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Dutta S, Kothari S, Singh D, Ghosh S, Narayan Sarangi A, Sanjita Behera S, Prajapati S, Kumar Sinha P, Prusty A, Tripathy S. Novel oceanic cyanobacterium isolated from Bangaram island with profound acid neutralizing ability is proposed as Leptolyngbya iicbica sp. nov. strain LK. Mol Phylogenet Evol 2024; 197:108092. [PMID: 38723790 DOI: 10.1016/j.ympev.2024.108092] [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: 11/10/2023] [Revised: 02/16/2024] [Accepted: 05/04/2024] [Indexed: 05/19/2024]
Abstract
An acid-neutralizing, filamentous, non-heterocytous, marine cyanobacterium named 'LK' has been isolated from the seashore of Bangaram Island, an atoll of Lakshadweep, India, and is described here as a novel species. LK has been characterized using morphological, ecological, and genomic features. Based on 16S rRNA, whole-genome sequencing, and marker gene-based analysis, LK has been identified as a new species. LK clustered with Leptolyngbya-like strains belonging to the LPP group but diverged from Leptolyngbya sensu stricto, indicating the polyphyletic nature of the Leptolyngbya genus. Leptolyngbya sp. SIOISBB and Halomicronema sp. CCY15110 were identified as LK's two closest phylogenetic neighbors in various phylogenetic studies. The analysis of 16S rRNA, ITS secondary structures, and genome relatedness indices such as AAI, ANI, and gANI strongly support LK as a novel species of the Leptolyngbya genus. The mechanism behind acid neutralization in LK has been delineated, attributing it to a surface phenomenon most likely due to the presence of salts of calcium, magnesium, sodium, and potassium. We name LK as Leptolyngbya iicbica strain LK which is a novel species with prominent acidic pH-neutralizing properties.
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Affiliation(s)
- Subhajeet Dutta
- Computational Genomics Lab, Structural Biology and Bioinformatics Division, CSIR- Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata 700032, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Shreya Kothari
- Computational Genomics Lab, Structural Biology and Bioinformatics Division, CSIR- Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata 700032, India
| | - Deeksha Singh
- Computational Genomics Lab, Structural Biology and Bioinformatics Division, CSIR- Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata 700032, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Samrat Ghosh
- Computational Genomics Lab, Structural Biology and Bioinformatics Division, CSIR- Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata 700032, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Aditya Narayan Sarangi
- Computational Genomics Lab, Structural Biology and Bioinformatics Division, CSIR- Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata 700032, India
| | - Smruti Sanjita Behera
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India; Molecular Genetics Division, CSIR Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata 700032, India
| | - Satish Prajapati
- Advanced Materials and Chemical Characterisation Division (AMCCD), CSIR-Central Glass & Ceramic Research Institute (CGCRI), Kolkata 700 032, West Bengal, India
| | - Prasanta Kumar Sinha
- Advanced Materials and Chemical Characterisation Division (AMCCD), CSIR-Central Glass & Ceramic Research Institute (CGCRI), Kolkata 700 032, West Bengal, India
| | - Asharani Prusty
- Computational Genomics Lab, Structural Biology and Bioinformatics Division, CSIR- Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata 700032, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Sucheta Tripathy
- Computational Genomics Lab, Structural Biology and Bioinformatics Division, CSIR- Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata 700032, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
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Prager KC, Danil K, Wurster E, Colegrove KM, Galloway R, Kettler N, Mani R, McDonough RF, Sahl JW, Stone NE, Wagner DM, Lloyd-Smith JO. Detection of Leptospira kirschneri in a short-beaked common dolphin (Delphinus delphis delphis) stranded off the coast of southern California, USA. BMC Vet Res 2024; 20:266. [PMID: 38902706 PMCID: PMC11188202 DOI: 10.1186/s12917-024-04111-x] [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: 01/22/2024] [Accepted: 06/04/2024] [Indexed: 06/22/2024] Open
Abstract
BACKGROUND Pathogenic Leptospira species are globally important zoonotic pathogens capable of infecting a wide range of host species. In marine mammals, reports of Leptospira have predominantly been in pinnipeds, with isolated reports of infections in cetaceans. CASE PRESENTATION On 28 June 2021, a 150.5 cm long female, short-beaked common dolphin (Delphinus delphis delphis) stranded alive on the coast of southern California and subsequently died. Gross necropsy revealed multifocal cortical pallor within the reniculi of the kidney, and lymphoplasmacytic tubulointerstitial nephritis was observed histologically. Immunohistochemistry confirmed Leptospira infection, and PCR followed by lfb1 gene amplicon sequencing suggested that the infecting organism was L.kirschneri. Leptospira DNA capture and enrichment allowed for whole-genome sequencing to be conducted. Phylogenetic analyses confirmed the causative agent was a previously undescribed, divergent lineage of L.kirschneri. CONCLUSIONS We report the first detection of pathogenic Leptospira in a short-beaked common dolphin, and the first detection in any cetacean in the northeastern Pacific Ocean. Renal lesions were consistent with leptospirosis in other host species, including marine mammals, and were the most significant lesions detected overall, suggesting leptospirosis as the likely cause of death. We identified the cause of the infection as L.kirschneri, a species detected only once before in a marine mammal - a northern elephant seal (Mirounga angustirostris) of the northeastern Pacific. These findings raise questions about the mechanism of transmission, given the obligate marine lifestyle of cetaceans (in contrast to pinnipeds, which spend time on land) and the commonly accepted view that Leptospira are quickly killed by salt water. They also raise important questions regarding the source of infection, and whether it arose from transmission among marine mammals or from terrestrial-to-marine spillover. Moving forward, surveillance and sampling must be expanded to better understand the extent to which Leptospira infections occur in the marine ecosystem and possible epidemiological linkages between and among marine and terrestrial host species. Generating Leptospira genomes from different host species will yield crucial information about possible transmission links, and our study highlights the power of new techniques such as DNA enrichment to illuminate the complex ecology of this important zoonotic pathogen.
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Affiliation(s)
- K C Prager
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, CA, 90095, USA.
| | - Kerri Danil
- Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, La Jolla, CA, 92037, USA
| | - Elyse Wurster
- Ocean Associates Inc. Under Contract to Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, La Jolla, CA, 92037, USA
| | - Kathleen M Colegrove
- Zoological Pathology Program, University of Illinois College of Veterinary Medicine, 3300 Golf Rd, Brookfield, IL, 60513, USA
| | - Renee Galloway
- National Center for Emerging and Zoonotic Infectious Diseases, Centers for Diseases Control and Prevention, Atlanta, GA, 30333, USA
| | - Niesa Kettler
- Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Michigan State University, East Lansing, Michigan, 48825, USA
| | - Rinosh Mani
- Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Michigan State University, East Lansing, Michigan, 48825, USA
| | - Ryelan F McDonough
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, 86011, USA
| | - Jason W Sahl
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, 86011, USA
| | - Nathan E Stone
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, 86011, USA
| | - David M Wagner
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, 86011, USA
| | - James O Lloyd-Smith
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, CA, 90095, USA
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Wang S, Nie W, Gu Q, Wang X, Yang D, Li H, Wang P, Liao W, Huang J, Yuan Q, Zhou S, Ahmad I, Kotaro K, Chen G, Zhu B. Spread of antibiotic resistance genes in drinking water reservoirs: Insights from a deep metagenomic study using a curated database. WATER RESEARCH 2024; 256:121572. [PMID: 38621316 DOI: 10.1016/j.watres.2024.121572] [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: 01/05/2024] [Revised: 03/13/2024] [Accepted: 04/03/2024] [Indexed: 04/17/2024]
Abstract
The exploration of antibiotic resistance genes (ARGs) in drinking water reservoirs is an emerging field. Using a curated database, we enhanced the ARG detection and conducted a comprehensive analysis using 2.2 Tb of deep metagenomic sequencing data to determine the distribution of ARGs across 16 drinking water reservoirs and associated environments. Our findings reveal a greater diversity of ARGs in sediments than in water, underscoring the importance of extensive background surveys. Crucial ARG carriers-specifically Acinetobacter, Pseudomonas, and Mycobacterium were identified in drinking water reservoirs. Extensive analysis of the data uncovered a considerable concern for drinking water safety, particularly in regions reliant on river sources. Mobile genetic elements have been found to contribute markedly to the propagation of ARGs. The results of this research suggest that the establishment of drinking water reservoirs for supplying raw water may be an effective strategy for alleviating the spread of water-mediated ARGs.
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Affiliation(s)
- Sai Wang
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Shanghai Cooperative Innovation Center for Modern Seed Industry, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Wenhan Nie
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Shanghai Cooperative Innovation Center for Modern Seed Industry, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China; Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, Tokyo, 162-8640, Japan.
| | - Qing Gu
- Zhejiang Province Ecological and Environmental Monitoring Centre, Zhejiang Key Laboratory of Ecological and Environmental Monitoring, Forewarning and Quality Control, Hangzhou, 310012, China
| | - Xie Wang
- Southwest China Mountain Agricultural Environment Key Laboratory, Ministry of Agriculture and Rural Areas, Institute of Agricultural Resources and Environment, Sichuan Academy of Agricultural Sciences, Shizishan Rd, Chengdu, 610066, China
| | - Danping Yang
- Observation and Research Station of Ecological Restoration for Chongqing Typical Mining Areas, Ministry of Natural Resources (Chongqing Institute of Geology and Mineral Resources), Chongqing, 401120. China
| | - Hongyu Li
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Shanghai Cooperative Innovation Center for Modern Seed Industry, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Peihong Wang
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Shanghai Cooperative Innovation Center for Modern Seed Industry, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Weixue Liao
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Shanghai Cooperative Innovation Center for Modern Seed Industry, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jin Huang
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Shanghai Cooperative Innovation Center for Modern Seed Industry, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Quan Yuan
- School of Energy and Power Engineering, Xihua University, Chengdu, 610039, China
| | - Shengli Zhou
- Zhejiang Province Ecological and Environmental Monitoring Centre, Zhejiang Key Laboratory of Ecological and Environmental Monitoring, Forewarning and Quality Control, Hangzhou, 310012, China
| | - Iftikhar Ahmad
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Shanghai Cooperative Innovation Center for Modern Seed Industry, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China; Department of Environmental Sciences, COMSATS University Islamabad, Vehari-Campus, Vehari, 61100, Pakistan
| | - Kiga Kotaro
- Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, Tokyo, 162-8640, Japan
| | - Gongyou Chen
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Shanghai Cooperative Innovation Center for Modern Seed Industry, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Bo Zhu
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Shanghai Cooperative Innovation Center for Modern Seed Industry, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China.
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Goravey W, Tsui CK, Ali GA, Najim MS, Shunnar K, Ibrahim EB, Ahmed MAS, Maslamani MA, Sultan A, Skariah S, Hadi HA. Clinical, phenotypic, and genotypic characteristics of ESBL-producing Salmonella enterica bloodstream infections from Qatar. IJID REGIONS 2024; 11:100368. [PMID: 38742235 PMCID: PMC11089346 DOI: 10.1016/j.ijregi.2024.100368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 04/16/2024] [Accepted: 04/17/2024] [Indexed: 05/16/2024]
Abstract
Background Resistant Salmonella infections are a major global public health challenge particularly for multidrug-resistant (MDR) isolates manifesting as bloodstream infections (BSIs). Objectives To evaluate clinical, phenotypic, and genotypic characteristics of extended-spectrum beta-lactamase (ESBL) producing Salmonella enterica BSIs from Qatar. Methods Phenotypic ESBL Salmonella enterica from adult patients presenting with positive BSIs were collected between January 2019 to May 2020. Microbiological identification and characterization were performed using standard methods while genetic characteristics were examined through whole genome sequencing studies. Results Of 151 episodes of Salmonella enterica BSI, 15 (10%) phenotypic ESBL isolates were collected. Recent travel was recorded in most cases (80%) with recent exposure to antimicrobials (27%). High-level resistance to quinolines, aminoglycosides, and cephalosporins was recorded (80-100%) while meropenem, tigecycline and colistin demonstrated universal susceptibility. Genomic evaluation demonstrated dominance of serotype Salmonella Typhi sequence type 1 (93%) while antimicrobial resistance genes revealed dominance of aminoglycoside resistance (100%), qnrS1 quinolones resistance (80%), blaCTX-M-15 ESBLs (86.7%), and paucity of AmpC resistance genes (6.7%). Conclusions Invasive MDR Salmonella enterica is mainly imported, connected to patients from high prevalent regions with recent travel and antimicrobial use caused by specific resistant clones. In suspected cases of multidrug resistance, carbapenem therapy is recommended.
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Affiliation(s)
- Wael Goravey
- Communicable Diseases Centre, Hamad Medical Corporation, Doha, Qatar
| | - Clement K.M. Tsui
- Infectious Diseases Research Laboratory, National Centre for Infectious Diseases, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
- Division of Infectious Diseases, Faculty of Medicine of British Columbia, Canada
| | - Gawahir A. Ali
- Communicable Diseases Centre, Hamad Medical Corporation, Doha, Qatar
| | | | - Khalid Shunnar
- Department of Internal Medicine, Hamad Medical Corporation, Doha, Qatar
| | - Emad B. Ibrahim
- Division of Microbiology, Department of Laboratory Medicine and Pathology, Hamad Medical Corporation, Doha, Qatar
- Biomedical Research Centre, Qatar University, Doha, Qatar
| | | | - Muna Al Maslamani
- Communicable Diseases Centre, Hamad Medical Corporation, Doha, Qatar
| | - Ali Sultan
- Department of Microbiology and Immunology, Weill Cornell Medicine, Education City, Qatar
| | - Sini Skariah
- Department of Microbiology and Immunology, Weill Cornell Medicine, Education City, Qatar
| | - Hamad Abdel Hadi
- Communicable Diseases Centre, Hamad Medical Corporation, Doha, Qatar
- College of Medicine, Qatar University, Doha, Qatar
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Gupta A, Mirarab S, Turakhia Y. Accurate, scalable, and fully automated inference of species trees from raw genome assemblies using ROADIES. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.27.596098. [PMID: 38854139 PMCID: PMC11160643 DOI: 10.1101/2024.05.27.596098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Inference of species trees plays a crucial role in advancing our understanding of evolutionary relationships and has immense significance for diverse biological and medical applications. Extensive genome sequencing efforts are currently in progress across a broad spectrum of life forms, holding the potential to unravel the intricate branching patterns within the tree of life. However, estimating species trees starting from raw genome sequences is quite challenging, and the current cutting-edge methodologies require a series of error-prone steps that are neither entirely automated nor standardized. In this paper, we present ROADIES, a novel pipeline for species tree inference from raw genome assemblies that is fully automated, easy to use, scalable, free from reference bias, and provides flexibility to adjust the tradeoff between accuracy and runtime. The ROADIES pipeline eliminates the need to align whole genomes, choose a single reference species, or pre-select loci such as functional genes found using cumbersome annotation steps. Moreover, it leverages recent advances in phylogenetic inference to allow multi-copy genes, eliminating the need to detect orthology. Using the genomic datasets released from large-scale sequencing consortia across three diverse life forms (placental mammals, pomace flies, and birds), we show that ROADIES infers species trees that are comparable in quality with the state-of-the-art approaches but in a fraction of the time. By incorporating optimal approaches and automating all steps from assembled genomes to species and gene trees, ROADIES is poised to improve the accuracy, scalability, and reproducibility of phylogenomic analyses.
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Affiliation(s)
- Anshu Gupta
- Department of Computer Science and Engineering, University of California, San Diego; San Diego, CA 92093, USA
| | - Siavash Mirarab
- Department of Electrical and Computer Engineering, University of California, San Diego; San Diego, CA 92093, USA
| | - Yatish Turakhia
- Department of Electrical and Computer Engineering, University of California, San Diego; San Diego, CA 92093, USA
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Břinda K, Lima L, Pignotti S, Quinones-Olvera N, Salikhov K, Chikhi R, Kucherov G, Iqbal Z, Baym M. Efficient and Robust Search of Microbial Genomes via Phylogenetic Compression. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.04.15.536996. [PMID: 37131636 PMCID: PMC10153118 DOI: 10.1101/2023.04.15.536996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Comprehensive collections approaching millions of sequenced genomes have become central information sources in the life sciences. However, the rapid growth of these collections has made it effectively impossible to search these data using tools such as BLAST and its successors. Here, we present a technique called phylogenetic compression, which uses evolutionary history to guide compression and efficiently search large collections of microbial genomes using existing algorithms and data structures. We show that, when applied to modern diverse collections approaching millions of genomes, lossless phylogenetic compression improves the compression ratios of assemblies, de Bruijn graphs, and k -mer indexes by one to two orders of magnitude. Additionally, we develop a pipeline for a BLAST-like search over these phylogeny-compressed reference data, and demonstrate it can align genes, plasmids, or entire sequencing experiments against all sequenced bacteria until 2019 on ordinary desktop computers within a few hours. Phylogenetic compression has broad applications in computational biology and may provide a fundamental design principle for future genomics infrastructure.
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7
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Hamond C, Adam EN, Stone NE, LeCount K, Anderson T, Putz EJ, Camp P, Hicks J, Stuber T, van der Linden H, Bayles DO, Sahl JW, Schlater LK, Wagner DM, Nally JE. Identification of equine mares as reservoir hosts for pathogenic species of Leptospira. Front Vet Sci 2024; 11:1346713. [PMID: 38784659 PMCID: PMC11112012 DOI: 10.3389/fvets.2024.1346713] [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: 11/29/2023] [Accepted: 04/24/2024] [Indexed: 05/25/2024] Open
Abstract
Equine leptospirosis can result in abortion, stillbirth, neonatal death, placentitis, and uveitis. Horses can also act as subclinical reservoir hosts of infection, which are characterized as asymptomatic carriers that persistently excrete leptospires and transmit disease. In this study, PCR and culture were used to assess urinary shedding of pathogenic Leptospira from 37 asymptomatic mares. Three asymptomatic mares, designated as H2, H8, and H9, were PCR-positive for lipL32, a gene specific for pathogenic species of Leptospira. One asymptomatic mare, H9, was culture-positive, and the recovered isolate was classified as L. kirschneri serogroup Australis serovar Rushan. DNA capture and enrichment of Leptospira genomic DNA from PCR-positive, culture-negative samples determined that asymptomatic mare H8 was also shedding L. kirschneri serogroup Australis, whereas asymptomatic mare H2 was shedding L. interrogans serogroup Icterohaemorrhagiae. Sera from all asymptomatic mares were tested by the microscopic agglutination test (MAT) and 35 of 37 (94.6%) were seropositive with titers ranging from 1:100 to 1:3200. In contrast to asymptomatic mares, mare H44 presented with acute spontaneous abortion and a serum MAT titer of 1:102,400 to L. interrogans serogroup Pomona serovar Pomona. Comparison of L. kirschneri serogroup Australis strain H9 with that of L. interrogans serogroup Pomona strain H44 in the hamster model of leptospirosis corroborated differences in virulence of strains. Since lipopolysaccharide (LPS) is a protective antigen in bacterin vaccines, the LPS of strain H9 (associated with subclinical carriage) was compared with strain H44 (associated with spontaneous abortion). This revealed different LPS profiles and immunoreactivity with reference antisera. It is essential to know what species and serovars of Leptospira are circulating in equine populations to design efficacious vaccines and diagnostic tests. Our results demonstrate that horses in the US can act as reservoir hosts of leptospirosis and shed diverse pathogenic Leptospira species via urine. This report also details the detection of L. kirschneri serogroup Australis serovar Rushan, a species and serotype of Leptospira, not previously reported in the US.
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Affiliation(s)
- Camila Hamond
- National Veterinary Services Laboratories, Animal and Plant Health Inspection Service, U.S. Department of Agriculture, Ames, IA, United States
- National Centers for Animal Health Leptospira Working Group, U.S. Department of Agriculture, Ames, IA, United States
| | - Emma N. Adam
- Department of Veterinary Science, University of Kentucky, Maxwell H. Gluck Equine Research Center, Lexington, KY, United States
| | - Nathan E. Stone
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, United States
| | - Karen LeCount
- National Veterinary Services Laboratories, Animal and Plant Health Inspection Service, U.S. Department of Agriculture, Ames, IA, United States
- National Centers for Animal Health Leptospira Working Group, U.S. Department of Agriculture, Ames, IA, United States
| | - Tammy Anderson
- National Veterinary Services Laboratories, Animal and Plant Health Inspection Service, U.S. Department of Agriculture, Ames, IA, United States
- National Centers for Animal Health Leptospira Working Group, U.S. Department of Agriculture, Ames, IA, United States
| | - Ellie J. Putz
- Infectious Bacterial Diseases Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Ames, IA, United States
| | - Patrick Camp
- National Veterinary Services Laboratories, Animal and Plant Health Inspection Service, U.S. Department of Agriculture, Ames, IA, United States
| | - Jessica Hicks
- National Veterinary Services Laboratories, Animal and Plant Health Inspection Service, U.S. Department of Agriculture, Ames, IA, United States
| | - Tod Stuber
- National Veterinary Services Laboratories, Animal and Plant Health Inspection Service, U.S. Department of Agriculture, Ames, IA, United States
| | - Hans van der Linden
- Department of Medical Microbiology and Infection Prevention, World Organisation for Animal Health (WOAH) and National Collaborating Centre for Reference and Research on Leptospirosis, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, Netherlands
| | - Darrell O. Bayles
- Infectious Bacterial Diseases Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Ames, IA, United States
| | - Jason W. Sahl
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, United States
| | - Linda K. Schlater
- National Veterinary Services Laboratories, Animal and Plant Health Inspection Service, U.S. Department of Agriculture, Ames, IA, United States
- National Centers for Animal Health Leptospira Working Group, U.S. Department of Agriculture, Ames, IA, United States
| | - David M. Wagner
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, United States
| | - Jarlath E. Nally
- National Centers for Animal Health Leptospira Working Group, U.S. Department of Agriculture, Ames, IA, United States
- Infectious Bacterial Diseases Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Ames, IA, United States
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Gündüz HA, Mreches R, Moosbauer J, Robertson G, To XY, Franzosa EA, Huttenhower C, Rezaei M, McHardy AC, Bischl B, Münch PC, Binder M. Optimized model architectures for deep learning on genomic data. Commun Biol 2024; 7:516. [PMID: 38693292 PMCID: PMC11063068 DOI: 10.1038/s42003-024-06161-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 04/08/2024] [Indexed: 05/03/2024] Open
Abstract
The success of deep learning in various applications depends on task-specific architecture design choices, including the types, hyperparameters, and number of layers. In computational biology, there is no consensus on the optimal architecture design, and decisions are often made using insights from more well-established fields such as computer vision. These may not consider the domain-specific characteristics of genome sequences, potentially limiting performance. Here, we present GenomeNet-Architect, a neural architecture design framework that automatically optimizes deep learning models for genome sequence data. It optimizes the overall layout of the architecture, with a search space specifically designed for genomics. Additionally, it optimizes hyperparameters of individual layers and the model training procedure. On a viral classification task, GenomeNet-Architect reduced the read-level misclassification rate by 19%, with 67% faster inference and 83% fewer parameters, and achieved similar contig-level accuracy with ~100 times fewer parameters compared to the best-performing deep learning baselines.
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Affiliation(s)
- Hüseyin Anil Gündüz
- Department of Statistics, LMU Munich, Munich, Germany
- Munich Center for Machine Learning, Munich, Germany
| | - René Mreches
- Department for Computational Biology of Infection Research, Helmholtz Center for Infection Research, 38124, Braunschweig, Germany
- Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany
| | - Julia Moosbauer
- Department of Statistics, LMU Munich, Munich, Germany
- Munich Center for Machine Learning, Munich, Germany
| | - Gary Robertson
- Department for Computational Biology of Infection Research, Helmholtz Center for Infection Research, 38124, Braunschweig, Germany
- Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany
| | - Xiao-Yin To
- Department of Statistics, LMU Munich, Munich, Germany
- Munich Center for Machine Learning, Munich, Germany
- Department for Computational Biology of Infection Research, Helmholtz Center for Infection Research, 38124, Braunschweig, Germany
- Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany
| | - Eric A Franzosa
- Department of Biostatistics, Harvard School of Public Health, Boston, MA, USA
| | - Curtis Huttenhower
- Department of Biostatistics, Harvard School of Public Health, Boston, MA, USA
| | - Mina Rezaei
- Department of Statistics, LMU Munich, Munich, Germany
- Munich Center for Machine Learning, Munich, Germany
| | - Alice C McHardy
- Department for Computational Biology of Infection Research, Helmholtz Center for Infection Research, 38124, Braunschweig, Germany
- Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany
- German Centre for Infection Research (DZIF), partner site Hannover Braunschweig, Braunschweig, Germany
| | - Bernd Bischl
- Department of Statistics, LMU Munich, Munich, Germany
- Munich Center for Machine Learning, Munich, Germany
| | - Philipp C Münch
- Department for Computational Biology of Infection Research, Helmholtz Center for Infection Research, 38124, Braunschweig, Germany.
- Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany.
- Department of Biostatistics, Harvard School of Public Health, Boston, MA, USA.
- German Centre for Infection Research (DZIF), partner site Hannover Braunschweig, Braunschweig, Germany.
| | - Martin Binder
- Department of Statistics, LMU Munich, Munich, Germany.
- Munich Center for Machine Learning, Munich, Germany.
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Zamudio R, Boerlin P, Mulvey MR, Haenni M, Beyrouthy R, Madec JY, Schwarz S, Cormier A, Chalmers G, Bonnet R, Zhanel GG, Kaspar H, Mather AE. Global transmission of extended-spectrum cephalosporin resistance in Escherichia coli driven by epidemic plasmids. EBioMedicine 2024; 103:105097. [PMID: 38608515 PMCID: PMC11024496 DOI: 10.1016/j.ebiom.2024.105097] [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: 09/07/2023] [Revised: 03/18/2024] [Accepted: 03/19/2024] [Indexed: 04/14/2024] Open
Abstract
BACKGROUND Extended-spectrum cephalosporins (ESCs) are third and fourth generation cephalosporin antimicrobials used in humans and animals to treat infections due to multidrug-resistant (MDR) bacteria. Resistance to ESCs (ESC-R) in Enterobacterales is predominantly due to the production of extended-spectrum β-lactamases (ESBLs) and plasmid-mediated AmpC β-lactamases (AmpCs). The dynamics of ESBLs and AmpCs are changing across countries and host species, the result of global transmission of ESC-R genes. Plasmids are known to play a key role in this dissemination, but the relative importance of different types of plasmids is not fully understood. METHODS In this study, Escherichia coli with the major ESC-R genes blaCTX-M-1, blaCTX-M-15, blaCTX-M-14 (ESBLs) and blaCMY-2 (AmpC), were selected from diverse host species and other sources across Canada, France and Germany, collected between 2003 and 2017. To examine in detail the vehicles of transmission of the ESC-R genes, long- and short-read sequences were generated to obtain complete contiguous chromosome and plasmid sequences (n = 192 ESC-R E. coli). The types, gene composition and genetic relatedness of these plasmids were investigated, along with association with isolate year, source and geographical origin, and put in context with publicly available plasmid sequences. FINDINGS We identified five epidemic resistance plasmid subtypes with distinct genetic properties that are associated with the global dissemination of ESC-R genes across multiple E. coli lineages and host species. The IncI1 pST3 blaCTX-M-1 plasmid subtype was found in more diverse sources than the other main plasmid subtypes, whereas IncI1 pST12 blaCMY-2 was more frequent in Canadian and German human and chicken isolates. Clonal expansion also contributed to the dissemination of the IncI1 pST12 blaCMY-2 plasmid in ST131 and ST117 E. coli harbouring this plasmid. The IncI1 pST2 blaCMY-2 subtype was predominant in isolates from humans in France, while the IncF F31:A4:B1 blaCTX-M-15 and F2:A-:B- blaCTX-M-14 plasmid subtypes were frequent in human and cattle isolates across multiple countries. Beyond their epidemic nature with respect to ESC-R genes, in our collection almost all IncI1 pST3 blaCTX-M-1 and IncF F31:A4:B1 blaCTX-M-15 epidemic plasmids also carried multiple antimicrobial resistance (AMR) genes conferring resistance to other antimicrobial classes. Finally, we found genetic signatures in the regions surrounding specific ESC-R genes, identifying the predominant mechanisms of ESC-R gene movement, and using publicly available databases, we identified these epidemic plasmids from widespread bacterial species, host species, countries and continents. INTERPRETATION We provide evidence that epidemic resistance plasmid subtypes contribute to the global dissemination of ESC-R genes, and in addition, some of these epidemic plasmids confer resistance to multiple other antimicrobial classes. The success of these plasmids suggests that they may have a fitness advantage over other plasmid types and subtypes. Identification and understanding of the vehicles of AMR transmission are crucial to develop and target strategies and interventions to reduce the spread of AMR. FUNDING This project was supported by the Joint Programming Initiative on Antimicrobial Resistance (JPIAMR), through the Medical Research Council (MRC, MR/R000948/1), the Canadian Institutes of Health Research (CFC-150770), and the Genomics Research and Development Initiative (Government of Canada), the German Federal Ministry of Education and Research (BMBF) grant no. 01KI1709, the French Agency for food environmental and occupational health & safety (Anses), and the French National Reference Center (CNR) for antimicrobial resistance. Support was also provided by the Biotechnology and Biological Sciences Research Council (BBSRC) through the BBSRC Institute Strategic Programme Microbes in the Food ChainBB/R012504/1 and its constituent project BBS/E/F/000PR10348 (Theme 1, Epidemiology and Evolution of Pathogens in the Food Chain).
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Affiliation(s)
- Roxana Zamudio
- Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, United Kingdom
| | - Patrick Boerlin
- Department of Pathobiology, University of Guelph, Guelph N1G 2W1, Canada
| | - Michael R Mulvey
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba R3E 3R2, Canada
| | - Marisa Haenni
- Unité Antibiorésistance et Virulence Bactériennes, Anses - Université de Lyon, Lyon 69007, France
| | - Racha Beyrouthy
- Microbes Intestin Inflammation et Susceptibilité de l'Hôte (M2ISH), Faculté de Médecine, Université Clermont Auvergne, Clermont-Ferrand 63001, France; Centre National de Référence de la Résistance Aux Antibiotiques, Centre Hospitalier Universitaire de Clermont-Ferrand, Clermont-Ferrand 63000, France
| | - Jean-Yves Madec
- Unité Antibiorésistance et Virulence Bactériennes, Anses - Université de Lyon, Lyon 69007, France
| | - Stefan Schwarz
- Institute of Microbiology and Epizootics, School of Veterinary Medicine, Freie Universität Berlin, Berlin 14163, Germany; Veterinary Centre for Resistance Research (TZR), School of Veterinary Medicine, Freie Universität Berlin, Berlin 14163, Germany
| | - Ashley Cormier
- Department of Pathobiology, University of Guelph, Guelph N1G 2W1, Canada
| | - Gabhan Chalmers
- Department of Pathobiology, University of Guelph, Guelph N1G 2W1, Canada
| | - Richard Bonnet
- Microbes Intestin Inflammation et Susceptibilité de l'Hôte (M2ISH), Faculté de Médecine, Université Clermont Auvergne, Clermont-Ferrand 63001, France; Centre National de Référence de la Résistance Aux Antibiotiques, Centre Hospitalier Universitaire de Clermont-Ferrand, Clermont-Ferrand 63000, France
| | - George G Zhanel
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba R3E 0J9, Canada
| | - Heike Kaspar
- Department Method Standardisation, Resistance to Antibiotics Unit Monitoring of Resistance to Antibiotics, Federal Office of Consumer Protection and Food Safety, Berlin 12277, Germany
| | - Alison E Mather
- Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, United Kingdom; University of East Anglia, Norwich NR4 7TJ, United Kingdom.
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10
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Posteraro B, De Maio F, Motro Y, Menchinelli G, De Lorenzis D, Marano RBM, Aljanazreh B, Errico FM, Massaria G, Spanu T, Posteraro P, Moran-Gilad J, Sanguinetti M. In-depth characterization of multidrug-resistant NDM-1 and KPC-3 co-producing Klebsiella pneumoniae bloodstream isolates from Italian hospital patients. Microbiol Spectr 2024; 12:e0330523. [PMID: 38411998 PMCID: PMC10986569 DOI: 10.1128/spectrum.03305-23] [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: 09/07/2023] [Accepted: 02/04/2024] [Indexed: 02/28/2024] Open
Abstract
Bloodstream infection (BSI) caused by carbapenem-resistant Klebsiella pneumoniae (KP) poses significant challenges, particularly when the infecting isolate carries multiple antimicrobial resistance (AMR) genes/determinants. This study, employing short- and long-read whole-genome sequencing, characterizes six New Delhi metallo-β-lactamase (NDM) 1 and KP carbapenemase (KPC) 3 co-producing KP isolates, the largest cohort investigated in Europe to date. Five [sequence type (ST) 512] and one (ST11) isolates were recovered from patients who developed BSI from February to August 2022 or February 2023 at two different hospitals in Rome, Italy. Phylogenetic analysis revealed two distinct clusters among ST512 isolates and a separate cluster for the ST11 isolate. Beyond blaNDM-1 and blaKPC-3, various AMR genes, indicative of a multidrug resistance phenotype, including colistin resistance, were found. Each cluster-representative ST512 isolate harbored a blaNDM-1 plasmid (IncC) and a blaKPC-3 plasmid [IncFIB(pQil)/IncFII(K)], while the ST11 isolate harbored a blaNDM-1 plasmid [IncFII(pKPX1)] and a blaKPC-3 plasmid [IncFIB(K)/IncFII(K)]. The blaNDM-1 plasmids carried genes conferring resistance to clinically relevant antimicrobial agents, and the aminoglycoside resistance gene aac(6')-Ib was found on different plasmids. Colistin resistance-associated mgrB/pmrB gene mutations were present in all isolates, and the yersiniabactin-encoding ybt gene was unique to the ST11 isolate. In conclusion, our findings provide insights into the genomic context of blaNDM-1/blaKPC-3 carbapenemase-producing KP isolates.IMPORTANCEThis study underscores the critical role of genomic surveillance as a proactive measure to restrict the spread of carbapenemase-producing KP isolates, especially when key antimicrobial resistance genes, such as blaNDM-1/blaKPC-3, are plasmid borne. In-depth characterization of these isolates may help identify plasmid similarities contributing to their intra-hospital/inter-hospital adaptation and transmission. Despite the lack of data on patient movements, it is possible that carbapenem-resistant isolates were selected to co-produce KP carbapenemase and New Delhi metallo-β-lactamase via plasmid acquisition. Studies employing long-read whole-genome sequencing should be encouraged to address the emergence of KP clones with converging phenotypes of virulence and resistance to last-resort antimicrobial agents.
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Affiliation(s)
- Brunella Posteraro
- Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, Rome, Italy
- Dipartimento di Scienze Mediche e Chirurgiche Addominali ed Endocrino Metaboliche, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Flavio De Maio
- Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, Rome, Italy
- Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Yair Motro
- Department of Health Policy and Management, School of Public Health, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Giulia Menchinelli
- Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Desy De Lorenzis
- Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Roberto B. M. Marano
- Department of Health Policy and Management, School of Public Health, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Bessan Aljanazreh
- Department of Health Policy and Management, School of Public Health, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Federica Maria Errico
- GVM - Ospedale San Carlo di Nancy, Laboratorio di Analisi Chimico-Cliniche e Microbiologiche, Rome, Italy
| | | | - Teresa Spanu
- Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, Rome, Italy
- Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Patrizia Posteraro
- GVM - Ospedale San Carlo di Nancy, Laboratorio di Analisi Chimico-Cliniche e Microbiologiche, Rome, Italy
| | - Jacob Moran-Gilad
- Department of Health Policy and Management, School of Public Health, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Maurizio Sanguinetti
- Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, Rome, Italy
- Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
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11
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Cook R, Telatin A, Hsieh SY, Newberry F, Tariq MA, Baker DJ, Carding SR, Adriaenssens EM. Nanopore and Illumina sequencing reveal different viral populations from human gut samples. Microb Genom 2024; 10. [PMID: 38683195 DOI: 10.1099/mgen.0.001236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2024] Open
Abstract
The advent of viral metagenomics, or viromics, has improved our knowledge and understanding of global viral diversity. High-throughput sequencing technologies enable explorations of the ecological roles, contributions to host metabolism, and the influence of viruses in various environments, including the human intestinal microbiome. However, bacterial metagenomic studies frequently have the advantage. The adoption of advanced technologies like long-read sequencing has the potential to be transformative in refining viromics and metagenomics. Here, we examined the effectiveness of long-read and hybrid sequencing by comparing Illumina short-read and Oxford Nanopore Technology (ONT) long-read sequencing technologies and different assembly strategies on recovering viral genomes from human faecal samples. Our findings showed that if a single sequencing technology is to be chosen for virome analysis, Illumina is preferable due to its superior ability to recover fully resolved viral genomes and minimise erroneous genomes. While ONT assemblies were effective in recovering viral diversity, the challenges related to input requirements and the necessity for amplification made it less ideal as a standalone solution. However, using a combined, hybrid approach enabled a more authentic representation of viral diversity to be obtained within samples.
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Affiliation(s)
- Ryan Cook
- Quadram Institute Bioscience, Norwich, NR4 7UQ, UK
| | | | | | - Fiona Newberry
- Department of Biosciences, Nottingham Trent University, Nottingham, NG11 8NS, UK
| | - Mohammad A Tariq
- Faculty of Health and Life Sciences, University of Northumbria, Newcastle upon Tyne, NE1 8ST, UK
| | - Dave J Baker
- Quadram Institute Bioscience, Norwich, NR4 7UQ, UK
| | - Simon R Carding
- Quadram Institute Bioscience, Norwich, NR4 7UQ, UK
- Norwich Medical School, University of East Anglia, Norwich, NR4 7TJ, UK
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12
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Sommer J, Reiter H, Sattler J, Cacace E, Eisfeld J, Gatermann S, Hamprecht A, Göttig S. Emergence of OXA-48-like producing Citrobacter species, Germany, 2011 to 2022. Euro Surveill 2024; 29:2300528. [PMID: 38606571 PMCID: PMC11010590 DOI: 10.2807/1560-7917.es.2024.29.15.2300528] [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: 09/29/2023] [Accepted: 01/10/2024] [Indexed: 04/13/2024] Open
Abstract
BackgroundCarbapenemase-producing Enterobacterales are a public health threat worldwide and OXA-48 is the most prevalent carbapenemase in Germany and western Europe. However, the molecular epidemiology of OXA-48 in species other than Escherichia coli and Klebsiella pneumoniae remains poorly understood.AimTo analyse the molecular epidemiology of OXA-48 and OXA-48-like carbapenemases in Citrobacter species (spp.) in Germany between 2011 and 2022.MethodsData of 26,822 Enterobacterales isolates sent to the National Reference Centre (NRC) for Gram-negative bacteria were evaluated. Ninety-one Citrobacter isolates from 40 German hospitals harbouring bla OXA-48/OXA-48‑like were analysed by whole genome sequencing and conjugation experiments.ResultsThe frequency of OXA-48 in Citrobacter freundii (CF) has increased steadily since 2011 and is now the most prevalent carbapenemase in this species in Germany. Among 91 in-depth analysed Citrobacter spp. isolates, CF (n = 73) and C. koseri (n = 8) were the most common species and OXA-48 was the most common variant (n = 77), followed by OXA-162 (n = 11) and OXA‑181 (n = 3). Forty percent of the isolates belonged to only two sequence types (ST19 and ST22), while most other STs were singletons. The plasmids harbouring bla OXA‑48 and bla OXA-162 belonged to the plasmid types IncL (n = 85) or IncF (n = 3), and plasmids harbouring bla OXA‑181 to IncX3 (n = 3). Three IncL plasmid clusters (57/85 IncL plasmids) were identified, which were highly transferable in contrast to sporadic plasmids.ConclusionIn CF in Germany, OXA-48 is the predominant carbapenemase. Dissemination is likely due to distinct highly transmissible plasmids harbouring bla OXA‑48 or bla OXA-48-like and the spread of the high-risk clonal lineages ST19 and ST22.
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Affiliation(s)
- Julian Sommer
- Goethe University Frankfurt, University Hospital, Institute of Medical Microbiology and Infection Control, Frankfurt am Main, Germany
| | - Hannah Reiter
- Goethe University Frankfurt, University Hospital, Institute of Medical Microbiology and Infection Control, Frankfurt am Main, Germany
| | - Janko Sattler
- University Hospital Cologne and Faculty of Medicine, University of Cologne, Institute for Medical Microbiology, Immunology and Hygiene, Cologne, Germany
| | - Elisabetta Cacace
- Institute of Microbiology, Department of Biology, ETH Zurich, Zurich, Switzerland
- Goethe University Frankfurt, University Hospital, Institute of Medical Microbiology and Infection Control, Frankfurt am Main, Germany
| | - Jessica Eisfeld
- German National Reference Centre for Multidrug-resistant Gram-negative Bacteria, Department of Medical Microbiology, Ruhr-University Bochum, Bochum, Germany
| | - Sören Gatermann
- German National Reference Centre for Multidrug-resistant Gram-negative Bacteria, Department of Medical Microbiology, Ruhr-University Bochum, Bochum, Germany
| | - Axel Hamprecht
- University of Oldenburg and Klinikum Oldenburg, Institute for Medical Microbiology and Virology, Oldenburg, Germany
- University Hospital Cologne and Faculty of Medicine, University of Cologne, Institute for Medical Microbiology, Immunology and Hygiene, Cologne, Germany
| | - Stephan Göttig
- Goethe University Frankfurt, University Hospital, Institute of Medical Microbiology and Infection Control, Frankfurt am Main, Germany
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Quarton S, McGee K, Cumley N, Behruznia M, Jeff C, Belchamber K, Cox M, Thickett D, Scott A, Parekh D, McNally A, Sapey E. Towards personalised anti-microbial and immune approaches to infections in acute care. Can real-time genomic-informed diagnosis of pathogens, and immune-focused therapies improve outcomes for patients? An observational, experimental study protocol. PLoS One 2024; 19:e0298425. [PMID: 38551904 PMCID: PMC10980213 DOI: 10.1371/journal.pone.0298425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 01/24/2024] [Indexed: 04/01/2024] Open
Abstract
INTRODUCTION Infection causes a vast burden of disease, with significant mortality, morbidity and costs to health-care systems. However, identifying the pathogen causative infection can be challenging, resulting in high use of broad-spectrum antibiotics, much of which may be inappropriate. Novel metagenomic methods have potential to rapidly identify pathogens, however their clinical utility for many infections is currently unclear. Outcome from infection is also impacted by the effectiveness of immune responses, which can be impaired by age, co-morbidity and the infection itself. The aims of this study are twofold: To compare diversity of organisms identified and time-to-result using metagenomic methods versus traditional culture -based techniques, to explore the potential clinical role of metagenomic approaches to pathogen identification in a range of infections.To characterise the ex vivo function of immune cells from patients with acute infection, exploring host and pathogen-specific factors which may affect immune function and overall outcomes. METHODS This is a prospective observational study of patients with acute infection. Patients with symptoms suggestive of an acute infection will be recruited, and blood and bodily fluid relevant to the site of infection collected (for example, sputum and naso-oropharyngeal swabs for respiratory tract infections, or urine for a suspected urinary tract infection). Metagenomic analysis of samples will be compared to traditional microbiology, alongside the antimicrobials received. Blood and respiratory samples such as bronchoalveolar lavage will be used to isolate immune cells and interrogate immune cell function. Where possible, similar samples will be collected from matched participants without a suspected infection to determine the impact of infection on both microbiome and immune cell function.
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Affiliation(s)
- Samuel Quarton
- Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom
- Institute of Inflammation & Ageing, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Kirsty McGee
- Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom
- Institute of Inflammation & Ageing, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Nicola Cumley
- Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom
- Institute of Microbiology & Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Mahboobeh Behruznia
- Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom
- Institute of Microbiology & Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Charlotte Jeff
- Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom
| | - Kylie Belchamber
- Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom
- Institute of Inflammation & Ageing, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Michael Cox
- Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom
- Institute of Microbiology & Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - David Thickett
- Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom
- Institute of Inflammation & Ageing, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Aaron Scott
- Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom
- Institute of Inflammation & Ageing, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Dhruv Parekh
- Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom
- Institute of Inflammation & Ageing, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Alan McNally
- Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom
- Institute of Microbiology & Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Elizabeth Sapey
- Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom
- Director of PIONEER: Health Data Research UK (HDRUK) Health Data Research Hub for Acute Care, Institute of Inflammation and Ageing, University of Birmingham, Birmingham, United Kingdom
- Patient Safety Research Collaborative, University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom
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Janet-Maitre M, Job V, Bour M, Robert-Genthon M, Brugière S, Triponney P, Cobessi D, Couté Y, Jeannot K, Attrée I. Pseudomonas aeruginosa MipA-MipB envelope proteins act as new sensors of polymyxins. mBio 2024; 15:e0221123. [PMID: 38345374 PMCID: PMC10936184 DOI: 10.1128/mbio.02211-23] [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: 08/16/2023] [Accepted: 01/09/2024] [Indexed: 03/14/2024] Open
Abstract
Due to the rising incidence of antibiotic-resistant infections, the last-line antibiotics, polymyxins, have resurged in the clinics in parallel with new bacterial strategies of escape. The Gram-negative opportunistic pathogen Pseudomonas aeruginosa develops resistance to colistin/polymyxin B by distinct molecular mechanisms, mostly through modification of the lipid A component of the LPS by proteins encoded within the arnBCDATEF-ugd (arn) operon. In this work, we characterized a polymyxin-induced operon named mipBA, present in P. aeruginosa strains devoid of the arn operon. We showed that mipBA is activated by the ParR/ParS two-component regulatory system in response to polymyxins. Structural modeling revealed that MipA folds as an outer-membrane β-barrel, harboring an internal negatively charged channel, able to host a polymyxin molecule, while the lipoprotein MipB adopts a β-lactamase fold with two additional C-terminal domains. Experimental work confirmed that MipA and MipB localize to the bacterial envelope, and they co-purify in vitro. Nano differential scanning fluorimetry showed that polymyxins stabilized MipA in a specific and dose-dependent manner. Mass spectrometry-based quantitative proteomics on P. aeruginosa membranes demonstrated that ∆mipBA synthesized fourfold less MexXY-OprA proteins in response to polymyxin B compared to the wild-type strain. The decrease was a direct consequence of impaired transcriptional activation of the mex operon operated by ParR/ParS. We propose MipA/MipB to act as membrane (co)sensors working in concert to activate ParS histidine kinase and help the bacterium to cope with polymyxin-mediated envelope stress through synthesis of the efflux pump, MexXY-OprA.IMPORTANCEDue to the emergence of multidrug-resistant isolates, antibiotic options may be limited to polymyxins to eradicate Gram-negative infections. Pseudomonas aeruginosa, a leading opportunistic pathogen, has the ability to develop resistance to these cationic lipopeptides by modifying its lipopolysaccharide through proteins encoded within the arn operon. Herein, we describe a sub-group of P. aeruginosa strains lacking the arn operon yet exhibiting adaptability to polymyxins. Exposition to sub-lethal polymyxin concentrations induced the expression and production of two envelope-associated proteins. Among those, MipA, an outer-membrane barrel, is able to specifically bind polymyxins with an affinity in the 10-µM range. Using membrane proteomics and phenotypic assays, we showed that MipA and MipB participate in the adaptive response to polymyxins via ParR/ParS regulatory signaling. We propose a new model wherein the MipA-MipB module functions as a novel polymyxin sensing mechanism.
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Affiliation(s)
- Manon Janet-Maitre
- Team Bacterial Pathogenesis and Cellular Responses, University Grenoble Alpes, IBS, UMR5075, Grenoble, France
| | - Viviana Job
- Team Bacterial Pathogenesis and Cellular Responses, University Grenoble Alpes, IBS, UMR5075, Grenoble, France
| | - Maxime Bour
- UMR6249 Chrono-Environnement, UFR Santé, University of Franche-Comté, Besançon, France
- French National Reference Center for Antibiotic Resistance, Besançon, France
| | - Mylène Robert-Genthon
- Team Bacterial Pathogenesis and Cellular Responses, University Grenoble Alpes, IBS, UMR5075, Grenoble, France
| | - Sabine Brugière
- University Grenoble Alpes, CEA, INSERM, UA13 BGE, CNRS, CEA, FranceGrenoble
| | - Pauline Triponney
- French National Reference Center for Antibiotic Resistance, Besançon, France
| | - David Cobessi
- University Grenoble Alpes, IBS, UMR5075, Team Synchrotron, Grenoble, France
| | - Yohann Couté
- University Grenoble Alpes, CEA, INSERM, UA13 BGE, CNRS, CEA, FranceGrenoble
| | - Katy Jeannot
- UMR6249 Chrono-Environnement, UFR Santé, University of Franche-Comté, Besançon, France
- French National Reference Center for Antibiotic Resistance, Besançon, France
- Department of Bacteriology, Teaching Hospital of Besançon, Besançon, France
| | - Ina Attrée
- Team Bacterial Pathogenesis and Cellular Responses, University Grenoble Alpes, IBS, UMR5075, Grenoble, France
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15
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Chopjitt P, Boueroy P, Morita M, Iida T, Akeda Y, Hamada S, Kerdsin A. Genetic characterization of multidrug-resistant Escherichia coli harboring colistin-resistant gene isolated from food animals in food supply chain. Front Cell Infect Microbiol 2024; 14:1289134. [PMID: 38384304 PMCID: PMC10880773 DOI: 10.3389/fcimb.2024.1289134] [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: 09/05/2023] [Accepted: 01/12/2024] [Indexed: 02/23/2024] Open
Abstract
Colistin is widely used for the prophylaxis and treatment of infectious disease in humans and livestock. However, the global food chain may actively promote the dissemination of colistin-resistant bacteria in the world. Mobile colistin-resistant (mcr) genes have spread globally, in both communities and hospitals. This study sought to genomically characterize mcr-mediated colistin resistance in 16 Escherichia coli strains isolated from retail meat samples using whole genome sequencing with short-read and long-read platforms. To assess colistin resistance and the transferability of mcr genes, antimicrobial susceptibility testing and conjugation experiments were conducted. Among the 16 isolates, 11 contained mcr-1, whereas three carried mcr-3 and two contained mcr-1 and mcr-3. All isolates had minimum inhibitory concentration (MIC) for colistin in the range 1-64 μg/mL. Notably, 15 out of the 16 isolates demonstrated successful transfer of mcr genes via conjugation, indicative of their presence on plasmids. In contrast, the KK3 strain did not exhibit such transferability. Replicon types of mcr-1-containing plasmids included IncI2 and IncX4, while IncFIB, IncFII, and IncP1 contained mcr-3. Another single strain carried mcr-1.1 on IncX4 and mcr-3.5 on IncP1. Notably, one isolate contained mcr-1.1 located on a chromosome and carrying mcr-3.1 on the IncFIB plasmid. The chromosomal location of the mcr gene may ensure a steady spread of resistance in the absence of selective pressure. Retail meat products may act as critical reservoirs of plasmid-mediated colistin resistance that has been transmitted to humans.
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Affiliation(s)
| | - Parichart Boueroy
- Faculty of Public Health, Kasetsart University, Sakon Nakhon, Thailand
| | - Masatomo Morita
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Tetsuya Iida
- Japan-Thailand Research Collaboration Center on Emerging and Re-emerging Infections, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
- Department of Bacterial Infections, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
- Center for Infectious Disease Education and Research, Osaka University, Osaka, Japan
| | - Yukihiro Akeda
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Sihigeyuki Hamada
- Department of Bacterial Infections, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Anusak Kerdsin
- Faculty of Public Health, Kasetsart University, Sakon Nakhon, Thailand
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16
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Duggett N, AbuOun M, Stubberfield E, Turner O, Randall L, Horton R, Nunez-Garcia J, Gates D, Chanter J, Teale C, Anjum MF. Genomic surveillance of extended-spectrum cephalosporin-resistant Escherichia coli isolated from poultry in the UK from 2016 to 2020. Front Microbiol 2024; 14:1335173. [PMID: 38352060 PMCID: PMC10861728 DOI: 10.3389/fmicb.2023.1335173] [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: 11/08/2023] [Accepted: 12/19/2023] [Indexed: 02/16/2024] Open
Abstract
Introduction Surveillance is vital for monitoring the increasing risk of antimicrobial resistance (AMR) in bacteria leading to failures in humans and animals to treat infections. In a One Health context, AMR bacteria from livestock and food can transfer through the food chain to humans, and vice versa, which can be characterized in detail through genomics. We investigated the critical aspects of AMR and the dynamics of AMR in poultry in the UK. Methods In this study, we performed whole genome sequencing for genomic characterization of 761 extended-spectrum cephalosporinases (ESCs) harboring Escherichia coli isolated from poultry caeca and meat through EU harmonized monitoring of AMR in zoonotic and commensal bacteria from 2016 and 2018 and UK national monitoring in 2020. Results The most common ESC in 2016 and 2018 was blaCTX-M-1; however, 2020 had a greater diversity of ESCs with blaCTX-M-55 dominant in chickens and blaCTX-M-15 more prevalent in turkeys. Co-resistance to sulphonamides, tetracycline, and trimethoprim was widespread, and there were several positive correlations between the sequence types (STs) and ESC genes. We identified certain AMR genotypes and STs that were frequent each year but not as successful in subsequent years, e.g., ST350 harboring blaCTX-M-1, sul2, and tetA-v4.Phylogenetic comparison of isolates prevalent in our panel with global ones from the same STs available in public databases showed that isolates from the UK generally clustered together, suggesting greater within-country than between-country transmission. Discussion We conclude that future genomic surveillance of indicator organisms will be invaluable as it will enable detailed comparisons of AMR between and within neighboring countries, potentially identifying the most successful sequence types, plasmids, or emerging threats.
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Affiliation(s)
- Nicholas Duggett
- Animal and Plant Health Agency, Addlestone, United Kingdom
- Animal and Plant Health Agency, Thirsk Veterinary Investigation Centre, Thirsk, United Kingdom
| | - Manal AbuOun
- Animal and Plant Health Agency, Addlestone, United Kingdom
| | | | - Olivia Turner
- Animal and Plant Health Agency, Addlestone, United Kingdom
| | - Luke Randall
- Animal and Plant Health Agency, Addlestone, United Kingdom
| | - Robert Horton
- Animal and Plant Health Agency, Addlestone, United Kingdom
| | | | - Daisy Gates
- Animal and Plant Health Agency, Addlestone, United Kingdom
| | - Jeremy Chanter
- Animal and Plant Health Agency, Starcross Veterinary Investigation Centre, Exeter, United Kingdom
| | - Chris Teale
- Animal and Plant Health Agency, Veterinary Investigation Centre, Shrewsbury, United Kingdom
| | - Muna F. Anjum
- Animal and Plant Health Agency, Addlestone, United Kingdom
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17
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Hem S, Cummins ML, Wyrsch ER, Drigo B, Hoye BJ, Maute K, Sanderson-Smith M, Gorman J, Bogema DR, Jenkins C, Deutscher AT, Yam J, Hai F, Donner E, Jarocki VM, Djordjevic SP. Genomic analysis of Citrobacter from Australian wastewater and silver gulls reveals novel sequence types carrying critically important antibiotic resistance genes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 909:168608. [PMID: 37977387 DOI: 10.1016/j.scitotenv.2023.168608] [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: 08/17/2023] [Revised: 11/08/2023] [Accepted: 11/14/2023] [Indexed: 11/19/2023]
Abstract
Antimicrobial resistance (AMR) is a major public health concern, and environmental bacteria have been recognized as important reservoirs of antimicrobial resistance genes (ARGs). Citrobacter, a common environmental bacterium and opportunistic pathogen in humans and other animals, has been largely understudied in terms of its diversity and AMR potential. Whole-genome (short-read) sequencing on a total of 77 Citrobacter isolates obtained from Australian silver gull (Chroicocephalus novaehollandiae) (n = 17) and influent wastewater samples (n = 60) was performed, revealing a diverse Citrobacter population, with seven different species and 33 sequence types, 17 of which were novel. From silver gull using non-selective media we isolated a broader range of species with little to no mobilised ARG carriage. Wastewater isolates (selected using Carbapenem- Resistant Enterobacterales (CRE) selective media) carried a heavy burden of ARGs (up to 21 ARGs, conferring resistance to nine classes of antibiotics), with several novel multidrug-resistant (MDR) lineages identified, including C. braakii ST1110, which carried ARGs conferring resistance to eight to nine classes of antibiotics, and C. freundii ST1105, which carried two carbapenemase genes, blaIMP-4 in class 1 integron structure, and blaKPC-2. Additionally, we identified an MDR C. portucalensis isolate carrying blaNDM-1, blaSHV-12, and mcr-9. We identified IncC, IncM2, and IncP6 plasmids as the likely vectors for many of the critically important mobilised ARGs. Phylogenetic analyses were performed to assess any epidemiological linkages between isolation sources, demonstrating low relatedness across sources beyond the ST level. However, these analyses did reveal some closer relationships between strains from disparate wastewater sources despite their collection some 13,000 km apart. These findings support the need for future surveillance of Citrobacter populations in wastewater and wildlife populations to monitor for potential opportunistic human pathogens.
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Affiliation(s)
- Sopheak Hem
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Ultimo, Australia; The Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, Ultimo, Australia
| | - Max L Cummins
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Ultimo, Australia; The Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, Ultimo, Australia
| | - Ethan R Wyrsch
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Ultimo, Australia; The Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, Ultimo, Australia
| | - Barbara Drigo
- UniSA STEM, University of South Australia, Adelaide, SA, Australia
| | - Bethany J Hoye
- School of Earth, Atmospheric and Life Sciences, University of Wollongong NSW, Australia; Environmental Futures Research Centre, University of Wollongong NSW, Australia
| | - Kimberly Maute
- School of Earth, Atmospheric and Life Sciences, University of Wollongong NSW, Australia; Environmental Futures Research Centre, University of Wollongong NSW, Australia
| | - Martina Sanderson-Smith
- School of Chemistry and Molecular Bioscience and Molecular Horizons, University of Wollongong, NSW, Australia
| | - Jody Gorman
- School of Chemistry and Molecular Bioscience and Molecular Horizons, University of Wollongong, NSW, Australia
| | - Daniel R Bogema
- Elizabeth Macarthur Agricultural Institute, NSW Department of Primary Industries, Menangle, NSW, Australia
| | - Cheryl Jenkins
- Elizabeth Macarthur Agricultural Institute, NSW Department of Primary Industries, Menangle, NSW, Australia
| | - Ania T Deutscher
- Elizabeth Macarthur Agricultural Institute, NSW Department of Primary Industries, Menangle, NSW, Australia
| | - Jerald Yam
- Elizabeth Macarthur Agricultural Institute, NSW Department of Primary Industries, Menangle, NSW, Australia
| | - Faisal Hai
- School of Civil, Mining, Environmental and Architectural Engineering, University of Wollongong, NSW, Australia
| | - Erica Donner
- Cooperative Research Centre for Solving Antimicrobial resistance in Agribusiness, Food, and Environments (CRC SAAFE), Adelaide, South Australia, Australia; Future Industries Institute, University of South Australia, Adelaide, South Australia, Australia
| | - Veronica M Jarocki
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Ultimo, Australia; The Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, Ultimo, Australia.
| | - Steven P Djordjevic
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Ultimo, Australia; The Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, Ultimo, Australia.
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18
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Silva EC, Quinde CA, Cieza B, Basu A, Vila MMDC, Balcão VM. Molecular Characterization and Genome Mechanical Features of Two Newly Isolated Polyvalent Bacteriophages Infecting Pseudomonas syringae pv. garcae. Genes (Basel) 2024; 15:113. [PMID: 38255005 PMCID: PMC10815195 DOI: 10.3390/genes15010113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Revised: 01/06/2024] [Accepted: 01/16/2024] [Indexed: 01/24/2024] Open
Abstract
Coffee plants have been targeted by a devastating bacterial disease, a condition known as bacterial blight, caused by the phytopathogen Pseudomonas syringae pv. garcae (Psg). Conventional treatments of coffee plantations affected by the disease involve frequent spraying with copper- and kasugamycin-derived compounds, but they are both highly toxic to the environment and stimulate the appearance of bacterial resistance. Herein, we report the molecular characterization and mechanical features of the genome of two newly isolated (putative polyvalent) lytic phages for Psg. The isolated phages belong to class Caudoviricetes and present a myovirus-like morphotype belonging to the genuses Tequatrovirus (PsgM02F) and Phapecoctavirus (PsgM04F) of the subfamilies Straboviridae (PsgM02F) and Stephanstirmvirinae (PsgM04F), according to recent bacterial viruses' taxonomy, based on their complete genome sequences. The 165,282 bp (PsgM02F) and 151,205 bp (PsgM04F) genomes do not feature any lysogenic-related (integrase) genes and, hence, can safely be assumed to follow a lytic lifestyle. While phage PsgM02F produced a morphogenesis yield of 124 virions per host cell, phage PsgM04F produced only 12 virions per host cell, indicating that they replicate well in Psg with a 50 min latency period. Genome mechanical analyses established a relationship between genome bendability and virion morphogenesis yield within infected host cells.
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Affiliation(s)
- Erica C. Silva
- VBlab—Laboratory of Bacterial Viruses, University of Sorocaba, Sorocaba 18023-000, SP, Brazil; (E.C.S.); (M.M.D.C.V.)
| | - Carlos A. Quinde
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA;
| | - Basilio Cieza
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University, Baltimore, MD 21218, USA;
| | - Aakash Basu
- Department of Biosciences, Durham University, Durham DH1 3LE, UK;
| | - Marta M. D. C. Vila
- VBlab—Laboratory of Bacterial Viruses, University of Sorocaba, Sorocaba 18023-000, SP, Brazil; (E.C.S.); (M.M.D.C.V.)
| | - Victor M. Balcão
- VBlab—Laboratory of Bacterial Viruses, University of Sorocaba, Sorocaba 18023-000, SP, Brazil; (E.C.S.); (M.M.D.C.V.)
- Department of Biology and CESAM, University of Aveiro, Campus Universitário de Santiago, P-3810-193 Aveiro, Portugal
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19
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Ma W, Cui X, Dong X, Li X, Liu K, Wang Y, Shi X, Chen L, Hao M. Characterization of nontyphoidal Salmonella strains from a tertiary hospital in China: serotype diversity, multidrug resistance, and genetic insights. Front Cell Infect Microbiol 2024; 13:1327092. [PMID: 38264733 PMCID: PMC10803454 DOI: 10.3389/fcimb.2023.1327092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 12/20/2023] [Indexed: 01/25/2024] Open
Abstract
Objective Nontyphoidal Salmonella is a significant public health concern due to its ability to cause foodborne illnesses worldwide. This study aims to characterize the nontyphoidal Salmonella strains isolated from patients in China. Methods A total of 19 nontyphoidal Salmonella strains were characterized through serovar identification, antimicrobial susceptibility testing (AST), biofilm formation assessment. Genetic relatedness was determined using pulsed-field gel electrophoresis (PFGE). WGS was employed to decipher the resistance mechanism and to contextualize the S. serovar Mbandaka strains among previously sequenced isolates in China. The biofilm associated mrkA gene was examined by PCR. Results The predominant serovar identified was S. Enteritidis, followed by S. Mbandaka, S. Thompson, S. Livingston, S. Alachua, and S. Infantis. PFGE analysis indicated a notable genetic similarity among the S. Mbandaka isolates. Phylogenetic analysis suggested that these strains were likely derived from a single source that had persisted in China for over five years. One multidrug resistance (MDR) S. Enteritidis isolate carried a highly transferable IncB/O/K/Z plasmid with bla CTX-M-15. One S. Thompson strain, harboring the mrkABCDF operon in an IncX1 plasmid, isolated from cutaneous lesions, demonstrated robust biofilm formation. However, no mrkABCDF loci were detected in other strains. Conclusion Our study emphasizes the importance of persisted surveillance and prompt response to Salmonella infections to protect public health. The dissemination of bla CTX-M-15-harboring IncB/O/K/Z plasmid and the spread of virulent mrkABCDF operon among Salmonella in China and other global regions warrant close monitoring.
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Affiliation(s)
- Wanshan Ma
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Shandong Medicine and Health Key Laboratory of Laboratory Medicine, Jinan, China
| | - Xiaodi Cui
- School of Clinical Medicine, Jining Medical University, Jining, China
| | - Xiutao Dong
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Shandong Medicine and Health Key Laboratory of Laboratory Medicine, Jinan, China
| | - Xinpeng Li
- Department of Bacterial Infectious Disease Control and Prevention, Shandong Center for Disease Control and Prevention, Jinan, China
| | - Ke Liu
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Shandong Medicine and Health Key Laboratory of Laboratory Medicine, Jinan, China
| | - Yujiao Wang
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Shandong Medicine and Health Key Laboratory of Laboratory Medicine, Jinan, China
| | - Xiaohong Shi
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Shandong Medicine and Health Key Laboratory of Laboratory Medicine, Jinan, China
| | - Liang Chen
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, United States
- Department of Medical Sciences, Hackensack Meridian School of Medicine, Nutley, NJ, United States
| | - Mingju Hao
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Shandong Medicine and Health Key Laboratory of Laboratory Medicine, Jinan, China
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20
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Chen C, Keunecke H, Bemm F, Gyetvai G, Neu E, Kopisch‐Obuch FJ, McDonald BA, Stapley J. GWAS reveals a rapidly evolving candidate avirulence effector in the Cercospora leaf spot pathogen. MOLECULAR PLANT PATHOLOGY 2024; 25:e13407. [PMID: 38009399 PMCID: PMC10799204 DOI: 10.1111/mpp.13407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 11/09/2023] [Accepted: 11/09/2023] [Indexed: 11/28/2023]
Abstract
The major resistance gene BvCR4 recently bred into sugar beet hybrids provides a high level of resistance to Cercospora leaf spot caused by the fungal pathogen Cercospora beticola. The occurrence of pathogen strains that overcome BvCR4 was studied using field trials in Switzerland conducted under natural disease pressure. Virulence of a subset of these strains was evaluated in a field trial conducted under elevated artificial disease pressure. We created a new C. beticola reference genome and mapped whole genome sequences of 256 isolates collected in Switzerland and Germany. These were combined with virulence phenotypes to conduct three separate genome-wide association studies (GWAS) to identify candidate avirulence genes. We identified a locus associated with avirulence containing a putative avirulence effector gene named AvrCR4. All virulent isolates either lacked AvrCR4 or had nonsynonymous mutations within the gene. AvrCR4 was present in all 74 isolates from non-BvCR4 hybrids, whereas 33 of 89 isolates from BvCR4 hybrids carried a deletion. We also mapped genomic data from 190 publicly available US isolates to our new reference genome. The AvrCR4 deletion was found in only one of 95 unique isolates from non-BvCR4 hybrids in the United States. AvrCR4 presents a unique example of an avirulence effector in which virulent alleles have only recently emerged. Most likely these were selected out of standing genetic variation after deployment of BvCR4. Identification of AvrCR4 will enable real-time screening of C. beticola populations for the emergence and spread of virulent isolates.
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Affiliation(s)
- Chen Chen
- Plant Pathology GroupInstitute of Integrative Biology, ETH ZurichZürichSwitzerland
| | | | | | | | - Enzo Neu
- KWS SAAT SE & Co. KGaAEinbeckGermany
| | | | - Bruce A. McDonald
- Plant Pathology GroupInstitute of Integrative Biology, ETH ZurichZürichSwitzerland
| | - Jessica Stapley
- Plant Pathology GroupInstitute of Integrative Biology, ETH ZurichZürichSwitzerland
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21
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Lo T, Coombe L, Gagalova KK, Marr A, Warren RL, Kirk H, Pandoh P, Zhao Y, Moore RA, Mungall AJ, Ritland C, Pavy N, Jones SJM, Bohlmann J, Bousquet J, Birol I, Thomson A. Assembly and annotation of the black spruce genome provide insights on spruce phylogeny and evolution of stress response. G3 (BETHESDA, MD.) 2023; 14:jkad247. [PMID: 37875130 PMCID: PMC10755193 DOI: 10.1093/g3journal/jkad247] [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: 05/17/2023] [Revised: 05/17/2023] [Accepted: 10/09/2023] [Indexed: 10/26/2023]
Abstract
Black spruce (Picea mariana [Mill.] B.S.P.) is a dominant conifer species in the North American boreal forest that plays important ecological and economic roles. Here, we present the first genome assembly of P. mariana with a reconstructed genome size of 18.3 Gbp and NG50 scaffold length of 36.0 kbp. A total of 66,332 protein-coding sequences were predicted in silico and annotated based on sequence homology. We analyzed the evolutionary relationships between P. mariana and 5 other spruces for which complete nuclear and organelle genome sequences were available. The phylogenetic tree estimated from mitochondrial genome sequences agrees with biogeography; specifically, P. mariana was strongly supported as a sister lineage to P. glauca and 3 other taxa found in western North America, followed by the European Picea abies. We obtained mixed topologies with weaker statistical support in phylogenetic trees estimated from nuclear and chloroplast genome sequences, indicative of ancient reticulate evolution affecting these 2 genomes. Clustering of protein-coding sequences from the 6 Picea taxa and 2 Pinus species resulted in 34,776 orthogroups, 560 of which appeared to be specific to P. mariana. Analysis of these specific orthogroups and dN/dS analysis of positive selection signatures for 497 single-copy orthogroups identified gene functions mostly related to plant development and stress response. The P. mariana genome assembly and annotation provides a valuable resource for forest genetics research and applications in this broadly distributed species, especially in relation to climate adaptation.
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Affiliation(s)
- Theodora Lo
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada
| | - Lauren Coombe
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada
| | - Kristina K Gagalova
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada
| | - Alex Marr
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada
| | - René L Warren
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada
| | - Heather Kirk
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada
| | - Pawan Pandoh
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada
| | - Yongjun Zhao
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada
| | - Richard A Moore
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada
| | - Andrew J Mungall
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada
| | - Carol Ritland
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Nathalie Pavy
- Canada Research Chair in Forest Genomics, Laval University, Quebec City, QC G1V 0A6, Canada
| | - Steven J M Jones
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada
| | - Joerg Bohlmann
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Jean Bousquet
- Canada Research Chair in Forest Genomics, Laval University, Quebec City, QC G1V 0A6, Canada
| | - Inanç Birol
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada
| | - Ashley Thomson
- Faculty of Natural Resources Management, Lakehead University, Thunder Bay, ON P7B 5E1, Canada
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22
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Alonso-del Valle A, Toribio-Celestino L, Quirant A, Pi CT, DelaFuente J, Canton R, Rocha EPC, Ubeda C, Peña-Miller R, San Millan A. Antimicrobial resistance level and conjugation permissiveness shape plasmid distribution in clinical enterobacteria. Proc Natl Acad Sci U S A 2023; 120:e2314135120. [PMID: 38096417 PMCID: PMC10741383 DOI: 10.1073/pnas.2314135120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Accepted: 10/26/2023] [Indexed: 12/18/2023] Open
Abstract
Conjugative plasmids play a key role in the dissemination of antimicrobial resistance (AMR) genes across bacterial pathogens. AMR plasmids are widespread in clinical settings, but their distribution is not random, and certain associations between plasmids and bacterial clones are particularly successful. For example, the globally spread carbapenem resistance plasmid pOXA-48 can use a wide range of enterobacterial species as hosts, but it is usually associated with a small number of specific Klebsiella pneumoniae clones. These successful associations represent an important threat for hospitalized patients. However, knowledge remains limited about the factors determining AMR plasmid distribution in clinically relevant bacteria. Here, we combined in vitro and in vivo experimental approaches to analyze pOXA-48-associated AMR levels and conjugation dynamics in a collection of wild-type enterobacterial strains isolated from hospitalized patients. Our results revealed significant variability in these traits across different bacterial hosts, with Klebsiella spp. strains showing higher pOXA-48-mediated AMR and conjugation frequencies than Escherichia coli strains. Using experimentally determined parameters, we developed a simple mathematical model to interrogate the contribution of AMR levels and conjugation permissiveness to plasmid distribution in bacterial communities. The simulations revealed that a small subset of clones, combining high AMR levels and conjugation permissiveness, play a critical role in stabilizing the plasmid in different polyclonal microbial communities. These results help to explain the preferential association of plasmid pOXA-48 with K. pneumoniae clones in clinical settings. More generally, our study reveals that species- and strain-specific variability in plasmid-associated phenotypes shape AMR evolution in clinically relevant bacterial communities.
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Affiliation(s)
- Aida Alonso-del Valle
- Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Cientificas, Madrid28049, Spain
| | - Laura Toribio-Celestino
- Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Cientificas, Madrid28049, Spain
| | - Anna Quirant
- Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana, Valencia46020, Spain
| | - Carles Tardio Pi
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca62209, México
- Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, Unidad Académica Yucatán, Universidad Nacional Autónoma de México, Yucatán04510, México
| | - Javier DelaFuente
- Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Cientificas, Madrid28049, Spain
| | - Rafael Canton
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal-Instituto Ramon y Cajal de Investigacion Sanitaria, Madrid28034, Spain
- Centro de Investigación Biológica en Red de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid28029, Spain
| | - Eduardo P. C. Rocha
- Institut Pasteur, Université de Paris Cité, CNRS UMR3525, Microbial Evolutionary Genomics, Paris75015, France
| | - Carles Ubeda
- Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana, Valencia46020, Spain
- Centro de Investigación Biológica en Red de Epidemiología y Salud Pública, Instituto de Salud Carlos III, Madrid28029, Spain
| | - Rafael Peña-Miller
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca62209, México
| | - Alvaro San Millan
- Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Cientificas, Madrid28049, Spain
- Centro de Investigación Biológica en Red de Epidemiología y Salud Pública, Instituto de Salud Carlos III, Madrid28029, Spain
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23
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Kochan TJ, Nozick SH, Valdes A, Mitra SD, Cheung BH, Lebrun-Corbin M, Medernach RL, Vessely MB, Mills JO, Axline CMR, Nelson JA, VanGosen EM, Ward TJ, Ozer EA, van Duin D, Chen L, Kreiswirth BN, Long SW, Musser JM, Bulman ZP, Wunderink RG, Hauser AR. Klebsiella pneumoniae clinical isolates with features of both multidrug-resistance and hypervirulence have unexpectedly low virulence. Nat Commun 2023; 14:7962. [PMID: 38042959 PMCID: PMC10693551 DOI: 10.1038/s41467-023-43802-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 11/21/2023] [Indexed: 12/04/2023] Open
Abstract
Klebsiella pneumoniae has been classified into two types, classical K. pneumoniae (cKP) and hypervirulent K. pneumoniae (hvKP). cKP isolates are highly diverse and important causes of nosocomial infections; they include globally disseminated antibiotic-resistant clones. hvKP isolates are sensitive to most antibiotics but are highly virulent, causing community-acquired infections in healthy individuals. The virulence phenotype of hvKP is associated with pathogenicity loci responsible for siderophore and hypermucoid capsule production. Recently, convergent strains of K. pneumoniae, which possess features of both cKP and hvKP, have emerged and are cause of much concern. Here, we screen the genomes of 2,608 multidrug-resistant K. pneumoniae isolates from the United States and identify 47 convergent isolates. We perform phenotypic and genomic characterization of 12 representative isolates. These 12 convergent isolates contain a variety of antimicrobial resistance plasmids and virulence plasmids. Most convergent isolates contain aerobactin biosynthesis genes and produce more siderophores than cKP isolates but not more capsule. Unexpectedly, only 1 of the 12 tested convergent isolates has a level of virulence consistent with hvKP isolates in a murine pneumonia model. These findings suggest that additional studies should be performed to clarify whether convergent strains are indeed more virulent than cKP in mouse and human infections.
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Affiliation(s)
- Travis J Kochan
- Laboratory of Respiratory and Special Pathogens, Division of Bacterial, Parasitic, and Allergenic Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA.
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
| | - Sophia H Nozick
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Aliki Valdes
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Sumitra D Mitra
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Bettina H Cheung
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Marine Lebrun-Corbin
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Rachel L Medernach
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Division of Infectious Diseases, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Madeleine B Vessely
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Jori O Mills
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Christopher M R Axline
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Julia A Nelson
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Ethan M VanGosen
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Timothy J Ward
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Egon A Ozer
- Division of Infectious Diseases, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - David van Duin
- Division of Infectious Diseases, University of North Carolina, Chapel Hill, NC, USA
| | - Liang Chen
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, USA
| | - Barry N Kreiswirth
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, USA
| | - S Wesley Long
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital Research Institute, Houston, TX, USA
| | - James M Musser
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital Research Institute, Houston, TX, USA
| | - Zackery P Bulman
- College of Pharmacy, University of Illinois at Chicago, Chicago, IL, USA
| | - Richard G Wunderink
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Simpson Querrey Institute for Epigenetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Alan R Hauser
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Division of Infectious Diseases, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
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24
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Veloso M, Waldisperg A, Arros P, Berríos-Pastén C, Acosta J, Colque H, Varas MA, Allende ML, Orellana LH, Marcoleta AE. Diversity, Taxonomic Novelty, and Encoded Functions of Salar de Ascotán Microbiota, as Revealed by Metagenome-Assembled Genomes. Microorganisms 2023; 11:2819. [PMID: 38004830 PMCID: PMC10673233 DOI: 10.3390/microorganisms11112819] [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: 09/21/2023] [Revised: 11/12/2023] [Accepted: 11/15/2023] [Indexed: 11/26/2023] Open
Abstract
Salar de Ascotán is a high-altitude arsenic-rich salt flat exposed to high ultraviolet radiation in the Atacama Desert, Chile. It hosts unique endemic flora and fauna and is an essential habitat for migratory birds, making it an important site for conservation and protection. However, there is limited information on the resident microbiota's diversity, genomic features, metabolic potential, and molecular mechanisms that enable it to thrive in this extreme environment. We used long- and short-read metagenomics to investigate the microbial communities in Ascotán's water, sediment, and soil. Bacteria predominated, mainly Pseudomonadota, Acidobacteriota, and Bacteroidota, with a remarkable diversity of archaea in the soil. Following hybrid assembly, we recovered high-quality bacterial (101) and archaeal (6) metagenome-assembled genomes (MAGs), including representatives of two putative novel families of Patescibacteria and Pseudomonadota and two novel orders from the archaeal classes Halobacteriota and Thermoplasmata. We found different metabolic capabilities across distinct lineages and a widespread presence of genes related to stress response, DNA repair, and resistance to arsenic and other metals. These results highlight the remarkable diversity and taxonomic novelty of the Salar de Ascotán microbiota and its rich functional repertoire, making it able to resist different harsh conditions. The highly complete MAGs described here could serve future studies and bioprospection efforts focused on salt flat extremophiles, and contribute to enriching databases with microbial genome data from underrepresented regions of our planet.
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Affiliation(s)
- Marcelo Veloso
- Grupo de Microbiología Integrativa, Laboratorio de Biología Estructural y Molecular BEM, Faculty of Science, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago 7800003, Chile; (M.V.); (A.W.); (P.A.); (C.B.-P.); (J.A.); (H.C.); (M.A.V.)
| | - Angie Waldisperg
- Grupo de Microbiología Integrativa, Laboratorio de Biología Estructural y Molecular BEM, Faculty of Science, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago 7800003, Chile; (M.V.); (A.W.); (P.A.); (C.B.-P.); (J.A.); (H.C.); (M.A.V.)
| | - Patricio Arros
- Grupo de Microbiología Integrativa, Laboratorio de Biología Estructural y Molecular BEM, Faculty of Science, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago 7800003, Chile; (M.V.); (A.W.); (P.A.); (C.B.-P.); (J.A.); (H.C.); (M.A.V.)
| | - Camilo Berríos-Pastén
- Grupo de Microbiología Integrativa, Laboratorio de Biología Estructural y Molecular BEM, Faculty of Science, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago 7800003, Chile; (M.V.); (A.W.); (P.A.); (C.B.-P.); (J.A.); (H.C.); (M.A.V.)
| | - Joaquín Acosta
- Grupo de Microbiología Integrativa, Laboratorio de Biología Estructural y Molecular BEM, Faculty of Science, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago 7800003, Chile; (M.V.); (A.W.); (P.A.); (C.B.-P.); (J.A.); (H.C.); (M.A.V.)
| | - Hazajem Colque
- Grupo de Microbiología Integrativa, Laboratorio de Biología Estructural y Molecular BEM, Faculty of Science, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago 7800003, Chile; (M.V.); (A.W.); (P.A.); (C.B.-P.); (J.A.); (H.C.); (M.A.V.)
| | - Macarena A. Varas
- Grupo de Microbiología Integrativa, Laboratorio de Biología Estructural y Molecular BEM, Faculty of Science, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago 7800003, Chile; (M.V.); (A.W.); (P.A.); (C.B.-P.); (J.A.); (H.C.); (M.A.V.)
- Millenium Institute Center for Genome Regulation, Faculty of Science, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago 7800003, Chile;
| | - Miguel L. Allende
- Millenium Institute Center for Genome Regulation, Faculty of Science, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago 7800003, Chile;
| | - Luis H. Orellana
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Celsiusstr. 1, D-28359 Bremen, Germany;
| | - Andrés E. Marcoleta
- Grupo de Microbiología Integrativa, Laboratorio de Biología Estructural y Molecular BEM, Faculty of Science, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago 7800003, Chile; (M.V.); (A.W.); (P.A.); (C.B.-P.); (J.A.); (H.C.); (M.A.V.)
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25
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Lei T, Luo N, Song C, Yu J, Zhou Y, Qi X, Liu Y. Comparative Genomics Reveals Three Genetic Groups of the Whitefly Obligate Endosymbiont Candidatus Portiera aleyrodidarum. INSECTS 2023; 14:888. [PMID: 37999087 PMCID: PMC10672337 DOI: 10.3390/insects14110888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Revised: 11/16/2023] [Accepted: 11/16/2023] [Indexed: 11/25/2023]
Abstract
Maternally inherited obligate endosymbionts codiverge with their invertebrate hosts and reflect their host's evolutionary history. Whiteflies (Hemiptera: Aleyrodidae) harbor one obligate endosymbiont, Candidatus Portiera aleyrodidarum (hereafter Portiera). Portiera was anciently acquired by whitefly and has been coevolving with its host ever since. Uncovering the divergence of endosymbionts provides a fundamental basis for inspecting the coevolutionary processes between the bacteria and their hosts. To illustrate the divergence of Portiera lineages across different whitefly species, we sequenced the Portiera genome from Aleyrodes shizuokensis and conducted a comparative analysis on the basic features and gene evolution with bacterial genomes from five whitefly genera, namely Aleurodicus, Aleyrodes, Bemisia, Pealius, and Trialeurodes. The results indicated that Portiera from Bemisia possessed significantly larger genomes, fewer coding sequences (CDSs), and a lower coding density. Their gene arrangement differed notably from those of other genera. The phylogeny of the nine Portiera lineages resembled that of their hosts. Moreover, the lineages were classified into three distinct genetic groups based on the genetic distance, one from Aleurodicus (Aleurodicinae), one from Bemisia (Aleyrodinae), and another from Aleyrodes, Pealius, and Trialeurrodes (Aleyrodinae). Synonymous and nonsynonymous rate analyses, parity rule 2 plot analyses, neutrality plot analyses, and effective number of codons analyses supported the distinction of the three genetic groups. Our results indicated that Portiera from distant hosts exhibit distinct genomic contents, implying codivergence between hosts and their endosymbionts. This work will enhance our understanding of coevolution between hosts and their endosymbionts.
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Affiliation(s)
- Teng Lei
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, School of Life Sciences, Taizhou University, Taizhou 318000, China; (T.L.)
| | - Ning Luo
- Natural Resources and Planning Bureau of Linhai City, Linhai 317000, China
| | - Chao Song
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, School of Life Sciences, Taizhou University, Taizhou 318000, China; (T.L.)
| | - Junwei Yu
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, School of Life Sciences, Taizhou University, Taizhou 318000, China; (T.L.)
| | - Yuhang Zhou
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, School of Life Sciences, Taizhou University, Taizhou 318000, China; (T.L.)
| | - Xin Qi
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, School of Life Sciences, Taizhou University, Taizhou 318000, China; (T.L.)
| | - Yinquan Liu
- Ministry of Agriculture and Rural Affairs Key Laboratory of Agricultural Entomology, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China
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26
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Paździor E, Bomba A, Tłuścik K, Nadolna-Ałtyn K, Podolska M, Reichert M, Wasyl D, Pękala-Safińska A. Phylogenetic analysis of Shewanella spp. isolated from fish. JOURNAL OF FISH DISEASES 2023; 46:1163-1171. [PMID: 37453080 DOI: 10.1111/jfd.13834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 06/30/2023] [Accepted: 07/03/2023] [Indexed: 07/18/2023]
Abstract
Different species of Shewanella spp. widely inhabit freshwater and marine environments. Some of them are opportunistic fish pathogens. The application of high-throughput sequencing enabled the characterization and taxonomic reclassification of many Shewanella spp. species. Still, some strains collected from fish need to be better recognized. The aim of the present study was to classify and determine the phylogenetic relationships of Shewanella spp. collected from fish. The complete genomes of 94 strains of Shewanella spp. from different fish species were sequenced using Illumina platform (MiSeq). The 16S rRNA gene, genomic features and whole-genome relationships of those bacteria were comprehensively analysed in comparison to reference strains. Whole-genome analysis showed that the tested Shewanella spp. strains were clustered into six groups similar to reference strains of S. xiamenensis, S. oneidensis, S. glacialipiscicola, S. hafniensis, S. baltica and S. oncorhynchi. Our study indicates that the whole-genome sequence analysis enabled taxonomic classification and assessment of the diversity of the Shewanella spp. strains, as opposed to recently the gold standard method of 16S rRNA amplicon sequencing. The high genetic diversity and low similarity to the reference genome of S. oneidensis indicate that the group of strains may be a subspecies or even new species. Furthermore, we showed that the most frequent Shewanella spp. species occurring in freshwater fish in our study is the recently described species S. oncorhynchi.
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Affiliation(s)
- Ewa Paździor
- Department of Fish Diseases, National Veterinary Research Institute, Puławy, Poland
| | - Arkadiusz Bomba
- Depratment of Omics Analyses, National Veterinary Research Institute, Puławy, Poland
| | - Katarzyna Tłuścik
- Depratment of Omics Analyses, National Veterinary Research Institute, Puławy, Poland
| | - Katarzyna Nadolna-Ałtyn
- Department of Fisheries Resources, National Marine Fisheries Research Institute, Gdynia, Poland
| | - Magdalena Podolska
- Department of Fisheries Resources, National Marine Fisheries Research Institute, Gdynia, Poland
| | - Michał Reichert
- Department of Fish Diseases, National Veterinary Research Institute, Puławy, Poland
| | - Dariusz Wasyl
- Depratment of Omics Analyses, National Veterinary Research Institute, Puławy, Poland
- Department of Microbiology, National Veterinary Research Institute, Puławy, Poland
| | - Agnieszka Pękala-Safińska
- Department of Preclinical Sciences and Infectious Diseases, Faculty of Veterinary Medicine and Animal Science, Poznań University of Life Sciences, Poznań, Poland
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27
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Hanze Villavicencio KL, Job MJ, Burghard AC, Taffet A, Banda FM, Vurayai M, Mokomane M, Arscott-Mills T, Mazhani T, Nchingane S, Thomas B, Steenhoff AP, Ratner AJ. Genomic Analysis of Group B Streptococcus Carriage Isolates From Botswana Reveals Distinct Local Epidemiology and Identifies Novel Strains. Open Forum Infect Dis 2023; 10:ofad496. [PMID: 37869411 PMCID: PMC10588617 DOI: 10.1093/ofid/ofad496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 09/29/2023] [Indexed: 10/24/2023] Open
Abstract
In pregnant people colonized with group B Streptococcus (GBS) in Botswana, we report the presence/expansion of sequence types 223 and 109, a low rate of erythromycin resistance, and 3 novel sequence types. These data highlight the importance of local epidemiologic studies of GBS, a significant source of neonatal disease.
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Affiliation(s)
- Karen L Hanze Villavicencio
- Division of Infectious Diseases, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Megan J Job
- Department of Pediatrics, NewYork University Grossman School of Medicine, New York, New York, USA
| | - Anne Claire Burghard
- Department of Pediatrics, NewYork University Grossman School of Medicine, New York, New York, USA
- Renaissance School of Medicine, Stony Brook University, Stony Brook, NewYork, USA
| | - Allison Taffet
- Department of Pediatrics, NewYork University Grossman School of Medicine, New York, New York, USA
| | - Francis M Banda
- Department of Pediatrics & Adolescent Health, Faculty of Medicine, University of Botswana, Gaborone, Botswana
| | - Moses Vurayai
- School of Allied Health Professionals, Faculty of Health Sciences, University of Botswana, Gaborone, Botswana
| | - Margaret Mokomane
- School of Allied Health Professionals, Faculty of Health Sciences, University of Botswana, Gaborone, Botswana
| | - Tonya Arscott-Mills
- Department of Pediatrics & Adolescent Health, Faculty of Medicine, University of Botswana, Gaborone, Botswana
- Botswana-UPenn Partnership, Faculty of Health Sciences, University of Botswana, Gaborone, Botswana
- Global Health Center, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Tiny Mazhani
- Department of Pediatrics & Adolescent Health, Faculty of Medicine, University of Botswana, Gaborone, Botswana
| | | | - Brady Thomas
- Department of Pediatrics, Stead Family Children's Hospital, University of Iowa, Iowa City, Iowa, USA
| | - Andrew P Steenhoff
- Division of Infectious Diseases, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
- Department of Pediatrics & Adolescent Health, Faculty of Medicine, University of Botswana, Gaborone, Botswana
- Botswana-UPenn Partnership, Faculty of Health Sciences, University of Botswana, Gaborone, Botswana
- Global Health Center, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Adam J Ratner
- Department of Pediatrics, NewYork University Grossman School of Medicine, New York, New York, USA
- Department of Microbiology, NewYork University Grossman School of Medicine, New York, New York, USA
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28
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Couvin D, Stattner E, Segretier W, Cazenave D, Rastogi N. simpiTB - a pipeline designed to extract meaningful information from whole genome sequencing data of Mycobacterium tuberculosis complex, allows to combine genomic, phylogenetic and clustering analyses in existing SITVIT databases. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2023; 113:105466. [PMID: 37331497 DOI: 10.1016/j.meegid.2023.105466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 06/11/2023] [Accepted: 06/14/2023] [Indexed: 06/20/2023]
Abstract
Data obtained from new sequencing technologies are evolving rapidly, leading to the development of specific bioinformatic tools, pipelines and softwares. Several algorithms and tools are today available allowing a better identification and description of Mycobacterium tuberculosis complex (MTBC) isolates worldwide. Our approach consists in applying existing methods to analyze DNA sequencing data (from FASTA or FASTQ files), and tentatively extract meaningful information that would facilitate identification as well as a better understanding and management of MTBC isolates (taking into account whole genome sequencing and classical genotyping data). The aim of this study is to propose a pipeline analysis allowing to potentially simplify MTBC data analysis by providing different ways to interpret genomic or genotyping information based on existing tools. Furthermore, we propose a "reconciledTB" list making a link with results directly obtained from whole genome sequencing (WGS) data and results obtained from classical genotyping analysis (data inferred from SpoTyping and MIRUReader). Data visualization graphics and trees generated provide additional elements to better understand and confer associations among information overlap analyses. Additionally, comparison between data entered in an international genotyping database (SITVITEXTEND) and ensuing data obtained from the pipeline not only provide meaningful information, but further suggest that simpiTB could also be suitable for new data integration in specific TB genotyping databases.
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Affiliation(s)
- David Couvin
- WHO Supranational TB Reference Laboratory, Tuberculosis and Mycobacteria Unit, Institut Pasteur de la Guadeloupe, Les Abymes, Guadeloupe, France; Transmission, Reservoir and Diversity of Pathogens Unit, Institut Pasteur de la Guadeloupe, Les Abymes, Guadeloupe, France.
| | - Erick Stattner
- Laboratoire de Mathématiques Informatique et Applications (LAMIA), Université des Antilles, Pointe-à-Pitre, Guadeloupe, France
| | - Wilfried Segretier
- Laboratoire de Mathématiques Informatique et Applications (LAMIA), Université des Antilles, Pointe-à-Pitre, Guadeloupe, France
| | - Damien Cazenave
- Transmission, Reservoir and Diversity of Pathogens Unit, Institut Pasteur de la Guadeloupe, Les Abymes, Guadeloupe, France
| | - Nalin Rastogi
- WHO Supranational TB Reference Laboratory, Tuberculosis and Mycobacteria Unit, Institut Pasteur de la Guadeloupe, Les Abymes, Guadeloupe, France
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29
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Zhang Z, Zhang J, Chen Q, He J, Li X, Wang Y, Lu Y. Complete De Novo Assembly of Wolbachia Endosymbiont of Frankliniella intonsa. Int J Mol Sci 2023; 24:13245. [PMID: 37686049 PMCID: PMC10487741 DOI: 10.3390/ijms241713245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Revised: 08/20/2023] [Accepted: 08/23/2023] [Indexed: 09/10/2023] Open
Abstract
As an endosymbiont, Wolbachia exerts significant effects on the host, including on reproduction, immunity, and metabolism. However, the study of Wolbachia in Thysanopteran insects, such as flower thrips Frankliniella intonsa, remains limited. Here, we assembled a gap-free looped genome assembly of Wolbachia strain wFI in a length of 1,463,884 bp (GC content 33.80%), using Nanopore long reads and Illumina short reads. The annotation of wFI identified a total of 1838 protein-coding genes (including 85 pseudogenes), 3 ribosomal RNAs (rRNAs), 35 transfer RNAs (tRNAs), and 1 transfer-messenger RNA (tmRNA). Beyond this basic description, we identified mobile genetic elements, such as prophage and insertion sequences (ISs), which make up 17% of the entire wFI genome, as well as genes involved in riboflavin and biotin synthesis and metabolism. This research lays the foundation for understanding the nutritional mutualism between Wolbachia and flower thrips. It also serves as a valuable resource for future studies delving into the intricate interactions between Wolbachia and its host.
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Affiliation(s)
- Zhijun Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (J.Z.); (Q.C.); (J.H.); (X.L.); (Y.L.)
| | - Jiahui Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (J.Z.); (Q.C.); (J.H.); (X.L.); (Y.L.)
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, College of Plant Protection, Hunan Agricultural University, Changsha 410128, China
| | - Qizhang Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (J.Z.); (Q.C.); (J.H.); (X.L.); (Y.L.)
| | - Jianyun He
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (J.Z.); (Q.C.); (J.H.); (X.L.); (Y.L.)
| | - Xiaowei Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (J.Z.); (Q.C.); (J.H.); (X.L.); (Y.L.)
| | - Yunsheng Wang
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, College of Plant Protection, Hunan Agricultural University, Changsha 410128, China
| | - Yaobin Lu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (J.Z.); (Q.C.); (J.H.); (X.L.); (Y.L.)
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30
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Macesic N, Hawkey J, Vezina B, Wisniewski JA, Cottingham H, Blakeway LV, Harshegyi T, Pragastis K, Badoordeen GZ, Dennison A, Spelman DW, Jenney AWJ, Peleg AY. Genomic dissection of endemic carbapenem resistance reveals metallo-beta-lactamase dissemination through clonal, plasmid and integron transfer. Nat Commun 2023; 14:4764. [PMID: 37553339 PMCID: PMC10409761 DOI: 10.1038/s41467-023-39915-2] [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: 03/29/2023] [Accepted: 07/03/2023] [Indexed: 08/10/2023] Open
Abstract
Infections caused by metallo-beta-lactamase-producing organisms (MBLs) are a global health threat. Our understanding of transmission dynamics and how MBLs establish endemicity remains limited. We analysed two decades of blaIMP-4 evolution in a hospital using sequence data from 270 clinical and environmental isolates (including 169 completed genomes) and identified the blaIMP-4 gene across 7 Gram-negative genera, 68 bacterial strains and 7 distinct plasmid types. We showed how an initial multi-species outbreak of conserved IncC plasmids (95 genomes across 37 strains) allowed endemicity to be established through the ability of blaIMP-4 to disseminate in successful strain-genetic setting pairs we termed propagators, in particular Serratia marcescens and Enterobacter hormaechei. From this reservoir, blaIMP-4 persisted through diversification of genetic settings that resulted from transfer of blaIMP-4 plasmids between bacterial hosts and of the integron carrying blaIMP-4 between plasmids. Our findings provide a framework for understanding endemicity and spread of MBLs and may have broader applicability to other carbapenemase-producing organisms.
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Affiliation(s)
- Nenad Macesic
- Department of Infectious Diseases, The Alfred Hospital and Central Clinical School, Monash University, Melbourne, Australia
- Centre to Impact AMR, Monash University, Clayton, Australia
| | - Jane Hawkey
- Department of Infectious Diseases, The Alfred Hospital and Central Clinical School, Monash University, Melbourne, Australia
| | - Ben Vezina
- Department of Infectious Diseases, The Alfred Hospital and Central Clinical School, Monash University, Melbourne, Australia
| | - Jessica A Wisniewski
- Department of Infectious Diseases, The Alfred Hospital and Central Clinical School, Monash University, Melbourne, Australia
| | - Hugh Cottingham
- Department of Infectious Diseases, The Alfred Hospital and Central Clinical School, Monash University, Melbourne, Australia
| | - Luke V Blakeway
- Department of Infectious Diseases, The Alfred Hospital and Central Clinical School, Monash University, Melbourne, Australia
| | - Taylor Harshegyi
- Department of Infectious Diseases, The Alfred Hospital and Central Clinical School, Monash University, Melbourne, Australia
| | - Katherine Pragastis
- Department of Infectious Diseases, The Alfred Hospital and Central Clinical School, Monash University, Melbourne, Australia
| | - Gnei Zweena Badoordeen
- Department of Infectious Diseases, The Alfred Hospital and Central Clinical School, Monash University, Melbourne, Australia
| | | | - Denis W Spelman
- Department of Infectious Diseases, The Alfred Hospital and Central Clinical School, Monash University, Melbourne, Australia
- Microbiology Unit, Alfred Hospital, Melbourne, Australia
| | - Adam W J Jenney
- Department of Infectious Diseases, The Alfred Hospital and Central Clinical School, Monash University, Melbourne, Australia
- Microbiology Unit, Alfred Hospital, Melbourne, Australia
| | - Anton Y Peleg
- Department of Infectious Diseases, The Alfred Hospital and Central Clinical School, Monash University, Melbourne, Australia.
- Centre to Impact AMR, Monash University, Clayton, Australia.
- Infection Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, Australia.
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31
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Sánchez-Gil JJ, Poppeliers SWM, Vacheron J, Zhang H, Odijk B, Keel C, de Jonge R. The conserved iol gene cluster in Pseudomonas is involved in rhizosphere competence. Curr Biol 2023; 33:3097-3110.e6. [PMID: 37419116 DOI: 10.1016/j.cub.2023.05.057] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 04/25/2023] [Accepted: 05/24/2023] [Indexed: 07/09/2023]
Abstract
The Pseudomonas genus has shown great potential as a sustainable solution to support agriculture through its plant-growth-promoting and biocontrol activities. However, their efficacy as bioinoculants is limited by unpredictable colonization in natural conditions. Our study identifies the iol locus, a gene cluster in Pseudomonas involved in inositol catabolism, as a feature enriched among superior root colonizers in natural soil. Further characterization revealed that the iol locus increases competitiveness, potentially caused by an observed induction of swimming motility and the production of fluorescent siderophore in response to inositol, a plant-derived compound. Public data analyses indicate that the iol locus is broadly conserved in the Pseudomonas genus and linked to diverse host-microbe interactions. Together, our findings suggest the iol locus as a potential target for developing more effective bioinoculants for sustainable agriculture.
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Affiliation(s)
- Juan J Sánchez-Gil
- Plant-Microbe Interactions, Department of Biology, Science for Life, Utrecht University, Utrecht 3584 CH, The Netherlands
| | - Sanne W M Poppeliers
- Plant-Microbe Interactions, Department of Biology, Science for Life, Utrecht University, Utrecht 3584 CH, The Netherlands
| | - Jordan Vacheron
- Department of Fundamental Microbiology, University of Lausanne, Lausanne CH-1015, Switzerland
| | - Hao Zhang
- Plant-Microbe Interactions, Department of Biology, Science for Life, Utrecht University, Utrecht 3584 CH, The Netherlands
| | - Bart Odijk
- Plant-Microbe Interactions, Department of Biology, Science for Life, Utrecht University, Utrecht 3584 CH, The Netherlands
| | - Christoph Keel
- Department of Fundamental Microbiology, University of Lausanne, Lausanne CH-1015, Switzerland
| | - Ronnie de Jonge
- Plant-Microbe Interactions, Department of Biology, Science for Life, Utrecht University, Utrecht 3584 CH, The Netherlands.
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32
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Ambrosio FJ, Scribner MR, Wright SM, Otieno JR, Doughty EL, Gorzalski A, Siao DD, Killian S, Hua C, Schneider E, Tran M, Varghese V, Libuit KG, Pandori M, Sevinsky JR, Hess D. TheiaEuk: a species-agnostic bioinformatics workflow for fungal genomic characterization. Front Public Health 2023; 11:1198213. [PMID: 37593727 PMCID: PMC10428623 DOI: 10.3389/fpubh.2023.1198213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 07/04/2023] [Indexed: 08/19/2023] Open
Abstract
Introduction The clinical incidence of antimicrobial-resistant fungal infections has dramatically increased in recent years. Certain fungal pathogens colonize various body cavities, leading to life-threatening bloodstream infections. However, the identification and characterization of fungal isolates in laboratories remain a significant diagnostic challenge in medicine and public health. Whole-genome sequencing provides an unbiased and uniform identification pipeline for fungal pathogens but most bioinformatic analysis pipelines focus on prokaryotic species. To this end, TheiaEuk_Illumina_PE_PHB (TheiaEuk) was designed to focus on genomic analysis specialized to fungal pathogens. Methods TheiaEuk was designed using containerized components and written in the workflow description language (WDL) to facilitate deployment on the cloud-based open bioinformatics platform Terra. This species-agnostic workflow enables the analysis of fungal genomes without requiring coding, thereby reducing the entry barrier for laboratory scientists. To demonstrate the usefulness of this pipeline, an ongoing outbreak of C. auris in southern Nevada was investigated. We performed whole-genome sequence analysis of 752 new C. auris isolates from this outbreak. Furthermore, TheiaEuk was utilized to observe the accumulation of mutations in the FKS1 gene over the course of the outbreak, highlighting the utility of TheiaEuk as a monitor of emerging public health threats when combined with whole-genome sequencing surveillance of fungal pathogens. Results A primary result of this work is a curated fungal database containing 5,667 unique genomes representing 245 species. TheiaEuk also incorporates taxon-specific submodules for specific species, including clade-typing for Candida auris (C. auris). In addition, for several fungal species, it performs dynamic reference genome selection and variant calling, reporting mutations found in genes currently associated with antifungal resistance (FKS1, ERG11, FUR1). Using genome assemblies from the ATCC Mycology collection, the taxonomic identification module used by TheiaEuk correctly assigned genomes to the species level in 126/135 (93.3%) instances and to the genus level in 131/135 (97%) of instances, and provided zero false calls. Application of TheiaEuk to actual specimens obtained in the course of work at a local public health laboratory resulted in 13/15 (86.7%) correct calls at the species level, with 2/15 called at the genus level. It made zero incorrect calls. TheiaEuk accurately assessed clade type of Candida auris in 297/302 (98.3%) of instances. Discussion TheiaEuk demonstrated effectiveness in identifying fungal species from whole genome sequence. It further showed accuracy in both clade-typing of C. auris and in the identification of mutations known to associate with drug resistance in that organism.
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Affiliation(s)
| | | | | | | | | | | | | | - Steve Killian
- Alameda County Public Health Laboratory, Oakland, CA, United States
| | - Chi Hua
- Public Health Laboratories, Division of Disease Control and Health Statistics, Washington State Department of Health, Shoreline, WA, United States
| | - Emily Schneider
- Public Health Laboratories, Division of Disease Control and Health Statistics, Washington State Department of Health, Shoreline, WA, United States
| | - Michael Tran
- Public Health Laboratories, Division of Disease Control and Health Statistics, Washington State Department of Health, Shoreline, WA, United States
| | - Vici Varghese
- Alameda County Public Health Laboratory, Oakland, CA, United States
| | | | - Mark Pandori
- Nevada State Public Health Laboratory, Reno, NV, United States
- Department of Pathology and Laboratory Medicine, Reno School of Medicine, University of Nevada, Reno, NV, United States
- Department of Microbiology and Immunology, Reno School of Medicine, University of Nevada, Reno, NV, United States
| | | | - David Hess
- Nevada State Public Health Laboratory, Reno, NV, United States
- Department of Pathology and Laboratory Medicine, Reno School of Medicine, University of Nevada, Reno, NV, United States
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33
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Fernández-Calvet A, Toribio-Celestino L, Alonso-del Valle A, Sastre-Dominguez J, Valdes-Chiara P, San Millan A, DelaFuente J. The distribution of fitness effects of plasmid pOXA-48 in clinical enterobacteria. MICROBIOLOGY (READING, ENGLAND) 2023; 169:001369. [PMID: 37505800 PMCID: PMC10433420 DOI: 10.1099/mic.0.001369] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 07/12/2023] [Indexed: 07/29/2023]
Abstract
Antimicrobial resistance (AMR) in bacteria is a major public health problem. The main route for AMR acquisition in clinically important bacteria is the horizontal transfer of plasmids carrying resistance genes. AMR plasmids allow bacteria to survive antibiotics, but they also entail physiological alterations in the host cell. Multiple studies over the last few years have indicated that these alterations can translate into a fitness cost when antibiotics are absent. However, due to technical limitations, most of these studies are based on analysing new associations between plasmids and bacteria generated in vitro, and we know very little about the effects of plasmids in their native bacterial hosts. In this study, we used a CRISPR-Cas9-tool to selectively cure plasmids from clinical enterobacteria to overcome this limitation. Using this approach, we were able to study the fitness effects of the carbapenem resistance plasmid pOXA-48 in 35 pOXA-48-carrying isolates recovered from hospitalized patients. Our results revealed that pOXA-48 produces variable effects across the collection of wild-type enterobacterial strains naturally carrying the plasmid, ranging from fitness costs to fitness benefits. Importantly, the plasmid was only associated with a significant fitness reduction in four out of 35 clones, and produced no significant changes in fitness in the great majority of isolates. Our results suggest that plasmids produce neutral fitness effects in most native bacterial hosts, helping to explain the great prevalence of plasmids in natural microbial communities.
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Affiliation(s)
| | | | | | | | | | - Alvaro San Millan
- Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
- Centro de Investigación Biológica en Red de Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain
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Kiu R, Shaw AG, Sim K, Acuna-Gonzalez A, Price CA, Bedwell H, Dreger SA, Fowler WJ, Cornwell E, Pickard D, Belteki G, Malsom J, Phillips S, Young GR, Schofield Z, Alcon-Giner C, Berrington JE, Stewart CJ, Dougan G, Clarke P, Douce G, Robinson SD, Kroll JS, Hall LJ. Particular genomic and virulence traits associated with preterm infant-derived toxigenic Clostridium perfringens strains. Nat Microbiol 2023; 8:1160-1175. [PMID: 37231089 PMCID: PMC10234813 DOI: 10.1038/s41564-023-01385-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 04/17/2023] [Indexed: 05/27/2023]
Abstract
Clostridium perfringens is an anaerobic toxin-producing bacterium associated with intestinal diseases, particularly in neonatal humans and animals. Infant gut microbiome studies have recently indicated a link between C. perfringens and the preterm infant disease necrotizing enterocolitis (NEC), with specific NEC cases associated with overabundant C. perfringens termed C. perfringens-associated NEC (CPA-NEC). In the present study, we carried out whole-genome sequencing of 272 C. perfringens isolates from 70 infants across 5 hospitals in the United Kingdom. In this retrospective analysis, we performed in-depth genomic analyses (virulence profiling, strain tracking and plasmid analysis) and experimentally characterized pathogenic traits of 31 strains, including 4 from CPA-NEC patients. We found that the gene encoding toxin perfringolysin O, pfoA, was largely deficient in a human-derived hypovirulent lineage, as well as certain colonization factors, in contrast to typical pfoA-encoding virulent lineages. We determined that infant-associated pfoA+ strains caused significantly more cellular damage than pfoA- strains in vitro, and further confirmed this virulence trait in vivo using an oral-challenge C57BL/6 murine model. These findings suggest both the importance of pfoA+ C. perfringens as a gut pathogen in preterm infants and areas for further investigation, including potential intervention and therapeutic strategies.
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Affiliation(s)
- Raymond Kiu
- Gut Microbes and Health, Quadram Institute Bioscience, Norwich, UK
| | | | - Kathleen Sim
- Faculty of Medicine, Imperial College London, London, UK
| | | | | | - Harley Bedwell
- Gut Microbes and Health, Quadram Institute Bioscience, Norwich, UK
| | - Sally A Dreger
- Gut Microbes and Health, Quadram Institute Bioscience, Norwich, UK
| | - Wesley J Fowler
- Gut Microbes and Health, Quadram Institute Bioscience, Norwich, UK
| | - Emma Cornwell
- Faculty of Medicine, Imperial College London, London, UK
| | - Derek Pickard
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Gusztav Belteki
- Neonatal Intensive Care Unit, The Rosie Hospital, Cambridge, UK
| | - Jennifer Malsom
- Gut Microbes and Health, Quadram Institute Bioscience, Norwich, UK
| | - Sarah Phillips
- Gut Microbes and Health, Quadram Institute Bioscience, Norwich, UK
| | - Gregory R Young
- Hub for Biotechnology in the Built Environment, Northumbria University, Newcastle upon Tyne, UK
| | - Zoe Schofield
- Gut Microbes and Health, Quadram Institute Bioscience, Norwich, UK
| | | | - Janet E Berrington
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
- Newcastle Neonatal Services, Newcastle upon Tyne NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Christopher J Stewart
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
- Newcastle Neonatal Services, Newcastle upon Tyne NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Gordon Dougan
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Paul Clarke
- Norfolk and Norwich University Hospital, Norwich, UK
- Norwich Medical School, University of East Anglia, Norwich, UK
| | - Gillian Douce
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Stephen D Robinson
- Gut Microbes and Health, Quadram Institute Bioscience, Norwich, UK
- School of Biological Sciences, University of East Anglia, Norwich, UK
| | - J Simon Kroll
- Faculty of Medicine, Imperial College London, London, UK
| | - Lindsay J Hall
- Gut Microbes and Health, Quadram Institute Bioscience, Norwich, UK.
- Norwich Medical School, University of East Anglia, Norwich, UK.
- Intestinal Microbiome, School of Life Sciences, ZIEL-Institute for Food & Health, Technical University of Munich, Freising, Germany.
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35
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Ma W, Zhu B, Wang W, Wang Q, Cui X, Wang Y, Dong X, Li X, Ma J, Cheng F, Shi X, Chen L, Niu S, Hao M. Genetic and enzymatic characterization of two novel bla NDM-36, -37 variants in Escherichia coli strains. Eur J Clin Microbiol Infect Dis 2023; 42:471-480. [PMID: 36810726 PMCID: PMC9998317 DOI: 10.1007/s10096-023-04576-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 02/13/2023] [Indexed: 02/23/2023]
Abstract
The widespread of different NDM variants in clinical Enterobacterales isolates poses a serious public health concern, which requires continuous monitoring. In this study, three E. coli strains carrying two novel blaNDM variants of blaNDM-36, -37 were identified from a patient with refractory urinary tract infection (UTI) in China. We conducted antimicrobial susceptibility testing (AST), enzyme kinetics analysis, conjugation experiment, whole-genome sequencing (WGS), and bioinformatics analysis to characterize the blaNDM-36, -37 enzymes and their carrying strains. The blaNDM-36, -37 harboring E. coli isolates belonged to ST227, O9:H10 serotype and exhibited intermediate or resistance to all β-lactams tested except aztreonam and aztreonam/avibactam. The genes of blaNDM-36, -37 were located on a conjugative IncHI2-type plasmid. NDM-37 differed from NDM-5 by a single amino acid substitution (His261Tyr). NDM-36 differed from NDM-37 by an additional missense mutation (Ala233Val). NDM-36 had increased hydrolytic activity toward ampicillin and cefotaxime relative to NDM-37 and NDM-5, while NDM-37 and NDM-36 had lower catalytic activity toward imipenem but higher activity against meropenem in comparison to NDM-5. This is the first report of co-occurrence of two novel blaNDM variants in E. coli isolated from the same patient. The work provides insights into the enzymatic function and demonstrates the ongoing evolution of NDM enzymes.
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Affiliation(s)
- Wanshan Ma
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Shandong Medicine and Health Key Laboratory of Laboratory Medicine, No. 16766 Jingshi Road, Lixia District, Jinan, China
| | - Bo Zhu
- Xiamen Key Laboratory of Genetic Testing, Department of Laboratory Medicine, The First Affiliated Hospital of Xiamen University, Xiamen, China
| | - Wen Wang
- Department of Laboratory Medicine, The First Affiliated Hospital of Chongqing Medical University, No. 1 Friendship Road, Yuzhong District, Chongqing, China
| | - Qian Wang
- Department of Laboratory Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, China
| | - Xiaodi Cui
- School of Clinical Medicine, Jining Medical University, Jining, China
| | - Yujiao Wang
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Shandong Medicine and Health Key Laboratory of Laboratory Medicine, No. 16766 Jingshi Road, Lixia District, Jinan, China
| | - Xiutao Dong
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Shandong Medicine and Health Key Laboratory of Laboratory Medicine, No. 16766 Jingshi Road, Lixia District, Jinan, China
| | - Xiaofeng Li
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Shandong Medicine and Health Key Laboratory of Laboratory Medicine, No. 16766 Jingshi Road, Lixia District, Jinan, China
| | - Jianping Ma
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Shandong Medicine and Health Key Laboratory of Laboratory Medicine, No. 16766 Jingshi Road, Lixia District, Jinan, China
| | - Fang Cheng
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Shandong Medicine and Health Key Laboratory of Laboratory Medicine, No. 16766 Jingshi Road, Lixia District, Jinan, China
| | - Xiaohong Shi
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Shandong Medicine and Health Key Laboratory of Laboratory Medicine, No. 16766 Jingshi Road, Lixia District, Jinan, China
| | - Liang Chen
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, USA
- Department of Medical Sciences, Hackensack Meridian School of Medicine, Nutley, NJ, USA
| | - Siqiang Niu
- Department of Laboratory Medicine, The First Affiliated Hospital of Chongqing Medical University, No. 1 Friendship Road, Yuzhong District, Chongqing, China.
| | - Mingju Hao
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Shandong Medicine and Health Key Laboratory of Laboratory Medicine, No. 16766 Jingshi Road, Lixia District, Jinan, China.
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36
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Mu A, Klare WP, Baines SL, Ignatius Pang CN, Guérillot R, Harbison-Price N, Keller N, Wilksch J, Nhu NTK, Phan MD, Keller B, Nijagal B, Tull D, Dayalan S, Chua HHC, Skoneczny D, Koval J, Hachani A, Shah AD, Neha N, Jadhav S, Partridge SR, Cork AJ, Peters K, Bertolla O, Brouwer S, Hancock SJ, Álvarez-Fraga L, De Oliveira DMP, Forde B, Dale A, Mujchariyakul W, Walsh CJ, Monk I, Fitzgerald A, Lum M, Correa-Ospina C, Roy Chowdhury P, Parton RG, De Voss J, Beckett J, Monty F, McKinnon J, Song X, Stephen JR, Everest M, Bellgard MI, Tinning M, Leeming M, Hocking D, Jebeli L, Wang N, Ben Zakour N, Yasar SA, Vecchiarelli S, Russell T, Zaw T, Chen T, Teng D, Kassir Z, Lithgow T, Jenney A, Cole JN, Nizet V, Sorrell TC, Peleg AY, Paterson DL, Beatson SA, Wu J, Molloy MP, Syme AE, Goode RJA, Hunter AA, Bowland G, West NP, Wilkins MR, Djordjevic SP, Davies MR, Seemann T, Howden BP, Pascovici D, Tyagi S, Schittenhelm RB, De Souza DP, McConville MJ, Iredell JR, Cordwell SJ, Strugnell RA, Stinear TP, Schembri MA, Walker MJ. Integrative omics identifies conserved and pathogen-specific responses of sepsis-causing bacteria. Nat Commun 2023; 14:1530. [PMID: 36934086 PMCID: PMC10024524 DOI: 10.1038/s41467-023-37200-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: 02/01/2023] [Accepted: 03/06/2023] [Indexed: 03/20/2023] Open
Abstract
Even in the setting of optimal resuscitation in high-income countries severe sepsis and septic shock have a mortality of 20-40%, with antibiotic resistance dramatically increasing this mortality risk. To develop a reference dataset enabling the identification of common bacterial targets for therapeutic intervention, we applied a standardized genomic, transcriptomic, proteomic and metabolomic technological framework to multiple clinical isolates of four sepsis-causing pathogens: Escherichia coli, Klebsiella pneumoniae species complex, Staphylococcus aureus and Streptococcus pyogenes. Exposure to human serum generated a sepsis molecular signature containing global increases in fatty acid and lipid biosynthesis and metabolism, consistent with cell envelope remodelling and nutrient adaptation for osmoprotection. In addition, acquisition of cholesterol was identified across the bacterial species. This detailed reference dataset has been established as an open resource to support discovery and translational research.
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Affiliation(s)
- Andre Mu
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
- Wellcome Sanger Institute, Hinxton, UK
| | - William P Klare
- Charles Perkins Centre and School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
| | - Sarah L Baines
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - C N Ignatius Pang
- Ramaciotti Centre for Genomics, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
- Bioinformatics Group, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Romain Guérillot
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Nichaela Harbison-Price
- Australian Infectious Diseases Research Centre and School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Nadia Keller
- Australian Infectious Diseases Research Centre and School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Jonathan Wilksch
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Nguyen Thi Khanh Nhu
- Australian Infectious Diseases Research Centre and School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Minh-Duy Phan
- Australian Infectious Diseases Research Centre and School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Bernhard Keller
- Australian Infectious Diseases Research Centre and School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Brunda Nijagal
- Metabolomics Australia, Bio21 Institute, The University of Melbourne, Melbourne, Australia
| | - Dedreia Tull
- Metabolomics Australia, Bio21 Institute, The University of Melbourne, Melbourne, Australia
| | - Saravanan Dayalan
- Metabolomics Australia, Bio21 Institute, The University of Melbourne, Melbourne, Australia
| | - Hwa Huat Charlie Chua
- Metabolomics Australia, Bio21 Institute, The University of Melbourne, Melbourne, Australia
| | - Dominik Skoneczny
- Metabolomics Australia, Bio21 Institute, The University of Melbourne, Melbourne, Australia
| | - Jason Koval
- Ramaciotti Centre for Genomics, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Abderrahman Hachani
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Anup D Shah
- Monash Proteomics and Metabolomics Facility, Monash Biomedicine Discovery Institute, Monash University, Melbourne, VIC, Australia
| | - Nitika Neha
- Metabolomics Australia, Bio21 Institute, The University of Melbourne, Melbourne, Australia
| | - Snehal Jadhav
- Metabolomics Australia, Bio21 Institute, The University of Melbourne, Melbourne, Australia
| | - Sally R Partridge
- Centre for Infectious Diseases and Microbiology, Westmead Hospital/ Westmead Institute, and Sydney ID, University of Sydney, Sydney, NSW, Australia
| | - Amanda J Cork
- Australian Infectious Diseases Research Centre and School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Kate Peters
- Australian Infectious Diseases Research Centre and School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Olivia Bertolla
- Australian Infectious Diseases Research Centre and School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Stephan Brouwer
- Australian Infectious Diseases Research Centre and School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Steven J Hancock
- Australian Infectious Diseases Research Centre and School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Laura Álvarez-Fraga
- Australian Infectious Diseases Research Centre and School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - David M P De Oliveira
- Australian Infectious Diseases Research Centre and School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Brian Forde
- Australian Infectious Diseases Research Centre and School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Ashleigh Dale
- Charles Perkins Centre and School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
| | - Warasinee Mujchariyakul
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Calum J Walsh
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Ian Monk
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | | | - Mabel Lum
- Bioplatforms Australia Ltd., Sydney, NSW, Australia
| | - Carolina Correa-Ospina
- Ramaciotti Centre for Genomics, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Piklu Roy Chowdhury
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Sydney, NSW, Australia
| | - Robert G Parton
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
- Centre for Microscopy and Microanalysis, The University of Queensland, Brisbane, QLD, Australia
| | - James De Voss
- Australian Infectious Diseases Research Centre and School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - James Beckett
- Australian Infectious Diseases Research Centre and School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Francois Monty
- Australian Genome Research Facility Ltd., Melbourne, VIC, Australia
| | - Jessica McKinnon
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Sydney, NSW, Australia
| | - Xiaomin Song
- Australian Proteome Analysis Facility, Macquarie University, Sydney, Australia
| | - John R Stephen
- Australian Genome Research Facility Ltd., Melbourne, VIC, Australia
| | - Marie Everest
- Australian Genome Research Facility Ltd., Melbourne, VIC, Australia
| | - Matt I Bellgard
- Office of eResearch, Queensland University of Technology, Brisbane, QLD, Australia
- Center for Comparative Genomics, Murdoch University, Perth, WA, Australia
| | - Matthew Tinning
- Australian Genome Research Facility Ltd., Melbourne, VIC, Australia
| | - Michael Leeming
- Metabolomics Australia, Bio21 Institute, The University of Melbourne, Melbourne, Australia
| | - Dianna Hocking
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Leila Jebeli
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Nancy Wang
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Nouri Ben Zakour
- Centre for Infectious Diseases and Microbiology, Westmead Hospital/ Westmead Institute, and Sydney ID, University of Sydney, Sydney, NSW, Australia
| | - Serhat A Yasar
- Ramaciotti Centre for Genomics, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Stefano Vecchiarelli
- Ramaciotti Centre for Genomics, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Tonia Russell
- Ramaciotti Centre for Genomics, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Thiri Zaw
- Australian Proteome Analysis Facility, Macquarie University, Sydney, Australia
| | - Tyrone Chen
- Department of Infectious Diseases, The Alfred Hospital and Central Clinical School, Monash University, Melbourne, VIC, Australia
| | - Don Teng
- Metabolomics Australia, Bio21 Institute, The University of Melbourne, Melbourne, Australia
| | - Zena Kassir
- Ramaciotti Centre for Genomics, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Trevor Lithgow
- Centre to Impact AMR and Infection Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Melbourne, VIC, Australia
| | - Adam Jenney
- Centre to Impact AMR and Infection Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Melbourne, VIC, Australia
| | - Jason N Cole
- Department of Pediatrics, School of Medicine, University of California at San Diego, La Jolla, CA, 92093, USA
- Skaggs School of Pharmaceutical Sciences, University of California at San Diego, La Jolla, CA, 92093, USA
| | - Victor Nizet
- Department of Pediatrics, School of Medicine, University of California at San Diego, La Jolla, CA, 92093, USA
- Skaggs School of Pharmaceutical Sciences, University of California at San Diego, La Jolla, CA, 92093, USA
| | - Tania C Sorrell
- Centre for Infectious Diseases and Microbiology, Westmead Hospital/ Westmead Institute, and Sydney ID, University of Sydney, Sydney, NSW, Australia
| | - Anton Y Peleg
- Department of Infectious Diseases, The Alfred Hospital and Central Clinical School, Monash University, Melbourne, VIC, Australia
- Centre to Impact AMR and Infection Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Melbourne, VIC, Australia
| | - David L Paterson
- Centre for Clinical Research, The University of Queensland, Brisbane, QLD, Australia
| | - Scott A Beatson
- Australian Infectious Diseases Research Centre and School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Jemma Wu
- Australian Proteome Analysis Facility, Macquarie University, Sydney, Australia
| | - Mark P Molloy
- Australian Proteome Analysis Facility, Macquarie University, Sydney, Australia
| | - Anna E Syme
- Melbourne Bioinformatics, The University of Melbourne, Melbourne, VIC, Australia
| | - Robert J A Goode
- Monash Proteomics and Metabolomics Facility, Monash Biomedicine Discovery Institute, Monash University, Melbourne, VIC, Australia
- Commonwealth Scientific and Industrial Research Organisation, Clayton, VIC, Australia
| | - Adam A Hunter
- Center for Comparative Genomics, Murdoch University, Perth, WA, Australia
| | - Grahame Bowland
- Center for Comparative Genomics, Murdoch University, Perth, WA, Australia
| | - Nicholas P West
- Australian Infectious Diseases Research Centre and School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Marc R Wilkins
- Ramaciotti Centre for Genomics, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Steven P Djordjevic
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Sydney, NSW, Australia
| | - Mark R Davies
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Torsten Seemann
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Benjamin P Howden
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Dana Pascovici
- Australian Proteome Analysis Facility, Macquarie University, Sydney, Australia
| | - Sonika Tyagi
- Department of Infectious Diseases, The Alfred Hospital and Central Clinical School, Monash University, Melbourne, VIC, Australia
| | - Ralf B Schittenhelm
- Monash Proteomics and Metabolomics Facility, Monash Biomedicine Discovery Institute, Monash University, Melbourne, VIC, Australia
| | - David P De Souza
- Metabolomics Australia, Bio21 Institute, The University of Melbourne, Melbourne, Australia
| | - Malcolm J McConville
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, VIC, Australia
| | - Jonathan R Iredell
- Centre for Infectious Diseases and Microbiology, Westmead Hospital/ Westmead Institute, and Sydney ID, University of Sydney, Sydney, NSW, Australia
| | - Stuart J Cordwell
- Charles Perkins Centre and School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
| | - Richard A Strugnell
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Timothy P Stinear
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Mark A Schembri
- Australian Infectious Diseases Research Centre and School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Mark J Walker
- Australian Infectious Diseases Research Centre and School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia.
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia.
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Raiyemo DA, Bobadilla LK, Tranel PJ. Genomic profiling of dioecious Amaranthus species provides novel insights into species relatedness and sex genes. BMC Biol 2023; 21:37. [PMID: 36804015 PMCID: PMC9940365 DOI: 10.1186/s12915-023-01539-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 02/08/2023] [Indexed: 02/21/2023] Open
Abstract
BACKGROUND Amaranthus L. is a diverse genus consisting of domesticated, weedy, and non-invasive species distributed around the world. Nine species are dioecious, of which Amaranthus palmeri S. Watson and Amaranthus tuberculatus (Moq.) J.D. Sauer are troublesome weeds of agronomic crops in the USA and elsewhere. Shallow relationships among the dioecious Amaranthus species and the conservation of candidate genes within previously identified A. palmeri and A. tuberculatus male-specific regions of the Y (MSYs) in other dioecious species are poorly understood. In this study, seven genomes of dioecious amaranths were obtained by paired-end short-read sequencing and combined with short reads of seventeen species in the family Amaranthaceae from NCBI database. The species were phylogenomically analyzed to understand their relatedness. Genome characteristics for the dioecious species were evaluated and coverage analysis was used to investigate the conservation of sequences within the MSY regions. RESULTS We provide genome size, heterozygosity, and ploidy level inference for seven newly sequenced dioecious Amaranthus species and two additional dioecious species from the NCBI database. We report a pattern of transposable element proliferation in the species, in which seven species had more Ty3 elements than copia elements while A. palmeri and A. watsonii had more copia elements than Ty3 elements, similar to the TE pattern in some monoecious amaranths. Using a Mash-based phylogenomic analysis, we accurately recovered taxonomic relationships among the dioecious Amaranthus species that were previously identified based on comparative morphology. Coverage analysis revealed eleven candidate gene models within the A. palmeri MSY region with male-enriched coverages, as well as regions on scaffold 19 with female-enriched coverage, based on A. watsonii read alignments. A previously reported FLOWERING LOCUS T (FT) within A. tuberculatus MSY contig was also found to exhibit male-enriched coverages for three species closely related to A. tuberculatus but not for A. watsonii reads. Additional characterization of the A. palmeri MSY region revealed that 78% of the region is made of repetitive elements, typical of a sex determination region with reduced recombination. CONCLUSIONS The results of this study further increase our understanding of the relationships among the dioecious species of the Amaranthus genus as well as revealed genes with potential roles in sex function in the species.
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Affiliation(s)
- Damilola A Raiyemo
- Department of Crop Sciences, University of Illinois, Urbana, IL, 61801, USA
| | - Lucas K Bobadilla
- Department of Crop Sciences, University of Illinois, Urbana, IL, 61801, USA
| | - Patrick J Tranel
- Department of Crop Sciences, University of Illinois, Urbana, IL, 61801, USA.
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38
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Liu K, Xie N, Wang Y, Liu X. Contribution bias of parental genomes to the hybrid lineages of black Amur bream and topmouth culter revealed by low-coverage whole-genome sequencing. Gene 2023; 852:147058. [PMID: 36423776 DOI: 10.1016/j.gene.2022.147058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 11/11/2022] [Accepted: 11/16/2022] [Indexed: 11/23/2022]
Abstract
Interspecific hybridization has the potential to increase animal genetic diversity, enable the introgression of advantageous genetic variation, and even create hybrid lineages. Using the low-coverage whole-genome sequencing data of black Amur bream (Megalobrama terminalis [SJ]), topmouth culter (Culter alburnus [QZ]), and their hybrid progeny, we focused on the sequence variation and contribution bias to the genomic composition of the hybrid lineages of SJ♀ × QZ♂ [ZJ] and QZ♀ × SJ♂ [FJ]. Both mash-based genetic distance analysis and variant analysis based on various reference genomes revealed that the hybrid lineages' genomes are more prone to QZ composition. Furthermore, we assess the degree of subgenomic intermixing between parents QZ and SJ in the FJ and ZJ hybrid lineages. In the Jaccard index-zero genomic area, 89.41% of the genomic region in ZJ and 90.23% in FJ are entirely from one of the parental genomes. This genomic area is primarily from QZ, regardless of FJ or ZJ. In FJ, the proportion is 55.70%; in ZJ, the proportion is 54.60%. Using the reference-free variant discovery tool, we identified two InDel markers (Both were SSR-type InDel markers) and one (T/A)-type SNP marker that displayed differences in agarose electrophoresis. Our current findings suggest that parental genomic contribution bias leads to an imbalance in the genomic composition of hybrid lineages. The genomic composition bias is connected to species but not maternal effects, giving insights into the development of vertebrate genomes shortly after hybridization.
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Affiliation(s)
- Kai Liu
- Institute of Fishery Science, Hangzhou Academy of Agricultural Sciences, Hangzhou 310024, China.
| | - Nan Xie
- Institute of Fishery Science, Hangzhou Academy of Agricultural Sciences, Hangzhou 310024, China
| | - Yuxi Wang
- Institute of Fishery Science, Hangzhou Academy of Agricultural Sciences, Hangzhou 310024, China
| | - Xinyi Liu
- Institute of Fishery Science, Hangzhou Academy of Agricultural Sciences, Hangzhou 310024, China
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39
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Biggel M, Johler S, Roloff T, Tschudin-Sutter S, Bassetti S, Siegemund M, Egli A, Stephan R, Seth-Smith HMB. PorinPredict: In Silico Identification of OprD Loss from WGS Data for Improved Genotype-Phenotype Predictions of P. aeruginosa Carbapenem Resistance. Microbiol Spectr 2023; 11:e0358822. [PMID: 36715510 PMCID: PMC10100854 DOI: 10.1128/spectrum.03588-22] [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: 09/06/2022] [Accepted: 12/29/2022] [Indexed: 01/31/2023] Open
Abstract
The increasing integration of genomics into routine clinical diagnostics requires reliable computational tools to identify determinants of antimicrobial resistance (AMR) from whole-genome sequencing data. Here, we developed PorinPredict, a bioinformatic tool that predicts defects of the Pseudomonas aeruginosa outer membrane porin OprD, which are strongly associated with reduced carbapenem susceptibility. PorinPredict relies on a database of intact OprD variants and reports inactivating mutations in the coding or promoter region. PorinPredict was validated against 987 carbapenemase-negative P. aeruginosa genomes, of which OprD loss was predicted for 454 out of 522 (87.0%) meropenem-nonsusceptible and 46 out of 465 (9.9%) meropenem-susceptible isolates. OprD loss was also found to be common among carbapenemase-producing isolates, resulting in even further increased MICs. Chromosomal mutations in quinolone resistance-determining regions and OprD loss commonly co-occurred, likely reflecting the restricted use of carbapenems for multidrug-resistant infections as recommended in antimicrobial stewardship programs. In combination with available AMR gene detection tools, PorinPredict provides a robust and standardized approach to link P. aeruginosa phenotypes to genotypes. IMPORTANCE Pseudomonas aeruginosa is a major cause of multidrug-resistant nosocomial infections. The emergence and spread of clones exhibiting resistance to carbapenems, a class of critical last-line antibiotics, is therefore closely monitored. Carbapenem resistance is frequently mediated by chromosomal mutations that lead to a defective outer membrane porin OprD. Here, we determined the genetic diversity of OprD variants across the P. aeruginosa population and developed PorinPredict, a bioinformatic tool that enables the prediction of OprD loss from whole-genome sequencing data. We show a high correlation between predicted OprD loss and meropenem nonsusceptibility irrespective of the presence of carbapenemases, which are a second widespread determinant of carbapenem resistance. Isolates with resistance determinants to other antibiotics were disproportionally affected by OprD loss, possibly due to an increased exposure to carbapenems. Integration of PorinPredict into genomic surveillance platforms will facilitate a better understanding of the clinical impact of OprD modifications and transmission dynamics of resistant clones.
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Affiliation(s)
- Michael Biggel
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Sophia Johler
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Tim Roloff
- Division of Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland
- Institute of Medical Microbiology, University of Zurich, Zurich
| | - Sarah Tschudin-Sutter
- Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Basel, Switzerland
| | - Stefano Bassetti
- Internal Medicine, University Hospital Basel, Basel, Switzerland
| | - Martin Siegemund
- Intensive Care Unit, University Hospital Basel, Basel, Switzerland
| | - Adrian Egli
- Division of Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland
- Institute of Medical Microbiology, University of Zurich, Zurich
| | - Roger Stephan
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Helena M. B. Seth-Smith
- Division of Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland
- Institute of Medical Microbiology, University of Zurich, Zurich
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40
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Zhang J, Wang Z, Chen Y, Zhou Z, Yang Q, Fu Y, Zhao F, Li X, Chen Q, Fang L, Jiang Y, Yu Y. Antifungal susceptibility and molecular characteristics of Cryptococcus spp. based on whole-genome sequencing in Zhejiang Province, China. Front Microbiol 2022; 13:991703. [PMID: 36466641 PMCID: PMC9712201 DOI: 10.3389/fmicb.2022.991703] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 10/31/2022] [Indexed: 06/05/2024] Open
Abstract
Cryptococcus spp. is a complex species that often causes cryptococcosis, which is one of the most common opportunistic infections in adults living with HIV and has very high morbidity and mortality rates. This study aimed to investigate the antifungal susceptibility profiles and epidemiological characteristics of the Cryptococcus neoformans species complex (CNSC) and the Cryptococcus gattii species complex (CGSC) in Zhejiang Province, China. A total of 177 CNSC and 3 CGSC isolates were collected, and antifungal susceptibility was tested by FUNGUS 3 and verified with an E-test. Moreover, multiple classification methods and genomic analyses were performed. The majority of the isolates (96.11%) were C. neoformans (formerly C. neoformans var. grubii) (ST5-VNI-A-α). Our study highlights that most of the patients with cryptococcosis were non-HIV patients in China, and nearly half of them did not have underlying diseases that led to immune insufficiency. Most of the Cryptococcus spp. isolates in this study were sensitive to common antifungal drugs. Two 5-flucytosine (5-FC)-resistant strains were identified, and FUR1 mutation was detected in the 5-FC-resistant isolates. Typing based on whole-genome sequencing (WGS) showed better discrimination than that achieved with multilocus sequence typing (MLST) and indicated a clear population structure. A phylogenetic analysis based on WGS included more genomic information than traditional classification methods.
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Affiliation(s)
- Junli Zhang
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
| | - Zhengan Wang
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
| | - Yan Chen
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
| | - Zhihui Zhou
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
| | - Qing Yang
- Department of Clinical Laboratory, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Ying Fu
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
- Department of Clinical Laboratory, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Feng Zhao
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
- Department of Clinical Laboratory, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xi Li
- Department of Clinical Laboratory, Zhejiang Provincial People's Hospital, Hangzhou, China
| | - Qiong Chen
- Department of Clinical Laboratory, Affiliated Hangzhou First People’s Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Li Fang
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
| | - Yan Jiang
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
| | - Yunsong Yu
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
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41
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Carfora V, Diaconu EL, Ianzano A, Di Matteo P, Amoruso R, Dell'Aira E, Sorbara L, Bottoni F, Guarneri F, Campana L, Franco A, Alba P, Battisti A. The hazard of carbapenemase (OXA-181)-producing Escherichia coli spreading in pig and veal calf holdings in Italy in the genomics era: Risk of spill over and spill back between humans and animals. Front Microbiol 2022; 13:1016895. [PMID: 36466661 PMCID: PMC9712188 DOI: 10.3389/fmicb.2022.1016895] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 10/10/2022] [Indexed: 08/26/2023] Open
Abstract
Carbapenemase-producing Enterobacterales (CPE) are considered a major public health issue. In the frame of the EU Harmonized AMR Monitoring program conducted in Italy in 2021, 21 epidemiological units of fattening pigs (6.98%; 95% CI 4.37-10.47%; 21/301) and four epidemiological units of bovines <12 months (1.29%; 95% CI 0.35-3.27%, 4/310) resulted positive to OXA-48-like-producing E. coli (n = 24 OXA-181, n = 1 OXA-48). Whole Genome Sequencing (WGS) for in-depth characterization, genomics and cluster analysis of OXA-181-(and one OXA-48) producing E. coli isolated, was performed. Tracing-back activities at: (a) the fattening holding of origin of one positive slaughter batch, (b) the breeding holding, and (c) one epidemiologically related dairy cattle holding, allowed detection of OXA-48-like-producing E. coli in different units and comparison of further human isolates from fecal samples of farm workers. The OXA-181-producing isolates were multidrug resistant (MDR), belonged to different Sequence Types (STs), harbored the IncX and IncF plasmid replicons and multiple virulence genes. Bioinformatics analysis of combined Oxford Nanopore Technologies (ONT) long reads and Illumina short reads identified bla OXA-181 as part of a transposon in IncX1, IncX3, and IncFII fully resolved plasmids from 16 selected E. coli, mostly belonging to ST5229, isolated during the survey at slaughter and tracing-back activities. Although human source could be the most likely cause for the introduction of the bla OXA-181-carrying IncX1 plasmid in the breeding holding, concerns arise from carbapenemase OXA-48-like-producing E. coli spreading in 2021 in Italian fattening pigs and, to a lesser extent, in veal calf holdings.
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Affiliation(s)
- Virginia Carfora
- Department of General Diagnostics, National Reference Laboratory for Antimicrobial Resistance, Istituto Zooprofilattico Sperimentale del Lazio e Della Toscana “M. Aleandri”, Rome, Italy
| | - Elena Lavinia Diaconu
- Department of General Diagnostics, National Reference Laboratory for Antimicrobial Resistance, Istituto Zooprofilattico Sperimentale del Lazio e Della Toscana “M. Aleandri”, Rome, Italy
| | - Angela Ianzano
- Department of General Diagnostics, National Reference Laboratory for Antimicrobial Resistance, Istituto Zooprofilattico Sperimentale del Lazio e Della Toscana “M. Aleandri”, Rome, Italy
| | - Paola Di Matteo
- Department of General Diagnostics, National Reference Laboratory for Antimicrobial Resistance, Istituto Zooprofilattico Sperimentale del Lazio e Della Toscana “M. Aleandri”, Rome, Italy
| | - Roberta Amoruso
- Department of General Diagnostics, National Reference Laboratory for Antimicrobial Resistance, Istituto Zooprofilattico Sperimentale del Lazio e Della Toscana “M. Aleandri”, Rome, Italy
| | - Elena Dell'Aira
- Department of General Diagnostics, National Reference Laboratory for Antimicrobial Resistance, Istituto Zooprofilattico Sperimentale del Lazio e Della Toscana “M. Aleandri”, Rome, Italy
| | - Luigi Sorbara
- Department of General Diagnostics, National Reference Laboratory for Antimicrobial Resistance, Istituto Zooprofilattico Sperimentale del Lazio e Della Toscana “M. Aleandri”, Rome, Italy
| | - Francesco Bottoni
- Department of General Diagnostics, National Reference Laboratory for Antimicrobial Resistance, Istituto Zooprofilattico Sperimentale del Lazio e Della Toscana “M. Aleandri”, Rome, Italy
| | - Flavia Guarneri
- Sede Territoriale di Brescia, Laboratorio Diagnostica Generale, Istituto Zooprofilattico Sperimentale Della Lombardia e Dell’Emilia-Romagna “Bruno Ubertini”, Brescia, Italy
| | | | - Alessia Franco
- Department of General Diagnostics, National Reference Laboratory for Antimicrobial Resistance, Istituto Zooprofilattico Sperimentale del Lazio e Della Toscana “M. Aleandri”, Rome, Italy
| | - Patricia Alba
- Department of General Diagnostics, National Reference Laboratory for Antimicrobial Resistance, Istituto Zooprofilattico Sperimentale del Lazio e Della Toscana “M. Aleandri”, Rome, Italy
| | - Antonio Battisti
- Department of General Diagnostics, National Reference Laboratory for Antimicrobial Resistance, Istituto Zooprofilattico Sperimentale del Lazio e Della Toscana “M. Aleandri”, Rome, Italy
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42
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Plasmidome in mcr-1 harboring carbapenem-resistant enterobacterales isolates from human in Thailand. Sci Rep 2022; 12:19051. [PMID: 36351969 PMCID: PMC9646850 DOI: 10.1038/s41598-022-21836-7] [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: 06/13/2022] [Accepted: 10/04/2022] [Indexed: 11/11/2022] Open
Abstract
The emergence of the mobile colistin-resistance genes mcr-1 has attracted significant attention worldwide. This study aimed to investigate the genetic features of mcr-1-carrying plasmid among carbapenem-resistant Enterobacterales (CRE) isolates and the potential genetic basis governing transmission. Seventeen mcr-harboring isolates were analyzed based on whole genome sequencing using short-read and long-read platforms. All the mcr-1-carrying isolates could be conjugatively transferred into a recipient Escherichia coli UB1637. Among these 17 isolates, mcr-1 was located on diverse plasmid Inc types, consisting of IncX4 (11/17; 64.7%), IncI2 (4/17; 23.53%), and IncHI/IncN (2/17; 11.76%). Each of these exhibited remarkable similarity in the backbone set that is responsible for plasmid replication, maintenance, and transfer, with differences being in the upstream and downstream regions containing mcr-1. The IncHI/IncN type also carried other resistance genes (blaTEM-1B or blaTEM-135). The mcr-1-harboring IncX4 plasmids were carried in E. coli ST410 (7/11; 63.6%) and ST10 (1/11; 9.1%) and Klebsiella pneumoniae ST15 (1/11; 9.1%), ST336 (1/11; 9.1%), and ST340 (1/11; 9.1%). The IncI2-type plasmid was harbored in E. coli ST3052 (1/4; 25%) and ST1287 (1/4; 25%) and in K. pneumoniae ST336 (2/4; 50%), whereas IncHI/IncN were carried in E. coli ST6721 (1/2; 50%) and new ST (1/2; 50%). The diverse promiscuous plasmids may facilitate the spread of mcr-1 among commensal E. coli or K. pneumoniae strains in patients. These results can provide information for a surveillance system and infection control for dynamic tracing.
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Watanabe K, Yaneshita M, Denda T, Yokota M, Hirota SK, Suyama Y, Tsumura Y. Genetic Structure of the Liriope muscari Polyploid Complex and the Possibility of Its Genetic Disturbance in Japan. PLANTS (BASEL, SWITZERLAND) 2022; 11:3015. [PMID: 36432743 PMCID: PMC9697476 DOI: 10.3390/plants11223015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 10/28/2022] [Accepted: 11/03/2022] [Indexed: 06/16/2023]
Abstract
Anthropogenic activities, such as the movement of plants through greening, can result in genetic disturbance that can interfere with local adaptation in wild populations. Although research is underway to prevent genetic disturbance associated with greening, genetic disturbance of intraspecific polyploidy, which is estimated to be present in 24% of vascular plants, has not been well studied. Liriope muscari is a polyploid complex with known diploid (2n = 36), tetraploid (2n = 72), and hexaploid (2n = 108) forms. The plants of this species tolerate dry and hot conditions and are therefore frequently used for greening and gardening. However, the distribution of this polyploid in Japan, its genetic structure, and genetic disturbance are not known. In this study, we investigated the polyploidy distribution and genetic structure in naturally distributed L. muscari in Japan using chloroplast DNA (cpDNA) haplotypes and nuclear DNA (nDNA). Commercially produced individuals were also studied and compared with natural populations to assess any genetic disturbance of the ploidy complex in this species. Chromosome counts, cpDNA, and nDNA results showed three genetically and cytologically distinct groups in Japan: first, a tetraploid group in mainland Japan; second, a hexaploid group in the Ryukyu Islands; and third, a diploid and tetraploid group in the Ryukyu Islands. Significant isolation by distance was also detected within the three groups (p = 0.001). Genetic disturbance due to greening and gardening should be avoided among the three groups. Genetic disturbance can be reduced by using individuals derived from natural populations that are close to the sites used for greening and gardening. For commercially produced individuals, genetic disturbance is unlikely in the Kanto region, an area of high usage, while genetic disturbance is thought possible in the Ryukyu Islands.
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Affiliation(s)
- Keita Watanabe
- Graduate School of Life and Environmental Science, University of Tsukuba, Tsukuba 305-8572, Japan
- Environment Research Section Urban Engineering Research Department, Taisei Corporation, Yokohama 245-0051, Japan
| | - Makoto Yaneshita
- Environment Research Section Urban Engineering Research Department, Taisei Corporation, Yokohama 245-0051, Japan
| | - Tetsuo Denda
- Laboratory of Ecology and Systematics, Faculty of Science, University of the Ryukyus, Nishihara 903-0213, Japan
| | - Masatsugu Yokota
- Laboratory of Ecology and Systematics, Faculty of Science, University of the Ryukyus, Nishihara 903-0213, Japan
| | - Shun K. Hirota
- Botanical Gardens, Osaka Metropolitan University, Katano 576-0004, Japan
| | - Yoshihisa Suyama
- Field Science Center, Graduate School of Agricultural Science, Tohoku University, Osaki 989-6711, Japan
| | - Yoshihiko Tsumura
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba 305-8786, Japan
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Lehotay-Kéry P, Kiss A. Membrane Clustering of Coronavirus Variants Using Document Similarity. Genes (Basel) 2022; 13:genes13111966. [PMID: 36360202 PMCID: PMC9689808 DOI: 10.3390/genes13111966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 10/19/2022] [Accepted: 10/24/2022] [Indexed: 11/29/2022] Open
Abstract
Currently, as an effect of the COVID-19 pandemic, bioinformatics, genomics, and biological computations are gaining increased attention. Genomes of viruses can be represented by character strings based on their nucleobases. Document similarity metrics can be applied to these strings to measure their similarities. Clustering algorithms can be applied to the results of their document similarities to cluster them. P systems or membrane systems are computation models inspired by the flow of information in the membrane cells. These can be used for various purposes, one of them being data clustering. This paper studies a novel and versatile clustering method for genomes and the utilization of such membrane clustering models using document similarity metrics, which is not yet a well-studied use of membrane clustering models.
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Affiliation(s)
- Péter Lehotay-Kéry
- Department of Information Systems, ELTE Eötvös Loránd University, 1117 Budapest, Hungary
| | - Attila Kiss
- Department of Information Systems, ELTE Eötvös Loránd University, 1117 Budapest, Hungary
- Department of Informatics, J. Selye University, 945 01 Komárno, Slovakia
- Correspondence:
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Greenrod STE, Stoycheva M, Elphinstone J, Friman VP. Global diversity and distribution of prophages are lineage-specific within the Ralstonia solanacearum species complex. BMC Genomics 2022; 23:689. [PMID: 36199029 PMCID: PMC9535894 DOI: 10.1186/s12864-022-08909-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 09/23/2022] [Indexed: 11/17/2022] Open
Abstract
Background Ralstonia solanacearum species complex (RSSC) strains are destructive plant pathogenic bacteria and the causative agents of bacterial wilt disease, infecting over 200 plant species worldwide. In addition to chromosomal genes, their virulence is mediated by mobile genetic elements including integrated DNA of bacteriophages, i.e., prophages, which may carry fitness-associated auxiliary genes or modulate host gene expression. Although experimental studies have characterised several prophages that shape RSSC virulence, the global diversity, distribution, and wider functional gene content of RSSC prophages are unknown. In this study, prophages were identified in a diverse collection of 192 RSSC draft genome assemblies originating from six continents. Results Prophages were identified bioinformatically and their diversity investigated using genetic distance measures, gene content, GC, and total length. Prophage distributions were characterised using metadata on RSSC strain geographic origin and lineage classification (phylotypes), and their functional gene content was assessed by identifying putative prophage-encoded auxiliary genes. In total, 313 intact prophages were identified, forming ten genetically distinct clusters. These included six prophage clusters with similarity to the Inoviridae, Myoviridae, and Siphoviridae phage families, and four uncharacterised clusters, possibly representing novel, previously undescribed phages. The prophages had broad geographical distributions, being present across multiple continents. However, they were generally host phylogenetic lineage-specific, and overall, prophage diversity was proportional to the genetic diversity of their hosts. The prophages contained many auxiliary genes involved in metabolism and virulence of both phage and bacteria. Conclusions Our results show that while RSSC prophages are highly diverse globally, they make lineage-specific contributions to the RSSC accessory genome, which could have resulted from shared coevolutionary history. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08909-7.
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Affiliation(s)
| | | | - John Elphinstone
- Fera Science Ltd, National Agri-Food Innovation Campus, Sand Hutton, York, UK
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Waglechner N, Tullis E, Stephenson AL, Waters V, McIntosh F, Ma J, Jamieson FB, Behr MA, Batt J, Lee RS. Genomic epidemiology of Mycobacterium abscessus in a Canadian cystic fibrosis centre. Sci Rep 2022; 12:16116. [PMID: 36167715 PMCID: PMC9514693 DOI: 10.1038/s41598-022-19666-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 09/01/2022] [Indexed: 11/09/2022] Open
Abstract
The Mycobacterium abscessus complex causes significant morbidity and mortality among patients with Cystic Fibrosis (CF). It has been hypothesized that these organisms are transmitted from patient to patient based on genomics. However, few studies incorporate epidemiologic data to confirm this hypothesis. We longitudinally sampled 27 CF and 7 non-CF patients attending a metropolitan hospital in Ontario, Canada from 2013 to 2018. Whole genome sequencing along with epidemiological data was used to evaluate the likelihood of transmission. Overall, the genetic diversity of M. abscessus was large, with a median pairwise distance (IQR) of 1,279 (143-134) SNVs between all Ontario M. abscessus isolates and 2,908 (21-3,204) single nucleotide variants (SNVs) between M. massiliense isolates. This reflects the global diversity of this pathogen, with Ontario isolates widely dispersed throughout global phylogenetic trees of each subspecies. Using a maximum distance of 25 SNVs as a threshold to identify possible transmission, we identified 23 (of 276 total) pairs of closely-related isolates. However, transmission was probable for only one pair based on both genomic and epidemiological data. This suggests that person-to-person transmission of M. abscessus among CF patients is indeed rare and reinforces the critical importance of epidemiological data for inferences of transmission.
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Affiliation(s)
- Nicholas Waglechner
- Dalla Lana School of Public Health, University of Toronto, 155 College St., Toronto, ON, M5T 3M7, Canada.
| | - Elizabeth Tullis
- Adult Cystic Fibrosis Program, Division of Respirology, St. Michael's Hospital, Unity Health Toronto, Toronto, ON, Canada.,Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, ON, Canada
| | - Anne L Stephenson
- Adult Cystic Fibrosis Program, Division of Respirology, St. Michael's Hospital, Unity Health Toronto, Toronto, ON, Canada.,Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, ON, Canada.,Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON, Canada
| | - Valerie Waters
- Department of Pediatrics, Division of Infectious Diseases, Hospital for Sick Children, 555 University Avenue, Toronto, ON, M5G 1X8, Canada
| | - Fiona McIntosh
- Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, Montreal, QC, Canada.,McGill International TB Centre, McGill University, Montreal, QC, Canada
| | - Jennifer Ma
- Public Health Ontario, Public Health Ontario Laboratories, 661 University Avenue, Suite 1701, Toronto, ON, M5G 1V2, Canada
| | - Frances B Jamieson
- Public Health Ontario, Public Health Ontario Laboratories, 661 University Avenue, Suite 1701, Toronto, ON, M5G 1V2, Canada
| | - Marcel A Behr
- Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, Montreal, QC, Canada.,McGill International TB Centre, McGill University, Montreal, QC, Canada.,Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, QC, Canada
| | - Jane Batt
- Keenan Research Center for Biomedical Science, St. Michael's Hospital, Toronto, ON, Canada.,Tuberculosis Program, St. Michael's Hospital Unity Health Toronto, Toronto, ON, M5B 1WB, Canada
| | - Robyn S Lee
- Dalla Lana School of Public Health, University of Toronto, 155 College St., Toronto, ON, M5T 3M7, Canada. .,McGill International TB Centre, McGill University, Montreal, QC, Canada. .,Center for Communicable Disease Dynamics, Harvard School of Public Health, Boston, MA, USA.
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Delineating Mycobacterium abscessus population structure and transmission employing high-resolution core genome multilocus sequence typing. Nat Commun 2022; 13:4936. [PMID: 35999208 PMCID: PMC9399081 DOI: 10.1038/s41467-022-32122-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 07/19/2022] [Indexed: 11/08/2022] Open
Abstract
Mycobacterium abscessus is an emerging multidrug-resistant non-tuberculous mycobacterium that causes a wide spectrum of infections and has caused several local outbreaks worldwide. To facilitate standardized prospective molecular surveillance, we established a novel core genome multilocus sequence typing (cgMLST) scheme. Whole genome sequencing data of 1991 isolates were employed to validate the scheme, re-analyze global population structure and set genetic distance thresholds for cluster detection and taxonomic identification. We confirmed and amended the nomenclature of the main dominant circulating clones and found that these also correlate well with traditional 7-loci MLST. Dominant circulating clones could be linked to a corresponding reference genome with less than 250 alleles while 99% of pairwise comparisons between epidemiologically linked isolates were below 25 alleles and 90% below 10 alleles. These thresholds can be used to guide further epidemiological investigations. Overall, the scheme will help to unravel the apparent global spread of certain clonal complexes and as yet undiscovered transmission routes.
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Biggel M, Jessberger N, Kovac J, Johler S. Recent paradigm shifts in the perception of the role of Bacillus thuringiensis in foodborne disease. Food Microbiol 2022; 105:104025. [DOI: 10.1016/j.fm.2022.104025] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 03/10/2022] [Accepted: 03/11/2022] [Indexed: 12/16/2022]
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Convergence of virulence and antimicrobial resistance in increasingly prevalent Escherichia coli ST131 papGII+ sublineages. Commun Biol 2022; 5:752. [PMID: 35902767 PMCID: PMC9334617 DOI: 10.1038/s42003-022-03660-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 06/29/2022] [Indexed: 12/26/2022] Open
Abstract
Escherichia coli lineage ST131 is an important cause of urinary tract and bloodstream infections worldwide and is highly resistant to antimicrobials. Specific ST131 lineages carrying invasiveness-associated papGII pathogenicity islands (PAIs) were previously described, but it is unknown how invasiveness relates to the acquisition of antimicrobial resistance (AMR). In this study, we analysed 1638 ST131 genomes and found that papGII+ isolates carry significantly more AMR genes than papGII-negative isolates, suggesting a convergence of virulence and AMR. The prevalence of papGII+ isolates among human clinical ST131 isolates increased dramatically since 2005, accounting for half of the recent E. coli bloodstream isolates. Emerging papGII+ lineages within clade C2 were characterized by a chromosomally integrated blaCTX-M-15 and the loss and replacement of F2:A1:B- plasmids. Convergence of virulence and AMR is worrying, and further dissemination of papGII+ ST131 lineages may lead to a rise in severe and difficult-to-treat extraintestinal infections. Genomic analyses indicate that the ST131 lineage of E. coli, responsible for urinary and bloodstream infections globally, is evolving towards both increased virulence and increased resistance to antimicrobials.
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Alikhan NF, Moreno LZ, Castellanos LR, Chattaway MA, McLauchlin J, Lodge M, O’Grady J, Zamudio R, Doughty E, Petrovska L, Cunha MPV, Knöbl T, Moreno AM, Mather AE. Dynamics of Salmonella enterica and antimicrobial resistance in the Brazilian poultry industry and global impacts on public health. PLoS Genet 2022; 18:e1010174. [PMID: 35653335 PMCID: PMC9162342 DOI: 10.1371/journal.pgen.1010174] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 03/29/2022] [Indexed: 11/19/2022] Open
Abstract
Non-typhoidal Salmonella enterica is a common cause of diarrhoeal disease; in humans, consumption of contaminated poultry meat is believed to be a major source. Brazil is the world’s largest exporter of chicken meat globally, and previous studies have indicated the introduction of Salmonella serovars through imported food products from Brazil. Here we provide an in-depth genomic characterisation and evolutionary analysis to investigate the most prevalent serovars and antimicrobial resistance (AMR) in Brazilian chickens and assess the impact to public health of products contaminated with S. enterica imported into the United Kingdom from Brazil. To do so, we examine 183 Salmonella genomes from chickens in Brazil and 357 genomes from humans, domestic poultry and imported Brazilian poultry products isolated in the United Kingdom. S. enterica serovars Heidelberg and Minnesota were the most prevalent serovars in Brazil and in meat products imported from Brazil into the UK. We extended our analysis to include 1,259 publicly available Salmonella Heidelberg and Salmonella Minnesota genomes for context. The Brazil genomes form clades distinct from global isolates, with temporal analysis suggesting emergence of these Salmonella Heidelberg and Salmonella Minnesota clades in the early 2000s, around the time of the 2003 introduction of the Enteritidis vaccine in Brazilian poultry. Analysis showed genomes within the Salmonella Heidelberg and Salmonella Minnesota clades shared resistance to sulphonamides, tetracyclines and beta-lactams conferred by sul2, tetA and blaCMY-2 genes, not widely observed in other co-circulating serovars despite similar selection pressures. The sul2 and tetA genes were concomitantly carried on IncC plasmids, whereas blaCMY-2 was either co-located with the sul2 and tetA genes on IncC plasmids or independently on IncI1 plasmids. Long-term surveillance data collected in the UK showed no increase in the incidence of Salmonella Heidelberg or Salmonella Minnesota in human cases of clinical disease in the UK following the increase of these two serovars in Brazilian poultry. In addition, almost all of the small number of UK-derived genomes which cluster with the Brazilian poultry-derived sequences could either be attributed to human cases with a recent history of foreign travel or were from imported Brazilian food products. These findings indicate that even should Salmonella from imported Brazilian poultry products reach UK consumers, they are very unlikely to be causing disease. No evidence of the Brazilian strains of Salmonella Heidelberg or Salmonella Minnesota were observed in UK domestic chickens. These findings suggest that introduction of the Salmonella Enteritidis vaccine, in addition to increasing antimicrobial use, could have resulted in replacement of salmonellae in Brazilian poultry flocks with serovars that are more drug resistant, but less associated with disease in humans in the UK. The plasmids conferring resistance to beta-lactams, sulphonamides and tetracyclines likely conferred a competitive advantage to the Salmonella Minnesota and Salmonella Heidelberg serovars in this setting of high antimicrobial use, but the apparent lack of transfer to other serovars present in the same setting suggests barriers to horizontal gene transfer that could be exploited in intervention strategies to reduce AMR. The insights obtained reinforce the importance of One Health genomic surveillance. Non-typhoidal Salmonella enterica is a common cause of diarrhoeal disease; in humans, consumption of contaminated poultry meat is believed to be a major source. Here we determine that S. enterica serovars Heidelberg and Minnesota were the most prevalent serovars in Brazilian poultry and in poultry products imported from Brazil into the UK. However, long-term surveillance data collected by the UK Health Security Agency showed no increase in the incidence of Salmonella Heidelberg or Salmonella Minnesota in human cases of clinical disease in the UK following the increase of these two serovars in Brazilian poultry. Salmonella Heidelberg and Salmonella Minnesota clades shared resistance to sulphonamides, tetracyclines and beta-lactams conferred by sul2, tetA and blaCMY-2 genes, not widely observed in other co-circulating serovars despite similar selection pressures. The sul2 and tetA genes were concomitantly carried on IncC plasmids, whereas blaCMY-2 was either co-located with the sul2 and tetA genes on IncC plasmids or independently on IncI1 plasmids. These findings suggest that introduction of the Salmonella Enteritidis vaccine, in addition to increasing antimicrobial use, could have resulted in replacement of salmonellae in Brazilian poultry flocks with serovars that are more drug resistant, but less associated with disease in humans in the UK.
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Affiliation(s)
| | - Luisa Zanolli Moreno
- Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine and Animal Science, University of São Paulo, São Paulo, Brazil
- Centro Universitário Max Planck (UniMax), Indaiatuba, São Paulo, Brazil
| | | | | | - Jim McLauchlin
- UK Health Security Agency National Infection Service, London, United Kingdom
| | - Martin Lodge
- UK Health Security Agency National Infection Service, London, United Kingdom
| | - Justin O’Grady
- Quadram Institute Bioscience, Norwich, United Kingdom
- University of East Anglia, Norwich, United Kingdom
| | | | - Emma Doughty
- Quadram Institute Bioscience, Norwich, United Kingdom
| | - Liljana Petrovska
- Department of Bacteriology and Food Safety, Animal and Plant Health Agency (APHA—Weybridge), Addlestone, United Kingdom
| | - Marcos Paulo Vieira Cunha
- Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine and Animal Science, University of São Paulo, São Paulo, Brazil
| | - Terezinha Knöbl
- Department of Pathology, School of Veterinary Medicine and Animal Science, University of São Paulo, São Paulo, Brazil
| | - Andrea Micke Moreno
- Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine and Animal Science, University of São Paulo, São Paulo, Brazil
- * E-mail: (AMM); (AEM)
| | - Alison E. Mather
- Quadram Institute Bioscience, Norwich, United Kingdom
- University of East Anglia, Norwich, United Kingdom
- * E-mail: (AMM); (AEM)
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