16S barcoding data, Proteobacteria appeared to be the dominant phylum in both locations, with Alteromonas, Methylophaga, Anaerospora, Marivita, and Vibrio dominating in Cox's Bazar and Pseudoalteromonas, Nautella, Marinomonas, Vibrio, and Alteromonas dominating the Saint Martin site. From the 18S barcoding data, Ochrophyta, Chlorophyta, and Protalveolata appeared among the most abundant eukaryotic divisions in both locations, with significantly higher abundance of Choanoflagellida, Florideophycidae, and Dinoflagellata in Cox's Bazar. The shotgun sequencing data reveals that in both locations, Alteromonas is the most prevalent bacterial genus, closely paralleling the dominance observed in the metabarcoding data, with Methylophaga in Cox's Bazar and Vibrio in Saint Martin. Functional annotations revealed that the microbial communities in these samples harbor genes for biofilm formation, quorum sensing, xenobiotics degradation, antimicrobial resistance, and a variety of other processes. Together, these results provide the first molecular insight into the functional and phylogenetic diversity of microbes along the BoB coast of Bangladesh. This baseline understanding of microbial community structure and functional potential will be critical for assessing impacts of climate change, pollution, and other anthropogenic disturbances on this ecologically and economically vital bay.
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Affiliation(s)
- Salma Akter
- Department of Microbiology, Jahangirnagar University, Savar, Dhaka, Bangladesh
| | - M Shaminur Rahman
- Department of Microbiology, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Hazrat Ali
- Department of Microbiology, Jahangirnagar University, Savar, Dhaka, Bangladesh
| | - Benjamin Minch
- Department of Marine Biology and Ecology, Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, Coral Gables, FL, USA
| | - Kaniz Mehzabin
- Department of Microbiology, Jahangirnagar University, Savar, Dhaka, Bangladesh
| | - Md Moradul Siddique
- Department of Computer Science and Engineering, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Syed Md Galib
- Department of Computer Science and Engineering, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Farida Yesmin
- Department of Microbiology, Jahangirnagar University, Savar, Dhaka, Bangladesh
| | - Nafisa Azmuda
- Department of Microbiology, Jahangirnagar University, Savar, Dhaka, Bangladesh
| | - Nihad Adnan
- Department of Microbiology, Jahangirnagar University, Savar, Dhaka, Bangladesh
| | - Nur A Hasan
- University of Maryland, College Park, MD, USA
| | | | - Mohammad Moniruzzaman
- Department of Marine Biology and Ecology, Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, Coral Gables, FL, USA.
| | - Md Firoz Ahmed
- Department of Microbiology, Jahangirnagar University, Savar, Dhaka, Bangladesh.
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49
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Hansen ZA, Vasco K, Rudrik JT, Scribner KT, Zhang L, Manning SD. Recovery of the gut microbiome following enteric infection and persistence of antimicrobial resistance genes in specific microbial hosts. Sci Rep 2023; 13:15524. [PMID: 37726374 PMCID: PMC10509190 DOI: 10.1038/s41598-023-42822-7] [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: 04/18/2023] [Accepted: 09/15/2023] [Indexed: 09/21/2023] Open
Abstract
Enteric pathogens cause widespread foodborne illness and are increasingly resistant to important antibiotics yet their ecological impact on the gut microbiome and resistome is not fully understood. Herein, shotgun metagenome sequencing was applied to stool DNA from 60 patients (cases) during an enteric bacterial infection and after recovery (follow-ups). Overall, the case samples harbored more antimicrobial resistance genes (ARGs) with greater resistome diversity than the follow-up samples (p < 0.001), while follow-ups had more diverse gut microbiota (p < 0.001). Although cases were primarily defined by genera Escherichia, Salmonella, and Shigella along with ARGs for multi-compound and multidrug resistance, follow-ups had a greater abundance of Bacteroidetes and Firmicutes phyla and resistance genes for tetracyclines, macrolides, lincosamides, and streptogramins, and aminoglycosides. A host-tracking analysis revealed that Escherichia was the primary bacterial host of ARGs in both cases and follow-ups, with a greater abundance occurring during infection. Eleven distinct extended spectrum beta-lactamase (ESBL) genes were identified during infection, with some detectable upon recovery, highlighting the potential for gene transfer within the community. Because of the increasing incidence of disease caused by foodborne pathogens and their role in harboring and transferring resistance determinants, this study enhances our understanding of how enteric infections impact human gut ecology.
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Affiliation(s)
- Zoe A Hansen
- Departments of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, 48824, USA
| | - Karla Vasco
- Departments of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, 48824, USA
| | - James T Rudrik
- Bureau of Laboratories, The Michigan Department of Health and Human Services, Lansing, MI, 48906, USA
| | - Kim T Scribner
- Fisheries and Wildlife, Michigan State University, East Lansing, MI, 48824, USA
| | - Lixin Zhang
- Departments of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, 48824, USA
- Epidemiology and Biostatistics, Michigan State University, East Lansing, MI, 48824, USA
| | - Shannon D Manning
- Departments of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, 48824, USA.
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Umanets A, Surono IS, Venema K. I am better than I look: genome based safety assessment of the probiotic Lactiplantibacillus plantarum IS-10506. BMC Genomics 2023; 24:518. [PMID: 37667166 PMCID: PMC10478331 DOI: 10.1186/s12864-023-09495-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 06/30/2023] [Indexed: 09/06/2023] Open
Abstract
BACKGROUND Safety of probiotic strains that are used in human and animal trials is a prerequisite. Genome based safety assessment of probiotics has gained popularity due its cost efficiency and speed, and even became a part of national regulation on foods containing probiotics in Indonesia. However, reliability of the safety assessment based only on a full genome sequence is not clear. Here, for the first time, we sequenced, assembled, and analysed the genome of the probiotic strain Lactiplantibacillus plantarum IS-10506, that was isolated from dadih, a traditional fermented buffalo milk. The strain has already been used as a probiotic for more than a decade, and in several clinical trials proven to be completely safe. METHODS The genome of the probiotic strain L. plantarum IS-10506 was sequenced using Nanopore sequencing technology, assembled, annotated and screened for potential harmful (PH) and beneficial genomic features. The presence of the PH features was assessed from general annotation, as well as with the use of specialised tools. In addition, PH regions in the genome were compared to all other probiotic and non-probiotic L. plantarum strains available in the NCBI RefSeq database. RESULTS For the first time, a high-quality complete genome of L. plantarum IS-10506 was obtained, and an extensive search for PH and a beneficial signature was performed. We discovered a number of PH features within the genome of L. plantarum IS-10506 based on the general annotation, including various antibiotic resistant genes (AMR); however, with a few exceptions, bioinformatics tools specifically developed for AMR detection did not confirm their presence. We further demonstrated the presence of the detected PH genes across multiple L. plantarum strains, including probiotics, and overall high genetic similarities between strains. CONCLUSION The genome of L. plantarum IS-10506 is predicted to have several PH features. However, the strain has been utilized as a probiotic for over a decade in several clinical trials without any adverse effects, even in immunocompromised children with HIV infection and undernourished children. This implies the presence of PH feature signatures within the probiotic genome does not necessarily indicate their manifestation during administration. Importantly, specialized tools for the search of PH features were found more robust and should be preferred over manual searches in a general annotation.
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Affiliation(s)
- Alexander Umanets
- Centre for Healthy Eating & Food Innovation (HEFI), Maastricht University - campus Venlo, Villafloraweg 1, Venlo, 5928 SZ, the Netherlands
- Chair Group Youth Food and Health, Faculty of Science and Engineering, Maastricht University - campus Venlo, Villafloraweg 1, Venlo, 5928 SZ, the Netherlands
| | - Ingrid S Surono
- Food Technology Department, Faculty of Engineering, Bina Nusantara University, Jakarta, 11480, Indonesia
| | - Koen Venema
- Centre for Healthy Eating & Food Innovation (HEFI), Maastricht University - campus Venlo, Villafloraweg 1, Venlo, 5928 SZ, the Netherlands.
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